Greek–Russian–English Alphabets
Greek letter Greek name English equivalent Russian letter English equivalent Α a Alpha (a¨) Аа(a¨) Β b Beta (b) Бб(b) Вв(v) GgGamma (g) Гг(g) DdDelta (d) Дд(d) Ε e Epsilon (e) Ее(ye) Ζ z Zeta (z) Жж(zh) Зз(z) Η Z Eta (a¯) Ии(i, e¯) YyTheta (th) Йй(e¯) Ι i Iota (e¯) Кк(k) Лл(l) Κ k Kappa (k) Мм(m) LlLambda (l) Нн(n) Оо(oˆ,o) Μ m Mu (m) Оо(oˆ,o) Пп(p) Ν n Nu (n) Рр(r) XxXi (ks) Сс(s) Тт(t) ΟοOmicron a Ууo¯o¯ PpPi (P) Фф(f) Хх(kh) Ρ r Rho (r) Хх(kh)
Цц(ts) SsSigma (s) Чч(ch) Τ t Tau (t) Шш(sh) Υ v Upsilon (u¨,o¯o¯) Щщ(shch) Ъъ8 F ø Phi (f) Ыы(e¨) Χ w Chi (H) Ьь(e¨) CcPsi (ps) Ээ(e) Юю(u¯) OoOmega (o¯) Яя(ya¨) 1088 Greek–Russian–English Alphabets
English–Greek–Latin numbers English Greek Latin 1 mono uni 2 bis di 3 tris Tri 4 tetrakis tetra 5 pentakis penta 6 hexakis hexa 7 heptakis hepta 8 octakis octa 9 nonakis nona 10 decakis deca
International Union of Pure and Applied Chemistry: Rules Concerning Numerical Terms Used in Organic Chemical Nomenclature (specifically as prefixes for hydrocarbons) 1 mono‐ or hen‐ 10 deca‐ 100 hecta‐ 1000 kilia‐ 2di‐ or do‐ 20 icosa‐ 200 Dicta‐ 2000 dilia‐ 3 tri‐ 0 triaconta‐ 300 tricta‐ 3000 trilia‐ 4 tetra‐ 40 tetraconta‐ 400 tetracta 4000 tetralia‐ 5 penta‐ 50 pentaconta‐ 500 pentactra 5000 pentalia‐ 6 hexa‐ 60 hexaconta‐ 600 Hexacta 6000 hexalia‐ 7 hepta‐ 70 hepaconta‐ 700 heptacta‐ 7000 hepalia‐ 8 octa‐ 80 octaconta‐ 800 ocacta‐ 8000 ocatlia‐ 9 nona‐ 90 nonaconta‐ 900 nonactta‐ 9000 nonalia‐
Source: IUPAC, Commission on Nomenclature of Organic Chemistry (N. Lorzac’h and published in Pure Appl. Chem. 1986, 58, 1693–1696). Mathematics signs
Sign Definition Sign Definition Operations Operations þ Addition ∑ Summation Subtraction ∏ Product Ð b Multiplication a Integral ˙ Multiplication ∮ Contour integral Division Logic / Division ∧ And, conjunction ∘ Composition ∨ Or, disjunction [ Union ¬ Negation \ Intersection ) Implies Plus or minus ! Implies Minus or plus , If and only if Convolution ↔ If and only if Direct sum, variation ∃ Existential quantifier pffi Cube root 8 Universal quantifier p3 ffi n nth root ∈ A member of : Ratio 2= Not a member of ц Amalgamation ├ Assertion ∵ Because ∴ Hence, therefore
Relations Radial units ¼ Equal to 0 Minute 6¼ Not equal to 00 Second Nearly equal to Degree ffi Equals approximately, isomorphic < Less than Constants Much less than p pi ( 3.14159265) > Greater than e Base of natural logarithms Much greater than ( 2.71828183) Less than or equal to Les than or equal to Geometry ≦ Less than or equal to ⊥ Perpendicular Greater than or equal to k Parallel Greater than or equal to ∦ Not parallel ≧ Greater than or equal to ∠ Angle Equivalent to, congruent to ∨ Spherical angle = ≢ Not equivalent to, not congruent to Equal angles 1090 Mathematics signs
j Divides, divisible by 00 Double prime Similar to, asymptotically equal to 000 Triple prime ≔ Assignment √ Square root, radical ∈ A member of ! Factorial Subset of !! Double factorial Subset of or equal to ∅ Empty set, null set Superset of 1 Infinity Superset of or equal to ∂ Partial differential / Varies as, proportional to D Delta ≐ Approaches a limit, definition ∇ Nabla, del ! Tends to, maps to r2, D Laplacian operator ← Maps from 7! Maps to Trigonometry Maps into sin sine Maps into cos cosine d’Alembertian operator tan tangent cot cotangent Miscellaneous sec secant i Square root of –1 csc cosecant 0 Prime Appendices
A. Conversion factors ...... 1093 B. International Standards Organization (ISO) units ...... 1096 C. Micro‐organisms, biochemistry, and nomenclature 1. Nomenclature of biochemistry and microbiology ...... 1105 2. Bacteria ...... 1195 3. Fungi, mildew and yeasts...... 1222 Appendix A: Conversion factors
To convert Into Multiply by in.3 1 0.01639 m3 ft3 35.31 A m3 in.3 61,023.0 atm cm of mercury 76.0 m3 gal (US liq.) 264.2 atm ft of water (at 4C) 33.90 atm in. of mercury 29.92 D (at 0C) days min 1,440.0 atm kg/cm2 1.0333 days s 86,400.0 atm lb/in.2 14.70 degrees rad 0.01745 atm tons/ft2 1.058 (angle) deg/s rad/s 0.01745 B dyne g 1.020Â103 Btu ft‐lb 778.3 dyne J/cm 10–7 Btu g‐cal 252.0 dyne lb 2.248Â106 Btu J 1,054.8 Btu k‐cal 0.2520 F 4 Btu kW‐h 2.928Â10–4 ft km 3.048Â10 Btu/h g‐cal/s 0.0700 ft m 0.3048 Btu/h W 0.2931 Ft of water atm 0.02950 ft of water in. of mercury 0.8826 C ft of water kg/cm2 0.03048 cm ft 3.281Â10–2 ft of water lb/in.2 0.4335 cm in. 0.3937 ft/min cm/s 0.5080 cm mile 6.214Â10–6 ft/min m/min 0.3048 cm mm 10.0 ft/s cm/s 30.48 cm/s ft/min 1.1969 ft/s m/min 18.29 cm/s ft/s 0.03281 ft‐lb Btu 1.286Â10–3 cm/s k/h 0.036 ft‐lb g‐cal 0.3238 cm/s m/min 0.6 ft‐lb hp‐h 5.050Â10–7 cc ft3 3.531Â10–5 ft‐lb J 1.356 cc in.3 0.06102 ft‐lb k‐h 3.766Â10–7 cc m3 10–6 ft‐lb/min Btu/min 1.286Â10–3 cc gal (US liq.) 2.642Â10–4 ft‐lb/min hp 3.030Â10–5 cc 0.001 ft‐lb/min kg‐cal/min 3.24Â10–4 ft3 in.3 1,728.0 ft‐lb/min kW 2.260Â10–5 ft3 m3 0.02832 ft3 gal (US liq.) 7.48052 G ft3 1 28.32 gal cc 3,785.0 ft3/min cm.3/s 472.0 gal ft3 0.1337 ft3/min gal/s 0.1247 gal in.3 231.0 ft3/min 1/s 0.4720 gal (liq. Br. gal (US liq.) 1.20095 in.3 cc 16.39 Impt) in.3 ft3 5.787Â10–4 gal (US) gal (Imp.) 0.83267 ft3/lb cm3/g 62.43 gal of water lb of water 8.3453 in.3/oz. cc/g 0.577 gal/min ft3/s 2.228Â10–3 in.3 gal 4.329Â10–3 gal/min 1/s 0.06308 1094 Appendix A: Conversion factors
To convert Into Multiply by kW hp 1.341 kW kg‐cal/min 14.34 Agal/min 1/min 3.785 kW‐h Btu 3,413 g oz (avdp) 0.03527 kW‐h hp 1.341 –3 g lb 2.205Â10 kW‐hkg‐cal 860.5 g/cm lb/in. 5.600Â10–3 g/cc lb/ft3 62.43 L l in.3 61.02 g/cc lb/ft3 0.03613 l gal (U.S. liq.) 0.2642 g/cc oz/in.3 0.5781 1/min ft2/s 5.886Â10–4 g/cc lb/in.3 0.03613 1/min gal/s 4.403Â10–3 g/cm2 lb/ft2 2.0481 M H m/min cm/s 1.667 hp Btu/min 42.44 m/min mile/h 0.03728 hp ft‐lb/s 550.0 m/s ft/s 2.281 hp W 745.7 m/s k/min 0.06 hp‐h Btu 2,547 m/s mile/h 2.237 hp‐hkg‐cal 641.1 m‐kg cm‐dyne 9.807Â107 hp‐hk‐h 0.7457 m‐kg lb‐ft 7.233 I mile ft 5,280 in. cm 2.540 (statute) in. of atm 0.03342 mile k 1.609 mercury (statute) in. of kg/cm2 0.03453 mile yard 1,760 mercury (statute) in. of lb/in.2 0.4912 mile/h cm/s 44.70 mercury mile/h ft/min 88. in. of Water atm 2.458Â10–3 mile/h m/min 26.82 (at 4C) mile/min cm/s 2,682 in. of Water in. of mercury 0.07355 mile/min natural knots/min 0.8684 (at 4C) mm ft 3.281Â10–3 in. of Water kg/cm2 2.540Â10–3 mm in. 0.03937 (at 4C) mils cm 2.540Â10–3 in. of Water lb/in.2 0.03613 mils in. 0.001 (at 4C) O J oz g 28.3495 J Btu 9.480Â10–4 oz lb 0.0625 J/cm g 1.020Â104 oz (fluid) in.3 1.805 J/cm lb 22.48 oz (fluid) l 0.02957 oz/in.2 lb/in.2 0.0625 K 2 kg/cm2 atm 0.9678 oz/in. g/cc 1.733 2 kg/cm ft of water 32.81 P kg/cm2 in. of mercury 28.96 lb dyne 44.4823Â kg/cm2 lb/in.2 14.22 104 kg‐cal Btu 3.968 lb g 453.59 kg‐cal J 4,186 lb of water ft3 0.01602 kg‐cal kW‐h 1.163Â10–3 lb of water in.3 27.68 kg‐m Btu 9.294Â10–3 lb of water gal 0.1198 kg‐mk‐h 2.723Â10–6 lb of ft3/s 2.670Â10–4 kW Btu/min 56.92 water/min Appendix A: Conversion factors 1095
To convert Into Multiply by m2 yard2 1.196 mm2 circular mils 1,973 7 lt‐ft cm‐dyne 1.356Â10 mm2 in.2 1.550Â10–3 lb‐ft m‐kg 0.1383 yard2 cm2 8,361 lb/ft3 g/cc 0.01602 lb/ft3 kg/m3 16.02 T lb/in.3 g.cc 27.68 tons (long) lb 2,240 lb/in. g/cm 178.6 tons (metric) k 1,000 lb/in.2 atm 0.06804 tons (metric) lb 2,205 lb/in.2 ft of water 2.307 tons (short) kg 907.18 lb/in.2 in. of mercury 2.036 tons (short) lb 2,000 kb/in.2 kg/m2 703.1 tons (short) tons (long) 0.89287 lb/in.2 kg/cm2 0.07031 tons (short) tons (metric) 0.9078 Q W quarts (liq.) cc 946.4 W Btu/h 3,413 quarts (liq.) in.3 57.75 W erg/s 107 quarts (liq.) l 0.9463 Wft‐lb/min 44.27 W hp 1.341Â10–3 S Wkg‐cal/min 0.01433 cm2 circular mils 1.973Â105 W‐h Btu 3.413 cm2 ft2 1.076Â10–3 W‐hg‐cal 859.85 cm2 in.2 0.1550 W‐hhp‐h 1.341Â10–3 ft2 cm2 929.0 W‐hkg‐m 367.2 in.2 ft2 6.452 m2 cm2 10.76 Y m2 in.2 1,550 Yard cm 91.4 Appendix B: International Standards Organization (ISO) units
The International System of units (SI) was adopted Second — The second is the duration of by the 11thgeneral Conference on Weights and 9,192,631,770 periods of the radiation correspon- Measures (CGPM) in 1960. It is a coherent system ding to the transition between the two hyperfine of units built from seven SI base units, one for each levels of theground state of the cesium‐133 atom of the seven dimensionally independent base (13th CGPM, 1967). quantities: they are meter, kilogram, second, am- Ampere — The ampere is that constant current pere, Kelvin, mole, and candela, for the dimensions which, if maintained in two straight parallel con- length, mass, time, electric current, thermody- ductors of infinite length, of negligible circular namic temperature, amount of substance, and lu- cross‐section, and placed 1m apart in vacuum, minous intensity, respectively. The definitions of would produce between these conductors a force the SI base units aregiven below. The SI derived equal to 2 10–7N/m of length (9th CGPM, units are expressed as products of powers of the 1948). base units, analogous to the corresponding rela- Kelvin — The Kelvin, unit of thermodynamic tions between physical quantities but with numer- temperature, is the fraction 1/27,316 of the ther- ical factors equal to unity. modynamic temperature of the triple point of In the International System there is only one SI water (13th CGPM, 1967). unit for each physical quantity. This is either the Mole — The mole is the amount of substance of a appropriate SI base unit itself or the appropriate SI system, which contains as many elementary enti- derived unit. However, any of the approved decimal ties as there are atoms in 0.012kg of cargon‐12. prefixes, called SI prefixes, may be used to construct When the mole is used, the elementary entities decimal multiples or submultiples of SI units. must be specific and may be atoms, molecules, It is recommended that only SI units be used in ions, electrons, other particles, or specified science and technology (with SI prefixes wherever groups of such particle (14thgCPM, 1971). appropriate). Where there are special reasons for Examples of the use of the mole: making an exception to this rule, it is recom- 23 2 1mol of H2 contains about 6.022 10 H mended always to define the units used in terms molecules, or 12.044 1023 H atoms of SI units. This section was reprinted with the 1mol of HgCl has a mass of 236.04 g permission of IUPAXC. 1mol of Hg22þCl2 has a mass of 472.08 g 1mol of Hg2 has a mass of 401.18 g and a Definitions of SI base units charge of 192.97 kC 1mol of Fe0.91S has a mass of 82.88 g Meter — The meter is the length of path traveled 1mol of e– has a mass of 548.60 mg and a by light in vacuum during a time interval of 1/ charge of –96.49kC 299,792,458 of a second (17th CGPM, 1983). 1mol of photons whose frequency is 1014Hz Kilogram — The kilogram is the unit of mass; it is has energy of about 39.90 kJ equal to the mass of the international prototype Candela — The candela is the luminous int- of the kilogram (3rd CGPM, 1901). ensity, in a given direction, of a source that Appendix B: International Standards Organization (ISO) units 1097
The SI unit of Celsius temperature interval is the degree Celsius, C, which emits monochromatic radiation of frequency is equal to the Kelvin, K. The C should be treated as a single symbol, with 540 1012Hz (0.556mm ¼ l) and that has a radi- no space between the sign and the letter C. (The symbol K, and the symbol , should no longer be used.) ant intensity in that direction of (1/683) watt per cThe unitsgray and sievert are admitted for reasons of safeguarding human health. steradian (16th CGPM, 1979). dThe units radian and steradian are described as ‘SI supplementary units’. However, in chemistry, as well as in physics, they are usually treated as Symbol dimensionless derived units, and this was recognized by CIPM in 1980. Physical Name of for Since they are then of dimension 1, this leaves open the possibility of including them or omitting them in expressions of SI derived units. In Quantity SI unit SI unit practice this means that rad and sr may be used when appropriate and may be omitted if clarity is not lost thereby. Length meter m Mass kilogram kg Time second s SI prefixes Electric current ampere A Thermodynamic Kelvin K To signify decimal multiples and submultiples of temperature Amount of mole mol SI units the following prefixes may be used. substance Luminous candela cd Factor Prefix Symbol Factor Prefix Symbol intensity Frequencya hertz Hz s–1 1024 yotta Y 10–1 deci d Force Newton N mkgs–2 1021 zetta Z 10–2 centi c Pressure, stress pascal Pa Nm–2 (¼m–1kgs–2) 1018 exa E 10–3 milli m Energy, work, joule J Nm (¼m2kgs–2) 1015 peta P 10–6 micro u heat 1012 tera T 10–9 nano n Power, radiant watt W Js–1 (¼m2kgs–3) 109 giga G 10–12 pico p flux 106 meta M 10–15 femto f Electric charge coulomb C As 103 kilo k 10–18 atto a Electric volt V JC–1 (¼m2kgs–3A–1) 102 hecto h 10–21 zepto z potential, 101 deka da 10–24 yocto y electromotive force Electric ohm VA–1 (¼m2kgs–3A–2) Prefix symbols should be printed in roman (up- resistance right) type with no space between the prefix and the Electric siemens S –1 (¼m–2kg–1s3A2) conductance unit symbol. Example: kilometer, km. Electric farad F CV–1 (¼m–2kg–1s4A2) When a prefix is used with a unit symbol, the capacitance combination is taken as a new symbol that can be Magnetic flux tesla T Vsm–2 (¼kgs–2A–1) density raised to any power without the use of parentheses. Magnetic flux weber Wb Vs (¼m2kgs–2A–1) Inductance henry H VA–1s(¼m2kgs–2A–2) Examples Celsius degree CK 1cm3 ¼ (0.01m)3¼106m3 b temperature Celsius m –1 ¼ –6 –1¼ 6 –1 Luminous flux lumen 1m cdsr 1 s (10 s) 10 s Illuminance lux lx cdsrm–2 1V/cm¼ 100V/m c 1 Activity becquerel Bq s 1mmol/dm3 ¼ molm–3 (radioactive) c –1 2 –2 Absorbed dose gray Gy Jkg (¼m s ) A prefix should never be used on its own, and (of radiation) Dose sievert Sv Jkg–1 (¼m2s–2) prefixes are not to be combined into compound equivalentc prefixes. Example: pm, not mmm. (dose equivalent The names and symbols of decimal multiples index) and sub‐multiples of the SI base unit of mass, the d –1 Plane angle radian rad 1 (¼mm ) kg, which already contains a prefix, are con- Solid angled stradian? sr 1 (¼m2m–2) structed by adding the appropriate prefix to the aFor radial (circular) frequency and for angular velocity the unit rads–1,or simply s–1, should be used, and this may not be simplified to Hz. The unit word gram and symbol g. Examples: mg, not mkg; Hz should be used only for frequency in the sense of cycles per second. bThe Celsius temperature y is defined by the equation: Mg, not kkg. y/ C ¼ T/K –273.15. The SI prefixes are not be used with C. 1098 Appendix B: International Standards Organization (ISO) units
Units in use together with the SI CGPM for treating them as units. The first five atomic units in the table below have special These units are not part of the SI, but it is recog- names and symbols. Only four of these nized that they will continue to be used in appro- are independent; all others may be derived by mul- priate contexts. SI prefixes may be attached to tiplication and division in the usual way, and the some of these units, such as milliliter, ml; millibar, table includes a number of examples. mbar; megaelectronvolt, MeV; kilotonne, ktonne. The relation of atomic units to the corresponding SI units involves the values of the fundamental Physical Name of Symbol value in SI quantity the unit For unit units physical constants, and is therefore not exact. The numerical values in the table are based on the Time minute min 60s Time hour h 3600s 1986 CODATA values of the fundamental con- Time day d 86 400s stants. The numerical results of calculations in Plane degree o (p/180)rad theoretical chemistry are frequently quoted in angle Plane minute 0 (p/10 800)rad atomic units, or as numerical values in the form angle (physical quantity)/(atomic unit), so that the read- Plane second 00 (p/648 000)rad angle er may make the conversion using the current best Length A¨ ngstro¨ma a˚ 10–10m estimates of the physical constants. Area barn b 10–28m2 Volume litre l, L dm3 (¼10–3m3) Mass tonne t Mg (¼103kg) Pressure bar1 bar 105Pa (¼105Nm–2) Energy electrovoltb eV (¼e V) 1.60218 10–19 Physical Symbol Definition and value of –27 quantity Name of unit for unit unit in SI Mass unified atomic U(¼m2) 1.66054 10 kg b,c3 12 mass unit ( C)/12) –31 Mass Electron rest me me 9.1095 10 kg mass aThe a¨ngstro¨m and the bar are approved by CIPM for ‘‘temporary use Charge Elementary ee 1.6022 10–19C with SI units’’, until CIPM makes a further recommendation. However, charge they should not be introduced where they are not used at present. Action Planck constant/ hh¼h/2p 1.0546 bThe values of these units in terms of the corresponding SI units are not 2p 10–34 Js exact, since they depend on the values of the physical constants e (for the 2 2 Length Bohr a0 4pE0h /mee 5.2918 electronvolt) and N (for the unified atomic mass unit), which are deter- A 10–11m mined by experiment. 2 2 –18 c Energy Hartree Eh h /mea0 4.3598 10 J TheunifiedatomicmassunitisalsosometimescalledtheDalton,withsymbol –17 Time au of time h/Eh 2.44189 10 s Da, although the name and symbol have not been approved by CGPM. a 6 –1 Velocity au of velocity a0Eh/h 2.1877 10 s –8 Force au of force Eh/a0 8.2389 10 N –24 Momentum au of momentum h/a0 1.9929 10 Ns linear –3 Atomic units Electric au of current eEh/h 6.6236 10 A current 11 –1 Electric field au of electric field Eh/ea0 5.1422 10 Vm –30 For the purpose of quantum mechanical calcula- Electric au of electric Ea0 8.4784 10 Cm tions of electronic wave functions, it is convenient dipole dipole moment moment 2 5 to regard certain fundamental constants (and Magnetic au of magnetic h/ea0 2.3505 10 T flux density flux density combinations of such constants) as though they –23 –1 Magnetic au of magnetic mh/me ¼2mB 1.8548 10 JT were units. They are customarily called atomic dipole dipole moment momentb units (abbreviated: au), and they may be regarded aThe numerical value of the speed of light, when expressed in atomic as forming a coherent system of units for the units, is equal to the reciprocal of the fine structure constant a; c/(au of –1 calculation of electronic properties in theoretical velocity) ¼ ch/a0Eh ¼ a 137.04. bThe atomic unit of magnetic dipole moment is twice the Bohr magne- chemistry, although there is no authority from tron, mB. Appendix B: International Standards Organization (ISO) units 1099
Conversion to SI units factors have been rounded to the figures given in accordance with accepted practice. Where less than The following tables give conversion factors from six decimal places are shown, more precision is not various unitsofmeasure toSIunits. It is reproduced warranted. from NIST Special Publication 811, guide for the use of the International System of units (Superin- To convert from To Multiply by tendent of Documents, US government Printing abampere ampere (A) 1.000 000*Eþ01 Office, 1991), which in turn was derived from abcoulomb coulomb (C) 1.000 000*Eþ01 abfaarad farad (F) 1.000 000*Eþ09 IEEE Std 268‐1982, IEEE Standard Metric Practice abhenry henry (H) 1.000 000*E 09 # abmho siemens (S) 1.000 000*Eþ09 ( 1982 by the Institute of Electrical and Electron- abohm ohm (Ω) 1.000 000*E 09 ics Engineers Inc.). abvolt volt (V) 1.000 000*E 08 acre foot meter3 (m3) 1.2335Eþ03 The SI values are expressed in terms of the base, acre meter2 (m2) 4.046 873Eþ03 supplementary, and derived units of SI in order ampere hour coulomb (C) 3.600 000*Eþ03 angstrom meter (m) 1.000 000*E 10 to provide a coherent presentation of the conver- are meter2 (m2) 1.000 000*Eþ02 astronomical unit meter (m) 1.495 979Eþ11 sion factors and facilitate computations (see the atmosphere (standard) pascal (Pa) 1.013 250*Eþ05 table ‘‘International System of Units’’ in this sec- atmosphere (technical¼ pascal (Pa) 9.806 650*Eþ04 1kgf/cm2) tion). Powers of 10 can be avoided by using SI bar pascal (Pa) 1.000 000*Eþ05 barn meter2 (m2) 1.000 000*E 28 prefixes and shifting the decimal point if neces- barrel (for petroleum, meter3 (m3) sary. Conversion from a non‐SI unit to a different 42gal) board foot meter3 (m3) 2.359 737E 03 non‐SI unit may be carried out by using this table British thermal unit joule (J) 1.055 056Eþ03 (international table) in two stages, e.g. British thermal unit joule (J) 1.055 87Eþ03 1cal (thermochemical) ¼ 4.184J and 1Btu (mean) British thermal unit joule (J) 1.054 350Eþ03 (mean)¼1.05587Eþ03J. (thermochemical) ¼ þ British thermal unit (39 F) joule (J) 1.059 67Eþ03 Thus, 1Btu (mean) (1.05587E 03/4.184 cal British thermal unit (59 ) joule (J) 1.054 68Eþ03 (thermochemical) ¼ 252.359cal (thermochemical). British thermal unit (60 ) joule (J) 1.054 68Eþ03 Btu (international table)/ watt per meter 1.730 735Eþ00 Conversion factors are presented for ready (ft/hft2 F) (thermal kelvin (W/mK) conductivity) adaptation to computer readout and electronic Btu (thermochemical)/(ft/ watt per meter 1.729 577Eþ00 data transmission. The factors are written as a hft2 F) (thermal kelvin (W/mK) conductivity) number equal to or greater than 1 and less than Btu (international table)/ watt per meter 1.442 279E–01 2 10 with six or less decimal places. This number is (in/hft F) (thermal kelvin (W/mK) conductivity) followed by the letter E (for exponent), plus or Btu (thermochemical) (in/ watt per meter 1.441 314E 01 hft2 F) (thermal kelvin (W/mK) minus symbol, and two digits which indicate the conductivity) power of 10 by which the number must be multi- Btu (international table)/ watt per meter 5.192 204Eþ02 in/(sft2 F) (thermal kelvin (W/mK) plied to obtain the correct value. conductivity) Btu (thermal chemical)/in/ watt per meter 5.188 732Eþ02 For example (sft2 F) (thermal kelvin (W/mk) 3.523 90E 02 is 3.523 907 10–2 or 0.035 239 07. conductivity) Btu (international table)/h watt (W) 2.930 711E 01 Similarly: Btu (international table)/s watt (W) 1.055 056Eþ03 þ 3 Btu (thermochemical)/h watt (W) 2.928 751E–01 3.386 389E 03 is 3.386 389 10 or 3 386.389. Btu (thermochemical)/ watt (W) 1,757 250Eþ01 An asterisk (*) after the sixth decimal place indi- min Btu (thermochemical)/s watt (W) 1.054 350Eþ03 cates that the conversion factor is exact and that all Btu (international table)/ joule per meter2 1.135 653Eþ04 2 2 subsequent digits are zero. All other conversion ft (J/m ) 1100 Appendix B: International Standards Organization (ISO) units
Btu (thermochemical)/ft2 joule per meter2 1.134 893Eþ04 centimeter of mercury pascal (Pa) 1.333 22Eþ03 (J/m2) (0 C) Btu (international table)/ watt per meter2 3.154 591Eþ00 centimeter of water (4 C) pascal (Pa) 9.806 38Eþ01 (ft2h) (W/m2) centipoises pascal second (Pas) 1.000 000*E 03 Btu (international table)/ watt per meter2 1.135 653Eþ04 centistokes meter2 per second 1.000 000*E 06 (ft2s) (W/m2) (m2/s Btu (thermochemical)/(ft2 watt per meter2 3.152 481Eþ00 chain meter2 (m2) 5.067 075Eþ01 h) (W/m2) circular mill meter2 (m2) 5.067 075E 10 Btu (thermochemical)/(ft2 watt per meter2 1.891 489Eþ02 clo Kelvin meter2 per 2.003 712E 01 min) (W/m2) watt (Km2/W) Btu (thermochemical)/(ft2 watt per meter2 1.134 893Eþ04 cup milliliter (ml) 2.366Eþ02 s) (W/m2) curie becquerel (BQ) 3,700 000*Eþ10 Btu (thermochemical)/(in2 watt per meter 1.634 246Eþ06 darcy2 meter2 (m2) 9.869 233E 13 s) (W/m2) day second (s) 8.640 000*Eþ04 Btu (international table)/(h watt per meter2 5.678 263Eþ00 day (sidereal) second (s) 8.616 409Eþ04 ft2 F) kelvin (W/m2K) degree (angle) radian (rad) 1.745 329E 02 2 Btu (thermalcohemical)/(h watt per meter 5.674 466Eþ00 degree Celsius kelvin (K) Tk¼tCþ273.15 ft2 F) kelvin (W/m2K) degree centigrade See note below 2 Btu (international table)/(s watt per meter 2.044 175Eþ04 degree Fahrenheit degree Celsius ( C) tC¼(tF 32)/1.8 2 2 ft F) kelvin (W/m K) degree Fahrenheit Kelvin (K) Tk¼tF/1.8 2 Btu (thermochemical)/(s watt per meter 2.042 808Eþ04 degree Rankine Kelvin (K) TK¼TR/1.8 ft2 F) kelvin (W/m2K) Fhft2/Btu (international kelvin meter2 per 1.761 102E 01 Btu joule per kilogram 2.326 000*Eþ03 table) watt (Km2/W) (international table)/lb (J/kg) Fhft2/Btu kelvin meter2 per 1.762 280E 01 Btu joule per kilogram 2.324 444Eþ03 (thermochemical) watt (Km2/W) (thermochemical)/lb (J/kg) Fhft2/Btu (international) kelvin meter2 per 6.933 472Eþ00 Btu (international table)/ joule per kilogram 4.186 800*Eþ03 watt (lb F) (specific heat kelvin (J/kgK) Table in (thermal Km2/W capability) resistivity) Btu (thermochemical) (lb joule per kilogram 4.184 000*Eþ03 Fhft2/[Btu kelvin meter2 per 6.938 112Eþ00 F) (specific heat capacity) kelvin (J/kgK) (thermochemical) in] watt (Km2/W) Btu (international table)/ joule per meter3 3.725 895Eþ04 (thermal resistivity) ft3 (J/m3) denier kilogram per meter 1.111 111E 07 Btu (thermochemical)/ft3 joule per meter3 3.723 402Eþ04 (kg/m) (J/m3) dyne newton (N) 1.000 000*E 05 bushel meter3 (m3) 3.523 907E 02 dyne/cm N/m 1.000 000E 03 calorie (international joule (J) 4.186 800*Eþ00 dyne/cm mN/m 1.000 000 table) dyne cm newton meter 1.000 000*E 07 calorie (mean) joule (J) 4.190 02Eþ00 (Nm) calorie (thermochemical) joule (J) 4.184 000*Eþ00 dyne/cm2 pascal (Pa) 1.000 000*E 01 calorie (15 C) joule (J) 4.185 80Eþ00 electronvolt joule (J) 1.602 19E 19 calorie (20 C) joule (J) 4.181 90Eþ00 EMU of capacitance farad (F) 1.000.000*Eþ09 calorie (kilogram, joule (J) 4.186 800*Eþ03 EMU of current ampere (A) 1.000 000*E 01 international table) EMU of electric potential volt (V) 1.000 000*E 08 calorie (kilogram, mean) joule (J) 4.190 02Eþ03 EMU of inductance henry (H) 1.000 000*E 09 calorie (kilogram, joule (J) 4.184 000*Eþ03 EMU of resistance ohm (m) 1.000 000*E 09 thermochemical) erg joule (J) 1.000 000*E 07 cal joule per meter2 4.184 000*Eþ04 erg/cm2s watt per meter2 (W/ 1.000 000*E 03 (thermochemical)/cm2 (J/m2) m2) cal (international table)/g joule per kilogram 4.186 800*Eþ03 erg/s watt(W) 1.000 000*E 07 (J/kg) faraday (based on carbon‐ coulomb (C) 9.648 70Eþ04 cal joule per kilogram 4.184 000*Eþ03 12) (thermochemical)/g (J/kg) faraday (chemical) coulomb (C) 9.649 57Eþ04 cal (international table)/ joule per kilogram 4.186 800*Eþ03 faraday (physical) coulomb (C) 9.652 19Eþ04 (g C) kelvin (J/kgK) fathom meter (m) 1.828 8Eþ00 cal (thermochemical)/(g joule per kilogram 4.184 000*Eþ03 fermi (femtometer) meter (m) 1.000 000*E 15 C) kelvin (J/kgK) fluid ounce (USA) meter3 (m3) 2.957 353E 05 cal (thermochemical)/min watt (W) 6.973 333E 02 foot meter (m) 3.048 000*E 01 cal (thermochemical)/s watt (W) 4.184 000*Eþ00 foot (USA survey) meter (m) 3.048 006E 01 cal watt per meter2 6.973 333E 02 foot of water (39.2 F) pascal (Pa) 2.988 98Eþ03 (thermochemical)/(cm2 (W/m2) ft2 meter2 (m2) 9.290 304E 02 min) ft2/h (thermal diffusivity) meter2 per second 2.580 640*E 05 cal (thermochemical)/(cm2 watt per meter2 4.184 000Eþ04 (m2/s) s) (W/m2) ft2/ meter2 per second 9.290 340E 02 cal (thermochemical)/(cm watt per meter 4.184 000Eþ02 s (m2/s) s C) kelvin (W/mK) ft3 (volume, section meter3 (m3) 2.831 685E 02 cd/in2 candela per meter2 1.550 003Eþ03 modulus) (cd/m2) ft3/min meter3 per second 4.719 474E 04 carat (metric) kilogram (kg) 2.000 000*E 04 (m3/s) Appendix B: International Standards Organization (ISO) units 1101
ft3/s meter3 per second 2.831 685E 02 in4 (second moment of meter4 (m4) 4.162 314E 07 (m3/s) area)b ft4 (second moment of meter4 (m4) 8.630 975E 03 in/s meter per second 2.540 000*E 02 area)b (m/s) ft/h meter per second 8.466 667E 05 in/s2 meter per second2 2.540 000*E 02 (m/s) (m/s2) ft/min meter per second 5.080 000*E 03 kayser 1 per meter (1/m) 1.000 000*Eþ02
(m/s) kelvin degree Celsius tC¼TK 273.15 ft/s meter per second 3.048 000*E 01 kilocalorie (international joule (J) 4.186 800*Eþ03 (m/s) table) ft/s2 meter per second2 3.048 000E 01 kilocalorie (mean) joule (J) 4.190 02Eþ03 (m/s2) kilocalorie joule (J) 4.184 000*Eþ03 footcandle lux (lx) 1.076 391Eþ01 (thermochemial) footlambert candela per meter2 3.426 259Eþ00 kilocalorie joule (J) 6.973 333Eþ01 (cd/m2) (thermochemical)/min ft lbf joule (J) 1.355 818Eþ00 kilocalorie watt (W) 4.184 000*Eþ03 ft lbf/h watt (W) 3.766 161E 04 (thermochemical)/s ft lbf/min watt (W) 2.259 697E 02 kilogram‐force (kgf) newton (N) 9.806 650*Eþ00 ft lbf/s watt (W) 1.355 818Eþ00 Kgfm newton meter (N m) 9.806 650*Eþ00 ft·poundal joule (J) 4.214 011E–02 Kgfs2/m (mass) kilogram (kg) 9.806 650*Eþ00 g, standard acceleration of meter per second2 9.806 650*Eþ00 Kgf/cm2 pascal (Pa) 9.806 650*Eþ04 free fall (m/s2) Kgf/m2 pascal (Pa) 9.806 650*Eþ00 gal meter per second2 1.000 000*E 02 Kgf/mm2 pascal (Pa) 9.806 650*Eþ06 (m/s2) Km/h meter per second 2.777 778E 01 gallon (Canadian liquid) meter3 (m3) 4.546 090*E 03 (m/s) gallon (UK liquid) meter3 (m3) 4.546 090*E 03 kilopond (1kp¼1kgf) newton (N) 9.806 650*Eþ00 gallons (USA liquid) meter3 (m3) 3.785 412E 03 KWh pascal (Pa) 6.894 757Eþ06 gallon (USA liquid) per meter3 per second 4.381 264E 08 Kip (1,000lbf) newton (N) 4.448 222Eþ03 day (m3/s) Kip/in2 (ksi) pascal (Pa) 6.894 757Eþ06 gallon (USA liquid) per meter3 per second 6.309 020E 05 knot (international) meter per second 5.144 444E 01 minute (m3/s) (m/s) gallon (USA liquid) per (hp meter3 per joule 1.410 089E 09 lambert candela per meter2 1/p*Eþ04 h), specific fuel (m3/J) (cd/m2) consumption (SFC) langley joule per meter2 4.184 000*Eþ04 gamma tesla (T) 1.000 000*E 09 (J/m2) gauss tesla (T) 1.000 000*E 04 light yeare meter (m) 9.460 73Eþ15 gilbert ampere (A) 7.957 747E 01 liter meter3 (m3) 1.000 000*E 03 gill (UK) meter3 (m3) 1.420 654E 04 lumen per ft2 lumen per meter2 1.076 391Eþ01 gill (USA) meter3 (m3) 1.182 941E 04 (lm/m2) grade degree (angular) 9.000 000E 01 maxwell weber (Wb) 1.000 000*E 08 grade radian (rad) 1.570 796E 02 mho siemens (S) 1.000 000*Eþ00 grain kilogram (kg) 6.497 891*E 05 microinch meter (m) 2.540 000*E 08 grain/gal (USA liquid) kilogram per meter3 1.711 806E 02 micron meter (m) 1.000 000*E 06 (kg/m3) Mil meter (m) 2.540 000*E 05 gram kilogram (kg) 1.000 000*E 03 mile (international) meter (m) 1.609 344*Eþ03 g/cm3 kilogram per meter3 1.000 000*Eþ01 mile (USA statute) meter (m) 1.609 3Eþ03 (kg/m3) mile (international meter (m) 1.852 000*Eþ03 gram/force/cm2 pascal (Pa) 9.801 650*Eþ03 nautical) hectare meter2 (m2) 1.000 000*Eþ04 m2 (international) meter2 (m2) 2.589 988Eþ06 horsepower watt (W) 7.456 999Eþ02 mi2 (USA statute) meter2 (m2) 2.589 998Eþ06 (550ftlbf/s) mi/h (international) meter per second 4.470 400*E 01 horsepower (boiler) watt (W) 9.809 50Eþ03 (m/s) hosepower (electric) watt (W) 7.460 000*Eþ02 mi/h (international) Kilometer per hour 1.609 344*Eþ00 horsepower (metric) watt (W) 7.354 99Eþ02 (km/h) horsepower (water) watt (W) 7.460 43Eþ02 mi/min (international) meters per second 2.682 240*Eþ01 horsepower (UK) watt (W) 7.457 0Eþ02 (m/s) hour second (s) 3.600 000*Eþ03 mi/s (international) meter per second 1.609 344*Eþ03 hour (sidereal) second (s) 3.590 170Eþ03 (m/s) hundredweight (long) kilogram 5.080 235Eþ01 millibar pascal (Pa) 1.000 000*Eþ02 hundredweight (short) kilogram (kg) 4.535 924Eþ01 millimeter of mercury pascal (Pa) 1.333 220Eþ02 inch meter (m) 2.540 000*E 02 (0 C)c inch of mercury (32 F)c pascal (Pa) 3.386 38Eþ03 millimeter meter (m) 1.000 000E 03 inch of mercury (60 F)c pascal (Pa) 3.376 85Eþ03 minute (angle) radian (rad) 2.908 882E 04 inch of water (39.2 F) pascal (Pa) 2.490 82Eþ02 minute second (s) 6.000 000*Eþ01 inch of water (60 F) pascal (Pa) 2.488 4Eþ02 minute (sidereal) second (s) 5.983 617Eþ01 in2 meter2 (m2) 6.451 600*E 04 nanometer meter (m) 1.000 000E 09 in2 (volume; section meter3 (m3) 1.638 706E 05 oersted ampere per meter 7.957 747Eþ01 modulus)d (A/m) in3/min meter3 per second 2.731 177E 07 ohm centimeter ohm meter (m) 1.000 000*E 02 (m3/s) ohm circular‐mil per ft ohm meter (m) 1.662 426E 09 1102 Appendix B: International Standards Organization (ISO) units
ounce (avoirdupois) kilogram (kg) 2.834 952E 02 lb/s kilogram per second 4.535 924E 01 ounce (troy or kilogram (kg) 3.110 348E 02 (kg/s) apothecary) lb/yd3 kilogram per meter3 5.932 E 01 ounce (UK fluid) meter3 (m3) 2.841 307E 05 (kg/m3) ounce (USA fluid) meter3 (m3) 2.957 353E 05 poundal newton (N) 1.382 550E 01 ounce‐force newton (N) 2.780 139E 01 poundal/ft2 pascal (Pa) 1.488 164Eþ00 Ozf in newton meter (N 7.061 552E 03 poundal s/ft2 pascal second (Pas) 1.488 164Eþ00 m) pound‐force (lbf)h newton (N) 4.448 222Eþ00 oz (avoirdupois)/gal (UK kilogram per meter3 6.236 023Eþ00 Lbf ft Newton meter (N 1.355 818Eþ00 liquid) (kg/m3) m) oz (avoirdupois)/gal (USA kilogram per meter3 7.489 152E 00 Lbf ft/in Newton meter per 5.337 866Eþ01 liquid) (kg/m3) meter (Nm/m) oz (avoirdupois)/in kilogram per 1.729 994E 03 Lbf in Newton meter (N 1.129 848E 01 meter3 m) Lbf in/in Newton meter per 4.448 222Eþ00 oz (avoirdupois)/ft2 kilogram per meter2 3.051 517E 01 meter (Nm/m) (kg/m2) Lbf s/ft2 pascal second (Pas) 4.788 026Eþ01 oz (avoirdupois)/yd2 kilogram per meter2 3.390 575E 02 Lbf s/in2 pascal second (Pas) 6.894 757Eþ03 (kg/m2) Lbf/ft newton per meter 1.459 390Eþ01 parsec meter (m) 3.085 678Eþ16 (N/m) peck (USA) meter3 (m3) 8.809 768E 03 Lbf/ft2 pascal (Pa) 4.788 026Eþ01 pennyweight kilogram (kg) 1.555 174E 03 Lbf/in newton per meter 1.751 268Eþ02 perm (0 C) kilogram per pascal 5.721 35E 11 (N/m) second meter2 (kg/ Lbf/in2 (psi) pascal (Pa) 6.894 757Eþ03 Pasm2) Lbf/lb [thrust/weight newton per 9.806 650Eþ00 perm (23 C) kilogram per pascal 5.745 25E 11 (mass) ratio] kilogram (N/kg) second meter2 (kg/ quad joule (J) 1.055Eþ18 Pasm2) quart (USA dry) meter3 (m3) 1.101 221E 03 perm in (0 C) kilogram per pascal 1.453 22E 12 quart (USA liquid) meter3 (m3) 9.463 529E 04 second meter (kg/Pa Rad (absorbed dose) gray (Gy) 1.000 000*E 02 sm) Rem (dose equivalent) sievert (Sv) 1.000 000*E 02 perm in (23 C) kilogram per pascal 1.459 29E 12 Rhe 1 per pascal second 1.000 000*Eþ01 second meter (kg/Pa (1/Pas) sm) rod meter (m) 5.029 210Eþ00 phot lumen per meter2 1.000 000*Eþ04 roentgen coulomb per 2.58E 04 (lm/m2) kilogram (C/kg) pica (printer’s) meter (m) 4.217 518E 03 second (angle) radian (rad) 4.848 137E 06 pint (USA dry) meter3 (m3) 5.506 105E 04 second (sidereal) second (s) 9.972 696E 01 ping (USA liquid) meter3 (m3) 4.731 765E 04 shake second (s) 1.000 000*E 08 point (printer’s) meter (m) 3.514 598*E 04 slug kilogram (kg) 1.459 390Eþ01 poise (absolute viscosity) pascal second (Pas) 1.000 000*E 01 slug/fts pascal second (Pas) 4.788 026Eþ01 pound (avoirdupois)g kilogram (kg) 4.535 924E 01 slug/ft3 kilogram per meter 5.153 788Eþ02 pound (troy or kilogram (kg) 3.732 417E 01 (kg/m3) apothecary) statampere ampere (A) 3.335 641E 10 lb/ft kilogram per meter 1.488 164Eþ00 statcoulomb coulomb (C) 3.335 641E 10 (kg/m) stratfarad farad (F) 1.112 650E 12 lbft2 (moment of inertia) kilogram meter2 (kg 4.214 011E 02 stathenry henry (H) 8.987 552Eþ11 m2) statmho siemens (S) 1.112 650E 12 lbft2 (moment of inertia) kilogram meter2 (kg 2.926 397E 04 statohm ohm () 8.987 552Eþ11 m2) statvolt volt (V) 2.997 925Eþ02 lb/fth pascal second (Pas) 4.133 789E 04 stere meter3 (m3) 1.000 000*Eþ00 lb/fts pascal second (Pas) 1.488 164E 00 stilb candela per meter2 1.000 000*Eþ04 lb/ft2 kilogram per meter2 4.882 428Eþ00 (cd/m2) (kg/m2) stokes (kinematic meter2 per second 1.000 000*E 04 lb/ft3 kilogram per meter3 1.601 846Eþ01 viscosity) (cd/m2) (kg/m3) tablespoon milliliter (ml) 1.479Eþ01 lb/gal (UK liquid) kilogram per meter3 9.977 633Eþ01 teaspoon meter3 (m3) milliliter 4.929Eþ01 (kg/m3) (ml) lb/gal (USA liquid) kilogram per meter3 1.198 264Eþ02 tex kilogram per meter 1.000 000*E 06 (kg/m3) (kg/m) lb/h kilogram per second 1.259 979E 04 therm (EEG)i joule (J) 1.055 060*Eþ08 (kg/s) therm (USA)i joule (J) 1.054 804*Eþ08 lb/hph (specific fuel kilogram per joule 1.689 659E 07 ton (assay) kilogram (kg) 2.916 667E 02 consumption, SFC) (kg/J) ton (long, 2240lb) kilogram (kg) 1.016 047Eþ03 lb/in kilogram per meter 1.785 797E 01 ton (metric) kilogram (kg) 1.000 000*Eþ03 (kgm) ton (explosive energy of joule (J) 4.184Eþ09j lb/in3 kilogram per meter3 2.767 990Eþ04 one tone of TNT) (kg/m3) ton of refrigeration watt (W) 3.517Eþ03 lb/min kilogram per second 7.559 873E 03 (12,000Btu/h) (kg/s) ton (register) meter3 (m3) 2.831 685Eþ00 Appendix B: International Standards Organization (ISO) units 1103
ton (short, 2,000lb) kilogram (kg) 9.071 847Eþ02 ton (long)/yd3 kilogram per meter3 1.328 939Eþ03 in others countries into agreement. The U.S. yard (kg/m3) was changed from 3600/3937 m to 0.9144 m ton (short)/yd3 kilogram per meter3 1.186 553Eþ03 (kg/m3) exactly. The new length is shorter by exactly two ton (short)/h kilogram per second 2.519 958E 01 (kg/s) parts in a million. At the same time it was decided ton‐force (2,000lbf) newton (N) 8.896 443Eþ03 that any data in feet derived from and published tonne kilogram (kg) 1.000 000*Eþ03 torr (mmHg, 0 C)c pascal (Pa) 1.333 22Eþ02 as a result ofgeodetic surveys within the United unit pole weber (Wb) 1.256 637E 07 ¼ Wh joule (J) 3.600 000*Eþ03 States would remain with the old standard (1 ft Ws joule (J) 1.000 000*Eþ00 1200/3937 m) until further decision. This foot is W/cm2 watt per meter2 (W/ 1.000 000*Eþ04 m2) named the U.S. survey foot and has the following W/in2 watt per meter2 (W/ 1.550 003*Eþ03 m2) relationships: Yard meter (m) 9.144 000*E 01 yd2 meter2 (m2) 8.361 274E 01 1 rod (pole or perch) ¼ 16 ½ feet yd3 meter3 (m3) 7.645 549E 01 ¼ yd3/min meter3 per second 1.274 258E 02 1 chain 66 feet m3/s) 1 mile (U.S. statute) ¼ 5280 feet year (365days) second (s) 3.153 600*Eþ07 year (sidereal) second (s) 3.155 815Eþ07 year (tropical) second (s) 3.155 693Eþ07 atmos Torr mmHz psi
Note—the centigrade temperature scale is obsolete. The unit, degree Torr 0.00131579 1 1000 0.01933672 centigrade, is only approximately equal to the degree Celsius mmHz 1.31579 0.001 1 1.933672 a The darcy is a unit for measuring permeability of porous solids 10 6 10 5 b This is sometimes called the moment of section or area moment of Psi 0.0680456 51.7151 51715.1 1 inertia of a plane section about a specified axis cConversion factors for mercury manometer pressure units are calculated using the standard value for the acceleration of gravity and the density of To convert a pressure value from a unit in the mercury at the stated temperature. Higher levels of precision are not left hand column to a new unit, multiply the justified because the definitions of the units do not take into account the compressibility of mercury or the density value change caused by the revised practical temperature scale, ITS‐90. dThe exact conversion factor is 1.638 706 4*E 05 eThis conversion factor is based on the astronomical unit of time of one Conversion of temperatures day (86,400s); an interval of 36, 525days is one Julian century See the Astronomical Almanac for the Year (1991) USA government From To Printing Office, Washington, DC, pK6 f In 1964 the general conference on weights and measures re‐established Celsius Fahrenheit tF ¼ (tc 1.8)þ32 the name liter as a special name for the cubic decimeter. Between 1901 Kelvin Tk ¼ tcþ273.15 3 and 1964, the liter was slightly larger (1.000028dm ); in the use of high‐ Rankin TR¼ (tcþ273.15) 1.8 ðtF 32Þ accuracy volume data of that time interval, this fact must be kept in mind Fahrenheit Celsius tc ¼ 1:8 g ðtF 32Þ The exact conversion factor is 4.535 923 7 *E 01 Kelvin tk ¼ 1:8 þ 273:15 h The exact conversion factor is 4.448 221 615 260 5 *Eþ00 Rankin TR¼tFþ459.67 i The therm (EEC) is legally defined in the Council Directive of 20 Decem- Kelvin Celsius tc ¼TK 273.15 ber 1979, Council of the European Communities. The therm (USA) is Rankin TR¼TK 1.8 legally defined in the Federal Register of July 27, 1968. Although, the Rankin Fahrenheit tF ¼TR–459.67 tR therm (EEC), which is based on the International Table Btu, is frequently Kelvin tk ¼ 1:8 used by engineers in the USA, the therm (USA) is the legal unit used by the USA natural gas industry jDefined (not measured) value
Note concerning the foot: Designation of large numbers The U.S. Metric Law of 1866gave the relation- U.S.A. Other countries ship, 1 meter equals 39.37 inches. Since 1893 the 106 million million 109 billion milliard U.S. yard has been derived from the meter. In 1012 trillion billion 1959 a refinement was made in the definition of 1015 quadrillion billard 1018 quintillion trillion the yard to bring the U.S. yard and the yard used 1104 Appendix B: International Standards Organization (ISO) units
Conversion factors for pressure units Commonly used units Pa kPa MPa bar
Pa 1 0.001 0.000001 0.00001 kPa 1000 1 0.001 0.01 Area MPa 1,000,000 1,000 1 10 bar 100,000 100 0.1 1 Density atmos 101,325 101.325 0.101325 1.01325 Torr 133.322 0.133322 0.000133322 0.00133322 Energy mmHz 0.133322 0.000133322 1.33322 107 1.33322 10 6 Flow rate psi 6894.757 6.894757 0.006894757 0.06894757 Force Frequency atmos Torr mmHz psi Heat Pa 9.8692 0.0075006 7.5006 0.0001450377 10 6 kPa 0.0098692 7.5006 7500.6 0.1450377 MPa 9.8692 7500.0 7,500,600 145.0377 Commonly used units bar 0.98692 750.06 750,060 14.50377 atmos 1 760 760,000 14.69594
Heat capacity value by the factor appearing in the column for Heat flux the new unit. For example: Length 1kPa¼ 9.8692 10–3 atmos Mass 1 Torr ¼ 1.33322 10–4 MPa Perms, permenance, and permeability Notes: mmHz is often referred to as ‘‘micron’’ Power Torr is essentially identical to mmHg Pressure psi is pounds per square inch Strength Sub‐units of the meter Stress 1m¼1.0 Eþ0m Temperature ¼ 1.0 E 1dm Thermal conductivity ¼1.0 E 2cm Thermal diffusivity ¼1.0 E 3mm Time ¼1.0 E 6mm Torque ¼1.0 E 9nm Velocity ¼1.0 E 10A˚ Viscosity Volume Work Appendix C: Micro‐organisms, biochemistry, and nomenclature
1. Nomenclature of Acid A substance that releases hydrogen biochemistry and micro‐ ions when it is dissolved in water. organisms Acidic dye See anionic dye. Acidophile An acid‐loving organism that Abiotic factor A physical feature of the en- grows best in an environment with a pH vironment that interacts with organisms. of 4.0–5.4. ABO blood group system One of the blood Acme (sometimes referred to a ful- typing systems that is based on the pres- minating) During the illness phase of the ence or absence of blood group antigens A disease process, the time of most intense and B on red blood cells. signs and symptoms. Abortive infection Viral infection in which Acne Skin condition caused by bacterial in- viruses enter a cell but are unable to express fection of hair follicles and the ducts of all of their genes to make infectious progeny. sebaceous glands. Abscess An accumulation of pus in a cavity Acquired Immune Deficiency Syndrome hollowed out by tissue damage. (AIDS) An infectious disease caused by Absorbance (Al) A dimensionless number the human immunodeficiency virus that that indicates how well a solution of a sub- destroys the individual’s immune system. stance absorbs light of a given wavelength. Acquired immunity Immunity obtained in It is defined as the negative logarithm of some manner other than by heredity. l the fraction of light wavelength that Acridine derivative A chemical mutagen passes through a sample of the solution; that can be inserted between bases of the its value depends on the length of the DNA double helix, causing frameshift light path, the concentration of the solu- mutations. tion, and the extinction coefficient of the Acrobe An organism that uses oxygen, in- substance at that wavelength. cluding ones that must have oxygen. Absorption Process in which light rays are Actinomycetes Gram‐positive bacteria that neither passed through nor reflected off an tends to form filaments. object but are retained and either trans- Action potential A wave of transient depo- formed to another form of energy or used larization that travels along the membrane in biological processes. of a nerve cell (or any other kind of excit- Accidental parasite A parasite that invades able cell, such as a muscle cell) as a result of an organism other than its normal host. fluxes of ions across the membrane. A Acetylcholinesterase An enzyme found in nerve impulse. cholinergic synapses that breaks down Activated sludge system Procedure in acetylcholine and thus terminates its action which the effluent from the primary stage on the postsynaptic cell. of sewage treatment is agitated, aerated, 1106 Appendix C: Micro‐organisms, biochemistry, and nomenclature
and added to sludge containing aerobic protein, that forms a non‐specific host‐ organisms that digest organic matter. defense mechanism during an acute phase Activated state With respect to a chemical response. reaction, a transient high‐energy state of a Acute phase response A response to an reactant molecule (such as an unfavorable acute illness that produces specific blood electron configuration or strained confor- proteins called acute phase proteins. mation) that enables the molecule to un- Acute respiratory disease (ARD) Viral dis- dergo the reaction. ease that occurs in epidemics with cold Activation energy The energy required to symptoms as well as fever, headache, start a chemical reaction. and malaise, sometimes causes viral pneu- Active immunity Immunity created when monia. an organism’s own immune system pro- Adenovirus A medium‐sized, naked DNA duces antibodies or other defenses against virus that is highly resistant to chemical an agent recognizes as foreign. agents and often causes respiratory infec- Active immunization Use of vaccines to con- tions or diarrhea. trol diseases by increasing herd immunity Adenylylation In cells, the transfer of an through stimulation of the immune response. adenylyl moiety from AT to another mole- Active site The site on an enzyme molecule cule. Some enzymes are regulated by re- where the substrate binds and where the versible adenylylation. reaction is facilitated. It is often a cleft or Adherence The attachment of a micro‐ pocket in the surface of the enzyme. organism to a host’s cell surface. Active transport (1) Movement of mole- Adhesin A protein or glycoprotein on at- cules or ions across a membrane against a tachment pili (fimbriae) or capsules that concentration gradient; requires expendi- help a micro‐organism attach to a host cell. ture of energy from ATP (2) The transport Adipocytes Fat cells; cells that are of a substance across a biological mem- specialized for storing triacylglycerols and brane by a mechanism that can work for releasing them to the blood in the form against a concentration (or electrochemi- of fatty acids and glycerol as required. cal) gradient. It always requires the ex- Adrenergic receptors Cell‐surface receptors penditure of cellular energy. Compare that bind epinephrine and norepinephrine. facilitated transport, passive transport. There are several different types with Acute disease A disease that develops rap- somewhat different ligand specificities idly and runs it course quickly. and effects (The term comes from adrena- Acute hemorrhagic conjunctivitis Eye dis- line, the old name for epinephrine.) ease caused by an enterovirus. Adsorption The attachment of the virus to Acute inflammation The relatively short the host cell in the replication process. duration of inflammation during which Aerobic respiration Processes in which aer- time host defenses destroy invading obic organisms gain energy from the catab- microbes and repair tissue damage. olism of organic molecules via the Krebs Acute necrotizing ulcerative gingivitis cycle and oxidative phosphorylation. (ANUG) A severe form of periodontal Aerosol A cloud of tiny liquid droplets sus- disease. pended in air. Also known as Trench Mouth. Aerotolerant anaerobe A bacterium that Acute phase protein Protein, such as can survive in the presence of oxygen but C‐reactive protein or mannose‐binding does not use oxygen in its metabolism. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1107
Affinity constant See association constant. monosaccharide (i.e. reducing R–CH¼O
Aflatoxin Fungal toxin that is a potent car- to R–CH2–OH) cinogen, found in food made from con- Aldose A monosaccharide in which the car- taminated grain or peanuts infested with bonyl group comes at the end of the chain Aspergillus flavus and other aspergilli. and thus represents an aldehyde group. African sleeping sickness Disease of equa- Compare ketose. torial Africa caused by protozoan blood Algae (singular: alga) Photosynthesis, eu- parasites of the genus Trypanosoma. karyotic organisms in the kingdoms Pro- Also known as Trypanosomiasis. tista and Plantae. Agammaglobulinemia Primary immunode- Alkaline Condition caused by an abundance ficiency disease caused by failure of B cells to of hydroxyl ions (OH–) resulting in a pH of develop, resulting in lack of antibodies. greater than 7.0. Agar A polysaccharide extracted from cer- Also known as basic. tain marine algae and used to solidify me- Alkaliphile A base‐ (alkaline) loving organ- dium for the growth of micro‐organisms. ism that grows best in an environment with Agar plate A plate of nutrient medium soli- a pH of 7.0–11.5. dified with agar. Alkaloids A large group of nitrogenous Agglutination reaction A reaction of anti- basic substances found in plants. Most of bodies with antigens the results in aggluti- them taste bitter, and many are pharmaco- nation, the clumping together of cells or logically active. The term can also be used other large particles. for synthetic compounds. Agonist In molecular biology, a substance Alkylating agent A chemical mutagen that
that mimics the cellular effects of a natural can add alkyl groups (–CH3)toDNA compound (such as a hormone or neuro- bases, altering their shapes and causing transmitter) by binding to and activating the errors in base pairing. same cellular receptor. Compare antagonist. Allele The form of a gene that occupies the Agranulocyte A leukocyte (monocyte or same place (locus) on the DNA molecule as lymphocyte) that lacks granules in the cy- another form but may carry different in- toplasm and has rounded nuclei. formation for a trait. A Helix A right‐hand helix structure of Allergen Anordinarilyinnocuousforeignsub- nucleic acid duplexes that has a smaller stancethatcanelicitanadverseimmunological pitch and a larger diameter than the B‐DNA response in a sensitized person. helix. It is the structure adopted by RNA Allergy When the immune system reacts in duplexes and RNA–DNA hybrid molecules an exaggerated or inappropriate way to a AIDS (Acquired Immune Deficiency Syn- foreign substance. drome) An infectious disease caused by Also known as hypersensitivity. the human immunodeficiency virus that Allograft A graft of tissue between two destroys the individual’s immune system. organisms of the same species those are Alcoholic fermentation Fermentation in not genetically identical. which pyruvic acid is reduced to ethyl al- Allosteric With respect to enzymes, an ef- cohol by electrons from reduced NAD fect that is produced on the activity of one (NADH) part of an enzyme (such as an active site) Alditols Compounds that are produced by the binding of an effector to a different by reducing the carbonyl group on a part of the enzyme. 1108 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Allosteric site The site at which a non‐com- Aminoglycoside An antimicrobial agent petitive inhibitor binds. that blocks bacterial protein synthesis. Alpha (a) hemolysin A type of enzyme that Amino terminus See N‐terminus. partially lyses red blood cells, leaving a Amoebic dysentery Severe, acute form of greenish ring in the blood agar medium amebiasis, caused by Entamoeba histolytica. around the colonies. Amoeboid movement Movement by means Alpha (a) hemolysis Incomplete lysis of red of pseudopodia that occurs in cells without blood cells by bacterial enzymes. walls, such as amoebas and some white Alternative pathway One of the sequences blood cells. of reactions in non‐specific host responses Amphibolic pathway A metabolic pathway by which proteins of the complement sys- that can yield either energy or building tem are activated. blocks for synthetic reactions. Alternative splicing The splicing of a eu- Amphipathic For a molecule, the property karyotic RNA transcript in different ways, of having both hydrophobic and hydro- to include or exclude certain exons from philic portions. Usually one end or side of the final mRNA. the molecule is hydrophilic and the other Alu elements DNA sequences about 300 end or side is hydrophobic. base pairs long that occur in many copies Amphitrichous The presence of flagella at scattered throughout the genome of mam- both ends of the bacterial cell. mals; the human genome has hundreds of Ampholyte A substance whose molecules thousands of them. They may serve an un- have both acidic and basic groups. known function, or they may be purely ‘‘par- Anabolic pathway A chain of chemical asitic,’’ spreading as mobile elements reactions in which energy is used to syn- through the genome. thesize biologically important molecules. Alveolus A saclike structure arranged in Anabolism Chemical reactions in which en- clusters at the ends of the respiratory ergy is used to synthesize large molecules bronchioles, having walls one cell layer from simple components. thick, where gas exchange occurs. Also known as synthesis. Amantadine An antiviral agent that pre- Anaerobe An organism that does not use vents penetration by influenza A virus. oxygen, including some organisms that are Ames test Test used to determine whether a killed by exposure to oxygen. particular substance is mutagenic, based on Anaerobic Refers to the absence of oxygen itsability toinducemutationsinauxotrophic or the absence of a need for it; processes bacteria. A strain of the bacterium Salmonel- that must or can occur without oxygen are la typhimurium having a mutation that called anaerobic processes. disables an enzyme necessary for histidine Anaerobic respiration Respiration in utilization is exposed to the substance in which the final electron acceptor in the question and plated on a medium lacking electron transport chain is an inorganic histidine. A reversion mutation that acti- molecule other than oxygen, e.g., sulfate, vates the mutant enzyme causes the cells to nitrate, etc. grow on this medium. Analytical study An epidemiological study Amino acid An organic acid containing an that focuses on establishing cause‐and‐ef- amino group and a carboxyl group, com- fect relationships in the occurrence of dis- posing the building blocks of proteins. eases in populations. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1109
Anamnestic response Prompt immune re- cellular receptor for the compound and sponse due to ‘‘recall’’ by memory cells. blocking its action. Compare agonist. See secondary response. Anthrax A zoonosis caused by Bacillus Anaphylactic shock Condition resulting anthracis that exists in cutaneous, respira- from a sudden extreme drop in blood pres- tory (‘‘woolsorters disease’’), or intestinal sure caused by an allergic reaction. forms; transmitted by endospores. Anaphylaxis An immediate, exaggerated al- Antibiosis The natural production of an an- lergic reaction to antigens, usually leading timicrobial agent by a bacterium or fungus. to detrimental effects. Antibiotic A chemical substance produced Androgens The male sex hormones; specif- by micro‐organisms that can inhibit the ically, the steroid hormones testosterone, growth of or destroy other micro‐organisms. dihydrotestosterone, and androstenedione, Antibodies A set of related proteins that are which act mainly to promote male sexual produced by B lymphocytes and can bind development and maintain male sex char- with specificity to antigens. Some types are acteristics. released into body fluids and mediate hu- Angstrom (A˚) Unit of measurement equal moral immunity; other types are retained to 0.0000000001 m, or 10–10 m. No longer on the surface of the B cell or are taken up officially recognized. and displayed by some other cell types. Animalia The kingdom of organisms to Antibody A protein in response to an anti- which all animals belong. gen that is capable of binding specifically to Animal passage The rapid transfer of a that antigen. pathogen through animals of a species sus- Also known as immunoglobulin. ceptible to infection by the pathogen. Antibody titer The quantity of a specific | Anion \ a‐|nı¯ ‐ ə n\ [GK, neut. of anio¯n, prp. antibody in an individual’s blood, often Of anienai to go up, fr. ana‐ þ ienai to go] measured by means of agglutination, (1834) n. A negatively charged ion. reactions. | Anionic \|a‐(|)n¯ ı‐ a¨‐nik\ (ca. 1920) adj. Anticodon A three‐base sequence in tRNA Anionic dye An ionic compound, used for that is complementary to one of the mRNA staining bacteria, in which the negative codons, forming a link between each codon ion imparts the color. and the corresponding amino acid. Also known as acidic dye. Antigen A substance that the body identi- Anomers Stereoisomes of cyclized mono- fies as foreign and toward which it counts saccharide molecules differing only in the an immune response. configuration of the substituents on the Also known as immunogen. carbonyl carbon (This carbon is a center Antigen binding site The site on the anti- of Chirality in the cyclized but not in the body to which the antigen (epitope) binds) open‐chain form of the molecule.) Antigen challenge Exposure to a foreign Antagonism The decreased effect when two antigen. antibiotics are administered together. Antigenic determinant See epitope. Antagonist In biochemistry, a substance Antigenic drift Process of antigenic varia- that counteracts the cellular effects of a tion that results from mutations in genes natural compound (such as a hormone coding for hemagglutinin and neuramin- or neurotransmitter) by binding to the dase. 1110 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Antigenic mimicry Self‐antigen that is simi- Antiseptic A chemical agent that can be lar to an antigen on a pathogen. safely used externally on tissues to destroy Antigenic shift Process of antigenic varia- micro‐organisms or to inhibit their growth. tion probably caused by a reassortment of Antiserum (plural: antisera) Serum that viral genes. contain a high concentration of antibodies Antigenic variation Mutations of influenza against a particular antigen. viruses that occur by antigenic drift and Antitoxin An antibody against a specific antigenic shift. toxin. Antigenic Presenting Cell An immunologi- Antiviral protein A protein induced by in- cal cell, such as a macrophage, dendritic terferon that interferes with the replication cell, or B cell, that processes antigen frag- of viruses. ments and presents peptide fragments Apicomplexan A parasite protozoan such as from the antigen on its cell surface. Plasmodium, that generally has a complex Antihistamine Drug that alleviates symp- life cycle. toms caused by histamines. Also known as Sporozoan. Antimetabolite A substance that is a struc- Aplastic crisis A period during which eryth- tural analog of a normal metabolite or oth- rocyte production ceases. erwise resembles it and that interferes with Apoenzyme The protein portion of an the utilization of the metabolite by the cell. enzyme. Antimicrobial Agent A chemotherapeutic Apolipoproteins The specific proteins that agent used to treat diseases caused by constitute the protein fraction of lipopro- microbes. teins; they mediate the interactions of lipo- Antioxidant A strongly reducing com- proteins with tissues. pound, such as ascorbic acid, which coun- Apoptosis Programmed cell death (as dis- teracts the tendency of a metabolite to tinguished from necrosis). undergo oxidation to a potentially toxic See autolysis. or harmful species. Arachnid An anthropod with two body Antiparallel The opposite head‐to‐tail ar- regions, four pairs of legs, and mount rangement of the two strands in a DNA parts that are used in capturing and tearing double helix. apart prey. Antiport A membrane transport process Archaea One of the three domains of living that couples the transport of a substance things; all members are bacterial. in one direction across a membrane to the Archaebacteria A group of prokaryotes that transport of a different substance in the are biochemically distinct from the true bac- other direction. Compare symport. teria (eubacteria) and that separated from Antisense RNA An RNA molecule that is them early in the history of life. Modern complementary to an mRNA; it can block archaebacteria mostly live in extreme envir- translation of the mRNA by forming a onments, such as acid hot springs. duplex with it. Gene expression can be Archaeobacteria Prokaryotic organisms regulated by the production of antisense lacking peptidoglycan in their cell walls and RNAs. differing from eubacteria in many ways. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1111
Arenavirus An enveloped RNA virus that in areas of poor sanitation and fecal con- causes Lassa fever and certain other hem- tamination of water. orrhagic fevers. Aspergillosis Skin infection caused by vari- Anthropod Makes up the largest group of ous species of Aspergillus, which can cause living organisms, characterized by a jointed severe pneumonia in immuno‐suppressed chitinous exoskeleton, segmented body, patients. and joined appendages, associated with Known also as farmer’s lung disease. some or all of the segments. Association constant (K) An equilibrium Arthus reaction A local reaction seen in the constant that indicates the tendency of skin after subcutaneous or intradermal in- two chemical species to associate with jection of an antigenic substance, immune each other; it is equal to the concentration complex (Type‐III) hypersensitivity. of the associated form divided by the prod- Artificially acquired active immunity When uct of the concentrations of the free species an individual is exposed to a vaccine at equilibrium. containing live, weakened, or dead organ- Known also as affinity constant. isms or their toxins, the host’s own im- Asthma Respiratory anaphylaxis caused mune system responds specifically to by inhaled or ingested allergies or by defend the body, e.g., by making specific hypersensitivity to endogenous micro‐ antibodies. organisms. Artificially acquired immunity When an Asymmetric carbon A carbon molecule that individual’s immune system is stimulated carries four different substituents and to react by some man‐made process, e.g., therefore acts as a center of chirality, mean- given a vaccine or an immune serum. ing that the substance can occur in two Artificially acquired passive immunity When different enantiomers (stereoisomers that antibodies made by other hosts are intro- are non‐superimposable mirror images of duced into a new host, e.g., via mother’s each other). milk or shots of gamma globulin. Atherosclerotic plaques The protruding Ascariasis Disease caused by a large round- masses that form on the inner walls of worm, Ascaris lumbricodes, acquired by in- arteries in atherosclerotic disease. A mature gestion of food or water contaminated plaque consists partly of lipid, mainly cho- with eggs. lesterol esters, which may be free or Ascomycota See sac fungus. contained in lipid‐engorged macrophages Ascospore One of the eight sexual spores called foam cells, and partly of an abnor- produced in each ascus of a sac fungus. mal proliferation of smooth‐muscle and Ascus (plural: asci) Saclike structures pro- connective‐tissue cells. duced by sac fungi during sexual reproduc- Athlete’s foot A form of ringworm in which tion. hyphae invade the skin between the toes, Aseptic technique A set of procedures used causing dry, scaly lesions. to minimize chances that cultures will be Also known as tinea pedis. contaminated by organisms from the envi- Atom The smallest chemical unit of matter. ronment. Atomic force microscope (AFM) Advanced Asiatic cholera Severe gastrointestinal dis- member of the family of scanning tunnel- ease caused by Vibrio cholerae, common ing microscopes, allowing 3‐dimensional 1112 Appendix C: Micro‐organisms, biochemistry, and nomenclature
views of structures from atomic size to multicellular organism. It is the process about 1 mm. by which unwanted cells are eliminated in Atomic number The number of protons in the body. Known also as apoptosis. an atom of a particular element. Autonomously replicating sequences Atomic weight The sum of the number of (ARSs) Sequences in yeast chromosomes protons and neutrons in an atom. that, when incorporated into an artificial Atopy Localized allergic reactions that plasmid, enable the plasmid to replicate occur first at the site where an allergen efficiently in yeast cells. enters the body. Autotroph Organisms that can synthesize Atrichous A bacterial cell without flagella. their organic compounds entirely from in- Attachment pilus Type of pilus that helps organic precursors in particular needing
bacteria adhere to surfaces. only CO2 as a carbon source. Compare Also known as fimbria. heterotrophs.
Attenuation (1) A genetic control mecha- Autotrophy ‘‘Self‐feeding’’ – the use of CO2 nism that terminates transcription of an op- as a source of carbon atoms for the synthe- eron prematurely when the gene products sis of biomolecules. are not needed (2) The weakening of the Auxotrophic mutant An organism that has disease‐producing ability of an organism. lost the ability to synthesize one or more Auditory canal Part of the outer ear lined metabolically important enzymes through with skin that contains many small hairs mutation, therefore requires special sub- and ceruminous glands. stances in its growth medium. Autoantibody An antibody against one’s Auxotrophs Micro‐organism strains that own tissue. requires as a nutrient a particular sub- Autocatalytic Refers to a reaction that an stance that is not required by the prototype enzyme catalyzes on part of its own struc- strain. Usually the requirement results ture, such as cleavage performed by a pro- from a mutation that disables an enzyme tease on its own polypeptide precursor. necessary for the endogenous synthesis of Autoclave An instrument for sterilization the substance. by means of moist heat under pressure. Axial filament A subsurface filament at- Autograft A graft of tissue from one part of tached near the ends of the cytoplasmic the body to another. cylinder of spirochetes that causes the spi- Autoimmune disorder An immune disor- rochete body to rotate like a corkscrew. der in which individuals are hypersensitive Also known as endoflagellum. to antigens on ells of their own body. Axis of symmetry An imaginary axis Autoimmunity A condition in which the through a structure, such that rotating the body mounts an immune response against structure around the axis through an ap- one of its own normal components. propriate angle leaves the appearance of Autoimmunization The process by which the structure unchanged. hypersensitivity to ‘‘self’’ develops, it Axon A threadlike process extending from occurs when the immune system responds a nerve cell by which impulses are trans- to a body components as if it were foreign. mitted to other nerve cells or to effector Autolysis Programmed cell death; the cells such as muscle or gland cells. Most orderly self‐destruction of a cell in a nerve cells have one axon; shorter processes Appendix C: Micro‐organisms, biochemistry, and nomenclature 1113
that function ion receiving impulses form Bacteriophage A virus that infects bacteria. other neutrons are called dendrites. Also known as phage. Babesiosis A protozoan disease caused by Bacteriostatic Referring to an agent that the Apicomplexan Babesia microti and inhibits the growth of bacteria. other species of Babesia. Bacteroid Irregularly shaped cells usually Bacillary angiomatosis A disease of the found in tight packets that develop from small blood vessels of the skin and internal Rhizobium swarmer cells and form nodules organs caused by the rickettsial organism in the roots of leguminous plants. Bartonella hensalae. Balantidiasis Type of dysentery caused by Bacillary dysentery See shigellosis. the ciliated protozoan Balantidium coli. Bacillus (plural: bacilli). A rod‐like bacte- Balantitis An infection of the penis. rium. Barophile An organism that lives under Bacteremia An infection in which bacteria high hydrostatic pressure. are transported in the blood but do not Barotholin gland A mucus‐secreting gland multiply in transit. of the female external genitalia. Bacteria (singular: bacterium). All prokary- Bartonellosis Rickettsial disease, caused by otic organisms. Bartonella bacilliformis, that occurs in two Bacteria When spelled with a capital B, it is forms. the name of one of the three domains of See also oroyo fever and verruga peruana. living things; all members are bacterial. Base A substance that absorbs hydrogen Bacterial conjunctivitis A highly contagious ions or donates hydroxyl ions. inflammation of the conjunctiva caused by Base analog A chemical mutagen similar in various bacterial species. molecular structure to one of the nitroge- Also known as pinkeye. nous bases found in DNA that causes point Bacterial endocarditis A life‐threatening in- mutations. fection and inflammation of the lining and Basic dye See cationic dye. valves of the heart. Basidiomycota See club fungus. Also known as infective endocarditis. Basidiospore A sexual spore of the club Bacterial enteritis An intestinal infection fungi. caused by bacterial invasion of intestinal Basidium (plural: basidia). A clublike struc- mucosa or deeper tissues. ture in club fungi bearing four external Bacterial lawn A uniform layer of bacteria spores on short, slender stalks. grown on the agar surface in a Petri dish. Basophil A leukocyte that migrates into tis- Bacterial meningitis An inflammation of the sues and helps initiate the inflammatory meninges that cover the brain and spinal response by secreting histamine. cord by any one of several bacterial species. B cell See b lymphocyte. Bactericidal Referring to an agent that kills B‐DNA A DNA duplex with a specific right‐ bacteria. hand helix structure. It is the usual form of Bacteriocin A protein released by some bac- DNA duplexes in vivo. teria that inhibits the growth of other Beer’s law The equation that relates the ab- strains of the same or closely related species. sorbance of a solution sample at a given Bacteriocinogen A plasmid that directs wavelength to the length of the light path, production of a bacteriocin. the concentration of the dissolved substance, 1114 Appendix C: Micro‐organisms, biochemistry, and nomenclature
and the extinction coefficient of the sub- Biohydrometallurgy The use of microbes to stance at that wavelength. extract metals from ores. See extinction coefficient. Biological oxygen demand (BOD) The oxy- Benign Not harmful. gen required to degrade organic wastes Beta (b) hemolysin A type of enzyme that suspended in water. completely lyses red blood cells, leaving a Biological vector An organism that actively clear ring in the blood agar medium transmits pathogens that complete part of around the colonies. their life cycle within the organism. Beta (b) hemolysis Complete lysis of red Bioremediation A process that uses natural- blood cells by bacterial enzymes. ly occurring or genetically engineered Beta oxidation A metabolic pathway that micro‐organisms to transform harmful breaks down fatty acids into 2‐carbon substances into less toxic or non‐toxic pieces. compounds. Bile acids A family of amphipathic choles- Biosphere The region of the earth inhibited terol derivatives that are produced in the by living organisms. liver and excreted in the bile; salts of the Biotic factor An organism in the biosphere. bile acids emulsify fat in the intestine. Blackfly fever Illness resulting from bites by Bilirubin A yellow substance, the product of blackflies, characterized by an inflammato- the breakdown of hemoglobin from red ry reaction, nausea, and headache. blood cells. Blackwater fever Malaria caused by Plas- Binary fission Process in which a bacterial modium falciparum that results in jaundice cell duplicates its components and divides and kidney damage. into two cells. Blastomycetic dermatitis Fungal skin dis- Binocular Referring to a light microscope ease caused by Blastomyces dermatitidis; having two eyepieces (oculars). characterized by disfiguring, granuloma- Binomial nomenclature The system of tax- tous, pus‐producing lesions. onomy developed by Linnaeus in which Blastomycosis Fungal skin disease caused each organism is assigned a genus and spe- by Blastomyces dermatitidis that enters the cific epithet. body through wounds. Biochemistry The branch of organic chem- Blocking antibody IgG antibody, elicited in istry that studies the chemical reactions of allergy patients by increasing doses of aller- living systems. gen, that complexes with allergen before it Bioconversion A reaction in which one can react with IgE antibody. compound is converted to another by Blood agar Type of medium containing enzymes in cells. sheep blood used to identify organisms Biogenic amines A set of low‐molecular‐ that cause Hemolysi, or breakdown of red weight amino acid derivatives that contain blood cells. a basic amino group and function in the Blood–brain barrier Formation in the brain body as intercellular mediators. Examples of special thick‐walled capillaries without are serotonin, histamine, and epinephrine. pores in their walls that limit entry of sub- Biogeochemical cycle Mechanism by which stances into brain cells. Physically the barrier water and elements that serve as nutrients consists of tight junctions between endothe- are recycled. lial cells; these cells have transporters for Appendix C: Micro‐organisms, biochemistry, and nomenclature 1115
polar substances such as glucose that need to head wound or via blood from another enter the brain. site. Blood group antigens A group of oligosac- Branch migration During recombination, charides that are carried in the form of the migration of a cross‐over point (holi- glycoproteins and glycolipids on the sur- day junction) by simultaneous unwinding face of cells, including blood cells; they are and rewinding in both duplexes. encoded by a large number of polymorphic Bread mold A fungus with complex mycelia gene loci and can provoke an immune re- composed of aseptate hyphae with chitin- sponse in an individual with different ous cross walls. blood group antigens. Known also as zygomycota or conjugation B Lymphocyte A lymphocyte that is pro- fungus. duced in and matures in bursal‐equivalent Bright‐field illumination Illumination pro- tissue, it gives rise to antibody‐producing duced by the passage of visible light through plasma cells. the condenser of a light microscope. Known also as B cell. Brill–Zinsser disease A recurrence of an ep- Body tube Microscope part that conveys an idemic typhus infection caused by reacti- image from the objective to the eyepiece. vation of latent organisms harbored in the Bohr effect The effect of pH on oxygen lymph nodes. binding by hemoglobin, by which a de- Known also as recrudescent typhus. crease in pH causes a decrease in oxygen Broad spectrum Referring to the range of affinity. The effect promotes both the re- activity of an antimicrobial agent that lease of oxygen from hemoglobin in the attacks a wide variety of micro‐organisms.
tissues and the release of CO2 from the Bronchial pneumonia Type of pneumonia blood to the air in the lungs. that begins in the bronchi and can spread Boil See furuncle. through surrounding tissue toward the Bolivian hemorrhagic fever A multisystem alveoli. disease caused by an arenavirus with insid- Bronchiole A finer subdivision of the air‐ ious onset and progressive effects. conveying bronchi. Bone Stink Putrefaction deep in the tissues Bronchitis An infection of the bronchi. of large carcasses that is caused by several Bronchus (plural: bronchi). A subdivision species of Clostridium. of the trachea that conveys air to and Bongkrek disease Type of food poisoning from the lungs. caused by Pseudomonas cocovenenans, Brucellosis A zoonosis highly infection for named for a native Polynesian coconut dish. humans, caused by any of several species of Botulism Disease caused by Clostridium Brucella. botulinum. The most common form, Also known as undulant fever and malta food‐borne botulism, results from inges- fever. tion of preformed toxin and is, therefore, Bubo Enlargement of infected lymph an intoxication rather than an infection. nodes, especially in the groin and armpit, Bradykinin Small peptide thought to cause due to accumulation of pus, characteristic the pain associated with tissue injury. of bubonic plague and other diseases. Brain abcess A pus‐filled cavity caused by Bubonic plague A bacterial disease, caused micro‐organisms reaching the brain from by Yersinia pestis and transmitted by flea 1116 Appendix C: Micro‐organisms, biochemistry, and nomenclature
bites, that spread in the blood and lym- Canning The use of moist heat under pres- phatic system. sure to preserve food. Budding Process that occurs in yeast and a Capillary A blood vessel that branches from few bacteria in which a small new cell devel- an arteriole. ops from the surface of an existing cell. Capnophile An organism that prefers car- Buffering The ability of a mixture of an acid bon dioxide gas for growth. and its conjugate base at a pH near their Capsid The protein coating of a virus,
pKa to minimize pH changes caused by an which protects the nucleic acid core from influx of acid or base. The Henderson– the environment and usually determines Hasselbach equation is useful relating pH, the shape of the virus. pK and [salt]/[acid]. Capsomere A protein aggregate that makes Bulking Phenomenon in which filamentous up a viral capsid. bacteria multiple, causing sludge to float on Capsule (1) A protective structure outside the surface of water rather than settling out. the cell wall, secreted by the organism. (2) Bunyavirus An enveloped RNA virus that A network of connective fibers covering causes some forms of respiratory distress organs such as the lymph nodes. and hemorrhagic fever. Carbapenem A bactericidal antibiotic that Burkitt’s lymphoma A tumor of the jaw, acts on bacterial cell walls. seen mainly in African children, caused by Carbohydrate A compound composed of the Epstein–Barr virus. carbon, hydrogen, and oxygen that serves Burst size The number of new virions re- as the main course of energy for most leased in the replication process. living things. Known also as viral yield. Carbohydrates In general, substances that
Burst time The time from absorption to have the stoichiometric formula (CH2)n, release of phages (in the replication pro- where n 3, or that are derived from cess). such a substance by the addition of func- Calorie A unit of energy defined as that tional groups. amount of heat energy that will raise the Carbon cycle Process by which carbon from temperature of 1 g of water by 1 C. atmospheric carbon dioxide enters living 1 calorie ¼ 4.182 J. and non‐living things and is recycled Calvin cycle The cycle of photosynthetic through them.
dark reactions by which CO2 is fixed, re- Carboxyl terminus See C‐terminus. duced, and converted to glyceraldehydes‐ Carbuncle A massive pus‐filled lesion 3‐phosphate (the precursor of hexose resulting from an infection, particularly of monophosphates). the neck and upper back. Cancer An uncontrolled, invasive growth of Carcinogen A cancer‐producing substance. abnormal cells. Cardiovascular system Body system that Candidiasis A yeast infection caused by supplies oxygen and nutrients to all parts Candida albicans that appears as thrust of the body and removes carbon dioxide (in the mount) or vaginitis. and other wastes from them. Known also as Moniliasis. Carnitine Alow‐molecular‐weight lysine Canine parvovirus A parvovirus that causes derivative that shuttles fatty acids through severe disease in dogs. the inner mitochondrial membrane to the Appendix C: Micro‐organisms, biochemistry, and nomenclature 1117
matrix. The fatty acyl moiety is transferred enzymes used to metabolize some alterna- from CoA to carnitine for transit through tive nutrient. the membrane and is then transferred back Catalase An enzyme that converts hydrogen to CoA; the carnitine released on the ma- peroxide to water and molecular oxygen. trix side of the membrane is shuttled back Caterrhal state Stage of whooping cough for reuse. characterized by fever, sneezing, vomiting, Carrier An individual who harbors an in- and a mild, dry persistent cough. fectious agent without having observable Cathepsins Lysosomal proteases that func- clinical signs or symptoms. tion in degrading proteins in lysosomes Cascade A set of reactions in which magni- and are also released into the cell at large fication of effect occurs, as in the comple- during cell autolysis (programmed cell ment system. death) | ‐ Casein hydrolsate A substance derived Cation \ kat |¯ı‐ən\ [Gk. kation, neut. of from milk protein that contains many katio¯n, prp. of katienai to go down, fr. amino acids, used to enrich certain media. kata‐cata þ ienai to go] (1834) n. A posi- Caseous Characterizing lesions with a tively charged ion. ‘‘cheesy’’ appearance that form in lung tis- Cationic dye An ionic compound, used for sue of patients with tuberculosis. staining bacteria in which the positive ion Caspases A family of proteases involved in imparts the color. apoptosis. Known also as basic dye. Catabolic pathway A chain of chemical Cat scratch fever A disease caused by Afipia reactions that capture energy by break- felis, or more commonly, Bartonella ing down large molecules into simpler (Rochalimaea) hensalae and transmitted components. in cat scratches and bites. Catabolism The sum of all the metabolic Cavitation The formation of a cavity inside processes by which complex molecules are the cytoplasm of a cell. broken down to simpler ones, including Cell culture A culture in the form of a the processes by which molecules are bro- monolayer from dispersed cells and con- ken down to yield cellular energy. Compare tinuous cultures of cell suspensions. anabolism. Cell‐mediated immune response The im- Catabolite activation In bacteria, a tran- mune response to an antigen carried out scriptional control system that induces at the cellular level by T cells. the synthesis of enzymes for the catabolism Cell‐mediated immunity The immune re- of energy substrates other than glucose sponse involving the direction action of when glucose levels are low. It involves an T cells to activate B cells or to destroy activator protein, CRP, that binds cyclic microbe‐infected cells, tumor cells, or AMP under conditions of low glucose; transplanted cells (organ transplants). this complex then binds to DNA sites and Cell‐mediated (Type‐IV) hypersensitivity promotes transcription of the appropriate Type of allergy elicited by foreign sub- genes. stances from the environment, infectious Catabolite repression Process by which the agents, transplanted tissue, and the body’s presence of a preferred nutrient (often glu- own malignant cells, mediated by T cells. cose) represses the genes coding for Known also as delayed hypersensitivity. 1118 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Cell membrane A selectively permeable li- to perform the initial fixation of CO2. This poprotein bilayer that forms the boundary enzyme is found in mesophyll cells, where
between a bacterial cell’s cytoplasm and its it fixes CO2 into a four‐carbon compound environment. (hence C4) This fixed carbon is shuttled Cell strain Dominant cell type resulting into sheltered bundle‐sheath cells, where
from subculturing. it is released as CO2 and enters the Calvin Cell theory Theory formulated by Schlei- cycle. den and Schwann that cells are the funda- Chagas’ disease Disease caused by Trypa- mental units of all living things. nosoma cruzi that occurs in the southern Cellular slime mold Fungus like protest United States and is endemic to Mexico; consisting of amoeboid, phagocytic cells transmitted by several kinds of reduviid that aggregate to form a pseudoplasmo- bugs. dium. Chancre A hard, painless, non‐discharging Cell wall Outer layer of most bacterial, lesion; a symptom of primary stage syphilis. algal, fungal, and plant cells that maintains Chancroid Sexually transmitted disease the shape of the cell. caused by Haemphilus ducreyi that causes Cementum The hard, bony covering of the soft, painful skin lesions on the genitals, tooth below the gumline. which bleeds easily. Center of chirality With respect to organic Chaotropic The property of being able to compounds, a carbon atom that has four disrupt the hydrogen bonding structure of different substituents attached to it; such a water. Substances that are good hydrogen group cannot be superimposed on its own bonders, such as urea or guanidine hydro- mirror image and therefore can occur in chloride, are chaotropic. Concentrated two enantiomers. solutions of these substances tend to dena- Central nervous system The brain and spi- ture proteins because they reduce the hy- nal cord. drophobic effect. Centromere The region of a chromosome Chaperonins Proteins that are involved in where the two sister chromatids are at- managing the folding of other proteins. tached together. It is also the site of attach- Some of them help proteins to fold cor- ment for spindle fibers during mitosis and rectly; some prevent premature folding; meiosis. and some prevent polypeptides from asso- Cephalosporin An antibacterial agent that ciating with other polypeptides until they inhibits cell wall synthesis. have folded properly. Cercaria A free‐swimming fluke larva that Chemical bond The interaction of electrons emerges from the snail or mollusk host. in atoms that form a molecule. Cerumen Earwax. Chemical cross‐linking A technique for Ceruminous gland A modified sebaceous investigating the mutual arrangement of gland that secrets cerumen. components in a complex. The complex is Cervix An opening at the narrow lower por- exposed to a reagent that can form chemical tion of the uterus. cross‐links between adjacent components C4 cycle A cycle in some plants that mini- and is then disaggregated and analyzed. mizes the wasteful effects of photorespira- Components that are linked together can tion by using an enzyme other than rubisco be assumed to be neighbors in the complex. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1119
Chemical equilibrium A steady state in Chemothrapeutic index The maximum tol- which there is no net change in the con- erable dose of a particular drug per kilo- centrations of substrates or products. gram body weight divided by the Chemically non‐defined medium See com- minimum dose per kilogram body weight plex medium. that will cure the disease. Chemical potential (G) In a system, the free Chemotherapy The use of chemical sub- energy that resides in a chemical compo- stances to treat various aspects of disease. nent per mole of the component present. Chickenpox A highly contagious disease, For example, in a system consisting of a characterized by skin lesions, caused by moles of component A and b moles of the varicella‐zoster herpes virus; usually component B, the total free energy G occurs in children. would be the sum of the free energy in Chigger dermatitis A violent allergic reac-
the two components: G ¼ aGA þ bGB. tion caused by chiggers, the larvae of Trom- Known also as partial molar free energy. bicula mites. Chemiosmosis Process of energy capture in Childbed fever See puerperal fever. which a proton gradient is created by Chiral With respect to a molecule or other means of electron transport and then object, the property of being non‐superim- used to drive the synthesis of ATP. posable on its mirror image. An atom that Chemiosmotic coupling The coupling of an makes a molecule chiral, such as a carbon enzyme‐catalyzed chemical reaction to the with four different substituents, is called a transport of a substance across a mem- chiral atom or center of chirality. brane either with or against its concentra- Chitin A polysaccharide found in the cell tion gradient. The outstanding example is walls of most fungi and the exoskeltons of the coupling of ATP synthesis to the move- anthropods. ment of protons across a membrane in Chlamydias Tiny, non‐motile, spherical response to a proton gradient. bacteria; all are obligate intracellular para- Chemoautotroph An autotroph that obtains sites with a complex life cycle. energy by oxidizing simple inorganic sub- Chloramphenicol A bacteriostatic agent stances such as sulfides and nitrates. that inhibits protein synthesis. Chemoheterotroph A heterotroph that Chlorination The addition of chlorine to obtains energy from breaking down water to kill bacteria. ready‐made organic molecules. Chloroplast A chlorophyll‐containing or- Chemolithotroph See chemoautotroph. ganelle found in eukaryotic cells that Chemostat A device for maintaining the carry out photosynthesis. logarithmic growth of a culture by the Chloroquine An antiprotozoan agent effec- continuous addition of fresh medium. tive against the malaria parasite. Chemotaxis The process by which bacteria Chocolate agar Type of medium made with sense a concentration gradient of a partic- heated blood, so named because it turns a ular substance in the medium and move chocolate brown color. either up or down the gradient. Chromatin The filamentous material of eu- Chemotherapeutic agent Any chemical karyotic chromosomes, consisting of DNA substance used to treat disease. with associated histones and other pro- Known also as drug. teins. During interphase it is dispersed 1120 Appendix C: Micro‐organisms, biochemistry, and nomenclature
and fills most of the nucleus; during nucle- extents. Stereoisomers exhibit circular di- ar division it condenses into compact chro- chroism. Also, some types of secondary mosomes. structure, such as a helices and b sheets in Chromatophore The internal membranes proteins, exhibit a predictable circular di- of photosynthetic bacteria and cyanobac- chroism at specific wavelengths. teria. Circular dichroism spectrum (CD spectrum) Chromophore A chemical group that An absorption spectrum obtained using absorbs light at characteristic wavelengths. circularly polarized light; it gives the circu- Chromosomal resistance Drug resistance of lar dichroism of the substance over a range a micro‐organism due to a mutation in of wavelengths. chromosomal DNA. Cis‐dominant Refers to a mutation in a Chromosome A structure that contains the genetic regulatory element that affects the DNA of organisms. expression of appropriate genes only on the Chromosome mapping The identification of same chromosome, not on another homol- the sequence of genes in a chromosome. ogous chromosome present in the same Chronic amebiasis Chronic infection caused call. Cis‐dominance demonstrates that a by the protozoan Entamoeba histolytica. regulatory element does not code for a Chronic disease A disease that develops diffusible factor. more slowly than an acute disease, is usu- Cistron The smallest unit of DNA that must ally less severe, and persists for a long, be intact to code for the amino acid se- interdeterminate period. quence of a polypeptide; thus, the coding Chronic fatigue syndrome Previously called part of a gene, minus 5’ and 3’ untranslated chronic EBV syndrome. Disease of uncer- sequences and regulatory elements. tain origin, similar to mononucleosis, with Citric acid cycle A cycle of reactions that symptoms including persistent fatigue and takes place in the mitochondrial matrix fever. and results in the oxidation of acetyl units
Chronic inflammation A condition in which to CO2 with the production of reducing there is a persistent, indecisive standoff equivalents and ATP. It is a central pathway between an inflammatory agent and the in oxidative respiration. Other substrates phagocytic cells and other host defenses besides acetyl‐CoA can enter the cycle at attempting to destroy it. intermediate points. Chylomicron A type of lipoprotein that is Known also as tricarboxylic acid cycle and produced in the intestinal villi and serves Krebs cycle. to transport dietary lipids in the circula- Classical pathway One of the two sequences tion. of reactions by which proteins of the com- Cilium (plural: cilia) A short cellular projec- plement system are activated. tion used for movement that beats in coor- Clathrate structure The cage‐like structure dinated waves. of organized water molecules that forms Ciliate A protozoan that moves by means of around a hydrophobic molecule in solu- cilia that cover most of its surface. tion. The structure has lower entropy Circular dichroism The property of absorb- than liquid water, which helps explain ing right circularly polarized light and left why hydrophobic substances dissolve circularly polarized light to different poorly in water. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1121
Clonal deletion The process in which the Coccidioidomycosis Fungal respiratory dis- binding of lymphocytes to self‐antigens ease caused by the soil fungus Coccidioides triggers a genetically programmed destruc- immitis. tion of those lymphocytes. Known also as valley fever. Clonal selection theory A model (proved Coccus (plural: cocci). A spherical bacterium. correct) describing how the body is ale to Codon A sequence of three bases in mRNA produce specific immune response against that specifies a particular amino acid in the a vast array of antigens. The B and T cells translation process. produced by the body have randomly gen- Coelom The body cavity between the erated antigen specificities. When a partic- digestive tract and body wall in higher ular antigen enters the body, it induces animals. proliferation only in B and T cells that Coenzyme An organic small molecule that happen to be specific for it. Thus, the anti- binds to an enzyme and is essential for its gen selects the cells that will mount an activity but is not permanently altered by immune response against it and stimulates the reaction. Most coenzymes are derived them to undergo Clonal proliferation. metabolically from vitamins. Clone A group of genetically identical cells, Cofactor An inorganic ion necessary for the organisms, or DNA sequences descending function of an enzyme. from a single parent cell. Colicin A protein released by some strains Club fungus A fungus, including mush- of Escherichia coli that inhibits growth of rooms, toadstools, rusts, and smuts, that other strains of the same organism. produces spores on basidia. Coliform bacterium Gram‐negative, non‐ Known also as basidiomycota. spore‐forming, aerobic or facultatively an- Cluster of differentiation marker An anti- aerobic bacterium that ferments lactose gen found on the cell surface of B and T and produces acid and gas, significant cells that can be used to distinguish the numbers may indicate water pollution. cells from one another. Colloid A mixture formed by particles too Coagulase A bacterially produced enzyme large to form a true solution dispersed in a that accelerates the coagulation (clotting) liquid. of blood. Colonization Growth of micro‐organisms Coarse adjustment Focusing mechanism of on epithelial surfaces such as skin or mu- a microscope that rapidly changes the dis- cous membranes. tance between the objective lens and the Colony A group of descendants of an origi- specimen. nal cell. Coated pit A cell membrane pit that is lined Colony hybridization A technique that is on its cytosolic side by a meshwork of the used to screen bacteria for the presence of protein clathrin. Coated pits participate in a specific recombinant DNA sequence. the mechanism of receptor‐mediated en- Colonies of the bacteria are transferred to docytosis, in which surface receptors that a filter, treated to lyse the cells and denature have bound specific extracellular sub- the DNA, and then exposed to a labeled stances are gathered into coated pits, DNA probe that is complementary to part which pinch off to become cytoplasmic of the sequence in question. Colonies that vesicles. bind the probe possess the sequence. 1122 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Colorado tick fever Disease caused by an Complement system See complement. orbivirus carried by dog ticks, character- Completed test The final test for coliforms ized by headache, backache, and fever. in multiple‐tube fermentation in which Colostrum The protein‐rich fluid secreted by organisms from colonies grown on eosin the mammary glands just after childbirth, methylene blue agar are used to inoculate prior to the appearance of breast milk. broth and agar slants. Commensal An organism that lives in or on Complex medium A growth medium another organism without harming it and that contains certain reasonable well‐ that benefits from the relationship. defined materials but that varies slightly Commensalism A symbiotic relationship in in chemical composition from batch to which one organism benefits and the other batch. one neither benefits nor is harmed by the Known also as a chemically non‐defined relationship. medium. Common‐source outbreak An epidemic Complex virus A virus, such as bacterio- that arises from contact with contaminated phage or poxvirus, that has an envelope substances. or specialized structures. Communicable infectious disease Infec- Compound A chemical substance made up tious disease that can be spread from one of atoms of two or more elements. host to another. Compound light microscope A light micro- Known also as a contagious disease. scope with more than one lens. Community All the kinds of organisms Compromised host An individual with re- present in an environment. duced resistance, being more susceptible to Competence factor A protein released into infection. the medium that facilitates the uptake of Concatemer A DNA molecule that consists DNA into a bacterial cell. of a tandem series of complete genomes. Competitive inhibitor A molecule similar in Some phage genomes form concatemers structure to a substrate that competes with during replication as part of a strategy for the substrate by binding to the active site. replicating the full length of a linear DNA The inhibitor can reversibly occupy the ac- duplex. tive site but does not undergo the reaction. Condenser Device in a microscope that Complementary base pairing Hydrogen converges light beams so that they will bonding between adenine and thymine pass through the specimen. (or uracil) bases or between guanine and Condyloma See genital wart. cytosine bases. Confirmed test Second stage of testing for Complement A set or more than 20 large coliforms in multiple‐tube fermentation in regulatory proteins that circulate in plasma which samples from the highest dilution and when activated form a non‐specific showing gas production are streaked into defense mechanism against many different eosin methylene blue agar. micro‐organisms. Confocal microscopy A light‐microscopy Known also as a contagious disease. technique that allows high resolution in Complement fixation test A complex sero- thick samples. logic test used to detect small quantities of Congenial rubella syndrome Complication antibodies. of German measles causing death or Appendix C: Micro‐organisms, biochemistry, and nomenclature 1123
damage to a developing embryo infected Contact transmission Amodeofdisease by virus that crosses the placenta. transmission effected directly, indirectly, or Congenital syphilis Syphilis passed to a by droplets. fetus when treponemes cross the placenta Contagious disease See communicable in- from mother to child before birth. fectious disease. Conidium (plural: conidia). A small, asexu- Contamination The presence of micro‐ al, aerial spore organized into chains in organisms on inanimate objects or surfaces some bacteria and fungi. of the skin and mucous membranes. Conjugation (1) The transfer of genetic infor- Continuous cell line Cell culture consisting mation from one bacterial cell to another by of cells that can be propagated over many meansofconjugationpili.(2)Theexchangeof generations. information between two ciliates (protests). Continuous reactor A device used in indus- Conjugation pilus A type of pilus that trial and pharmaceutical microbiology to attaches two bacterial together and pro- isolate and purify a microbial product vides a means for the exchange of genetic often without killing the organism. material. Control variable A factor that is prevented Known also as sex pilus. from changing during an experiment. Conjuctiva Mucous membranes of the eye. Convalescent stage The stage of an infec- Consensus sequence For a group of nucle- tious disease during which tissues are otide or amino acid sequences that show repaired, healing takes place, and the similarity but are not identical (e.g., the body regains strength and recovers. sequences for a family of related regulatory Comb’s antiglobulin test An immunological gene sequences), an artificial sequence that test designed to detect anti‐Rh antibodies. is compiled by choosing at each position Cooperative transition A transition in a the residue that is found there mot often in multipart structure such that the occur- the sequences under study. rence of the transition in one part of the Consolidation Blockage of air spaces as a structure makes the transition likelier to result of fibrin deposits in lobar pneumonia. happen in other parts. Constitutive With respect to gene expres- Copy number The number of copies per cell sion, refers to proteins that are synthesized of a particular gene or other DNA at a fairly steady rate at all times instead of sequence. being induced and repressed in response to Core The living part of an endospores. changing conditions. Cori cycle The metabolic cycle by which Constitutive enzyme An enzyme that is lactate produced by tissues engaging in an- synthesized continuously regardless of the aerobic glycolysis, such as exercising mus- nutrients available to the organism. cle, is regenerated to glucose in the liver Consumer An organism that obtains nutri- and returned to the tissue via the blood- ents by eating producers orother consumers. stream. Known also as heterotroph. Cornea The transparent part of the eyeball Contact dermatitis Cell‐mediated (Type‐ exposed to the environment. IV) hypersensitivity disorder that occurs Coronavirus Virus with clublike projections in sensitized individuals on second expo- that causes colds and acute upper respira- sure of the skin to allergens. tory distress. 1124 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Cortex A laminated layer of peptidoglycan Cruiform In a DNA duplex, a structure that between the membranes of the endospores can be adopted by a palindromic sequence, in septum. whicheachstrandbase‐pairs with itself to Corynebacteria Club‐shaped, irregular, form an arm that projects from the main non‐spore‐forming, Gram‐positive rods. duplex and terminates in a hairpin loop. The Coryza The common cold. twoarmsforma‘‘cross’’withthemainduplex. Countable number A number of colonies Crustacean A usually aquatic anthropod on an agar plate small enough so that one that has a pair of appendages associated can clearly distinguish and count them with each body segment. (30–300 per plate). Cryoelectron microscopy A variation of Counterion atmosphere A cloud of oppo- electron microscopy in which samples are sitely charged small ions (Counterions) that frozen in a glassy ice matrix. collects around a macroion dissolved in a Cryptococcois Fungal respiratory disease salt solution. Counterion atmospheres caused by a budding, encapsulated yeast, partly shield macroions from each other’s Filobasidiella neoformans. charges and thus affect their interactions. Cryptosporidiosis Disease caused by proto- Covalent bond A bond between atoms cre- zoans of the genus Cryptosporidium, com- ated by the sharing of pairs of electrons. mon in AIDS patients. Cowpox Disease caused by the vaccinia C‐Terminus The end of a polypeptide chain virus and characterized by lesions, inflam- that carries an unreacted carboxyl group. mation of lymph nodes, and fever, virus is Known also as carboxyl terminus. See also used to make vaccine against smallpox and N‐terminus. monkeypox. Curd The solid portion of milk resulting Crepitant tissue Distorted tissue caused by from bacterial enzyme addition and used gas bubbles in gas gangrene. to make cheese. Creutzfeldt–Jakob disease (CJD) A trans- Curie The basic unit of radioactive decay; missible spongiform encephalopathy of an amount of radioactivity equivalent to the human brain caused by prions. that produced by 1 g of radium, mainly Crista (cristae) A fold in the inner mito- 2.22 1012 disintegrations per minute. chondrial membrane that project into the Cyanobacteria Photosynthetic, prokaryot- mitochondrial matrix. The enzymes of the ic, typically unicellular organisms that are electron transport chain and oxidative members of the kingdom Monera. phosphorylation are located mainly on Cyanosis Blush skin characteristic of the cristae. oxygen‐poor blood. Cross‐reaction Immune reaction of a single Cyclic photophosphorylation In photosyn- antibody with different antigens that are thesis, Photophosphorylation (light‐ similar in structure. dependent ATP synthesis) that is linked to Cross‐resistance Resistance against two or a cyclic flow of electrons from photosystem more similar antimicrobial agents through II down an electron transport chain and a common mechanism. back to photosystem II; it is not coupled
Croup Acute obstruction of the larynx that to the oxidation of H2O or to the reduction þ produces a characteristic high‐pitched of NADP . Compare non‐cyclic photophos- barking cough. phorylation. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1125
Cyclins Proteins that regulate the cell cycle Cytosol The fluid medium that is lo- by binding to and activating specific nucle- cated inside a cell but outside the nu- ar protein kinases. Cyclin‐dependent kinase cleus and organelles (for eukaryotes) or activations occur at three points during the the nucleoid (for prokaryotes). It is a cell cycle, thus providing three decision semiliquid concentrated solution or sus- points as to whether the cycle will proceed. pension. Cyst A spherical, thick‐walled cell that Cytotoxic drug A drug that interferes with resembles an endospores, formed by cer- DNA synthesis, used to suppress the im- tain bacteria. mune system and prevent the rejection of Cysticercus An oval white sac with a tape- transplants. worm head invaginated into it. Cytotoxic (Type‐II) hypersensitivity Type of Known also as a bladder worm. allergy elicited by antigens on cells, espe- Cystitis Inflammation of the bladder. cially red blood cells, that the immune Cytochrome An electron carrier function- system treats are foreign. ing in the electron transport chain; heme Cytotoxin Toxin produced by cytotoxic cells protein. that kills infected host cells. Cytokine One of a diverse group of soluble Dark‐field illumination In light micros- proteins that have specific roles in host copy, the light that is reflected from an defenses. object rather than passing through it, Cytokinesis The division of a eukaryotic resulting in a bright image on a dark back- cell to form two cells. It usually accompa- ground. nies nuclear division, although nuclear di- Dark reactions Part of photosynthesis in vision can occur without cytokinesis. which carbon dioxide gas is reduced by Cytomegalovirus One of a widespread and electrons form reduced NADP (NADPH) diverse group of herpsviruses that often to form various carbohydrate molecules, produces no symptoms in normal adults chiefly glucose. These photosynthetic sub- but can severely affect AIDS patients and processes do not depend directly on light congenitally infected children. energy; specifically, the synthesis of carbo-
Cytopathic effect (CPE) The visible effect hydrate from CO2 and H2O. Compare light viruses have on cells. reactions. Cytoplasm The semifluid substance inside Dark repair Mechanism for repair of dam- a cell, excluding, in eukaryotes, the cell aged DNA by several enzymes that do not nucleus. require light for activation; they excise de- Cytoplasmic streaming Process by which fective nucleotide sequences and replace cytoplasm flows from one part of a eukary- then with DNA complementary to the un- otic cell to another. altered DNA strand. Cytoskelton An organized network of rod‐ Daughter cell One of the two identical pro- like and fiber‐like proteins that pervades a ducts of cell division. cell and helps give it its shape and motility. Deaminating agent A chemical mutagen
The cytoskelton includes action filaments, that can remove an amino group (–NH2) microtubules, and a diverse group of fila- from a nitrogenous base, causing a point mentous proteins collectively called inter- mutation. mediate filaments. Death phase See decline phase. 1126 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Debridement Surgical scraping to remove so that the polymer becomes a random coil. the thick crust or scab that forms over For DNA, this change involves the separa- burnt tissue (eschar) tion of the two strands. Denaturation can Decimal reduction time (DRT; also called be induced by heating and by certain D‐value) The length of time needed to changes in chemical environment. It can kill 90% of the organisms in a given popu- also be stated as the disruption of hydrogen lation at a specified temperature. bonds and other weak forces that maintain Decline phase (1) The fourth of four major the structure of a globular protein, resulting phases of the bacterial growth curve in in the loss of its biological activity. which cells lose their ability to divide Dengue fever Viral systemic disease that (due to less supportive conditions in the causes severe bone and joint pain. medium) and thus die. (2) In the stages of Known also as breakbone fever. a disease, the period during which the host Denitrification The process by which defense finally overcome the pathogen and nitrates are reduced to nitrous oxide or symptoms begin to subside. nitrogen gas. Known also as death phase. Dental caries The erosion of enamel and Decomposer Organism that obtains energy deeper parts of teeth. by digesting dead bodies or wastes of pro- Known also as tooth decay. ducers and consumers. Dental plaque A continuously formed Defined synthetic medium A synthetic me- coating of micro‐organisms and organic dium that contains known specific kinds matter on tooth enamel. and amounts of chemical substances. Deoxyribonucleic acid (DNA) Nucleic acid Definitive host An organism that harbors that carries hereditary information from the adult, sexually reproducing form of a one generation to the next. parasite. Depurination Cleavage of the glycosidic Degranulation Release of histamine and bond between C‐10 of deoxyribose and a other preformed mediators of allergic reac- purine base in DNA. Used in Maxam– tions by sensitized mast cells and basophils Gilbert sequence analysis. after a second encounter with an allergen. Dermal wart A fungal skin disease. Dehydration synthesis A chemical reaction Dermatophyte A fungus that invades kera- that builds complex organic molecules. tinized tissue of the skin and nails. Delayed (Type‐IV) hypersensitivity See cell‐ Dermis The thick inner layer of the skin. mediated (Type‐iv) hypersensitivity. Descriptive study An epidemiologic study Delayed hypersensitivity (TDH) cells Those that notes the number of cases of a disease,
T cells (inflammatory TH1) that produce which segments of the population are af- lymphokines in cell‐mediated (Type‐IV) fected, where the cases have occurred, and hypersensitivity reactions. over what time period. Deletion The removal of one or more ni- Desensitization Treatment designed to cure trogenous bases from DNA, usually pro- allergies by means of injections with grad- ducing a frameshift mutation. ually increasing does of allergen. Delta hepatitis See hepatitis D. Deuteromycota See fungi imperfecti. Denaturation For a nucleic acid or protein, Diabetes melllitus A disease caused by a the loss of tertiary and secondary structure deficiency in the action of insulin in the Appendix C: Micro‐organisms, biochemistry, and nomenclature 1127
body, resulting either from low insulin le- Differential medium A growth medium vels or from inadequate insulin levels com- with a constituent that causes an observ- bined with unresponsiveness of the target able change (in color or pH) in the medi- cells to insulin. The disease is manifested um when a particular chemical reaction primarily by disturbances in fuel homeo- occurs, making it possible to distinguish stasis, including hyperglycemia (abnor- between organisms. mally high blood glucose levels). Differential stain Use of two or more dyes Dialysis The process by which low‐molecu- to differentiate among bacterial species or lar‐weight solutes are added to or removed to distinguish various structures of an or- from a solution by means of diffusion ganism; for example, the Gram stain. across a semipermeable membrane. Diffraction Phenomenon in which light Diapedsis The process in which leukocytes waves, as they pass through a small open- pass out of blood into inflamed tissues by ing, are broken up into bands of different squeezing between cells of capillary walls. wavelengths. Diarrhea Excessive frequency and looseness Diffraction pattern The pattern that is pro- of bowel movements. duced when electromagnetic radiation Diastereomers Molecules that are stereoi- passes through a regularly repeating struc- somers but not enantiomers of each ture; it results because the waves scattered other. Isomers that differ in configuration by the structure interact destructively in about two or more asymmetric carbon most directions (creating dark zones) but atoms and are not complete mirror images. constructively in a few directions (creating Diatom An alga or plantlike protest bright spots) For the pattern to be sharp, that lacks flagella and has a glasslike outer the radiation wavelength must be some- shell. what shorter than the repeat distance in Dichotomous key Taxonomic key used to the structure. identify organisms, composed of paired See also X‐ray diffraction. (either‐or) statements describing charac- Diffusion coefficient (D) A coefficient that teristics. indicates how quickly a particular sub- Dielectric constant A dimensionless con- stance will diffuse in a particular medium stant that expresses the screening effect of under the influence of a given concentra- an intervening medium on the interaction tion gradient. between two charged particles. Every me- DiGeorge syndrome Primary immunodefi- dium (such as a water solution or an inter- ciency disease caused by failure of the thy- vening portion of an organic molecule) has mus to develop properly, resulting in a a characteristic dielectric constant. deficiency of T cells. Difference spectrum With respect to ab- Digestive system The body system that sorption spectra, a spectrum obtained by converts ingested food into material suit- loading the sample cuvette with the sub- able for the liberation of energy or for stances under study and a reference cuvette assimilation into body tissues. with an equimolar sample of the same Dikaryotic Referring to fungal cells within substances in a known state (e.g., fully hyphae that have two nuclei, produced by oxidized) and recording the difference plasmogany in which the nuclei have not between the two spectra. united. 1128 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Dilution method A method of testing antibi- Disaccharide A carbohydrate formed by the otic sensitivity in which organisms are incu- joining of two monosaccharides. bated in a series of tubes containing known Disease A disturbance in the state of health quantities of a chemotherapeutic agent. wherein the body cannot carry out all its Dimer Two adjacent pyrimidines bonded normal functions. together in a DNA strand, usually as a See also epidemiology and infectious disease. result of exposure to ultraviolet rays. Disinfectant A chemical agent used on inan- Dimorphism The ability of an organism to imate objects to destroy micro‐organisms. alter its structure when it changes habitats. Disinfection Reducing the number of path- Dinoflagellate An alga or plantlike protest, ogenic organisms on objects or in materials usually with two flagella. so that they pose no threat of disease. Diphtheria A severe upper respiratory dis- Dismutation A reaction in which two iden- ease caused by Corynebacterium diphther- tical substrate molecules have different iae, can produce subsequent myocarditis fates; particularly, a reaction in which one and polyneuritis. of the substrate molecules is oxidized and Diphtheroid Organism found in normal the other reduced. throat cultures that fails to produce exo- Disk diffusion method A method used to toxin but is otherwise indistinguishable determine microbial sensitivity to antimi- from diphtheria‐causing organisms. crobial agents in which antibiotic disks are Dipicolonic acid Acid found in the core of placed on an inoculated Petri dish, incu- endospores that contributes to its heat re- bated, and observed for inhibition of sistance. growth. Diploid For a cell or an organism, the pos- Dispersion forces Weak intermolecular at- session of two homologous sets of chromo- tractive forces that arise between molecules somes per nucleus (with the possible are close together, because the fluctuating exception of sex chromosomes, which electron distributions of the molecules be- may be present in only one copy). Compare come synchronized so as to produce a haploid. slight electrostatic attraction. These forces Diploid fibroblast strain A culture derived play a role in the internal packing of many from fetal tissues that retains fetal capacity biomolecules. for rapid, repeated cell division. Disseminated tuberculosis Type of tubercu- Direct contact transmission Mode of dis- losis spread throughout body, not seen in ease transmission requiring person‐to‐per- AIDS patients, usually caused by Mycobac- son body contact. terium avium‐intercellulare. Direct fecal – oral transmission Direct con- Dissociation constant For an acid, the equi-
tact transmission of disease in which librium constant Ka for the dissociation of pathogens from fecal matter are spread by the acid into its conjugate base and a pro- unwashed hands to the mouth. ton. For a complex of two biomolecules,
Direct microscopic count A method of mea- the equilibrium constant Kd for dissocia- suring bacterial growth by counting cells in tion into the component molecules. a known volume of medium that fills a Distillation The separation of alcohol and specially calibrated counting chamber on other volatile substances from solid and a microscope slide. non‐volatile substances. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1129
Divergent evolution Process in which des- Drug resistance factors Bacterial plasmids cendants of a common ancestor species that carry genes coding for resistance to undergo sufficient change to be identified antibiotics. as separate species. DTaP vaccine Diphtheria, tetanus, and acel- DNA gyrase An enzyme that is able to in- lular pertussis vaccine. troduce negative superhelical turns into a D‐value See decimal reduction time. circular DNA helix. Dyad A set of paired chromosomes in DNA hybridization Process in which the eukayotic cells that are prepared to divided double strands of DNA of each of two organ- by mitosis or meiosis. isms are split apart and the split strands from Dyad axis A twofold axis of symmetry. the two organisms are allowed to combine. Dysentery A severe diarrhea that often con- DNA polymerase An enzyme that moves tains mucus and sometimes blood or pus. along behind each replication fork, synthe- Dysuria Pain and burning on urination. sizing new DNA strands complementary to Eastern equine encephalitis Type of viral the original ones. encephalitis seen most often in the eastern DNA replication Formation of new DNA United States, infects horses more fre- molecules. quently than human. DNA tumor virus An animal virus capable Ebola virus A filovirus that causes hemor- of causing tumors. rhagic fevers. Domain A portion of a polypeptide chain Eclipse period Period during which viruses that folds on itself to form a compact unit have absorbed to and penetrated host cells that remains recognizably distinct within but cannot yet be detected in cells. the tertiary structure of the whole protein. Ecology The study of relationships among Large globular proteins often consist of organisms and their environment. several domains, which are connected to Ecosystem All the biotic and abiotic com- each other by stretches of relatively extend- ponents of an environment. ed polypeptide. A new taxonomic category Ectoparasite A parasite that lives on the above the kingdom level, consisting of the surface of another organism. archaea, bacteria, and eukarya. Eczema herpecticum A generalized erup- Donovan body A large monon‐uclear cell tion caused by entry of the herpevirus found in scrapings of lesions that confirms through the skin, often fatal. the presence of granuloma inguinale. Edema An accumulation of fluid in tissues DPT vaccine Diphtheria, killed whole cell that causes swelling. pertussis and tetanus vaccine. Editing See RNA editing. Dracunculiasis Skin disease caused by a Ehrlichiosis A tick‐borne disease found in parasitic helminth, the guinea worm Dra- dogs and human and caused by Ehrlichia cunculus medinensis. canis and E. chaeffeenis. Droplet nucleus A particle consisting of Einstein One mole of photons. dried mucus in which micro‐organisms Electrolyte A substance that is ionizable in are embedded. solution. Droplet transmission Contact transmission Electron A negatively charged subatomic of disease through small liquid droplets. particle that moves around the nucleus of Drug See chemotherapeutic agent. an atom. 1130 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Electron acceptor An oxidizing agent in a membrane, allowing entrance of vectors chemical reaction. carrying foreign DNA. Electron donor A reducing agent in a chem- Element Matter composed of one kind of ical reaction. atom. Electron micrograph A ‘‘photograph’’ of an Elementary body An infectious stage in the image taken with an electron microscope. life cycle of chlamydias. Electron microscope Microscope that uses a Elephantiasis Gross enlargement of limbs, beam of electrons rather than a beam of scrotum, and sometimes other body parts light and electromagnets instead of glass from accululation of fluid due to blockage lenses to produce an image. of lymph ducts by the helminth Wuchereria Electron spin resonance A form of spectros- bancrofti. copy that is sensitive to the environment of Elongation factors Non‐ribosomal protein unpaired electrons in a sample. factors that are necessary participants in Known also as electron paramagnetic reso- the chain‐elongation cycle of polypeptide nance or EPR. synthesis; they interact with the ribosome‐ Electron transport Processes in which pairs mRNA complex or with other major cycle of electrons are transferred between cyto- participants. chromes and other compounds. Enamel The hard substance covering the Electron transport chain (1) A series of crown of a tooth. compounds that pass electrons to oxygen Enantiomers Stereoisomers that are non‐ (the final electron acceptor). (2) A sequence superimposable mirror images of each of electron carriers of progressively higher other. The term optical isomers comes from reduction potential in a cell that is linked so the fact that the enantiomers of a compound that electrons can pass from one carrier to rotate polarized light in opposite directions. the next. The chain captures some of the Known also as optical isomers. energy released by the flow of electrons and Encephalitis An inflammation of the brain- uses it to drive the synthesis of ATP. caused by a variety of viruses or bacteria. Known also as respiratory chain. Endemic Referring to a disease that is con- Electrophoresis (1) Process used to separate stantly present in a specific population. large molecules such as antigens or proteins Endemic relapsing fever Tick‐borne cases by passing an electrical current through a of relapsing fever caused by several species sample on a gel. (2) A method for separa- of Borrelia. ting electrically charged substances in a Endemic typhus A flea‐borne typhus mixture. A sample of the mixture is placed caused by Rickettsia typhi. on a supporting medium (a piece of filter Endergonic In a non‐isolated system, a pro- paper or a gel) to which an electrical field is cess that is accompanied by a positive applied. Each charged substance migrates change in free energy (positive DG) and toward the cathode or the anode at a speed therefore is thermodynamically not fa- that depends on its net charge and its fric- vored. Compare exergonic. tional interaction with the medium. Endocrine glands Glands that synthesize See also gel electrophoresis. hormones and release them into the Electroporation A brief electric pulse pro- circulation. The hormone‐producing gland duces temporary pores in the cell cells are called endocrine cells. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1131
Endocytosis Process in which vesicles form Endosymbiotic theory Holds that the orga- by invagination of the plasma membrane nelles of eukaryotic cells arose from pro- to move substances into eukaryotic cells. karyotes that came to live, in a symbiotic Endoenzyme An enzyme that acts within relationship, inside the eukayote‐to‐be cell. the cell producing it. Endotoxin A toxin incorporated in Gram‐ Endoflagellum See axial filament. negative bacterial cell walls and released Endogenous infection An infection caused when the bacterium dies. by opportunistic micro‐organism already Known also as lipopolysaccharide. present in the body. End‐product inhibition See feedback inhibi- Endogenous pyrogen Pyrogen secreted tion. mainly by monocytes and macrophages Energy See internal energy. that circulates to the hypothalamus and Energy charge A quantity that indicates the causes an increase in body temperature. state of a cell’s energy reserves. It is equal to Endometrium The mucous membrane lin- the cell’s reverses of the free energy sources ing the uterus. ATP and ADP (taking into account that Endonuclease An enzyme that cleaves a ADP stores less free energy than ATP) nucleic acid chain at an internal phospho- divided by the total supply of ATP and its diester bond. breakdown products ADP and AMP ([ATP] Endoparasite A parasite that lives within þ ½[ADP])/([ATP] þ [ADP] þ (AMP]). the body of another organism. Enhancer sequence A DNA sequence that is Endoplasmic reticulum A highly folded distant from a gene but to which a protein membranous compartment within the cy- factor that affects the gene’s transcription toplasm that is responsible for a great vari- can bind to exert its action. It is possible ety of cellular tasks, including the that DNA looping brings enhancer‐bound glycosylation and trafficking of proteins proteins into proximity with the gene’s destined for secretion or for the cell mem- promoter. brane or some organelles. It also functions Enrichment medium A medium that con- in lipid synthesis, and the enzymes of many tains special. nutrients that allow growth pathways of intermediate metabolism are of a particular organism. located on its surface. Enteric bacteria Members of the family Endorphins A class of endogenous brain enterobacteriaceae, many of which are in- peptides that exert analgesic effects in the testinal, small facultatively anerobic Gram‐ central nervous system by binding to negative rods with peritrichous flagella. opiate receptors. They are produced by Enteric fever Systemic infection, such as ty- cleavage of the large polypeptide pro‐ phoid fever, spread throughout the body opiomelanocortin. from the intestinal mucosa. Endospore A resistant, dormant structure, Enteritis An inflammation of the intestine. formed inside some bacteria, such as Bacil- Enterocolitis Disease caused by Salmonella lus and Clostridium, that can survive ad- typhimurium and five paratyphi that invade verse conditions. intestinal tissue and produce bacteremia. Endospore septum A cell membrane with- Enterohemorrhagic strain of Escherichia out a cell wall that grows around the core of coli One that causes bloody diarrhea and endospores. is often fatal; often from contaminated food. 1132 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Enteroinvasive strain Strain of Escherichia of being radioactive, is attached to an coli with a plasmid‐borne gene for a surface enzyme that causes a color change in its antigen (K antigen) then enables it to at- substrate. tach to and invade mucosal cells. Enzyme repression Mechanism by which Enterotoxicosis See food poisoning. the presence of a particular metabolite Enterotoxigenic strain Strain of Escherichia represses the genes coding for enzymes coli carrying a plasmid that enables it to used in its synthesis. make an enterotoxin. Enzyme–substrate complex A loose associ- Enterotoxin An exotoxin that acts on tis- ation of an enzyme with its substrate. sues of the gut. Eosinophil A leukocyte present in large Enterovirus One of the three major groups numbers during allergic reactions and of picornaviruses that can infect nerve and worm infections. muscle cells, the respiratory tract lining, Epidemic Referring to a disease that has a and skin. higher than normal incidence in a popula- Enthalpy (H) A thermodynamic quantity tion over a relatively short period of time. (function of state) that is equal to the in- Epidemic keratoconjunctivitis Eye disease ternal energy of a system plus the product caused by an adenovirus. of the pressure and volume: H ¼ E þ PV.It Known also as shipyard eye. is equal to the heat change in constant‐ Epidemic relapsing fever Louseborne cases pressure reactions, such as most reactions of relapsing fever caused by several species in biological systems. of Borrelia. Entropy (S) A thermodynamic quantity Epidemic typhus Louseborne rickettsial (function of state) that expresses the degree disease caused by Rickettsia prowazekii, of disorder or randomness in a system. seen most frequently in conditions of over- According to the second law of thermody- crowding and poor sanitation. namics, the entropy of an opens system Known also as classic, European, or louse- tends to increase unless energy is expended borne typhus. to keep the system orderly. Epidemiologic study A study conducted in Envelope A bilayer membrane found out- order to learn more about the spread of a side the capsid of some viruses, acquired as disease in a population. the virus buds through one of the host’s Epidemiologist A scientist who studies epi- membrane. demiology. Enveloped virus A virus with a bilayer Epidemiology The study of factors and membrane outside its capsid. mechanisms involved in the spread of dis- Enzyme A protein catalyst that controls the ease within a population. rate of chemical reaction in cells. Epidermis The thin outer layer of the skin. Enzyme induction A mechanism whereby Epiglottitis An infection of the epiglottis. the genes coding for enzymes needed Episomes Plasmids that can undergo inte- to metabolize a particular nutrient are acti- gration into the bacterial chromosome. vated by the presence of that nutrient. Epitope The specific portion of an antigen Enzyme‐linked immunosorbent assay particle that is recognized by a given (ELISA) Modification of radioimmuno- antibody or T‐cell receptor. assay in which the anti‐antibody, instead Known also as antigenic determinant. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1133
Epstein‐Barr virus (EBV) Virus that causes Eukaryote An organism composed of eu- infectious monon‐ucleosis and Burkitt’s karyotic cells. lymphoma. Eukaryotic cell A cell that has a distinct Ergot Toxin produced by Claviceps, pur- cell nucleus and other membrane‐bound purea, a parasite fungus of rye and wheat structures. that causes ergot poisoning when ingested Eutophication The nutrient enrichment of by humans. water from detergents, fertilizes, and ani- Ergot poisoning Disease caused by inges- mal manures, which cause overgrowth of tion of ergot, the toxin produced by Clavi- algae and subsequent depletion of oxygen. ceps purpurea, a fungus of rye and wheat. Exanthema A skin rash. Erysipelas Infection caused by hemolytic Exergonic (1) In a non‐isolated system, a streptococci that spreads through lym- process that is accompanied by a negative phatics, resulting in septicemia and other change in free energy (negative DG) and diseases. therefore is thermodynamically favored. Erythrocyte A red blood cell. Compare endergonic. (2) Releasing energy Erythromycin An antibacterial agent that from a chemical reaction. has a bacteriostatic effect on protein syn- Exocrine cell A cell that secretes a substance thesis. that is excreted through a duct either into Eschar The thick crust or scab that forms the alimentary tract or to the outside of the over a severe burn. organism. Exocrine cells are grouped to- Essential amino acids Amino acids that gether in exocrine glands. must be obtained in the diet because they Exocytosis Process by which vesicles inside cannot be synthesized in the body (at least a eukaryotic cell fuse with the plasma not in adequate amounts) membrane and release their contents from Essential fatty acids Fatty acids that must the eukaryotic cell. be obtained in the diet because they cannot Exoenzyme An enzyme that is synthesized be synthesized in the body in adequate in a cell but crosses the cell membrane to amounts. Examples are linoleic acid and act in the periplasmic space or the cell’s linolenic acid. immediate environment. Ethanbutol An antibacterial agent effective Known also as extracellular enzyme. against certain strains of mycobacteria. Exogenous infection An infection caused Etiology The assignment or study of causes by micro‐organisms that enter the body and origins of a disease. from the environment. Eubacteria True bacteria. Exogenous pyrogen Exotoxins and endo- Englenoid An alga or plantlike protest, usu- toxins from infectious agents that cause ally with a single flagella and a pigmented fever by stimulating the release of an en- eyespot (stigma). dogenous pyrogen. Eukarya One of the three domains of living Exon A region in the coding sequence of a things; all members are eukaryotic. gene that is translated into protein (as op- Eukaryotes Organisms whose cells are posed to introns, which are not) The name compartmentalized by internal cellular comes from the fact that exons are the only membranes to produce a nucleus and orga- parts of an RNA transcript that are seen nelles. Compare prokaryotes. outside the nucleus. Compare intron. 1134 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Exonuclease An enzyme that removes seg- Facilitated transport The movement of a ments of DNA. substance across a biological membrane Exosporium A lipid‐protein membrane for- in response to a concentration or electro- med outside the coat of some endospores chemical gradient where the movement is by the mother cell. facilitated by membrane pores or by spe- Exotoxin A soluble toxin secreted by cific transport proteins. Compare active microbes into their surroundings, includ- transport, passive transport. ing host tissues. Known also as facilitated diffusion. Experimental study An epidemiological Facultative Able to tolerate the presence study designed to test a hypothesis about or absence of a particular environmental an outbreak of disease, often about the condition. value of a particular treatment. Facultative anaerobe A bacterium that car- Experimental variable The factor that is ries on aerobic metabolism when oxygen is purposely changed in an experiment. present but shifts to anerobic metabolism Exponential rate The rate of growth in a when oxygen is absent. bacterial culture characterized by doubl- Facultative parasite A parasite that can live ing of the population in a fixed interval either on a host or freely. of time. Facultative psychrophile An organism Known also as logarithmic rate. that grows best at temperatures below Exportins A class of proteins involved in 20 C but can also grow at temperatures transporting materials out of nuclei. above 20 C. See importins. Facultative thermophile An organism that Extinction coefficient (el) A coefficient that can grow both above and below 37 C. indicates the ability of a particular sub- FAD Flavin adenine dinucleotide, a coen- stance in solution to absorb light of wave- zyme that carries hydrogen atoms and elec- length l. The molar extinction coefficient, trons. e Fastidious ‐ M, is the absorbance that would be dis- Referring to micro organisms played by a 1 M solution in a 1 cm light that have special nutritional needs that path. are difficult to meet in the laboratory. Extracellular enzyme See exoenzyme. Fat A complex organic molecule formed Extrachromosomal resistance Drug resis- from glycerol and one or more fatty acids. tance of a micro‐organism due to the pres- Fatty acid A long chain of carbon atoms ence of resistance (R) plasmids. and their associated hydrogens with a car- Extreme T hermoacidophile Organism re- boxyl group at one end. quiring very hot and acidic environment, Fc fragment The tail region of an antibody usually belonging to domain archaea. that may contain sites for macrophage and Fab fragment The portion of an antibody complement binding. that contains an antigen‐binding site. Feces Solid waste produced in the large Faciliated diffusion Diffusion (down a con- intestine and stored in the rectum until centration gradient) across a membrane eliminated from the body. (from an area of higher concentration to Feedback inhibition Regulation of a meta- lower concentration) with the assistance of bolic pathway by the concentration of a carrier molecule, but not requiring ATP. one of its intermediates or, typically, its Appendix C: Micro‐organisms, biochemistry, and nomenclature 1135
end product, which inhibits an enzyme in Filtration (1) A method of estimating the the pathway. size of bacterial populations in which a Known also as end‐product inhibition. known volume of air or water is drawn Feline panleukopenia virus (FPV) A parvo- through a filter with pores too small to virus that causes severe disease in cats. allow passage of bacteria. (2) A method of Female reproductive system The host sys- sterilization that uses a membrane filter tem consisting of the ovaries, uterine tubes, to separate bacteria from growth media. uterus, vagina, and external genitalia. (3) The filtering of water through beds of Fermentation Anaerobic metabolism of the sand to remove most of the remaining pyruvic acid produced in glycolysis. micro‐organisms after flocculation in Fermentations Processes in which cellular water treatment plants. energy is generated from the breakdown Fimbria See attachment pilus. of nutrient molecules where there is no Fine adjustment Focusing mechanism of a net change in the oxidation state of the pro- microscope that very slowly changes the ducts as Compare d with that of the reac- distance between the objective lens and tants; fermentation can occur in the the specimen. absence of oxygen. First law of thermodynamics The law that Fever A body temperature that is abnor- states that energy cannot be created or mally high. destroyed and that it is therefore possible Fibroblast A new connective tissue cell that to account for any change in the internal replaces fibrin as a blood clot dissolves, energy of a system DE by an exchange of forming grandulation tissue. heat (q) and/or work (w) with the sur- Fibrous proteins Proteins of elongated roundings DE ¼ Q–w. shape, often used as structural materials First‐order reaction A reaction whose rate in cells and tissues. Compare globular pro- depends on the first power of the concen- teins. tration of the reactant. Compare second‐ Fifth disease A normal disease in children order reaction. caused by the Erythrovirus called B19, char- Fischer projection A convention for re- acterized by a bright red rash on the cheeks presenting stereoisomers in a plane. The and a low‐grade fever. tetrahedron of bonds on a carbon is repre- Known also as erythema infectiosum. sented as a plane cross, where the bonds to Filariasis Disease of the blood and lymph the right and left are assumed to be point- caused by any of several different round- ing toward the viewer and the bonds to worms carried by mosquitoes. the top and bottom are assumed to be Filovirus A filamentous virus that displays pointing away from the viewer. Fischer unusual variability in shape. Two filo- projections of monosaccharides are ori- viruses, the Ebola virus and the Marburg ented with the carbonyl group at the top; virus, have been associated with human the chiral carbon farthest from the car- disease. bonyl group (which is the one that deter- Filter paper disk method Method of evalu- mines whether the sugar is the D or the L ating the antimicrobial properties of a form) is then drawn with its hydroxyl to chemical agent using filter paper disks the right for the D form and to the left for placed on an inoculated agar plate. the L form. 1136 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Five‐kingdom system System of classifying move in the plane of the membrane. This organisms into one of five kingdoms: model is basically correct. Monera (Prokaryotae), Protista, Fungi, Fluke A flatworm with a complex life cycle; Plantae, and Animalia. can be an internal or external parasite. Flagellar staining A technique for ob- Fluorescence (1) Emission of light of one serving flagella by coating the surfaces color when irradiated with another, shorter of flagella with a dye or a metal such as wavelength of light (2) The phenomenon silver. by which a substance that absorbs light at a Flagellum (plural: flagella). A long, thin, given wavelength reradiates a portion of helical appendage of certain cells that pro- the energy as light of a longer wavelength. vides a means of locomotion. Flourescence activated cell sorter (FACS) De- Flash pasteurization See high‐temperature vice that separates cells within a population short‐time pasteurization. based on whether or not they fluoresce. Flat sur spoilage Spoilage due to the growth Flourescence miscroscopy Use of ultravio- of spores that does not cause cans to bulge let light in a microscope to excite molecules with gas. so that they release light of different colors. Flatworm A primitive, unsegmented, her- Fluorescent antibody staining Procedure in maphroditic often parasitic worm. fluorescence microscopy that uses a fluoro- Known also as platyhelminthes. chrome attached to antibodies to detect the Flavin adenine dinucleotide (FAD), flavin presence of an antigen. mononucleotide (FMN) Coenzymes deri- Fluoride Chemical that helps in reducing
ved from vitamin B2 (riboflavin) that func- tooth decay by poisoning bacterial tion as electron acceptors in enzymes that enzymes and hardening the surface enamel catalyze electron transfer reactions. of teeth. Flavivirus A small, enveloped, (þ) sense Flux With reference to a chemical pathway, RNA virus that causes a variety of encepha- the rate (in moles per unit time) at which litides, including yellow fever. reactant ‘‘flows through’’ the pathway to Flavorprotein An electron carrier in oxida- emerge as product. The term can be used tive phosphorylation. for the rate at which particles undergo any Flocculation The addition of alum to cause process in which they either flow or can be precipitation of suspended colloids, such thought of metaphorically as flowing. as clay, in the water purification process. Focal infection An infection confined to a Flourescence‐activated cell sorter (FACS) A specific area from which pathogens can machine that collects quantities of a partic- spread to other areas. ular cell type under sterile conditions for Folliculitis Local infection produced when study. hair follicles are invaded by pathogenic Fluctuation test A test to determine that bacteria. resistance to chemical substances occurs Known also as pimple or pustule. spontaneously rather than being induced. Fomite A non‐living substance capable of Fluid‐mosaic model A model describing transmitting disease, such as clothing, cellular membrane structure, according to dishes, or paper money. which the proteins are embedded in a Food poisoning A gastrointestinal disease phosopholipid bilayer and are free to caused by ingestion of foods contaminated Appendix C: Micro‐organisms, biochemistry, and nomenclature 1137
with preformed toxins or other toxic sub- in enthalpy and entropy and indicates stances. whether the process will be thermodynam- Known also as enterotoxicosis. ically favored at a given temperature. Footprinting With respect to molecular ge- Known also as Gibbs free energy. netics, a technique used to identify the Freeze‐etching Technique in which water is DNA segment in contact with a given evaporated under vacuum from the freeze‐ DNA‐binding protein. The DNA‐protein fractured surface of a specimen before the complex is subjected to digestion with a observation with electron microscopy. non‐specific nuclease, which cleaves at Freeze‐fracturing Technique in which a cell the residues that are not protected by the is first frozen and then broken with a knife protein. so that the fracture reveals structures inside Formed elements Cells and cell fragments the cell when observed by electron micros- comprising about 40% of the blood. copy. F Pilus A bridge formed from an F1 cell to Frictional coefficient A coefficient that an F2 cell for conjugation. determines the frictional force on a partic- F Plasmid Fertility plasmid containing ular particle (such as a molecule) in a par- genes direction synthesis of proteins that ticular medium at a given velocity. In the form an F pilus (sex pilus, or conjugation context of electrophoresis or centrifuga- pilus) tion, it determines how fast a chemical F Cell A cell lacking the F plasmid; called species will move in a particular medium recipient or female cell. in response to a given electrical field or Fþ Cell A cell having an F plasmid, called centrifugal force. donor or male cell. Fulminating See ACME. F’ Plasmid An F plasmid that has been im- Functional group Part o a molecule that precisely separated from the bacterial chro- generally participates in chemical reactions mosome so that it carries a fragment of the as a unit and gives the molecule some of its bacterial chromosome. chemical properties. Frameshift mutation A mutation that Fungi (singular: fungus). The kingdom of changes the reading for a gene by adding non‐photosynthetic, eukaryotic organisms or deleting one or two nucleotides, thereby that absorb nutrients from their environ- reducing the remainder of the message 30 ment. to the mutation to gibberish. Fungi imperfecti Group of fungi termed Frameshift suppressor A mutant tRNA that ‘‘imperfect’’ because no sexual stage has contains either two or four bases in the been observed in their life cycles. anticodon loop and can suppress the effects Known also as deuteromycota. of a particular frameshift mutation in a gene. Furuncle A large, deep pus‐filled infection. Free energy (G) A thermodynamic quantity Known also as a boil. (function of state) that takes into account Fusion proteins Genetically engineered both enthalpy and entropy: G ¼ H–TS, proteins that are made by splicing toge- where H is enthalpy, S is entropy, and T is ther coding sequences from two or more absolute temperature. The change in free genes. The resulting protein thus combi- energy (DG) for a process, such as a chemi- nes portions from two different parent cal reaction, takes into account the changes proteins. 1138 Appendix C: Micro‐organisms, biochemistry, and nomenclature
F0F1 complex The enzyme complex in the Generation time Time required for a inner mitochondrial membrane that uses population of organisms to double in energy from the transmembrane proton number.
gradient to catalyze ATP synthesis. The F0 Genetic code The code by which the nucle- portion of the complex spans the mem- otide sequence of a DNA or RNA molecule
brane, and the F1 portion, which performs specifies the amino acid sequence of a poly- the ATP synthase activity, projects into the peptide. It consists of three‐nucleotide mitochondrial matrix. codons that either specify a particular Gamete A male or female reproductive cell. amino acid or tell the ribosome to stop Gametocyte A male or female sex cell. translating and release the polypeptide. Gamma globulin See immune serum globu- With a few minor exceptions, all living lin. things use the same code. Ganglion An aggregation of neuron cell Genetic engineering The use of various bodies. techniques to purposefully manipulate ge- Gas gangrene A deep would infection, de- netic material to alter the characteristics of structive of tissue, often caused by a com- an organism in a desired way. bination of two or more species of Genetic fusion A technique of genetic engi- Clostridium. neering that allows transposition of genes Gated channel A membrane ion channel from one location on a chromosome to that can open or close in response to sig- another location; the coupling of genes nals from outside or within the cell. from two different operons. Gel electrophoresis A type of electrophore- Genetic homology The similarity of DNA sis in which the supporting medium is a base sequences among organisms. thin slab of gel held between glass plates. Genetic immunity Inborn or innate immu- The technique is widely used for separating nity. proteins and nucleic acids. Genetic recombination Any process that See also electrophoresis, isoelectric focusing. results in the transfer of genetic material Gene A linear sequence of DNA nucleo- from one DNA molecule to another. In tides that form a functional unit within a eukaryotes, it can refer specifically to the chromosome or plasmid. exchange of matching segments between Gene amplification A technique of genetic homologous chromosomes by the process engineering in which plasmids or bacterio- of crossing over. phages carrying a specific gene are induced Genetics The science of heredity, including to reproduce at a rapid rate within host cells. the structure and regulation of genes and Generalized anaphylaxis See anaphylactic how these genes are passed between gen- shock. erations. Generalized transduction Type of transduc- Gene transfer Movement of genetic infor- tion in which a fragment of DNA from mation between organisms by transforma- the degraded chromosome of an infected tion, transduction, or conjugation. bacteria cell is accidentally incorporated Genital herpes See herpes simplex virus into a new phage particle during viral rep- Type‐2. lication and thereby transferred to another Genital wart An often malignant wart asso- bacterial cell. ciated with sexual transmitted viral disease Appendix C: Micro‐organisms, biochemistry, and nomenclature 1139
having a very high association rate with that can be used as substrates for glucose cervical cancer. synthesis. Known also ad condyloma. Gluconeogenesis The processes by which Genome The total genetic information glucose is synthesized from non‐ contained in a cell, an organism, or virus. carbohydrate precursors such as glycerol, Genotype The genetic information lactate, some amino acids, and (in plants) contained in the DNA of an organism. acetyl‐CoA. Compare phenotype. Glucose transporter A membrane protein Genus A taxon consisting of one or more that is responsible for transporting glucose species, the first name of an organism in across a cell membrane. Different tissues the binomial system of nomenclature; for may have glucose transporters with differ- example, Escherichia in Escherichia coli. ent properties. German measles See rubella. Glycan Another name for polysaccharide. Germination The start of the process of de- Glycocalyx Term used to refer to all sub- velopment of a spore or an endospore. stances containing polysaccharides found Germ theory of disease Theory that micro‐ external to the cell wall. organisms (germs) can invade other organ- Clycolipids Lipids that have saccharides at- isms and cause disease. tached to their head groups. Giardiasis A gastrointestinal disorder Glycolysis The initial pathway in the catab- caused by the flagellated protozoan Giardia olism of carbohydrates, by which a mole- intestinalis. cule of glucose is broken down to two Gibberellins A family of diterpene plant molecules of pyruvate, with a net produc- growth hormones. tion of ATP molecules and the reduction of þ Gibbs free energy See free energy. two NAD molecules to NADH. Under Gingivitis The mildest form of periodontal aerobic conditions, these NADH molecules disease, characterized by inflammation of are reoxidized by the electron transport the gums. chain; under anaerobic conditions, a dif- Gingivostomatitis Inflammation of and ferent electron acceptor is used. An anaer- damage to the glomeruli of the kidneys. obic metabolic pathway used to break Known also as Bright’s disease. down glucose into pyruvic acid while Globular proteins Proteins whose three‐ producing some ATP. dimensional folded shape is relatively com- Glycoprotein A long, spikelike molecule pact. Compare fibrous proteins. made of carbohydrate and protein that Glomerulus A coiled cluster of capillaries in projects beyond the surface of a cell or the nephron. viral envelope; some viral glycoproteins at- Glucocorticoids The steroid hormones tach the virus to receptor sites on host cells, cortisol and corticosterone, which are se- while other said fusion of viral and cellular creted by the adrenal cortex. In addition to membranes. other functions, they promote gluconeo- Glycosaminoglycans Polysaccharides com- genesis in response to low blood sugar posed of repeating disaccharide units in levels. which one sugar is either N‐acetylgalacto- Glucogenic In fuel metabolism, refers to samine or N‐acetylglucosamine. Typically substances (such as some amino acids) the disaccharide unit carries a carboxyl 1140 Appendix C: Micro‐organisms, biochemistry, and nomenclature
group and often one or more sulfates, so Gram molecular weight See mole. that most glycosaminoglycans have a high Gram stain A differential stain that uses density of negative charges. Glycosamino- crystal violet, iodine, alcohol, and safranin glycans are often combined with protein to to differentiate bacteria. Gram‐positive form proteoglycans and are an important bacteria stain dark purple; Gram‐negative component of the extracellular matrix of ones stain pink/red. vertebrates. Granulation tissue Fragile, reddish, grainy Known also as mucopolysaccharides. tissue made up of capillaries and fibro- Glycosidic bond A covalent bond between blasts that appears with the healing of an two monosaccharides. injury. Glyoxysome A specialized type of peroxi- Granule An inclusion that is not bounded some found in plant cells. It performs by a membrane and contains compacted some of the reactions of photorespira- substances that do not dissolve in the cyto- tion, and it also breaks down fatty acids plasm. to acetyl‐CoA by b‐oxidation and converts Granulocyte A leukocyte (basophil, mast the acetyl‐CoA to succinate via the glyox- cell, eosinophil, and neutrophil) with gran- ylate cycle, thus enabling plants to convert ular cytoplasm and irregularly shaped, fatty acids to carbohydrates. lobed nuclei. Golgi apparatus An organelle in eukaryotic Granuloma In a chronic inflammation, a cells that receives, modifies, and transports collection of epithelial cells, macrophages, substances coming from the endoplasmic lymphocytes, and collagen fibers. reticulum. Granuloma inguinale A sexually transmit- Golgi complex A stack of flattened mem- ted disease caused by Calymmatobacterium branous vesicles in the cytoplasm. It serves Granulomatis. as a routing center for proteins destined for Known also as Donovanosis. secretion or for lysosomes or the cell mem- Granulomatous hypersensitivity Cell‐ brane; it performs similar functions for mediated hypersensitivity reaction that membrane lipids, and it also modifies and occurs when macrophages have engulfed finishes the oligosaccharide moieties of pathogens but have failed to kill them. glycoproteins. Granulomatous inflammation A special Gonorrhea A sexually transmitted disease kind of chronic inflammation character- caused by Neisseria Gonorrhoeae. ized by the presence of granulomas. G Proteins A family of membrane‐associated Granzyme A cytotoxin produced by cyto- proteins that transduce signals received by toxic T cells that help kill infected host various cell‐surface receptors. They are cells. called G proteins because binding of GTP Griseofulvin An antifungal agent that inter- and GDP is essential to their action. feres with fungal growth. Graft tissue Tissue that is transplanted Ground itch Bacterial infection of sites of from one site to another. penetration by hookworms. Graft‐versus‐host (GVH) disease Disease in Group translocation An active transport which host antigens elicit an immunologi- process in bacteria that chemically modi- cal response from graft cells that destroys fies substance so it cannot diffuse out of the host tissue. cell. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1141
Growth curve The different growth periods munogenic carrier molecule (usually a of a bacterial or phage population. protein). Growth factors Peptide mediators that in- Hapten A small molecule that can act as an fluence the growth and/or differentiation antigenic determinant when combined of cells; they differ from growth hormones with a larger molecule. in being produced by many tissues and in Haworth projection A conventional planar acting locally. representation of a cyclized monosaccha- Gumma A granulomatous inflammation, ride molecule. The hydroxyls that are symptomatic of syphilis, that destroys represented to the right of the chain in a tissue. Fischer projection are shown below the Gut‐associated lymphatic tissue (GALT) Col- plane in a Haworth projection. lective name for the tissues of lymphoid Heat fixation Technique in which air‐dried nodules, especially those in the digestive, smears are passed through an open flame respiratory, and urogenital tracts; main site so that organisms are killed, adhere better of antibody production. to the side, and take up dye more easily. Half‐life For a chemical reaction, the time Heat‐shock proteins A group of Chapero- at which half the substrate has been con- nins that accumulates in a cell after it has sumed and turned into product. The term been subjected to a sudden temperature can also refer to the analogous point in jump or other stress. They are thought to other processes, such as the radioactive help deal with the accumulation of im- decay of an isotope. properly folded or assembled proteins in Known also as half‐time. stressed cells. Halobacteria One of the groups of the Heavy chain (H chain) Larger of the two archaeobacteria that lives in very concen- identical pairs of chains comprising immu- trated salt environments. noglobulin molecules. Halophile A salt‐loving organism that Helicases Enzymes that catalyze the requires moderate to large concentrations unwinding of duplex nucleic acids. of salt. Helix‐loop‐helix motif A binding motif that Hanging drop A special type of wet. mount is found in calmodulin and some other often used with dark‐field illumination to calcium‐binding proteins as well as in study motility of organisms. some DNA‐binding proteins. It consists of Hansen’s disease The preferred name for two a‐helix segments connected by a loop. leprosy, caused by Mycobacterium leprae, Helix‐turn‐helix motif ADNA‐binding it exhibits various clinical forms ranging motif that is responsible for sequence‐ from tuberculoid to lepromatous. specific DNA binding in many transcrip- Hantavirus pulmonary syndrome (HPS) The tion factors. It consists of two a‐helix ‘‘Sin Nombre’’ hantavirus responsible for segments connected by a b turn; one of severe respiratory illness. the helices occupies the DNA major groove Haploid (1) A eukaryotic cell that contains and makes specific base contacts. a single, unpaired set of chromosomes. Helminth A worm, with bilateral symmetry; (2) A molecule that is too small to stimu- includes the roundworms and flatworms. late an immune response by itself but Helper T cell (TH) (1) Lymphocytes that can do so when coupled to a larger, im- stimulate other immune cells, such as B 1142 Appendix C: Micro‐organisms, biochemistry, and nomenclature
cells and macrophages. (2) T lymphocytes causing kidney damage and bleeding in the whose role is to recognize antigens and urinary tract. help other defensive cells to mount an im- Hepadnavirus A small, enveloped DNA mune response. They help activate antigen‐ virus with circular DNA, one such virus stimulated B cells (resulting in production causes hepatitis B. of specific antibodies) and/or antigen‐ Hepatitis An inflammation of the liver, stimulated cytotoxic T cells (resulting in usually caused by viruses but sometimes attack on antigenic cells), and they also by an amoeba or various toxic chemicals. produce immune mediators that stimulate Hepatitis A (formerly called infectious non‐specific defense responses. hepatitis) Common form of viral hepati- Hemagglutination Agglutination (clump- tis caused by a single‐stranded RNS virus ing) of red blood cells, used in blood typing. transmitted by the fecal‐oral route. Hemagglutination inhibition test Serologic Hepatitis B (formerly called serum hepati- test used to diagnose measles, influenza, tis) Type of hepatitis caused by a double‐ and other viral diseases, based on the abili- stranded DNA virus usually transmitted in ty of antibodies to viruses to prevent viral blood or semen. hemagglutination. Hepatitis C (formerly called non‐A, non‐B Heme A molecule consisting of a porphyrin hepatitis) Type of hepatitis distinguished ring (either protoporphyrin IX or a deriva- by a high level of the liver enzyme alanine tive) with a central complexed iron; it serves transferase, usually mild or inapparent in- as a prosthetic group in proteins such as fection but can be severe in compromised myoglobin, hemoglobin, and cytochromes. individuals. Hemimethylated With respect to DNA, Hepatitis D Severe type of hepatitis caused refers to the condition in which one strand by presence of both hepatitis D and hepati- of the duplex is methylated and the other is tis B viruses, hepatitis D virus is an incom- not. Newly replicated DNA is hemimethy- plete virus and cannot replicate without lated; normally a methylase enzyme then presence of hepatitis B virus as a helper. methylates appropriate bases in the new Known also as delta hapatitis. strand. Hepatitis E Type of hepatitis transmitted Hemoglobin The oxygen‐binding com- through fecally contaminated water pound found in erythocytes. supplies. Hemolysin An enzyme that lyses red blood Hepatovirus One of three major groups of cells. picornaviruses that can infect nerves and is Hemolysis The lysis of red blood cells. responsible for causing hepatitis A. Hemolytic disease of the newborn Disease Herd immunity The proportion of indivi- in which a baby is born with enlarged liver duals in a population who are immune to and spleen caused by efforts of these organs a particular disease. to destroy red blood cells damaged by ma- Known also as group immunity. ternal antibodies; mother is Rh‐negative Heredity Having both male and female re- and baby is Rh‐positive. productive systems in one organism. Known also as erythroblastosis fetalis. Herpes gladiatorium Herpesvirus infection Hemorrhagic uremic syndrome (HUS) Infec- that occurs in skin injuries of wrestlers, tion with 0157‐H7 strain of Escherichia coli transmitted by contact or on mats. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1143
Herpes labialis Fever blisters (cold sores) Hib vaccine Vaccine against Haemophilus on lips. influenzae b. Herpes meningoencephalitis A serious dis- High‐density lipoprotein (HDL) Atypeof ease caused by herpesvirus that can cause lipoprotein particle that functions mainly permanent neurological damage or death to scavenge excess cholesterol from tissue and that sometimes follows a generalized cells and transport it to the liver, where it herpes infection or ascends from the tri- can be excreted in the form of bile acids. geminal ganglion. High‐energy bond A chemical bond that Herpes pneumonia A rare form of herpes releases energy when hydrolyzed; the ener- infection seen in burn patients, AIDS gy can be used to transfer the hydrolyzed patients, and alcoholics. product to another compound. Herpes simplex virus Type‐1 (HSV‐1) A virus High frequency of recombination (Hfr) þ that most frequently causes fever blisters strain A strain of F bacteria in which (cold sores) and other lesions of the the F plasmid is incorporated into the bac- oral cavity, and less often causes genital terial chromosome. lesions. High‐temperature short‐time (HTST) pasteur- Herpes simplex virus Type‐2 (HSV‐2) A virus ization Process in which milk is heated to that typically causes genital herpes, but 71.6 C for at least 15 s. which can also cause oral lesions. Known also as flash pasteurization. Known also as herpes hominis virus. Hill coefficient (nH) A coefficient that indi- Herpesvirus A relatively large, enveloped cates the degree of cooperativity of a coop- DNA virus that can remain latent in host erative transition; it is the maximum slope cells for long periods of time. of a Hill plot of the transition. Heterogencity The ability of the immune Histamine Amine release by basophils and system to produce many different kinds of tissues in allergic reactions. antibodies, each specific for a different an- Histocompatibility antigen An antigen tigenic determinant. found in the membranes of all human Heterotroph An organism that uses com- cells that is unique in all individuals except pounds to produce biomolecules. identical twins. Heterotrophs Organisms that cannot syn- Histone A protein that contributes directly thesize their organic compounds entirely to the structure of eukaryotic chromosomes. from inorganic precursors but most con- Histones The proteins that participate in sume at least some organic compounds forming the nucleosomal structure of made by other organisms. In particular, chromatin. Four of the five kinds of his-
these organisms cannot use CO2 as a car- tones make up the core particle of the bon source. Compare autotrophs. nucleosome; the 50 is associated with the Heterotrophy ‘‘Other‐feeding’’ the use of linker DNA between nucleosomes. All carbon atoms from organic compounds histones are small, very basic proteins. for the synthesis of biomolecules. Histoplasmosis Fungal respiratory disease Heterozygous In a diploid organism, the endemic to the central and eastern United possession of two different alleles for a States, caused by the soil fungus Histo- given gene (as opposed to two copies of plasma capsulatium. the same allele). Compare homozygous. Known also as darling’s disease. 1144 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Holding method See low‐temperature long‐ Homozygous In a diploid organism, the time pasteurization. possession of two identical alleles for a Holliday junction An intermediate during given gene. Compare heterozygous. homologous recombination; a four‐armed Hookworm A disease caused by two species structure in which each of the participating of small roundworms, Ancylostoma duode- DNA duplexes has exchanged one strand nale and Necator americanus, whose larvae with the other duplex. burrow through skin and feet, enter the Holoenzyme A functional enzyme consist- blood vessels, and penetrate lung and ing of an apoenzyme and a coenzyme or intestinal tissue. cofactor. Horizontal transmission Direct contact Homeo box A common sequence element transmission of disease in which pathogens of about 180 base pairs that is found in are usually passed by handshaking, kissing, homeotic genes. It codes for a sequence‐ contact with sores, or sexual contact. specific DNA‐binding element of the Hormone A substance that is synthesized helix‐loop‐helix class. and secreted by specialized cells and carried See also homeotic genes. via the circulation to target cells, where it Homeotic genes Genes that contain homeo elicits specific changes in the metabolic box elements and typically are involved in behavior of the cell by interacting with a controlling the pattern of organismal de- hormone‐specific receptor. velopment. Homeotic mutations, which Hormone‐responsive element A DNA site scramble portions of this pattern, affect that binds an intracellular hormone– homeotic genes. The nuclear DNA‐binding receptor complex; binding of the complex proteins encoded by these genes presum- to a hormone‐responsive element affects ably serve as transcriptional regulators for the transcription of specific genes. the coordinated expression of groups of Host Any organism that harbors another genes. organism. See also homeo box. Host‐induced restriction and modification A Homolactic acid fermentation A pathway in genetic system found in bacteria whereby a which pyruvic acid is directly converted to genetic element (often a plasmid) encodes lactic acid using electrons from reduced both an enzyme for the methylation of NAS (NADH) DNA at a specific base sequence and an Homologous recombination Genetic recom- Endonuclease that cleaves unmethylated bination that requires extensive sequence DNA at that sequence. The system thus homology between the recombining restricts the DNA that can survive in the DNA molecules. Meiotic recombination cell to DNA that is modified by methylation by crossing over in eukaryotes is an at the correct sequences. example. Host range The different types of organ- Homopolymer (biological) A polymer that is isms that a microbe can infect. made of only one kind of monomer. Starch, Host specificity The range of different made only of glucosyl units, is an example. ghosts in which a parasite can mature. Polymers that include more than one kind of Human immunodeficiency virus (HIV) One monomer, like polypeptides and nucleic of the retroviruses that is responsible for acids, are called heteropolymers. AIDS. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1145
Human leukocyte antigen (HLA) A lympho- Hydrologic cycle See water cycle. cyte antigen used in laboratory tests to Hydrolysis A chemical reaction that pro- determine compatibility of donor and re- duces simpler products from more com- cipient tissues for transplants. plex organic molecules. Human papillomavirus (HPV) Virus that Hydrophilic Refers to the ability of an atom attacks skin and mucous membranes, caus- or a molecule to engage in attractive inter- ing papillomas or warts. actions with water molecules. Substances Humoral immune response A response to that are ionic or can engage in hydrogen foreign antigens carried out by antibodies bonding are hydrophilic. Hydrophilic sub- circulating in the blood. stances are either soluble in water or, at Humoral immunity The immune response least, wettable. Compare hydrophobic. most effective in defending the body Hydrophobic The molecular property of against bacteria, bacterial toxins, and vi- being unable to engage in attractive inter- ruses that have not entered cells. actions with water molecules. Hydro- Humus The non‐living organic compo- phobic substances are non‐ionic and nents of soil. non‐polar; they are non‐wettable and do Hyaluronidase A bacterially produced en- not readily dissolve in water. Compare hy- zyme that digests hyaluronic acid, which drophilic. helps hold the cells of certain tissues to- Hydrophobic effect With respect to globu- gether, thereby making tissues more acces- lar proteins, the stabilization of tertiary sible to microbes. structure that results from the packing of Known also as spreading factor. hydrophobic side chains in the interior of Hybridoma A hybrid cell resulting from the the protein. fusion of a cancer cell with another cell, Hydrostatic pressure Pressure exerted by usually an antibody‐producing white standing water. blood cell. Hyperimmune serum A preparation of im- Hybridomas Cultured cell lines that are mune serum globulins having high titers of made by fusing antibody‐producing B lym- specific kinds of antibodies. phocytes with cells derived from a mouse Known also as convalescent serum. myeloma (a type of lymphocyte cancer). Hyperparasitism The phenomenon of a Like B cells, they produce specific anti- parasite itself having parasites. bodies, and like myeloma cells, they can Hypersensitivity Disorder in which the proliferate indefinitely in culture. immune system reacts inappropriately, Hydatid cyst An enlarged cyst containing usually by responding to an antigen it nor- many tapeworm heads. mally ignores. Hydrogen bond An attractive interaction Known also as an allergy. between the hydrogen atom of a donor Hypertonic solution A solution containing group, such as –OH or =NH, and a pair a concentration of dissolved material great- of non‐bonding electrons on an acceptor er than that within a cell. group, such as O=C. The donor group Hypha (plural. hyphae). A long, threadlike atom that carries the hydrogen must be structure of cells in fungi or actinomycetes. fairly electronegative for the attraction to Hypochromism With respect to DNA, a re- be significant. duction in the absorbance of ultraviolet 1146 Appendix C: Micro‐organisms, biochemistry, and nomenclature
light of wavelength of about 260 nm that Immune complex disorder A disorder accompanies the transition from random‐ caused by antigen–antibody complexes coil denatured strands to a double‐strand that precipitate in the blood and injure helix. It can be used to track the process of tissues; elicited by antigens in vaccines, on denaturation or renaturation. micro‐organisms, or on a person’s own Hypothesis A tentative explanation for an cells. observed condition or event. Known also as immune complex (Type‐III) Hypotonic solution A solution containing a hypersensitivity. concentration of dissolved material lower Immune cytolysis Process in which the than that within a cell. membrane attack complex of complement IgA Class of antibody found in the blood produces lesions on cell membranes and secretions. through which the contents of the bacterial IgD Class of antibody found on the surface cells leak out. of B cells and rarely secreted. Immune serum globulin A pooled sample IgE Class of antibody that binds to receptors of antibody‐containing fractions of serum on basophils in the blood or mast cells in the from many individuals. tissues, responsible for allergic or immediate Known also as gamma globulin. (Type‐I) hypersensitivity reactions. Immune system Body system that provides IgG The main class of antibodies found in the host organism with specific immunity the blood; produced in largest quantities to infectious agents. during secondary response. Immunity The ability of an organism to IgM The first class of antibody secreted into defend itself against infectious agents. the blood during the early stages of a pri- Immunocompromised Referring to an in- mary immune response (a rosette of five dividual whose immune defenses are immunoglobulin molecules) or found on weakened due to fighting another infec- the surface of B cells (a single immuno- tious disease, or because of an immunode- globulin molecule). ficiency disease or an immunosuppressive Illness phase In an infectious disease, the agent. period during which the individual experi- Immunodeficiency Inborn or acquired ences the typical signs and symptoms of defects in lymphocytes (B or T cells). the disease. Immunodeficiency disease A disease of Imidazole An antifungal agent that disrupts impaired immunity caused by lack of lym- fungal plasma membranes. phocytes, defective lymphocytes, or des- Immediate (Type‐I) hypersensitivity Res- tructive lymphocytes. ponse to a foreign substance (allergen) re- Immunodiffusion test A serologic test simi- sulting from prior exposure to the allergen. lar to the precipitin test but carried out in Known also as anaphylactic hypersensitivity. agar gel medium. Immersion oil Substance used to avoid re- Immunoelectrophoresis Serologic test in fraction at a glass–air interface when exam- which antigens are first separated by gel ining objects through a microscope. electrophoresis and then allowed to react Immune complex An antigen–antibody with antibody placed in a trough in the gel. complex that is normally eliminated by Immunofluorescence Referring to the use of phagocytic cells. antibodies to which a fluorescent substance Appendix C: Micro‐organisms, biochemistry, and nomenclature 1147
is bound and used to detect antigens, Incidence rate The number of new cases of other antibodies, or complement within a particular disease per 100,000 population tissue. seen in a specific period of time. Immunogen See antigen. Inclusion A granule or vesicle found in the Immunogenic Something that is a potent cytoplasm of a bacterial cell. stimulator of antibody production and de- Inclusion blennorrhea A mild chlamydial fense cell activity. infection of the eyes in infants. Immunoglobulin (Ig) The class of protective Inclusion body (1) An aggregation of retic- proteins produced by the immune system ulate bodies within chlamydias. (2) A form in response to a particular epitope. of cytopathic effect consisting of viral com- Known also as an antibody. See antibodies. ponents, masses of viruses, or remnants of Immunological disorder Disorder that viruses. results from an inappropriate or inade- Inclusion conjunctivitis A chlamydial infec- quate immune system. tion that can result from self‐inoculation Immunological memory The ability of the with Chlamydia trachomatis. immune system to recognize substances it Incubation period In the stages of infec- has previously encountered. tious disease, the time between infection Immunology The study of specific immuni- and the appearance of signs and symp- ty and how the immune system responds toms. to specific infectious agents. Index case The first case of a disease to be Immunosuppression Minimizing of im- identified. mune reactions using radiation or cytotox- Index of refraction A measure of the ic drugs. amount that light rays bend when passing Impetigo A highly contagious pyoderma from one medium to another. caused by staphylococci, streptococci, or Indicator organism An organism such as both. Escherichia coli whose presence indicates Importins A class of proteins involved in the contamination of water by fecal matter. importing molecules into the nucleus. Indigenous organism An organism native See exportins. to a given environment. Inapparent infection An infection that fails Known also as a native organism. to produce symptoms, either because too Indirect contact transmission Transmission few organisms are present or because host of disease through fomites. defenses effectively combat the pathogens. Indirect fecal‐oral transmission Transmis- Known also as subclinical infection. sion of disease in which pathogens from Inborn errors of metabolism Human muta- feces of one organism infect another tions that result in specific derangements organism. of intermediary metabolism. Usually the Induced Dipole A molecule has an induced problem is an enzyme that is inactive, over- dipole if an external electric field induces active, too scarce, or too abundant; symp- an asymmetric distribution of charge with- toms may result from the insufficient in it. production of a necessary metabolite and/ Induced fit model A model for how or from the accumulation of another enzymes interact with substrates to achieve metabolite to toxic levels. catalysis. According to this model, the 1148 Appendix C: Micro‐organisms, biochemistry, and nomenclature
empty active site of the enzyme only Infectious mononucleosis An acute disease roughly fits the substrate(s), and the entry that affects many systems, caused by the of substrate causes the enzyme to change Epstein‐Barr virus. its shape so as to both tighten the fit and Infestation The presence of heminths causes the substrate to adopt an intermedi- (worms) or anthropods in or on a living ate state that resembles the transition state host. of the uncatalyzed reaction. This is cur- Inflammation The body’s defensive res- rently the dominant model for enzymatic ponse to tissue damage caused by microbi- catalysis. al infection. Induced mutation A mutation produced by Influenza Viral respiratory infection caused agents called mutagen that increases the by orthomyxoviruses that appears as epi- mutation rate. demics. Inducer A substance that binds to and inac- Initiating segment It is the part of the F tivates a repressor protein. plasmid that is transferred to the recipient Inducible enzyme An enzyme coded for by cell in conjugation with an Hfr bacterium. a gene that is sometimes active and some- Innate immunity Immunity to infection times inactive. that exists in an organism because of ge- Induction (1) The stimulation of a temper- netically determined characteristics. ature phase (prophage) to excise itself from Insect An anthropod with three body the host chromosome and initiate a lytic regions, three pairs of legs, and highly cycle of replication. (2) In cellular metabo- specialized mouthparts. lism, the synthesis of a particular protein in Insertion The addition of one or more response to a signal; for example, the syn- bases to DNA, usually producing a frame- thesis of an enzyme in response to the shift mutation. appearance of its substrate. In situ hybridization A technique for Induration A raised, hard, red region on the finding the chromosomal location of a par- skin resulting from tuberculin hypersensi- ticular DNA sequence by probing the chro- tivity. mosomes with a radiolabeled sequence that Industrial microbiology Branch of microbi- will hybridize with the sequence in ques- ology concerned with the use of micro‐ tion. The location of the probe is then organisms to assist in the manufacture visualized with radioautography. of useful products or disposal of waste Intercalation With respect to DNA, refers products. to the fitting (intercalation) of a small mol- Infant botulism Form of botulism in infants ecule between adjacent bases in a DNA associated with ingestion of honey. helix. Known also as ‘‘floppy baby’’ syndrome. Interferon (1) A small protein often re- Infection The multiplication of a parasite leased from virus‐infected cells that binds organism, usually microscopic, within or to adjacent uninfected cells, causing them upon the host’s body. to produce antiviral proteins that interfere Infectious disease Disease caused by infec- with viral replication. (2) All of the reac- tious agents (bacteria viruses, fungi, proto- tions in an organism that are concerned zoa, and helminths). with storing and generating metabolic Infectious hepatitis See hepatitis A. energy and with the biosynthesis of Appendix C: Micro‐organisms, biochemistry, and nomenclature 1149
low‐molecular‐weight compounds and en- Ionic strength (I ) A quantity that reflects the ergy‐storage compounds. It does not in- total concentration of ions in a solution and clude nucleic acid and protein synthesis. the stoichiometric charge (charge per atom Interleukin A cytokine produced by leuko- or molecule)P of each ion. It is defined as I ¼ 1 MiZ2 M Z cytes. 2 i i where i and i are, re- Intermediate host An organism that harbors spectively the molarity and stoichiometeric a sexually immature stage of a parasite. charge of ion i. It is used, for example, in Internal energy (E) The energy contained in calculating the effective radius of a coun- a system. For the purposes of biochemistry, terion atmosphere. the term encompasses all the types of energy Ion pore A pore in a cellular membrane that might be changed by chemical or non‐ through which ions can diffuse. It is nuclear physical processes, including the formed by a transmembrane protein and kinetic energy of motion and vibration of can discriminate among ions to some atoms and molecules and the energy stored degree on the basis of size and charge. in bonds and non‐covalent interactions. Many ions pores are gated, meaning that Intoxication The ingestion of a microbial they can open and close in response to toxin that leads to a disease. signals. Intron (1) Region of a gene (or mRNA) in Iris diaphragm Adjustable device in a mi- eukaryotic cells that does not code for a croscope that controls the amount of light protein. (2) A region in the coding se- passing through the specimen. quence of a gene that is not translated Ischemia Reduced blood flow to tissues into protein. Introns are common in eu- with oxygen and nutrient deficiency and karyotic genes but are rarely found in waste accumulation. prokaryotes. They are excised from the Isoelectric focusing A version of gel electro- RNA transcript before translation. Com- phoresis that allows ampholytes to be sepa- pare exon. rated almost purely on the basis of their Known also as the intervening region. isoelectric points. The ampholytes are Invasiveness The ability of a micro‐organ- added to a gel that contains a pH gradient ism to take up residence in a host. and are subjected to an electric field,. Each Invasive stage Disease spreads into body ampholyte migrates until it reaches the pH from site of energy causing symptoms to that represents its isoelectric point, at appear. which point it ceases to have a net electric Ion An electrically charged atom produced charge and therefore comes to a halt and when an atom gains or loses one or more accumulates. electrons. See also gel electrophoresis, isoelectric point. Ion‐exchange resins Polycationic or polya- Isoelectric point (pI) The pH at which the nionic polymers that are used in ion‐ net charge on an ampholyte is, on average, exchange column chromatography to zero. separate substances on the basis of electri- Isoenzymes Different but related forms of cal charge. an enzyme that catalyze the same reaction. Ionic bond A chemical bond between atoms Often differ in only a few amino acid sub- resulting from attraction of ions with op- stitutions. posite charges. Known also as isozymes. 1150 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Isograft A graft of tissue between geneti- Keratitis An inflammation of the cornea. cally identical individuals. Keratoconjunctivitis Condition in which Isolation Situation in which a patient with a vesicles appear in the cornea and eyelids. communicable disease is prevented from Ketone bodies The substances acetoace- contact with the general population. tate, b‐hydroxybutyrate, and acetone, Isomer An alternative form of a molecule which are produced from excess acetyl‐ having the same molecular formula but CoA in the liver when the rate of fatty different structure. acid b‐oxidation in liver mitochondria Isomorphorous replacement The replace- exceeds the rate at which acetyl‐CoA is ment of one atom in a macromolecule used for energy generation or fatty acid with a heavy metal atom in such a way synthesis. that the structure of the macromolecule Ketose A monosaccharide in which the car- does not change. It is used in the determi- bonyl group occurs within the chain and nation of molecular structure by X‐ray hence represents a ketone group. Compare crystal diffraction. aldose. Isoniazid An antimetabolite that is bacteri- Kidney One of a pair of organs responsible ostatic against the tuberculosis‐causing for the formation of urine. mycobacterium. Kirby–Bauer method See disk diffusion Isotonic Fluid containing the same concen- method. tration of dissolved materials as is in a cell; Koch’s postulates Four postulated formu- causes no change in cell volume. lated by Robert Koch in the 19th century, Isotope An atom of a particular element that used to prove that a particular organism contains a different number of neutrons. causes a particular disease. Isozymes See isoenzymes. Koplik’s spots Red spots with central bluish Joule (J) A unit for energy or work, defined specks that appear on the upper lip mucosa as the work done by a force of 1 N when its in early stages of measles. point of application moves 1 m in the di- Krebs cycle A sequence of enzyme‐ rection of the force. It is the unit of energy catalyzed chemical reactions that metabo- used in the Syste`me Internationale (SI). lizes 2‐carbon units called acetyl groups to
Kala azar Visceral leishmaniasis caused by CO2 and H2O. Leishmania donovani. Known also as tricarboxylic acid cycle and Kaposi’s sarcoma A malignancy often the citric acid cycle. found in AIDS patients in which blood Kupffer cells Phagocytic cells that remove vessels grow into tangled masses that are foreign matter from the blood as it passes filled with blood and easily ruptured. through sinusoids. Karyogamy Process by which nuclei fuse to Kura Transmissible spongiform encepha- produce a diploid cell. lopathy disease of the human brain, caused Keratin A waterproofing protein found in by prions, associated with cannibalism and epidermal cells. tissue/organ transplants. a‐Keratins A class of keratins that are the Lacrimal gland Tear‐producing gland of major proteins of hair. They consist of long the eye. a‐helical polypeptides, which are wound Lactobacilli Type of regular, non‐sporing, around each other to form triplet helices. Gram‐positive rod found in many foods; Appendix C: Micro‐organisms, biochemistry, and nomenclature 1151
used in production of cheeses, yogurt, molecule that precedes the initiation sourdough, and other fermented foods. codon. For a protein, a short N‐terminal Lagging strand During DNA replication, hydrophobic sequence that causes the pro- the strand that is synthesized in the oppo- tein to be translocated into or through a site direction to the direction of movement cellular membrane. of the replication fork; it is synthesized as a Known also as signal sequence. series of fragments that are subsequently Leading strand During DNA replication, joined. Compare leading strand. the strand that is synthesized in the same Lag phase First of four major phases of the direction as the direction of movement bacterial growth curve, in which organisms of the replication fork; it is synthesized grow in size but do not increase in number. continuously rather than in fragments. Large intestine The lower area of the intes- Compare lagging strand. tine that absorbs water and converts undi- Leavening agent An agent, such as yeast, gested food into feces. that produces gas to make dough rise. Laryngeal papilloma Benign growth caused Legionellas The causative bacterial agent in by herpesviruses that can be dangerous is Legionnaires’ disease, Legionella pneumo- such papillomas block the airway, infants phila. are often infected during birth by mothers Leishmaniasis A parasitic systemic disease having genital warts. caused by three species of protozoa of the Laryngitis An infection of the larynx, often genus Leishmania and transmitted by with loss of voice. sandflies. Larynx The voicebox. Leproma An enlarged, disfiguring skin le- Lassa fever Hemorrhagic fever, caused by sion that occurs in the lepromatous form arenaviruses, that begins with pharyngeal of Hansen’s disease. lesions and proceeds to severe liver damage. Lepromatous Referring to the nodular Latency The ability of a virus to remain the form of Hansen’s disease (leprosy) in host cells for long periods of time while which a granulomatous response causes retaining the ability to replicate. enlarged, disfiguring skin lesions called Latent disease A disease characterized by leptromas. periods of inactivity either before symp- Lepromin skin test Test used to detect toms appear or between attacks. Hansen’s disease (leprosy), similar to the Latent Period Period of a bacteriophage tuberculin test. growth curve that spans the time from Leprosy See hansen’s disease. penetration through biosynthesis. Leptospirosis A zoonosis caused by the spi- Latent viral infection An infection typical of rochete Leptospira interrogans, which herpesviruses in which an infection in enters the body through mucous mem- childhood that is brought under control branes or skin abrasions. later in life is reactivated. Leukocidin An exotoxin produced by many Lateral gene transfer Genes pass from one bacteria, including the streptococci and organism to another within the same gen- staphylococci, that kills phagocytes. eration. Leukocyte A white blood cell. Leader sequence For an mRNA, the non‐ Leukocyte‐endogenous mediator A substan- translated sequence at the 50 end of the ce that helps to raise the body temperature 1152 Appendix C: Micro‐organisms, biochemistry, and nomenclature
while decreasing iron absorption (increasing Light reaction The part of photosynthesis iron storage). in which light energy is used to excite elec- Leukocytosis An increase in the number of trons from chlorophyll, which are then white blood cells (leukocytes) circulating used to generate ATP and NADPH. in the blood. Light reactions The photosynthetic subpro- Leukostatin An exotoxin that interferes cesses that depend directly on light energy; with the ability of leukocytes to engulf specifically, the synthesis of ATP by photo- micro‐organisms that release the toxin. phosphorylation and the reduction of þ Leukotriene A reaction mediator released NADP to NADPH via the oxidation of from mast cells after degranulation that water. Compare dark reactions. causes prolonged airway construction, di- Light repair Repair of DNA dimers by a lation, and increased permeability of capil- light‐activated enzyme. laries, increased thick mucous secretion, Known also as photoreactivation. and stimulation of nerve endings that Lineweaver‐burk plot A plot that allows
cause pain and itching. one to derive the rate constant kcat and Leukotrienes K ‐ A family of molecules that are the Michaelis constant M for an enzyme synthesized from arachidonic acid by the catalyzed reaction. It is constructed by lipoxygenase pathway and function as local measuring the initial reaction rate V at hormones, primarily to promote inflam- various substrate concentration [S] and matory and allergic reactions (such as the plotting the values on a graph of 1/V versus bronchial construction of asthma). 1/[S]. L Forms Irregularly shaped naturally occur- Linkage map A map showing the arrange- ring bacteria with defective cell walls. ment of genes on a chromosome; it is con- Library With respect to molecular genetics, structed by measuring the frequency of a large collection of random cloned DNA recombination between pairs of genes. fragments from a given organism, some- Linking number (L) The total number of times representing the entire nuclear times the two strands of a closed, circular genome. DNA helix cross each other by means of Ligand In general, a small molecule that either twist or writhe; this equals the num- binds specifically to a larger one – for ex- ber of times the two strands are interlinked. ample, a hormone that binds to a receptor, It reflects both the winding of the native the term can also be used to mean a chem- DNA helix and the presence of any super- ical species that forms a coordination com- coiling. plex with a central atom, which is usually a See also twist, writhe. metal atom. Lipid One of a group of complex, water‐ Ligase An enzyme that joins together DNA insoluble compounds. segments. Lipid A Toxic substance found in the cell Light chain (L chain) Smaller of the two wall of a Gram‐negative bacteria. identical pairs of chains constituting im- Lipid bilayer A membrane structure that munoglobulin molecules. can be formed by amphipathic molecules Light microscopy The use of any type of in an aqueous environment; it consists of microscope that uses visible light to make two back‐to‐back layers of molecules, in specimens observable. each of which the polar head groups face Appendix C: Micro‐organisms, biochemistry, and nomenclature 1153
the water and the non‐polar tails face that are found at either end of a retroviral the center of the membrane. The fabric of genome. They are involved in integration cellular membranes is a lipid bilayer. into the host genome and in viral gene Lipids A chemically diverse group of expression. biological compounds that are classified Lophotrichous Having two or more flagella together on the basis of their generally at one or both ends of a bacterial cell. apolar structure and resulting poor solu- Low‐angle neutron scattering A set of tech- bility in water. niques that can be used to find the size of a Lipopolysaccharide Part of the outer layer particle in solution or to find the size or of the cell wall in Gram‐negative bacteria. spacing of internal regions that can be dis- Known also as an endoxtoxin. tinguished by different neutron scattering Lipoproteins Any lipid–protein conjugate. power, such as the protein and nucleic acid Specifically refers to lipid–protein associa- components of a nucleoprotein particle or tions that transport lipids in the circulation,. labeled proteins within a multisubunit Each consists of a core of hydrophobic complex. lipids surrounded by a skin of amphipathic Low‐density lipoprotein (LDL) A type of li- lipids with embedded apolipoproteins. Dif- poprotein particle that functions mainly to ferent kinds of lipoproteins play different distribute cholesterol from the liver to roles in lipid transport. other tissues. Its protein component con- Listeriosis A type of meningitis caused by sists of a single molecule of apoprotein B‐ Listeria monocytogenes that is especially 100. threatening to those with impaired im- Lower respiratory tract Thin‐walled bron- mune systems. chioles and alveoli where gas exchange Loaiasis Tropical eye disease caused by the occurs. filarial worm Loa loa. Low‐temperature long‐time (LTLT) pasteuri- Lobar pneumonia Type of pneumonia that zation Procedure in which milk is heated affects one or more of the five major lobes to 62.0 C for at least 30 min. of the lungs. Known also as holding method. Local infection An infection confirmed to a Luminescence Process in which absorbed specific area of the body. light rays are reemitted at longer wave- Localized anaphylaxis An immediate (Type‐ lengths. I) hypersensitivity restricted to only some Lyme disease Disease caused by Borrelia tissue/organs resulting in, e.g., reddening of burgdorferi, carried by the deer tick. the skin, watery eyes, hives, etc. Lymph The excess fluid and plasma pro- Locus The location of a gene on a chromo- teins lost through capillary walls that are some. found in the lymphatic capillaries. Logarithmic rate See exponential rate. Lymphangitis Symptom of septicemia in Log phase Second of four major phases of which red streaks due to inflamed lympha- the bacterial growth curve, in which cells tics appear beneath the skin. divide at an exponential or logarithmic Lymphatic system Body system, closely rate. associated with the cardiovascular system, Long terminal repeats (LTRs) A pair of di- that transports lymph in lymphatic vessels rect repeats several hundred base pairs long through body tissues and organs, performs 1154 Appendix C: Micro‐organisms, biochemistry, and nomenclature
important functions in host defenses and the integration of the viral DNA into the specific immunity. host chromosome and without the replica- Lymphatic vessel Vessel that returns lymph tion of new viruses or cell lysis. to the blood circulatory system. Lysosome A small membrane‐bound or- Lymph node An encapsulated globular ganelle in animal cells that contains diges- structure located along the routes of the tive enzymes. lymphatic vessels that helps clear the Lytic cycle The sequence of events in which lymph of micro‐organisms. a bacteriophage infects a bacterial cell, Lymphocyte A leukocyte (white blood cell) replicates, and eventually causes lysis of found in large numbers in lymphoid tis- the cell. sues that contribute to specific immunity. Lytic phage See virulent phage. Lymphogranuloma venereum A sexually Macrolide A large‐ring compound, such as transmitted disease, caused by Chlamydia erythromycin, that is antibacterial by af- trachomatis, that attacks the lymphatic fecting protein synthesis. system. Macrophage Ravenously phagocytic leuko- Lymphoid nodule A small, unencapsulated cytes found in tissues. aggregation of lymphatic tissue that devel- Mad cow disease Transmissible spongiform ops in many tissues, especially the diges- encephalopathy disease of the brain of tive, respiratory, and unogenital tracts, cattle, caused by prions. collectively called gut‐associated lymphatic Madura foot Tropical disease caused by a tissue (GALT); they are the body’s main variety of soil organisms (fungi and acti- sites of antibody production. nomycetes) that often enter the skin Lymphoid stem cell A cell in the bone mar- through bare feet. row from which lymphocytes develop. Known also as maduromycosis. Lyophokine A cytokine secreted by T cells Maduromycosis See madura foot. when they encounter an antigen. Major histocompatibility complex (MHC) A Lymphilization The drying of a material group of cell surface proteins that are es- from the frozen state, freeze‐drying. sential to immune recognition reactions. Lysis The destruction of a cell by the rup- Malaria A severe parasitic disease caused by ture of a cell or plasma membrane, result- several species of the protozoan Plasmodi- ing in the loss of cytoplasm. um and transmitted by mosquitoes. Lysogen The combination of a bacterium Male reproductive system The host system and a temperate phage. consisting of the testes, ducts, specific Lysogenic Pertaining to a bacterial cell in glands, and the penis. the state of lysogeny. Malignant Relating to a tumor that is Lysogenic conversion The ability of a cancerous. prophage to prevent additional infec- Malta fever See brucellosis. tions of the same cell by the same type Malted Referring to cereal grains that are of phage; also the conversion of a non‐ partially germinated to increase the con- toxin‐producing bacterium into a toxin‐ centration of starch‐digesting enzymes. producing one by a temperate phage. Mammary gland A modified sweat gland Lysogeny The ability of temperature bac- that produces milk and ducts that carry teriophages to persist in a bacterium by milk to the nipple. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1155
Mash Malted grain that is crushed and Meiosis Division process in eukaryotic cells mixed with hot water. that reduces the chromosome number in Mass spectrometry A method for determin- half. ing the molecular mass from the velocity of Membrane attack complex A set of proteins motion of ions in a vacuum. in the complement system that lyses invad- Mast cell A leukocyte that releases hista- ing bacteria by producing lesions in their mine during an allergic response. cell membranes. Mastigophoran A flagellate protozoan such Membrane electrical potential With respect as Giardia. to biological membranes, a voltage differ- Mastoid area Portion of the temporal bone ence that exists across a membrane owing prominent behind the ear opening. to differences in the concentrations of ions Matrix Fluid‐filled inner portion of a mito- on either side of the membrane. chondrion. Membrane filter method Method of testing Maturation The process by which complete for coliform bacteria in water in which virions are assembled from newly synthe- bacteria are filtered through a membrane sized components in the replication process. and then incubated on the membrane sur- Measles A febrile disease with rash caused face in growth medium. by the rubeola virus, which invades lym- Memory cell Long‐lived B or T lymphocyte phatic tissue and blood. that can carry out an anamestic or second- Known also as rubeola. ary response. Measles encephalitis A serious complica- Meninges Three layers of membrane that tion of measles that leaves many survivors protect the brain and spinal cord. with permanent brain damage. Merozoite A malaria trophozoite found in Mebendazole An antihelminthic agent that infected red blood or liver cells. blocks glucose uptake by parasitic round- Mesophile An organism that grows best at worms. temperatures between 25 and 45 C, in- Mechanical stage Attachment to a micro- cluding most bacteria. scope stage that holds the slide and allow- Mesophilic spoilage Spoilage due to im- sprecise control in moving the slide. proper canning procedures or because the Mechanical vector A vector in which the seal has been broken. parasite does not complete any part of its Messenger RNA (mRNA) (1) A type of RNA life cycle during transit. that carries the information from DNA to Mechanism‐based inhibitor An enzyme in- dictate the arrangement of amino acids in a hibitor whose action depends on the protein. (2) RNA molecules that act as enzyme’s catalytic mechanism. Typically, templates for the synthesis of polypeptides it is a substrate analog that irreversibly by ribosomes. modifies the enzyme at a particular step Metabolic pathway A chain of chemical in the catalytic cycle. reactions in which the product of one reac- Medium A mixture of nutritional substances tion serves as the substrate for the next. on or in which micro‐organisms grow. Metabolism The totality of the chemical Megakaryocyte Large cell normally pre- reactions that occur in an organism. Com- sent in bone marrow that gives rise to pare anabolism, catabolism, and intermedi- platelets. ary metabolism. 1156 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Metacercaria The postcercarial encysted Microbial antagonism The ability of normal stage in the development of a fluke, prior microbiota to compete with pathogenic to transfer to the final host. organisms and in some instances to effec- Metachromasia Property of exhibiting a va- tively combat their growth. riety of colors when stained with a simple Microbial antagonism The ability of. nor- stain. mal microbiota to compete with pathogen- Metachromatic granule A polyphosphate ic organisms and in some instances to granule that exhibits metachromasia. effectively combat their growth. Known also as volutin. Microbial growth Increase in the number of Metastability For a system, the condition of cells, due to cell division. being in a state that does not represent Microbiology The study of micro‐organisms. thermodynamic equilibrium but is nearly Micrococci Aerobes or facultative anerobes stable at the time scale of interest because that form irregular clusters by dividing in progress toward equilibrium is slow. two or more planes. Metastasize Relating to the spread of ma- Microenvironment A habitat in which the lignant tumors to other body tissues. oxygen, nutrients, and light are stable, in- Methanogens One of the groups of the cluding the environment immediately sur- archaeobacteria that produce methane gas. rounding the microbe. Metronidazole An antiprotozoan agent ef- Microfilament A protein fiber that makes fective against Trichomonas infections. up part of the cytoskeleton in eukaryotic Micelles Tiny droplets that form when an cells. amphipathic substance that has a polar Microfilaria An immature microscopic head group and a non‐polar tail region roundworm larva. (such as a fatty acid) is added to an aque- Micrometer (mm) Unit of measure equal to ous medium and shaken. Each droplet 0.000001 m or 10–6 m; formerly called a consists of a spherical cluster of amphi- micron (m). pathic molecules arranged with their Micro‐organism Organism studied with a polar head groups facing out toward the microscope; includes the viruses. water and their non‐polar tails facing in Known also as a microbe. toward the center. Microscopy The technology for making Michaelis–Menten equation An equation very small things visible to the unaided eye. that gives the rate of an enzyme‐catalyzed Microtubule A protein tubule that forms reaction in terms of the concentrations of the structure of cilia, flagella, and part of substrate and enzyme as well as two con- the cytoskeleton in eukaryotic cells. stants that are specific for a particular com- Microtubule‐associated proteins (MAPs) A bination of enzyme and substrate: a rate class of proteins associated with microtu-
constant, kcat, for the catalytic production bules that assist in dynamic processes. of product when the enzyme is saturated, Microtubules Fiber‐like cytoplasmic struc- K and the Michaelis constant, M. tures that consist of units of the protein Microaerophile A bacterium that grows tubulin arranged helically to form a hollow best in the presence of a small amount of tube. They are involved in various kinds free oxygen. of cellular motility, including the beating Microbe See micro‐organism. of cilia and flagella and the movement of Appendix C: Micro‐organisms, biochemistry, and nomenclature 1157
organelles from one part of the cell to an- Mitochondrion An organelle in eukaryotic other. cells that carries out oxidative reactions Microvillus (plural: Microvilli). A minute that capture energy. projection from the surface of an animal Mitosis Process by which the cell nucleus in cell. a eukaryotic cell divides to form identical Miliary tuberculosis Type of tuberculosis daughter nuclei. that invades all tissues producing tiny Mixed‐functional oxidase An oxygenase en- lesions. zyme that analyzes a reaction in which two Minimum bactericidal concentration (MBC) different substrates are oxidized, one by the
The lowest concentration of an antimicro- addition of an oxygen atom from O2 and bial agent that kills micro‐organisms, as the other by supplying two hydrogen indicated by absence of growth following atoms to reduce the remaining oxygen
subculturing in the dilution method. atom to H2O. Minimum inhibitory concentration (MIC) Mixed infection An infection caused by sev- The lowest concentration of an antimicro- eral species of organisms present at the bial agent that prevents growth in the dilu- same time. tion method of determining antibiotic Mixture Two or more substances combined sensitivity. in any proportion and not chemically Minus strand In viral genomes, a nucleic bound. acid strand that is complementary to the MMR vaccine Measles, mumps, and rubella RNA strand that serves as mRNA. Compare vaccine. plus strand. Mole The weight of a substance in grams Miracidium Ciliated, free‐swimming first‐ equal to the sum of the atomic weights of stage fluke larva that emerges from an the atoms in a molecule of the substance. egg. Known also as gram molecular weight. Mismatch repair A system for the correc- Molecular mimicry Imitation of the behav- tion of mismatched nucleotides or single‐ ior of a normal molecule by an antimetab- base insertions or deletions produced olite. during DNA replication; it scans the nearly Molecule Two or more atoms chemically replicated DNA, and when it finds an error, bonded together. it removes and replaces a stretch of the Molluscum contagiosum A viral infection strand containing the error. characterized by flesh‐colored, painless Missense mutation A mutation that alters a lesions. DNA codon so as to cause one amino acid Molten globule A hypothetical interme- in a protein to be replaced by a different diate state in the folding of a globular one. protein, in which the overall tertiary Mitochondria The organelles whose chief framework has been established but inter- task it is to supply the cell with ATP via nal side chains (especially hydrophobic oxidative phosphorylation. They contain ones) are still free to move about. the enzymes for pyruvate oxidation, the Monera The kingdom of prokaryotic organ- citric acid cycle, the b‐oxidation of fatty isms that are unicellular and lack a true cell acids, and oxidative phosphorylation, as nucleus. well as the electron transport chain. Known also as prokaryotae. 1158 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Moniliasis See candidiasis. Mucopolysaccharides See glycosaminogly- Monoclonal antibody A single, pure anti- cans. body produced in the laboratory by a Mucous membrane A covering over those clone of cultured hybridoma cells. tissues and organs of the body cavity that Monocular Refers to a light microscope are exposed to the exterior. having one eyepiece (ocular) Known also as mucosa. Monocyte A ravenously phagocytic leuko- Mucus A thick but watery secretion of gly- cyte, called a macrophage after it migrates coproteins and electrolytes secreted by the into tissues. mucous membranes. Monolayer A suspension of cells that attach Multicatalytic proteinase complex (MPC) A to plastic or glass surfaces as a sheet one cell massive complex of proteolytic enzymes layer thick. that is found in the cytosol of many eu- Monosaccharide A simple carbohydrate, karyotic cells and seems to function in consisting of a carbon chain or ring with the programmed destruction of cellular several alcohol groups and either an alde- proteins. hyde or ketone group. Multiple‐tube fermentation method Three‐ Monotrichous A bacterial cell with a single step method of testing for coliform bacte- flagellum. ria in drinking water. Morbidity rate The number of persons Mumps Disease caused by a paramyxovirus contracting a specific disease in relation that is transmitted by saliva and invades to the total population (cases per cells of the oropharynx. 100,000). Murine typhus See endemic typhus. Mordant A chemical that helps a stain ad- Muscarinic acetylcholine receptors A class here to the cell or cell structure. of receptors for the neurotransmitter Mortality rate The number of deaths from a acetylcholine that are characterized by an specific disease in relation to the total pop- ability to bind the toadstool toxin musca- ulation. rine. Synapses that have these receptors Most probable number (MPN) A statistical may be either excitatory or inhibitory. method of measuring bacterial growth, Compare nicotinic acetylcholine receptors. used when samples contain too few organ- Mutagen An agent that increases the rate of isms to give reliable measures by the plate‐ mutations. count method. Mutation Any inheritable change in the Mother cell A cell that has approximately nucleotide sequence of genomic DNA (or doubled in size and is about to divide genomic RNA, in the case of an RNA into two daughter cells. virus). Known also as a parent cell. Mutualism A form of symbiosis in which Mucin A glycoprotein in mucus that coats two organisms of different species live bacteria and prevents their attaching to in a relationship that benefits both of surfaces. them. Mucociliary escalator Mechanism involving Myasthenia gravis Autoimmune disease ciliated cells that allows materials in the specific to skeletal muscle, especially mus- bronchi, trapped in mucus, to be lifted to cles of the limbs and those involved in eye the pharynx and spit or swallowed. movements, speech, and swallowing. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1159
Mycelium (plural: mycelia). In fungi, a mass birth, without the intervention or use of of long, threadlike structures (hyphae) that man‐made products such as vaccines or branch and intertwine. gamma globulin. Mycobacteria Slender, acid‐fast rods, often Naturally acquired passive immunity When filamentous, include organisms that cause antibodies made by another individual are tuberculosis, leprosy, and chronic infec- given to a host, e.g., in mother’s milk, tions. without intervention by man. Mycology The study of fungi. Natural killer (NK) cell A lymphocyte that Mycoplasmas Very small bacteria with cell can destroy virus‐infected cells, malignant membranes, RNA and DNA, but no cell tumor cells, and cells of transplanted tis- walls. sues. Mycosis (plural: Mycoses). A disease caused Negative (–) sense RNA An RNA strand by a fungus. made up of bases complementary to those Myiasis An infestation caused by maggots of a positive (þ) sense RNA. (fly larvae). Negative staining Technique of staining the Mycarditis An inflammation of the heart background around a specimen, leaving muscle. the specimen clear and unstained. Nacardioforms Gram‐positive, non‐motile, Nematode See roundworm. pheomorphic, aerobic bacteria, often fila- Neonatal herpes Infection in infants usual- mentous and acid‐fast, include some skin ly with HSV‐2, most often acquired during and respiratory pathogens. passage through a birth canal contami- NAD Nicotinamide dinucleotide, a coen- nated with the virus. zyme that carries hydrogen atoms and elec- Neoplasm A localized tumor. trons. Neoplastic transformation The uncontrol- Naked virus A virus that lacks an envelope. lable division of host cells caused by infec- Nanometer (nm). Unit of measure equal to tion with a DNA tumor virus. 0.000000001 m or 10–9; formerly called a Nephron A functional unit of the kidney in millimicron (nm). which fluid from the blood is filtered. Narrow spectrum The range of activity of Nernst equation An equation that relates an antimicrobial agent that attacks only a the electrical potential across a membrane few kinds of micro‐organisms. to the concentrations of ions on either side Nasal cavity Part of the upper respiratory of the membrane. tract where air is warmed and particles are Nerve A bundle of neuron fibers that relays removed by hairs as they pass through. sensory and motor signals throughout the Nasal sinus A hollow cavity within the skull body. that is lined with mucous membrane. Nervous system The body system, compris- Naturally acquired active immunity When ing the brain, spinal cord, and nerves, that an individual is exposed to an infectious coordinates the body’s activities in relation agent, often having the disease, and their to the environment. own immune system responds in a protec- Neurohormones Substances that are re- tive way. leased from neurons and modulate the be- Naturally acquired immunity Defense against havior of target cells, which are often other a specific disease is acquired sometime after neurons. Unlike neurotransmitters, they do 1160 Appendix C: Micro‐organisms, biochemistry, and nomenclature
not act strictly across a synapse. Most neu- Nick translation A process in which nucleo- rohormones are peptides. tides in one strand of a nucleic acid duplex Neuron A conducting nerve cell. are replaced one by one with nucleotides Neurotoxin A toxin that acts by disrupting complementary to the other strand. The nerve cell function. Fast‐acting neurotoxins process starts at a nick in the strand and often act by blocking the action of an ion causes the location of the nick to migrate gate necessary for the development of an (hence the origin of the term) action potential. Niclosamide An antihelminthic agent that Neurosyphilis Neurological damage, in- interferes with carbohydrate metabolism. cluding thickening of the meninges, ataxia, Nitrification The process by which ammo- paralysis, and insanity, that results from nia or ammonium ions are oxidized to syphilis. nitrites or nitrates. Neurotoxin A toxin that acts on nervous Nitrofuran An antibacterial drug that system tissues. damages cellular respiratory systems. Neurotransmitter Alow‐molecular‐weight Nitrogenase Enzyme in nitrogen‐fixing substance that is released from an axon bacteroids that catalyzes the reaction of terminal in response to the arrival of an nitrogen gas and hydrogen gas to form action potential and then diffuses across ammonia. the synapse to influence the post‐synaptic Nitrogen cycle Process by which nitrogen cell, which may be either another neuron moves from the atmospheric through vari- or a muscle or gland cell. ous organisms and back into the atmo- Neutral Referring to a solution with a pH sphere. of 7. Nitrogen fixation The reduction of atmo- Neutralization Inactivation of microbes spheric nitrogen gas to ammonia. or their toxins through the formation of Nocardiosis Respiratory disease character- antigen–antibody complexes. ized by tissue lesions and abscesses, caused Neutralization reaction An immunological by the filamentous bacterium Nocardia test used to detect bacterial toxins and asteroids. antibodies to viruses. Nocturia Nightime urination, often a result Neutron An uncharged subatomic particle of urinary tract infections. in the nucleus of an atom. Nomarski microscopy Differential inter- Neutrophil A phagocytic leukocyte. ference contrast microscopy; utilizes dif- Known also as Polymorphonuclear leukocyte, ferences in refractive index to visualize PMNL. structures producing a nearly three‐ Neutrophile An organism that grows best dimensional image. in an environment with a pH of 5.4–8.5. Non‐communicable infectious disease Di- Nicotinic acetylcholine receptors A class sease caused by infectious agents but not of receptors for the neurotransmitter spread from one host to another. acetylcholine that are characterized by Non‐competitive inhibitor A molecule that their ability to bind nicotine. Synapses attaches to an enzyme at an allosteric site with this king of receptor are excita- (a site other than the active site), distorting tory. Compare muscarinic acetylcholine the shape of the active site so that the receptors. enzyme can no longer function. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1161
Non‐covalent interactions All kinds of Non‐specific immunity Product by general interactions between atoms and molecules defenses, such as skin, lysozyme and com- that do not involve the actual sharing of plement, that protect against many differ- electrons in a covalent bond; they include ent kinds of organisms rather than a electrostatic interactions, permanent and specific one or two. induced dipole interactions, and hydrogen Non‐synchronous growth Natural pattern of bonding. growth during the log phase in which every Non‐cyclic photophosphorylation In pho- cell in a culture divides at some point during tosynthesis, photophosphorylation (light‐ the generation time, but not simultaneously. dependent ATP synthesis) that is linked Normal microflora Micro‐organisms that to a one‐way flow of electrons from live on or in the body but do not usually water through photosystems II and I and cause disease. finally to NADPH; it is thus coupled to Known also as normal flora.
the oxidation of H2O and the reduction Northern blotting A technique for detecting þ of NADP . Compare cyclic photophosphory- the presence of a specific RNA sequence in lation. a cell and determining its size. The total Non‐cyclic photoreduction The photosyn- RNA of the cell is extracted, resolved by gel thetic pathway in which excited electrons electrophoresis, and blotted onto a filter. from chlorophyll are used to generate ATP There it is incubated under annealing con- and reduce NADP with the splitting of ditions with a radiolabeled probe for the water molecules. sequence in question, and heteroduplexes Non‐gonococcal urethritis (NGU) A gonor- of the probe with RNA are detected by rhealike sexually transmitted disease most radioautography. often caused by Chlamydia trachomatis and Nosocomial infection An inflection acqui- mycoplasmas. red in a hospital or other medical facility. Non‐indigenous organism An organism Notifiable disease A disease that a physician temporarily found in a given environment. is required to report to public health offi- Non‐infection disease Disease caused by cials. any factor other than infectious agents. N‐Terminus The end of a polypeptide chain Non‐self Antigens recognized as foreign by that carries an unreacted amino group. an organism. A ribosome synthesizes a polypeptide in Nonsense codon A set of three bases in a the direction from the N‐terminus to the gene (or mRNA) that does not code for an C‐terminus. amino acid. Known also as amino terminus. See also Known also as terminator codon. C‐terminus. Nonsense mutation A mutation that creates Nuclear envelope The double membrane an abnormal stop codon and thus causes surrounding the cell nucleus in a eukaryot- translation to terminate prematurely; the ic cell. It is pierced by nuclear pores that resulting truncated protein is usually non‐ allow even quite large molecules, such as functional. mRNAs and nuclear proteins, to enter or Non‐specific defenses Those host defenses leave the nucleus. against pathogens that operate regardless Nuclear magnetic resonance (NMR) spectro- of the invading agent. scopy A type of spectroscopy that depends 1162 Appendix C: Micro‐organisms, biochemistry, and nomenclature
on the fact that isotope nuclei having RNA and serves as the site for the assembly the property of spin will resonate with spe- of ribosomes. cific frequencies of microwave radiation Nucleoplasm The semifluid portion of the when placed in a magnetic field of given cell nucleus in eukaryotic cells that is sur- strength. The resonance energy is sensitive rounded by the nuclear envelope. to the local molecular environment, so Nucleoside A molecule that, upon com- NMR spectroscopy can be used to explore plete hydrolysis, yields 1 mol per mol of a molecular structure. Also, different living purine or pyrimidine base and a sugar. tissues have characteristic overall NMR Nucleotide An organic compound consist- spectra, which are sensitive to changes in ing of a nitrogenous base, a five‐carbon the tissue environment. NMR can thus be sugar, and one or more phosphate groups. used in the study of tissue metabolism and Nucleosome The first‐order structural unit the diagnosis of disease. for the packing of DNA in chromatin, con- Nuclear matrix A protein web that is left sisting of 146 bp of DNA wrapped 1.75 in the nucleus when histones and other times around a core octamer of histone weakly bound proteins are removed and proteins. Successive nucleosomes are most of the DNA is digested away. It is connected by stretches of ‘‘linker’’ DNA. presumed to act as an organizing scaffold Nucleotide A molecule that, upon com- for the chromatin. plete hydrolysis, yields at least 1 mol per Nuclear pore An opening in the nuclear mol of a Purine or pyrimidine base, a envelope that allows for the transport of sugar, and inorganic phosphate. materials between nucleus and cytoplasm. Nucleus The membrane‐bound structure in Nuclear region Central location of DNA, a eukaryotic cell that contains the chromo- RNA, and some proteins in bacteria; not a somal genetic material and associated true nucleus. components. It is also the place where Known also as nucleoid. RNA molecules are processed and ribo- Nuclease An enzyme that cleaves nucleic somes are assembled. acids. Null cells Undifferentiated cells that cannot Nucleic acids Long polymers of nucleotides be identified as either B cells or T cells; that encode genetic information and direct include the natural killer (NK) cells. protein synthesis. Numerical aperature The widest cone of Nucleocapsid The nucleic acid and capsid light that can enter a lens. of a virus. Numerical taxonomy Comparison of Nucleoid The large, circular DNA molecule organisms based on quantitative assess- of a prokaryotic cell, along with its asso- ment of a large number of characteristics. ciated proteins; also sometimes called the Nutritional complexity The number of bacterial chromosome. It is supercoiled nutrients an organism must obtain to grow. and forms a dense mass within the cell, Nutritional factor One factor that influ- and the term Nucleoid is often used for ences both kinds of organisms found in the cell region occupied by this mass. an environment and their growth. See nuclear region. Objective lens Lens in a microscope closest Nucleolus (plural: Nucleoli). Area in the to the specimen that creates an enlarged nucleus of a eukaryotic cell that contains image of the object viewed. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1163
Obligate Requiring a particular environ- ONPG and MUG test Water purity test that mental condition. relies on the ability of coliform bacteria to Obligate aerobe A bacterium that must secrete enzymes that convert a substrate have free oxygen to grow. into a product that can be detected by a Obligate anaerobe A bacterium that is color change. killed by free oxygen. Oomycota see water mold. Obligate intracellular parasite An organism Open‐promoter complex A complex be- or virus that can live or multiply only in- tween RNA polymerase holoenzyme and a side a living host cell. promoter that has undergone initial Obligate parasite A parasite that must spend unwinding (has ‘‘opened’’) preparatory to some or all of its life cycle in or on a host. the start of transcription. It is preceded by a Obligate psychrophile An organism that much less stable closed‐promoter complex, cannot grow at temperatures about 20 C. in which the promoter has not unwound, Obligate thermophile An organism that that may either fall apart or proceed to an can grow only at temperatures above 37 C. open‐promoter complex. Ocular lens Lens in the microscope that Open reading frame A sequence within a further magnifies the image creased by the messenger RNA that is bounded by start objective lens. and stop codons and can be continuously Ocular micrometer A glass disk with an translated. It represents the coding se- inscribed scale that is placed inside the quence for a polypeptide. eyepiece of a microscope; used to measure Operator A DNA site where a repressor the actual size of an object being viewed. protein binds to block the initiation of Okazaki fragment One of the short, discon- transcription from an adjacent promoter. tinuous DNA segments formed on the Operon (1) A sequence of a closely asso- lagging strand during DNA replication. ciated genes that includes both structural Okazaki fragments The discontinuous genes and regulatory sites that control stretches in which the lagging strand is transcription. (2) A set of contiguous pro- initially synthesized during DNA replica- karyotic structural genes that are tran- tion; these fragments are later joined to scribed as a unit, along with the adjacent form a continuous strand. regulatory elements that control their Onchocerciasis Ana eye disease caused by expressions. the filarial larvae of the nematode Oncho- Opthalmia neonatorium Pyrogenic infection cerca volvulus, transmitted by blackflies, of the eyes caused by Neisseria Gonorrhoeae. common in Africa and Central America. Known also as conjunctivitis of the newborn. Known also as river blindness. Opportunist A species of resident or tran- Oncogene A gene that, in a mutated ver- sient microbiota that does not ordinarily sion, can help to transform a normal cell to cause disease but can do so under certain a cancer cell. Many oncogene codes for conditions. mutant proteins that are involved in the Opsonin An antibody that promotes reception and transduction of growth fac- phagocytosis when bound to the surface tor signals. A cancer‐causing gene. of a micro‐organism. Oncoprotein The protein product of an on- Opsonization The process by which micro‐ cogene. organisms are rendered more attractive to 1164 Appendix C: Micro‐organisms, biochemistry, and nomenclature
phagocytes by being coated with antibodies Outer membrane A bilayer membrane, (opsonins) and C3b complement protein. forming part of the cell wall of Gram‐ Known also as immune adherence. negative bacteria. Optical isomers See enantiomers. Ovarian follicle An aggregation of cells in Optical microscope See compound light mi- the ovary containing an ovum. croscope. Ovary In the female, one of a pair of glands Optimum pH The pH at which micro‐ that produces ovarian follicles, which con- organisms grow best. tain an ovum and hormone‐secreting cells. Orbivirus Type of virus that causes color- Oxidase An enzyme that catalyzes the oxi- ado tick fever. dation of a substrate with oxygen as the Orchitis Inflammation of the testes; a electron acceptor. symptom of mumps in postpubertal males. Oxidation The loss of electrons and hydro- Organelle An internal membrane‐enclosed gen atoms. structure found in eukaryotic cells. Oxidative phosphorylation (1) Process in Organelles Membrane‐bound compart- which the energy of electrons is captured ments in the cytoplasm of eukaryotic in high‐energy bonds as phosphate groups cells. Each kind of organelle carries out a combine with ADP to form ATP. (2) The specific set of functions. Examples are phosphorylation of ADP to ATP that mitochondria, chloroplasts, and nuclei. occurs in conjunction with the transit of Organic chemistry The study of com- electrons down the electron transport pounds that contain carbon. chain in the inner mitochondrial mem- Ornithosis Disease with pneumonialike brane. symptoms, caused by Chlamydia psittaci Oxygenase An enzyme that catalyzes the and acquired from birds (previously called incorporation of oxygen into a substrate. psittacosis and parrot fever). Palindrome With respect to DNA, a seg- Oroyo fever One form of bartonellosis; an ment in which the sequence is the same acute fatal fever with severe anemia. on one strand read right to left as on the Known also as carrion’s disease. other strand read left to right; thus, a back‐ Orthomyxovirus A medium‐sized, envel- to‐back pair of inverted repeats. oped RNA virus that varies in shape from Pandemic An epidemic that has become spherical to filamentous and has an affinity worldwide. for mucus. Papilloma See wart. Osmosis A special type of diffusion in Papovavirus A small, naked DNA virus which water molecules move from an area that causes both benign and malignant of higher concentration to one of lower warts in humans, some types cause cervical concentration across a selectively perme- cancer. able membrane. Parainfluenza Viral disease characterized by Osmotic pressure The pressure required to nasal inflammation, pharyngitis, Bronchi- prevent the net flow of water molecules by tis, and sometimes pneumonia, mainly in osmosis. children. Otitis externa Infection of the external ear Parainfluenza virus Virus that initially canal. attacks the mucous membranes of the Otitis media Infection of the middle ear. nose and throat. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1165
Paramyxovirus A medium‐sized, enveloped Pasteurella‐Haemophilus Group Very small RNA virus that has an affinity for mucus. Gram‐negative bacilli and coccobacilli Parasite An organism that lives in or on, that lack flagella and are nutritionally and at the expense of, another organism, fastidious. the host. Pasteurization Mild heating to destroy Parasitism A symbiotic relationship in pathogens and other organisms that cause which one organism, the parasite, benefits spoilage. from the relationship, whereas the other Pathogen An organism capable of causing organism, the host, is harmed by it. disease in its host. Parasitology The study of parasites. Pathogenicity The capacity to produce dis- Parfocal For a microscope, remaining in ease. approximate focus when minor focus Pediculosis Lice infestation, resulting in red- adjustments are made. dened areas at bites, dermatitis, and itch. Paroxysmal stage State of whooping cough Pellicle (1) A thin layer of bacteria adhering in which mucus and masses of bacterial fill to the air‐water interface of a broth culture the airway, causing violet coughing. by their attachment pili (2) A strengthened Partial molar free energy See chemical po- plasma membrane of a protozoan cell tential. (3) Film over the surface of a tooth at the Partition coefficient (K) A coefficient that beginning of plaque formation. indicates how a particular substance will Pelvic Inflammatory Disease (PID) An infec- distribute itself between two media if tion of the pelvic cavity in females, caused allowed to diffuse to equilibrium betw- by any of several organisms including Neis- een them; it is equal to the ratio of the seria Gonorrhoeae and Chlamydia. solubilities of the substance in the two Penetration The entry of the virus (or its media. nucleic acid) into the host cell in the repli- Parvovirus A small, naked DNA virus. cation process. Passive immunity Immunity created when Penicillin An antibacterial agent that inhi- ready‐made antibodies are introduced into, bits cell wall synthesis. rather than created by, an organism. Penis Part of the male reproductive system Passive immunization The process of in- used to deliver semen to the female repro- ducing immunity by introducing ready‐ ductive tract during sexual intercourse. made antibodies into a host. Peptide bond A covalent bond joining the Passive transport With respect to mem- amino group of one amino acid and the brane transport, the movement of a sub- carboxyl group of another amino acid. It stance across a biological membrane consists of an amide bond between the by molecular diffusion through the lipid a‐carboxyl group of one amino acid and bilayer. Compare active transport, facili- the a‐amino group of the next. tated transport. Peptidoglycan A structural polymer in the Known also as Passive Diffusion. bacterial cell wall that forms a supporting Pasteur Effect The inhibition of glycolysis net. Known also as murein. by oxygen; discovered by Pasteur when he Peptidyltransferase During ribosomal po- found that aerobic yeast cultures metabo- lypeptide synthesis, the enzyme complex lize glucose relatively slowly. that transfers the polypeptide chain from 1166 Appendix C: Micro‐organisms, biochemistry, and nomenclature
the tRNA in the P site to the amino acid distribution of charge such that one end carried by the tRNA in the A site, thereby is negative and the other end positive. The adding another amino acid to the chain, water molecule is an example. The oxygen the complex is an integral part of the large end has a partial negative charge, and the ribosomal subunit. hydrogen end has a partial positive charge. Peptococci Anerobes that form pairs, tet- Permanent parasite A parasite that remains rads, or irregular clusters, they lac both in or on a host once it has invaded the host. catalase and the enzyme to ferment lactic Permease An enzyme complex involved acid. in active transport through the cell mem- Peptone A product of enzyme digestion of brane. proteins that contains many small pep- Peroxisome (1) An organelle filled with tides; a common ingredient of a complex enzymes that in animal cells oxidate medium. amino acids and in plant cells oxidize fats. Perforin A cytotoxin produced by cytotoxic (2) A small vesicular organelle that specia- T cells that bores holes in the plasma mem- lizes in carrying out cellular reactions in- brane of infection host cells. volving the transfer of hydrogen from a
Pericarditis An inflammation of the protec- substrate to O2. These reactions produce tive membrane around the heart. the by‐product H2O2, which is split to Periodontal disease A combination of gum H2O and O2 by the peroxisomal enzyme inflammation, decay of cementum, and catalase. erosion of periodontal ligaments and Persistent viral infection The continued bone that support teeth. production of viruses within the host over Periodontitis A chronic periodontal disease many months or years. that affects the bone and tissue that sup- Pertussis See whooping cough. ports the teeth and gums. PEST sequences A family of amino acid Peripheral nervous system All nerves out- sequences that have been found on cellular side the central nervous system. proteins that undergo rapid turnover; they Periplasm Those substances (enzymes, may target proteins for rapid proteolysis. transport proteins) located in the peri- They consist of a region about 12–60 resi- plasmic space of Gram‐negative bacteria dues long that is rich in praline, glutamate, or in the older cell wall of Gram‐positive serine, and threonine (P, E, E, and T in the bacteria. one‐letter abbreviation system). Periplasmic enzyme An exoenzyme pro- Petechia (plural: petechiae). A pinpoint‐ duced by Gram‐negative organisms, size hemorrhage, most common in skin which acts in the periplasmic space. folds, that often occurs in rickettsial dis- Periplasmic space The space between the eases. cell membrane and the outer membrane pH A means of expressing the hydrogen‐ion in Gram‐negative bacteria that is filled concentration, and thus the acidity, of a with periplasm. solution. Peritrichous Having flagella distributed all Phage See bacteriophage. over the surface of a bacterial cell. Phage typing Use of bacteriophages to de- Permanent dipole In chemistry, a mole- termine similarities or differences among cule that has a permanent, asymmetric different bacteria. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1167
Phagocyte A cell that ingests and digests (DAG) in part of their structure and can foreign particles. act as tumor promoters. This effect sug- Phagocytosis Ingestion of solids into cells gests that the DAG second‐messenger sys- by means of the formation of vacuoles. tem may be involved in growth factor Phagolysosome A structure resulting from action. the fusion of lysosomes and a phagosome. Phosphodiester link The linkage that con- Phagosome A vacuole that forms around a nects the nucleotide monomers in a nucleic microbe within the phagocyte that acid. It consists of a phosphate residue that engulfed it. links the sugar moieties of successive Pharmaceutical microbiology A special monomers by forming an ester bond with branch of industrial microbiology con- the 50 carbon of one sugar and the 30 car- cerned with the manufacture of products bon of the next. used in treating or preventing disease. Phospholipid A lipid composed of glycerol, Pharyngitis An infection of the pharynx, two fatty acids, and a polar head group; usually caused by a virus but sometimes found in all membranes. bacterial in origin, a sore throat. Phosphorescence Continued emission of Pharnyx The throat, a common passage‐ light by an object when light rays no longer way for the respiratory and digestive sys- strike it. tems with tubes connecting to the middle Phosphorus cycle The cyclic movement of ear. phosphorous between inorganic and or- Phase‐contrast microscopy Use of micro- ganic forms. scope having a condenser that accentuates Phosphorylation The addition of a phos- small differences in the refractive index of phate group to a molecule, often from various structures within the cell. ATP, generally increasing the molecule’s Phenol coefficient A numerical expression energy. for the effectiveness of a disinfectant rela- Phosphotransferase system A mechanism tive to that of phenol. that uses energy from phosphorenolyru- Phenotype The specific observable charac- vate to move sugar molecules into cells by teristics displayed by an organism. It results active transport. from the interaction of the organism’s Photoautotroph An autotroph that obtains genetic makeup with the environment. energy from light. Compare genotype. Photoheterrotroph A heterotroph that Pheromones Intercellular mediator com- obtains energy from light. pounds that are released from one organ- Photolysis Process in which light energy is ism and influence the metabolism or used to split water molecules into protons, behavior of another organism, usually of electrons, and oxygen molecule. the same species. Sex attractants, which Photophosphorylation Phosphorylation of elicit reproductive behavior in suitable ADP to ATP that depends directly on ener- recipients, are the examples. gy from sunlight. The light energy is cap- Phlebovirus Bunyavirus that is carried by tured by a pigment such as chlorophyll the sandfly Phlebotomus papatsii. and is passed in the form of excited elec- Phorbol esters A group of natural sub- trons to an electron transport chain; the stances that resemble sn‐1,2‐diacyglycerol electron transport chain uses energy from 1168 Appendix C: Micro‐organisms, biochemistry, and nomenclature
the electrons to create a proton gradient radiation, that influences the kinds of across a membrane, which drives the syn- organisms found and their growth. thesis of ATP. Picornavirus A small, naked RNA virus; dif- Photoproducts The products that result ferent genera are responsible for polio, the when light energy causes a chemical reac- common cold, and hepatitis. tion to occur in a substance. With respect Pilus (plural: pili). A tiny hollow projection to DNA, the term refers to the types of used to attach bacteria to surfaces (attach- damaged DNA that can be caused by UV ment pilus) or for conjugation (conjuga- irradiation. tion pilus). Photoreactivation A DNA repair process in Pimple See folliculitis. which an enzyme uses light energy to break Pinna Flap‐like external structure of the ear. cyclobutane pyrimidine dimers created by Pinworm A small roundworm, Enterobius UV irradiation and to restore the correct vermicularis, that causes gastrointestinal bonding. disease. See light repair. Placebo An unmedicated, usually harmless Photorespiration The cycle of reactions that substance given to a recipient as a substi- occurs in place of the Calvin cycle when the tute for or to test the efficacy of a medica-
photosynthetic enzyme rubisco adds O2 tion or treatment. rather than CO2 to ribulose bisphosphate Plantae The kingdom of organisms to carboxylase. It takes place partly in chlor- which all plants belong. oplasts, partly in peroxisomes, and partly Plaque (1) A clean area in a bacterial lawn in mitochondria; it expends ATP energy culture where viruses have lysed cells. (2) A
and loses a previously fixed CO2 molecule clear area that is formed by a local phage in the process of regenerating the Calvin infection in a lawn of cultured bacteria in a cycle intermediate 3‐phosphoglycerate. Petri dish; for purposes of experimenta- Photosynthesis The capture of energy from tion, it is the phage equivalent of a bacterial light and use of this energy to manufacture colony. carbohydrates from carbon dioxide. Plaque assay A viral assay used to deter- Photosystem A structural unit in a cellular mine viral yield by culturing viruses on a membrane that captures light energy and bacterial lawn and counting plaques. converts a portion of it to chemical energy. Plaque‐forming unit A plaque counted on a The photosynthesis practiced by plants, bacterial lawn that gives only an approxi- algae and cyanobacteria involves two mate number of phages present, because a types of photosystem, both of which cap- given plaque may have been due to more ture energy in the form of high‐energy than one phage. electrons and transduce it via an electron Plasma Liquid portion of the blood, ex- transport chain. cluding the formed elements. Phototaxis A non‐random movement of an Plasma cell A large lymphocyte differen- organism toward or away from light. tiated from a B cell that synthesizes and Phylogenetic Pertaining to evolutionary releases antibodies like those on the B cell relationships. surface. Physical factor Factor in the environment, Plasma membrane A selectively permeable such as temperature, moisture, pressure, or lipoprotein bilayer that forms the boundary Appendix C: Micro‐organisms, biochemistry, and nomenclature 1169
between the cytoplasm of a eukaryotic cell (minus) strand. Most viruses with single‐ and its environment. strand genomes package only the plus or Known also as cell membrane. minus strand in virions; the other strand is Plasmid A small, circular, independent made transiently during replication. Com- replicating piece of DNA in a cell that is pare minus strand. not part of its chromosome and can be Pneumocystis pneumonia A fungal respira- transferred to another cell. tory disease caused by Pneumocystis carinii. Known also as extrachromosomal DNA. Pneumonia An inflammation of lung tissue Plasmids Small, extrachromosomal circular caused by bacteria, viruses, or fungi. DNA molecules found in many bacteria, Pneumonic plague Usually fatal form of they replicate independently of the main plague transmitted by aerosol droplets chromosome and may occur in multiple from a coughing patient. copies per cell. Point mutation Mutation in which one base Plasmodial slime mold Funguslike protest is substituted for another at a specific loca- consisting of a multinucleate amoeboid tion in a gene. mass, or plasmodium, that moves about Polar compound A molecule with an un- slowly and phagocytizes dead matter. equal distribution of charge due to an Plasmodium A multinucleate mass of cyto- unequal sharing of electrons from between plasm that forms one of the stages in the atoms. life cycle of a plasmodial slime mold. Poliomyelitis Disease caused by any of sev- Plasmogamy Sexual reproduction in fungi eral strains of polioviruses that attack in which haploid gametes unite and their motor neutrons of the spinal cord and cytoplasm mingles. brain. Plasmolysis Shrinking of a cell, with sepa- Polyacrylamide gel electrophoresis (PAGE) A ration of the cell membrane from the cell technique for separating proteins from a wall, resulting from loss of water in a cell based in their molecular size. hypertonic solution. Polyene An antifungal agent that increases Platelet A short‐lived fragment of large cells membrane permeability. called megakaryocytes, important compo- Polymer (1) A large molecule that is made nent of the blood‐clotting mechanism. by linking together prefabricated molecu- Pleomorphism Phenomenon in which bac- lar units (monomers) that are similar or teria vary widely in form, even within a identical to each other. The number of single culture under optimal conditions. monomers in a polymer may range up to Pleura Serious membrane covering the sur- millions. (2) A long chain of repeating faces of the lungs and the cavities they subunits. occupy. Polymerase chain reaction (PCR) A tech- Pleurisy Inflammation of pleural mem- nique that rapidly produces a billion or branes that causes painful breathing often more identical copies of a DNA fragment accompanies lobar pneumonia. without needing a cell. Plus strand In viral genomes, a nucleic acid Polymyxin An antibacterial agent that dis- strand that can serve as mRNA or (for DNA rupts the cell membrane. strand) that is homologous to one that Polynucleotide A chain of many nucleotides. can; as distinct from the complementary Polypeptide A chain of many amino acids. 1170 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Polyribosome A long chain of ribosomes Precipitation reaction Immunological test attached at different points along an in which antibodies called precipitans mRNA molecule. react with antigens to form latticelike net- Known also as polysome. works of molecules that precipitate from Polysaccharide A carbohydrate formed solution. when many monosaccharides are linked Precipitin test Immunological test used to together by glycosidic bonds. detect antibodies that is based on the pre- Polytene chromosome An extra‐thick chro- cipitation reaction. mosome that includes many parallel copies Prediction The expected outcome if a hy- of the original DNA molecule; it is pro- pothesis is correct. duced by repeated rounds of DNA replica- Preserved culture A culture in which tion without separation of the resulting organisms are maintained in a dormant copies. Polytene chromosomes are found state. in various cell types, notably Drosophilia Presumptive test First stage of testing in salivary gland cells; they are useful in chro- multiple‐tube fermentation in which gas mosome mapping because they are large production in lactose broth provides pre- and because the genes on the strands are sumptive evidence that coliform bacteria arranged in strict register. are present. Pontiac fever A mild variety of legionellosis. Prevalence rate The number of people Porin A protein in the outer membrane infected with a particular disease at any of Gram‐negative bacteria that non‐ one time. selectively transports polar molecules into Primaquine An antiprotozoan agent that the periplasmic space. interferes with a protein synthesis. Portal of entry A site at which micro‐ Primary atypical pneumonia A mild form organisms an gain access to body tissues. of pneumonia with insidious onset. Portal of exit A site at which micro‐ Known also as mycoplasma pneumonia and organisms can leave the body. walking pneumonia. Positive chemotaxis Movement of an or- Primary cell culture A culture that comes ganism toward a chemical. directly from an animal and is not subcul- Positive (þ) sense RNA An RNA strand that tured. encodes information for making proteins Primary immunodeficiency disease A genet- needed by a virus. ic or developmental defect in which T cells Potable water Water that is fit for human or B cells are lacking or non‐functional. consumption. Primary infection An initial infection in a Pour plate A plate containing separate previously healthy person. colonies and used to prepare a pure cul- Primary response Humoral immune re- ture. sponse that occurs when an antigen is Pour plate method Method used to prepare first recognized by host B cells. pure cultures using serial dilutions, each of Primary structure For a nucleic acid or a which is mixed with melted agar and protein, the sequence of the bases or poured into a sterile Petri plate. amino acids in the polynucleotide or po- Poxvirus DNA virus that is the largest and lypeptide. Compare quaternary structure most complex of all viruses. second structure tertiary structure. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1171
Primary treatment Physical treatment to re- Progressive multifocal leukoencephalo- move solid wastes from sewage. pathy Disease caused by the JC polyoma- Primer A short piece of DNA or RNA that is virus with symptoms including mental base‐paired with a DNA template strand deterioration, limb paralysis, and blind- and provide a free 30 –OH end from ness. which a DNA polymerase can extend a Prokaryote Micro‐organism that lacks a cell DNA strand. Also refers to DNA oligo- nucleus and membrane‐enclosed internal mers used in the polymerase chain structures, all bacteria in the kingdom reaction. Monera (Prokaryotae) are prokaryotes. Primosome An enzyme complex that is lo- Prokaryotes Primitive single‐celled organ- cated in the replication fork during DNA ism that are not compartmentalized by in- replication; it synthesizes the RNA primers ternal cellular membranes; the eubacteria on the lagging strand and also participates and archaebacteria. Compare eukaryotes. in unwinding the parental DNA helix. Prokaryotic cell A cell that lacks a cell nu- Prion An exceedingly small infectious par- cleus; includes all bacteria. ticle consisting of protein without any Promoter A DNA sequence that can bind nucleic acid. RNA polymerase, resulting in the initiation Probe A single‐stranded DNA fragment of transcription. that has a sequence of bases that can be Propagated epidemic An epidemic that used to identify complementary DNA base arises from person‐to‐person contacts. sequences. Prophage An inactive phage genome that is Processivity For a DNA or an RNA poly- present in a bacterial cell and its progeny. It merase, the average number of nucleotides is integrated into the host chromosome. incorporated per event of binding between Propionibacteria Pleomorphic, irregular, the polymerase and a 30 primer terminus. It non‐sporing, Gram‐positive rods. describes the tendency of a polymerase to Prostaglandin A reaction mediator that remain bound to a template. acts as a cellular regulator, often intensify- Prodromal phase In an infectious disease, ing pain. the short period during which non‐specific Prostaglandins A family of compounds symptoms such as malaise and headache that are derived from certain long‐chain sometimes appear. unsaturated fatty acids (particularly ara- Prodrome A symptom indicating the onset chidonic acid) by a cyclooxygenase path- of a disease. way and that function as local hormones. Producer Organism that captures energy Prostate gland The gland located at the be- from the sun and synthesizes food. ginning of the male urethra whose milky Known also as autotroph. fluid discharge forms a component of Product The material resulting from an en- semen. zymatic reaction. Prostatitis Inflammation of the prostate Productive infection Viral infection in gland. which viruses enter a cell and produce in- Prosthetic group A metal ion or small mol- fectious progeny. ecule (other than an amino acid) that Proglottid One of the segments of a tape- forms part of a protein in the protein’s na- worm, containing the reproductive organs. tive state and is essential to the protein’s 1172 Appendix C: Micro‐organisms, biochemistry, and nomenclature
functioning; its attachment to the protein down their gradient across the membrane, may be either covalent or non‐covalent. they can drive processes such as ATP Proteases Enzymes that cleave peptide synthesis. bonds in a polypeptide. Many show speci- Proton pumping The active pumping of ficity for a particular amino acid sequence. protons across a cellular membrane to Proteasome A large, ATP‐dependent prote- form a proton gradient. For example, the ase complex that is found in the cytosol of electron transport chains of the inner cells and is involved in the selective degra- mitochondrial and thylakoid membranes dation of short‐lived cytoplasmic proteins. incorporate proton pumps, which create Protein A polymer of amino acids joined by the proton gradient that powers the ATP peptide bonds. synthases of these membranes. Protein profile A technique for visualizing Proto‐oncogene A normal gene that can the proteins contained in a cell; obtained cause cancer in uncontrolled situations; by the use of polyacrylamide gel electro- often the normal gene comes under the phoresis. control of a virus. Proteoglycans Glycoproteins in which car- Protoplast A Gram‐positive bacterium bohydrate is the dominant element. The from which the cell wall has been removed. carbohydrate is in the form of glycosam- Protoplast fusion A technique of genetic minoglycan polysaccharides, which are engineering in which genetic material is connected to extended core polypeptides combined by removing the cell walls of to form huge, feathery molecules. Proteo- two different types of cells and allowing glycans are important components of the the resulting protoplasts to fuse. intercellular. matrix. Prototroph A normal, non‐mutant Protista The kingdom of organisms that are organism. unicellular but contain internal organelles Known also as wild type. typical of the eukaryotes. Protozoa (singular: protozoan). Single‐ Protist A unicellular eukaryotic organism celled, microscopic, animallike protests in that is a member of the kingdom Protista. the kingdom Protista. Protofilaments The 13 linear columns of Provirus Viral DNA that is incorporated tubulin units that can be visualized in the into a host‐cell chromosome. structure of a microtubule; they result be- Pseudocoelom A primitive body cavity, cause each turn of the microtubule helix typical of nematodes, that lacks the com- contains exactly 13 tubulin units. Each plete lining found in higher animals. protofilament consists of alternating a Pseudocyst An aggregate of trypanosome and b tubulin subunits. protozoa that forms in lymph nodes in Proton A positively charged subatomic par- Chagas’ disease. ticle located in the nucleus of an atom. Pseudogenes Non‐transcribed stretches of Proton motive force (pmf) An electrochem- DNA that bear a strong sequence similarity þ ical H gradient that is set up across a to functioning genes and obviously arose cellular membrane by membrane‐bound from them during evolution. Many gene proton pumps, such as the ones in the families contain pseudogene members. inner mitochondrial membrane or thyla- Pseudomembrane A combination of koid membrane. As the protons flow back bacilli, damaged epithelial cells, fibrin, Appendix C: Micro‐organisms, biochemistry, and nomenclature 1173
and blood cells resulting from infection Pyrogen A substance that acts on the hypo- with diphtheria that can block the airway, thalamus to set the body’s ‘‘thermostat’’ to causing suffocation. a higher‐than‐normal temperature. Pseudomonads Aerobic motile rods with Q Fever Pneumonialike disease caused by polar flagella. Coxiella burnetii, a rickettsia that survives Paeudoplasmodium A multicellular mass long periods outside cells and can be trans- composed of individual cellular slime mitted aerially as well as by ticks. mold cells that have aggregated. Quantum efficiency (Q) With respect to Pseudopodium A temporary footlike pro- photosynthesis, the ratio of oxygen mole- jection of cytoplasm associated with amoe- cules released to photons absorbed. boid movement. Quarantine The separation of human or Psittacosis See ornithosis. animals from the general population Psychrophile A cold‐loving organism that when they have a communicable disease grows best at temperatures of 15–20 C. or have been exposed to one. Puerperal fever Disease caused by b‐ Quaternary ammonium compound (quat) A hemolytic streptococci, which are normal cationic detergent that has four organic vaginal and respiratory microbiota that groups attached to a nitrogen atom. can be introduced during child delivery Quaternary structure (1) The three‐ by medical personnel. dimensional structure of a protein mole- Known also as childbed fever or puerperal cule formed by the association of two or sepsis. more polypeptide chains. (2) For a protein, Pulsed field gel electrophoresis Atypeof the level of structure that results when sep- gel electrophoresis in which the orientation arate, folded polypeptide chains (subunits) of the electric field is charged periodically. associate in a specific way to produce a This technique makes it possible to sepa- complete protein. Compare primary struc- rate very large DNA molecules, up to the ture, secondary structure tertiary structure. size of whole chromosomes. Quinine An antiprotozoan agent used to Pure culture A culture that contains only a treat malaria. single species of organism. Quinolone A bactericidal agent that inhi- Purine The nucleic acid bases adenine and bits DNA replication. guanine. Quinone A non‐protein, lipid‐soluble elec- Pus Fluid formed by the accumulation of tron carrier in oxidative phosphorylation. dead phagocytes, the material they have Known also as coenzyme Q. ingested, and tissue debris. Rabies A viral disease that affects the brain Pustule See folliculitis. and nervous system with symptoms in- Pyelonephritis Inflammation of the cluding hydrophobia and aerophobia; kidneys. transmitted by animal bites. Pyoderma A pus‐producing skin infec- Rabies virus An RNA‐containing rhabdovi- tion caused by staphylococci, strepto- rus that is transmitted through animal bites. cocci, and corynebacteria, singly or in Rad A unit of radiation energy absorbed combination. per gram of tissue. Pyrimidine Any of the nucleic acid bases Radial immunodiffusion Serological test thymine, cytosine, and uracil. used to provide a quantitative measure of 1174 Appendix C: Micro‐organisms, biochemistry, and nomenclature
antigen or antibody concentration by Reactant Substance that takes part in a measuring the diameter of the ring of chemical (enzymatic) reaction. precipitation around an antigen. Reaction center In photosynthesis, a specif- Radiation Light rays, such as X‐rays and ic pair of chlorophyll molecules in a pho- ultraviolet rays, that can act as mutagens. tosystem that collect light energy absorbed Radioautography A technique in which an by other chlorophyll molecules and pass it item containing radioactively labeled ele- to an electron acceptor, normally the first ments (for example, a tissue slice or a compound of an electron transport chain. chromatography gel) is laid against a pho- Reactive oxygen species (ROS) Oxygen spe- tographic film; the radioactivity exposes cies intermediate in oxidation level between
the film to form an image of the labeled O2 and H2O, which are more reactive than elements. Also called autoradiography. O2; ROS includes superoxide, peroxide, Radioimmunoassay (RIA) Technique that peroxynitrite, and hydroxyl radical. uses a radioactive anti‐antibody to detect Reagin Older name for immunoglobulin E very small quantities of antigens or anti- (IgE); very important in allergies. bodies. Receptor A protein that binds selectively to Radioisotope Isotope with unstable nuclei a specific molecule (such as an intercellular that tends to emit subatomic particles and mediator or antigen) and initiates a radiation. biological response. Ramachandran plot A plot that constitutes a Recognition helix In a helix‐turn‐helix DNA map of all possible backbone configurations binding motif, the a‐3 helix, which fits deep for an amino acid in a polypeptide. The axes in the major groove and is responsible for of the plot consist of the rotation angles of the sequence specificity of binding. the two backbone bonds that are free to Recombinant DNA DNA combined from rotate (f and c, respectively); each point two different species by restriction f, c on the plot thus represents a conceiv- enzymes and ligases. able amino acid backbone configuration. Recombinant DNA molecule A DNA mole- Random coil Refers to a linear polymer that cule that includes segments from two or has no secondary or tertiary structure but more precursor DNA molecules. instead is wholly flexible with a randomly Recombination (1) The combining of DNA varying geometry. This is the state of a from two different cells, resulting in a re- denatured protein or nucleic acid. combinant cell. (2) A process in an organ- Rat bite fever A disease caused by Strepto- ism in which two parent DNA molecules bacillus moniliformis transmitted by bites give rise to daughter DNA that combines from wild and laboratory rats. segments from both parent molecules. It Rate constant With respect to chemical may involve the integration of one DNA reactions, a constant that relates the reac- molecule into another, the substitution of a tion rate for a particular reaction to sub- DNA segment for a homologous segment strate concentrations. on another DNA molecule, or the exchange Rate equation An equation, such as the of homologous segments between two Michaelis–Menten equation that relates ve- DNA molecules. locity of an enzyme‐catalyzed reaction to Redia The development stage of the fluke measurable parameters. immediately following the sporocyst stage. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1175
Reducing equivalent An amount of a reduc- Replication cycle The series of steps of virus ing compound that donates the equivalent replication in a host cell. of 1 mol of electrons in an oxidation– Replication fork A site at which the two reduction reaction. The electrons may be strands of the DNA double helix separate expressed in the form of hydrogen atoms. during replication and new complementa- Reduction The gain of electrons and hydro- ry DNA strands form. gen atoms. Replicon A unit in the genome that consists Reference culture A preserved culture used of an origin of replication and all the DNA to maintain an organism with its charac- that is replicated from that origin. teristics ad originally defined. Repressor In an operon it is the protein Reflection The bouncing of light off an ob- that binds to the operator, thereby prevent- ject. ing transcription of adjacent genes. Refraction The bending of light as it passes Repressor protein Substance produced by from one medium to another medium of host cells that keeps a virus in an inactive different density. state and prevents the infections of the cell Regulator gene Gene that controls the ex- by another phage. pression of structural genes of an operon Reservoir host An infected organism that through the synthesis of a repressor protein. makes parasites available for transmission Regulatory site The promotor and operator to other hosts. regions of an operon. Reservoir of infection Site where micro‐ Regulon A group of unlinked (non‐ organisms can persist and maintain their adjacent) genes that are all regulated by a ability to infect. common mechanism. Resident microflora Species of micro‐ Relapsing fever Disease caused by various organisms that are always present on or in species of Borrelia, most commonly by B an organism. recurrentis; transmitted by lice. Resistance The ability of a micro‐organism Release The exit from the host cell of new to remain unharmed by an antimicrobial virions, which usually kills the host cell. agent. Release factors Independent protein fac- Resistance (R) gene A component of a re- tors that are necessary participants in the sistance plasmid that confers resistance to a release of a finished polypeptide chain specific antibiotic or to a toxic metal. from a ribosome. Resistance (R) plasmid A plasmid that car- Rennin An enzyme from calves’ stomachs ries genes that provide resistance to various used in cheese manufacture. antibiotics or toxic metals. Reovirus A medium‐sized RNA virus that Known also as R factor. has a double‐capsid with no envelope; Resistance transfer factor (RTF) A compo- causes upper respiratory and gastrointesti- nent of a resistance plasmid that imple- nal infections in humans. ments transfer by conjugation of the Replica plating A technique used to transfer plasmid. colonies from one medium to another. Resolution The ability of an optical device Replication Process by which an organism to show two items as separate and discrete or structure (especially a DNA molecule) entities rather than a fuzzily overlapping duplicates itself. image. 1176 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Resolving power A numerical measure of Restriction enzyme Another term for re- the resolution of an optical instrument. striction endonuclease. Respiration With respect to energy metab- Restriction fragment length polymophism olism, the process in which cellular energy (RFLP) (1) A short piece of DNA snipped is generated through the oxidation of nu- out by restriction enzymes. (2) A type of
trient molecules with O2 as the ultimate genetic polymorphism that is readily electron acceptor. This type of respiration detected by Southern blotting and can be is also called cellular respiration to distin- used to screen for genetic diseases. It is guish it from respiration in the sense of based on the fact that alleles often have breathing. different restriction endonuclease cleavage Respiratory anaphylaxis Life‐threatening sites and therefore produce different arrays allergy in which airways become con- of fragments upon cleavage with appropri- structed and filled with mucous secretions. ate endonucleases. Respiratory bronchiole Microscopic chan- Reticulate body An intracellular stage in nel in the lower respiratory system that the life cycle of chlamydias. ends in a series of alveoli. Retinoids Substances that are derived from Respiratory chain The electron transport retinoic acid (a form of vitamin A) and chain that is employed during cellular res- act as intercellular mediators; they are
piration and has O2 as the ultimate elec- particularly important in regulating de- tron acceptor. velopment. Respiratory syncytial virus (RSV) Cause of Retrovirus An enveloped RNA virus that lower respiratory infections affecting chil- uses its own reverse transcriptase to tran- dren under 1 year old causes cells in culture scribe its RNA into DNA in the cytoplasm to fuse their plasma membranes and be- of the host cell. come multinucleate masses (syncytia). Retroviruses A family of RNA viruses that Respiratory system Body system that moves possess reverse transcriptase. After the oxygen from the atmosphere to the blood virus infects a cell, this enzyme transcribes and removes carbon dioxide and other the RNA genome into a double‐strand wastes from the blood. DNA version, which integrates into a host Resting potential The voltage difference chromosome. Human immunodeficiency that exists across the membrane of an ex- virus (HIV) is a retrovirus. citable cell, such as a nerve cell, except in Reverse transcriptase An enzyme found in places when an action potential is in prog- retroviruses that synthesizes a double‐ ress. It is a consequence of the ion gradients strand DNA molecule from a single‐strand that are maintained across the membrane. RNA template. It is an important tool in Restriction endonuclease Enzymes that molecular genetics. catalyze the double‐strand cleavage of Reverse transcription An enzyme found in DNA at specific base sequences. Many re- retroviruses that copies RNA into DNA. striction endonucleases with different se- R factor See resistance (R) plasmid. quence specificities have been found in R group An organic chemical group at- bacteria; they are used extensively in mo- tached to the central carbon atom in an lecular genetics. amino acid. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1177
Rhabdovirus Arod‐shaped, enveloped Rift valley fever Disease caused by bunya- RNA virus that infects insects, fish, various viruses that occurs in epidemics. other animals, and some plants. Ringworm A highly contagious fungal skin Rh antigen An antigen found on some red disease that can cause ringlike lesions. blood cells, discovered in the cells of rhesus River blindness See onchocerciasis. monkeys. Rheumatic fever. A multisystem RNA editing A type of RNA processing that disorder following infection by b‐ has been found in the mitochondrial hemolytic Streptococcus pyogenes that can mRNAs of certain eukaryotes, in which cause heart damage. the RNA sequence is altered by the inser- Rheumatoid arthritis Autoimmune disease tion of uridine residues at specific sites. that affects mainly the joints but can ex- RNA polymerase An enzyme that binds to tend to other tissues. one strand of exposed DNA during tran- Rheumatoid factor IgM found in the blood scription and catalyzes the synthesis of of patients with rheumatoid arthritis, and RNA from the DNA template. their relatives. RNA primer During DNA replication, the Rhinovirus A virus that replicates in cells of short stretch of RNA nucleotides that the upper respiratory tract and causes the is laid down at the beginning of each common cold. Okazaki fragment; it provides a 30 –OH Ribonucleic acid (RNA) Nucleic acid that end from which DNA polymerase can ex- carries information from DNA to sites tend the fragment. It is later replaced with where proteins are manufactured in cells DNA. and that directs and participates in the RNA tumor virus Any retrovirus that causes assembly of proteins. tumors and cancer. Ribosomal RNA (rRNA) A type of RNA that, Rocky mountain spotted fever Disease together with specific proteins, makes up caused by Rickettsia rickettsia and transmit- the ribosomes. ted by ticks. Ribosome Site for protein synthesis consist- Rotavirus Virus transmitted by the fecal‐ ing of RNA and protein, located in the oral route that replicates in the intestine, cytoplasm. causing diarrhea and enteritis. Ribosomes Large protein – RNA complexes Roundworm A worm with a long, cylindri- that are responsible for synthesizing poly- cal, unsegmented body and a heavy cuticle. peptides under the direction of mRNA Known also as a nematode. templates. Rubella Viral disease characterized by a skin Rickettsialpox Mild rickettsial disease with rash; can cause severe congenital damage. symptoms resembling those of chickenpox; Known also as German measles. caused by Rickettsia akari and carried by Rubeola See measles. mites found on house mice. Rubisco (ribulose bisphosphate carboxylase– Rickettsias Small, non‐motile, Gram‐ oxygenase) The enzyme that accom- negative organisms, obligate intercellular plishes carbon fixation in photosynthesis
parasites of mammalian and anthropod cells. by adding CO2 to ribulose‐1,5‐ Rifamycin An antibacterial agent that inhi- bisphosphate. It can also add O2 in place bits ribonucleic and (RNA) synthesis. of CO2, initiating photorespiration. 1178 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Rule of octets Principle that an element is Scalded skin syndrome Infection caused chemically stable if it contains eight elec- by staphylococci consisting of large, soft trons in its outer shell. vesicles over the whole body. Sac fungus Amemberofadiversegroup Scanning electron microscope (SEM) Atype of fungi that produces saclike asci during of electron microscopy in which a beam sexual reproduction. of electrons is scanned across an object, Known also as ascomycota. and the pattern of reflected electrons is St. Anthony’s fire See erysipelas. analyzed to crease an image of the object’s St. Louis encephalitis Type of viral enceph- surface. This type of microscope is used to alitis most often seen in humans in the study the surfaces of specimens. Compare central United States. transmission electron microscopy. Salmonellosis A common enteritis charac- Scanning tunneling microscope (STM) Also terized by abdominal pain, fever, and diar- called scanning probe microscope; type of rhea with blood and mucus; caused by microscope in which electron tunnel into Salmonella species. each other’s clouds, can show individual Sapremia A condition caused when sapro- molecules, live specimens, and work un- phytes release metabolic products into the derwater. blood. Scarlet fever (sometimes called scarlatina) In- Saprophyte An organism that feeds on fection caused by Streptococcus pyogenes dead or decaying organic matter. that produces an erythrogenic toxin. Sarcina A group of eight cocci in a cubicle Schaeffer–Fulton fpore staining A differen- packet. tial stain used to make endospores easier to Sarcodine An amoeboid protozoan. visualize. Sarcoplasmic reticulum A network of mem- Schick test Test to determine immunity to branous tubules that surrounds each myo- diphtheria. fibril in a skeletal muscle cell. It is a Schistosomiasis Disease of the blood and specialized region of endoplasmic reticu- lymph caused by blood fluke of the genus lum; its main function is to sequester and Schistosoma. þ then release the Ca2 that triggers myofi- Known also as Bilharzia. bril contraction. Schizogony Multiple fission, in which one Sarcoptic manage See scabies. cell gives rise to many cells. Satellite DNA DNA consisting of multiple Scolex Head end of a tapeworm, with suck- tandem repeats of very short, simple nucle- ers and sometimes hooks that attach to the otide sequences. It typically makes up intestinal wall. 10–20% of the genome of higher eukar- Scrapie Transmissible spongiform encepha- yotes; at least some of it may play a role lopathy disease of the brain of sheep, causing in chromosome structure. extreme itching so that the sheep repeatedly Saturated fatty acid A fatty acid containing scrape themselves against posts, trees, etc. only carbon–hydrogen single bonds. Scrub typhus A typhus caused by Rickettsia Scabies Highly contagious skin disease tsutsugamushi, transmitted by mites that caused by the itch mite Sarcoptes scabiei. feed on rats. Known also as Sarcoptic mange. Known also as tsutsugamushi. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1179
Sebaceous gland Epidermal structure, rate depends on the square of reactant associated with hair follicles, that secretes concentration (for two molecules of the an oily substance called sebum. same reactant) or on the product of two Sebum Oily substance secreted by the seba- reactant concentrations (for two different ceous glands. reactants) Compare first‐order reaction. Secondary immunodeficiency disease Re- Secretory piece A part of the IgA antibody sult of damage to T cells or B cells after that protects the immunoglobulin from they have developed normally. degradation and helps in the secretion of Secondary infection Infection that follows a the antibody. primary infection, especially in patients Secretory vesicle Small membrane‐ weakened by the primary infection. enclosed structure that stores substances Secondary response The folding or coiling coming from the Golgi apparatus. of a polypeptide chain into a particular Sedimentation coefficient (S) A coefficient pattern, such as a helix or pleated sheet. that determines the velocity at which a Secondary structure (1) Local folding of particular particle will sediment during the backbone of a linear polymer to form centrifugation; it depends on the density a regular, repeating structure. The B‐ and of the medium, the specific density of the Z‐forms of the DNA helix and the a‐helix particle, and the size, shape, and mass of and b‐sheet structures of polypeptides are the particle. examples. Compare primary structure, qua- Sedimentation equilibrium A technique for ternary structure, tertiary structure. (2) The using centrifugation to measure the mass folding or coiling of a polypeptide chain of a large molecule such as a protein. A into a particular pattern such as a helix or solution of the substance is centrifuged at pleated sheet. low speed until the tendency of the Secondary treatment Treatment of sewage substance to sediment is balanced by its by biological means to remove remaining tendency to diffuse to uniform concen- solid wastes after primary treatment. tration; the resulting concentration gradient Second law of thermodynamics The law is used to measure the molecular mass. that states that the entropy in a closed Selectively permeable Able to prevent the system never decreases. An alternative passage of certain specific molecules and statement is that processes that are thermo- ions while allowing others through. dynamically favored at constant tempera- Selective medium A medium that encou- ture and pressure involve a decrease in free rages growth of some organisms and sup- energy. presses growth of others. Second messenger An intercellular sub- Selective toxicity The ability of an antimi- stance that relays an extracellular signal crobial agent to harm microbes without (such as a hormonal signal) from the cell causing significant damage to the host. membrane to intracellular effector proteins. Self Molecules that are not recognized as Second‐order reaction A reaction in which antigenic or foreign by an organism. two reactant molecules must come togeth- Semen The male fluid discharge at the time er for the reaction to occur. The reaction is of ejaculation, containing sperm and vari- called second‐order because the reaction ous glandular and other secretions. 1180 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Semiconservative replication Replication in Seroconversion The identification of a spe- which a new DNA double helix is synthe- cific antibody in serum as a result of an sized from one strand of parent DNA and infection. one strand of new DNA. Serology The branch of immunology deal- Seminal vesicle A saclike structure whose ing with laboratory tests to detect antigens secretions form a component of semen. and antibodies. Semisynthetic drug An antimicrobial agent Serovar Strain; a subspecies category. made partly by laboratory synthesis and Serum The liquid part of blood after cells partly by micro‐organisms. and clotting factors have been removed. Sense codon A set of three DNA (or Serum hepatitis See hepatitis B. mRNA) bases that code for an amino acid. Serum killing power Test used to determine Sense strand For a gene, the DNA strand effectiveness of an antimicrobial agent in that is homologous to an RNA transcript of which a bacterial suspension is added to the gene – that is, it carries the same se- the serum of a patient whose is receiving an quence as the transcript, except with T in antibiotic; and incubated. place of U. It is thus complementary to the Serum sickness Immune complex disorder strand that served as a template for the that occurs when foreign antigens in seta RNA. cause immune complexes to be deposited Sensitization Initial exposure to an antigen, in tissues. which causes the host to mount an im- Severe combined immunodeficiency mune response against it. (SCID) Primary immunodeficiency dis- Septicemia An infection caused y rapid ease caused by failure of stem cells to de- multiplication of pathogens in the blood. velop properly, resulting in deficiency of Known also as blood poisoning. both B and T cells. Septicemic plague Fatal form of plague Sewage Used water and the wastes it con- that occurs when bubonic plague bacteria tains. move from the lymphatics to the circulato- Sex factors Plasmids that specify gene pro- ry system. ducts that enable bacteria to engage in Septic shock A life‐threatening septicemia conjugation (bacterial mating). with low blood pressure and blood‐vessel Sexually transmitted disease (STD) An in- collapse, caused by endotoxins. fectious disease spread by sexual activities. Septic tank An underground tank for re- Shadow casting The coating of electron mi- ceiving sewage, where solid material settle croscopy specimens with a heavy metal, out as sludge, which must be pumped such as gold or palladium, to create a periodically. three‐dimensional effect. Septum (plural: septa). A cross‐wall separ- Shigellosis Gastrointestinal disease caused ating two fungal cells. by several strains of Shigella that invade Sequela (plural: sequelae). The aftereffect intestinal lining cells. of a disease; after recovery from it. Known also as bacillary dysentery. Serial dilution A method of measurement Shinbone fever See trench fever. in which successive 1:10 dilutions are made Shingles Sporadic disease caused by reacti- from the original sample. vation of varicella‐zoster herpesvirus that Appendix C: Micro‐organisms, biochemistry, and nomenclature 1181
appears most frequently in older and im- forms between carbon‐6 of one pyrimidine munocompromised individuals. base and carbon‐4 of an adjacent pyrimi- Shrub of life A diagram that represents our dine base. This type of photoproduct current understanding of the early evolution appears to be the chief cause of UV‐ of life. There are many roots rather than a induced mutations. single ancestral line, and the branches criss‐ Skin The largest single organ of the body cross and merge again and again. that presents a physical barrier to infection Sickle‐cell disease A genetic disease result- by micro‐organisms. ing from a hemoglobin mutation. It pro- Slime layer A thin protective structure duces fragile erythrocytes, leading to loosely bound to the cell wall that protects anemia. the cell against drying, helps trap nutrients, Sign A disease characteristic that can be and sometimes binds cells together. observed by examining the patient, such Slime mold A funguslike protist. as swelling or redness. Sludge Solid matter remaining from water Signal recognition particles (SRPs) Cyto- treatment that contains aerobic organisms plasmic particles that dock ribosomes on that digest organic matter. the surface of the endoplasmic reticulum Sludge digester Large fermentation tank in (ER) if the nascent polypeptide is desti- which sludge is digested by anerobic bacte- ned to be processed by the ER. The SRP ria into simple organic molecules, carbon recognizes and binds to a specific N‐ dioxide, and methane gas. terminal signal sequence on the nascent Small intestine The upper area of the intes- polypeptide. tine where digestion is completed. Simple diffusion The net movement of par- Smallpox A formerly worldwide and seri- ticles from a region of higher to one of ous viral disease that has now been eradi- lower concentration; does not require en- cated. ergy from a cell. Smear A thin layer of liquid specimen Signal sequence See leader sequence. spread out on a microscopic slide. Simple stain A single dye used to reveal Solute The substance dissolved in a solvent basic cell shapes and arrangements. to form a solution. Single‐cell protein (SCP) Animal feed con- Solution A mixture of two or more sub- sisting of micro‐organisms. stances in which the molecules are evenly Sinus A large passageway in tissues, lined distributed and will not separate out on with phagocytic cells. standing. Sinusitis An infection of the sinus cavities. Solvent The medium in which substances Sinusoid An enlarged capillary. are dissolved to form a solution. Site‐directed mutagenesis A technique by Somatic mutation A mutation that occurs which a specific mutation is introduced at in a cell of an organism other than a germ‐ a specific site in a cloned gene. The gene like cell; it may affect the organism in can then be introduced into an organism which it occurs, but it cannot be passed and expressed. on to progeny. 6‐4 Photoproduct A type of DNA damage Sonication The disruption of cells by sound caused by UV irradiation in which a bond waves. 1182 Appendix C: Micro‐organisms, biochemistry, and nomenclature
SOS response A bacterial response to vari- cells (3) The ability of the immune system ous potentially lethal stresses, including to mount a unique immune response to severe UV irradiation. It involves the coor- each antigen it encounters. dinated expression of a set of proteins that Spectrophotometer An instrument that carry out survival maneuvers, including an exposes a sample to light of defined wave- error‐prone type of repair for thymine lengths and measures the absorbance. dimers in DNA. Different types of spectrophotometers op- Southern blotting A technique for detecting erate in different wavelength ranges, such the presence of a specific DNA sequence in as ultraviolet, visible, and infrared. a genome. The DNA is extracted, cleaved Spectrum of ctivity Refers to the range of into fragments, separated by gel electro- different microbes against which are anti- phoresis, denatured, and blotted onto a microbial agent is effective. nitrocellulose filter. There it is incubated Spheroplast A Gram‐negative bacterium under annealing conditions with a ra- that lacks the cell wall but had not lysed. diolabeled probe for the sequence in ques- Spike A glycoprotein projection that extend tion, and heteroduplexes of the probe with to form the viral capsid or envelope and is genomic DNA are detected by radioauto- used to attach to or fuse with host cells. graphy. Spindle apparatus A system of microtu- Specialized transduction Type of transduc- bules in the cytoplasm of a eukaryotic cell tion in which the bacterial DNA trans- that guides the movement of chromosomes duced is limited to one or a few genes during mitosis and meiosis. lying adjacent to a prophage that are acci- Spin label A substance that has an unpaired dentally included when the prophage is electron detectable by electron spin reso- excised from the bacterial chromosome. nance and that is used as a chemical label. Species A group of organisms wit many Spirillar fever A form of rat bite fever, common characteristics; the narrowest caused by Spirillum minor, first described taxon. as sodoku in Japan. Species immunity Innate or inborn genetic Spirillum (plural: spirilla). A flexible, wavy‐ immunity. shaped bacterium. Specific defense A host defense that oper- Spirochetes Corkscrew‐shaped motile bac- ates in response to a particular invading teria. pathogen. Spleen The largest lymphatic organ; acts as Specific epithet The second name of an or- a blood filter. ganism in the binomial system of nomen- Spliceosome A protein–RNA complex in clature, following that of the genus – for the nucleus that is responsible for splicing example, coli in Escherichia coli. introns out of RNA transcripts. Specific immunity Defense against a partic- Spontaneous generation The theory that ular microbe. living organisms can arise from non‐living Specificity (1) The property of an enzyme things. that allows it to accept only certain sub- Spontaneous mutation A mutation that strates and catalyze only one particular re- occurs in the absence of any agent known action. (2) The property of a virus that to cause changes in DNA; usually caused by restricts it to certain specific types of host errors during DNA replication. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1183
Sporadic disease A disease that is limited to amino acids in protein synthesis; in bacte- a small number of isolated case posing no ria it always codes for methionine. great threat to a large population. Stationary phase The third of four major Spore A resistant reproductive structure phases of the bacterial growth curve in formed by fungi and actinomycetes; differ- which new cells are produced at the same ent from a bacterial endospore. rate that old cells die, leaving the number Spore coat A keratinlike protein material of live cells constant. that is lad down around the cortex of an Sterility The state in which there are no endospore by the mother cell. living organisms in or on a material. Sporocyst Larval form of a fluke that devel- Sterilization The killing or removal of all ops in the body of its snail or mollusk host. micro‐organisms in a material or on an Sporotrichosis Fungal skin disease caused object. by Sporothrix schenckii that often enters Steroid A lip having a four‐ring structure, the body from plants. includes cholesterol, steroid hormones, Sporozoite A malaria trophozoite present in and vitamin D. the salivary glands of infected mosquitoes. Stock culture A reserve culture used to Sporulation The formation of spores such store an isolated organism in pure condi- as endospores. tion for use in the laboratory. Spread plate method A technique used to Stop codon (1) The last codon to be trans- prepare pure cultures by placing a diluted lated in a molecule of mRNA, causing sample of cells on the surface of an agar the ribosome to release from the mRNA. plate and then spreading the sample evenly (2) RNA codons that signal a ribosome to over the surface. stop translating an mRNA and to release Stain A molecule that can bind to a struc- the polypeptide. In the normal genetic ture and give it color. code, they are UAG, UGA, and UAA. Known also as a dye. Strain A subgroup of a species with one or Standard bacterial growth curve Agraph more characteristics that distinguish it plotting the number of bacteria versus time from other subgroups of that species. and showing the phases of bacterial growth. Streak plate method Method used to pre-
Standard reduction potential (E0) For a pare pure cultures in which bacterial are given pair consisting of an electron donor lightly spread over the surface of agar and its conjugate acceptor, the reduction plates, resulting in isolated colonies. potential under standard conditions (25 C; Streptococci Aerotolerant anerobes that donor and acceptor both at 1 m concentra- form pairs, tetrads, or chains by dividing tion). in one or two planes; most lack the enzyme Standard state A reference state, with re- catalase. spect to which thermodynamic quantities Streptokinase A bacterially produced en- (such as chemical potentials) are defined. zyme that digests (dissolves) blood clots. For substances in solution, standard state Streptolysin Toxin produced by strepto- indicates 1 m concentration at 1 atm pres- cocci that kills phagocytes. sure and 25 C. Streptomycetes Gram‐positive, filamen- Start codon The first codon in a molecule tous, sporing, soil‐dwelling bacteria, pro- of mRNA, which begins the sequence of duces of many antibiotics. 1184 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Streptomycin An antibacterial agent that the enzyme in the process. (It is called a blocks protein synthesis. suicide inhibitor because the enzyme Stringent response A mechanism that inhi- ‘‘commits suicide’’ by acting on it.) bits the expression of all structural genes in Sulfate reduction The reduction of sulfate bacteria under conditions of amino acid ions to hydrogen sulfide. starvation. It involves inhibition of the Sulfonamide A synthetic, bacteriostatic synthesis of ribosomal and transfer RNAs. agent that blocks the synthesis of folic acid. Stroma The fluid‐filled inner portion of a Known also as sulfa drugs. chloroplast. Sulfur cycle The cyclic movement of sulfur Stromatolite Live or fossilized layered mats through an ecosystem. of photosynthetic prokaryotes associated Sulfur oxidation The oxidation of various with warm lagoons or hot springs. forms of sulfur to sulfate. Strongyloidiasis Parasitic disease caused by Sulfur reduction The reduction of elemen- the roundworm Stongyloides stercoralis and tal sulfur to hydrogen sulfide. a few closely related species. Superantigens Powerful antigens, such as Structural gene A gene that carries infor- bacterial toxins, that activate large num- mation for the synthesis of a specific poly- bers of T cells, causing a large immune peptide. response that can cause diseases such as Structural protein A protein that contri- toxic shock. butes to the structure of cells, cell parts, Supercoiling For a DNA double helix, turns and membranes. of the two strands around each other that Sty An infection at the base of an eyelash. either exceed or are fewer than the number Subacute disease A disease that is interme- of turns in the most stable helical confor- diate between an acute and a chronic disease. mation. Only a helix that is circular or else Subacute sclerosing panencephalitis fixed at both ends can support supercoiling. (SSPE) A complication of measles, nearly See twist, writhe. always fatal, that is due to the persistence of Superhelix density (s) A measure of the measles viruses in brain tissue. superhelicity of a DNA molecule. It is Subclinical infection See inapparent infection. equal to the change in linking number Subculturing The process by which cells caused by the introduction of supercoiling from an existing culture are transferred to divided by the linking number the DNA fresh medium in new containers. molecule would have in its relaxed state. Substrate (1) The substance on which an Superinfection A secondary infection from enzyme acts. (2) A surface or food source the removal of normal microbiota, allow- on which a cell can grow or a spore can ing colonization by pathogenic, and often germinate. antibiotic‐resistant, microbes. Substrate‐level phosphorylation Synthesis Superoxide A highly reactive form of oxy- of a nucleoside triphosphate (usually ATP) gen that kills obligate anaerobes. driven by the breakdown of a compound Superoxide dismutase An enzyme that with higher phosphate transfer potential. converts superoxide to molecular oxygen Suicide inhibitor An enzyme inhibitor on and hydrogen peroxide. which the enzyme can act catalytically but Suppression With respect to mutations, a which irreversibly alters the active site of mutation that occurs at a different site Appendix C: Micro‐organisms, biochemistry, and nomenclature 1185
from that of an existing mutation in a gene together that is greater than either can but restores the wild‐type phenotype. achieve alone. Suppressor T cell (T5) Possibly a type of Synthesis The step of viral replication dur- cytotoxic or helper T cells that inhibits ing which new nucleic acids and viral pro- immune responses. teins are made. Surface tension A phenomenon in which Synthetic drug An antimicrobial agent the surface of water behaves like a thin synthesized chemically in the laboratory. invisible elastic membrane. Synthetic medium A growth medium Surfactant A substance that reduces surface prepared in the laboratory from materials tension. of precise or reasonably well‐defined com- Susceptibility The vulnerability of an or- position. ganism to harm by infectious agents. Syphilis A sexually transmitted disease, Svedberg unit (S) In ultracentrifugation, a caused by the spirochete Treponema palli- unit used for the sedimentation coefficient; dum, characterized by a chancre at the site it is equal to 10–13 s. of entry and often eventual neurological Swarmer cell Spherical, flagellated Rhizobi- damage. um cell that invades the root hairs of legu- Systemic blastomycosis Disease resulting minous plants, eventually to form nodules. from invasion by Blastomyces dermatitides Sweat gland Epidermal structure that of internal organs, especially the lungs. empties a watery secretion through pores Systemic infection An infection that affects in the skin. the entire body. Swimmer’s itch Skin reaction to cercariae of Known also as a generalized infection. some species of the helminth Schistosoma. Systemic lupus erythematosus A widely Symbiosis The living together of two differ- disseminated, systemic autoimmune dis- ent kinds of organisms. ease resulting from production of anti- Symport A membrane transport process bodies against DNA and other body that couples the transport of a substrate components. in one direction across a membrane to the Tapeworm Flatworm that lives in the adult transport of a different substrate in the stage as a parasite in the small intestine of same direction. Compare antiport. animals. Symptom A disease characteristic that can Tartar Calcium deposition on dental be observed or felt only by the patient, such plaque forming a very rough, hard crust. as pain or nausea. Tautomers Structural isomers that differ in Synchronous growth Hypothetical pattern the location of their hydrogen and double of growth during the log phase in which all bonds. the cells in a culture divide at the same time. Taxon (plural: taxa). A category used in Syncytium (plural: syncytia). A multinucle- classification, such as species, genus, ate mass in a cell culture, for example, order, family. caused by the respiratory syncytial virus. Taxonomy The science of classification. Syndrome A combination of signs and Tay‐sachs disease A genetic disease caused symptoms that occur together. by a deficiency of the lysosomal enzyme Synergism Referring to an inhibitory effect N‐acetylhexosaminidase A, which is in- produced by two antibiotics working volved in sphingolipid degradation. The 1186 Appendix C: Micro‐organisms, biochemistry, and nomenclature
deficiency results in accumulation of the Terminator codon A codon that signals the
ganglioside sphingolipid GM2, particularly end of the information for a particular in the brain. protein. T Cell See t lymphocyte. Known also as nonsense codon or stop codon. T‐Dependent antigen Antigen requiring Tertiary structure (1) The folding of a pro-
helper T cell (TH2) activity to activate B tein molecule into globular shapes. (2) cells. Large‐scale folding structure in a linear Teichoic acid A polymer attached to pepti- polymer that is at a higher order than sec- doglycan in Gram‐positive cell walls. ondary structure. For proteins and RNA Telomerase A DNA polymerase that adds a molecules, the tertiary structure is the spe- short repeating sequence to the 30 strand at cific three‐dimensional shape into which either end of a chromosomal DNA mole- the entire chain is folded. Compare primary cule, thus creating a single‐strand over- structure, quaternary structure, and second- hand. This overhand gives room for ary structure. priming the origin of a final Okazaki frag- Tertiary treatment Chemical and physical ment during DNA replication so that treatment of sewage to produce an effluent the full length of the chromosome can be of water pure enough to drink. copied. Test A shell made of calcium carbonate and Telomeres Special DNA sequences at the common to some protists. ends of eukaryotic chromosomes. See also diagnostic procedures and tests; Temperate phage A bacteriophage that specific tests. does not cause a virulent infection; rather, Testis (plural: testes). One of a pair of male its DNA is incorporated into the host cell reproductive glands that produce testoster- chromosome, as a prophage, and repli- one and sperm. cated with the chromosome. Tetanus Disease caused by Clostridium Temperate phages Bacterial phages that tetani in which muscle stiffness progresses can establish a condition of lysogeny. to eventual paralysis and death. See also lysogeny. Known also as lockjaw. Template DNA used as a pattern for the Tetanus neonatorum Type of tetanus ac- synthesis of a new nucleotide polymer in quired through the raw stump of the um- replication or transcription. bilical cord. Template strand A DNA or an RNA strand Tetracycline An antibacterial agent that that directs the synthesis of a complemen- inhibits protein synthesis. tary nucleic acid strand. Tetrad Cuboidal groups of four cocci. Temporary parasite A parasite that feeds on Thallus The body of a fungus. and then leaves its host (such as a biting Theca A tightly affixed, secreted outer insect). layer of dinoflagellates that often contains Teratogen An agent that induces defects cellulose. during embryonic development. Therapeutic dosage lLevel Level of drug Teratogenesis The induction of defects dosage that successfully eliminates a path- during embryonic development. ogenic organism if maintained over a Terminator See stop codon. period of time. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1187
Thermal death point The temperature that Tinea cruris Groin ringworm, a form of kills all the bacteria in a 24‐hour‐old broth ringworm that occurs in skin folds in the culture at neutral pH in 10 min. pubic region. Thermal death time The time required to Known also as jock itch. kill all the bacteria in a particular culture at Tinea pedis See athlete’s foot. a specified temperature. Tinea unguium A form of ringworm that Thermoacidophile A member of one of the causes hardening and discoloration of fin- groups of the archaeobacteria that live in gernails and toenails. extremely hot, acidic environments. Tissue culture Culture made from a single Thermophile A heat‐loving organism that tissue, assuring a reasonably homogenous grows best at temperatures from 50 to set of cultures in which to test the effects of 60 C. a virus or to culture an organism. Thermophilic anaerobic spoilage Spoilage Titer The quantity of a substance needed to due to endospore germination and growth produce a given reaction. in which gas and acid are produced, T‐Lymphocyte Thymus‐derived cell of the making cans bulge. immune system and agent of cellular im- Thrush Milky patches of inflammation mune responses. on oral mucous membranes; a symp- Known also as T cell. tom Candidiasis, caused by Candida Togavirus A small, enveloped RNA virus albicans. that multiplies in many mammalian and Thylakoid An internal membrane of chlor- anthropod cells. oplasts that contains chlorophyll. Tolerance A state in which antigens no lon- Thymus gland Multilobed lymphatic organ ger elicit an immune response. located beneath the sternum that posses Tonsilitis A bacterial infection of the tonsils. lymphocytes into T cells. Tonsil Lymphoid tissue that contributes Tick paralysis A disease characterized by immune defenses in the form of B cells fever and paralysis due to anticoagulants and T cells. and toxins secreted into a tick’s bite via Topoisomerases Enzymes that change the the ectoparasite’s saliva. supercoiling of DNA helices by either Tincture An alcoholic solution. allowing the superhelical torsion to relax T‐Independent antigen Antigen not requir- (thus reducing the supercoiling) or adding
ing helper T cells (TH2) activity to activate more twists (thus increasing the super- B cells. coiling) Tinea barbae Barber’s itch; a type of ring- Topoisomers With respect to DNA, closed worm that causes lesions in the beard. circular DNA molecules that are identical Tinea capitis Scalp ringworm, a form of except in their sense or degree of super- ringworm in which hyphae grow in hair coiling. DNA topoisomers can be inter- follicles, often leaving circular patterns of changed only by cutting one or both baldness. strands using topoisomerases. Tinea corporis Body ringworm, a form of TORCH series A group of blood tests used to ringworm that causes ringlike lesions with identify teratogenic diseases in pregnant a central scaly area. women and newborn infants. 1188 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Total magnification Obtained by multiplying Transfer RNA (tRNA) Type of RNA that the magnifying power of the objective lens transfers amino acids from the cytoplasm by the magnifying power of the ocular lens. to the ribosomes for placement in a protein Toxemia The presence and spread of exo- molecule. toxins in the blood. Transformation A change in an organism’s Toxic dosage level Amount of a drug nec- characteristics through the transfer of essary to cause host damage. naked DNA. Toxic shock syndrome (TSS) Condition Transfusion reaction Reaction that occurs caused by infection with certain toxigenic when matching antigens and antibodies strains of Staphylococcus aureus; often asso- are present in the blood at the same time. ciated with the use of super absorbent but Transgenic (1) State of permanently abrasive tampons. changing an organism’s characteristics by Toxin Any substance that is poisonous to integrating foreign DNA (genes) into the other organisms. organism. (2) Refers to an organism whose Toxoid An exotoxin inactivated by chemi- genome contains one or more DNA cal treatment but which retains its antige- sequences from a different species (trans- nicity and therefore can be used to genes). Genetic engineering can be used to immunize against the toxin. create transgenic animals. Toxoplasmosis Disease caused by the pro- Transient microflora Micro‐organisms that tozoan Toxoplasma gondii that can cause may be present in or on an organism congenital defects in newborns. under certain conditions and for certain Trace element Minerals, such as copper, lengths of time t sites where resident iron, zinc, and cobalt ions, that are re- microbiota. quired in minute amounts for growth. Transition state In any chemical reaction, Trachea The windpipe. the high‐energy or unlikely state that must Trachoma Eye disease caused by Chlamydia be achieved by the reacting molecule(s) for trachomatis that can result in blindness. the reaction to occur. Transamination In the cell, the enzymatic Translation The synthesis of a polypeptide transfer of an amino group from an under the direction of an mRNA, so that amino group a keto acid. The keto acid the nucleotide sequence of the mRNA is becomes an amino acid and vice versa. ‘‘translated’’ into the amino acid sequence Transcription The synthesis of an RNA of the protein. Compare transcription. molecule complementary to a DNA strand; Transmissible spongiform encephalopathies the information encoded in the base se- Prion‐caused diseases resulting in brain quence of the DNA is thus ‘‘transcribed’’ tissue developing multiple holds such that into the RNA version of the same code. it resembles a sponge, includes Creutz- Compare translation. feldt–Jakob disease, mad cow disease, Transcription factors Proteins that influence kuru, scrapie and others. the transcription of particular genes, usually Transmission The passage of light through by binding to specific promoter sites. an object. Transduction The transfer of genetic mate- Transmission electron microscope (TEM) A rial from one bacterium to another by a type of electron microscopy in which a bacteriophage. beam of electrons passes through the object Appendix C: Micro‐organisms, biochemistry, and nomenclature 1189
to be viewed and creates an image on a epidemic typhus in that is transmitted by photographic plate or screen. Very thin lice and is prevalent during wars and under slices of specimens are used. Compare scan- unsanitary conditions. ning electron microscopy. Known also as shinbone fever. Transovarian transmission Passing of path- Treponemes Spirochetes belonging to the ogen from one generation of ticks to the genus Treponema. next as eggs leave the ovaries. Triacylglycerol A molecule formed from Transplantation The moving of tissue from three fatty acids bonded to glycerol. one site to another. Tricarboxylic acid cycle See citric acid cycle Transplant rejection Destruction of grafted and krebs cycle. tissue or of a transplanted organ by the Trichinosis A disease caused by a small host immune system. nematode, Trichinella spiralis, that enters Transposable element A mobile genetic se- the digestive tract as encysted larvae in quence that can move from one plasmid to poorly cooked meat, usually pork. another plasmid or chromosome. Trichocyst Tentaclelike structure on ciliates Transposable genetic elements Genetic ele- for catching prey for attachment. ments that are able to move from place to Trichomoniasis A parasitic urogenital dis- place within a genome. A Transposon is ease, transmitted primarily by sexual inter- one type of transposable element. course, that causes intense itching and a Transposal of virulence A laboratory tech- copious white discharge, especially in nique in which a pathogen is passed from females. its normal host sequentially through many Trichuriasis Parasitic disease caused by the individual members of a new host species, whipworm, Trichuris trichiura, that resulting in a lessening or even total loss of damages intestinal mucosa and causes its virulence in the original host. chronic bleeding. Transposase An enzyme that is involved in Trickling filter system Procedure in which the insertion of a bacterial Transposon into sewage is spread over a bed of rocks coated a target site. with aerobic organisms that decompose Transposition The process whereby certain the organic matter in it. genetic sequences in bacteria or eukaryotes Trophozoite Vegetative form of a protozo- can move from one location to another. an such as Plasmodium. Transposon A mobile genetic sequence that Trypanosomiasis See african sleeping sickness. contains the genes for transposition as well Tube agglutination test Serologic test that as one or more other genes not related to measures antibody titers by comparing transposition. various dilutions of the patient’s serum Traumatic herpes Type of herpes infection against known quantities of an antigen. in which the virus enters traumatized skin Tubercle A solidified lesion or chronic in the area of a burn or other injury. granuloma that forms in the lungs in Traveler’s diarrhea Gastrointestinal disor- patients with tuberculosis. der generally caused by pathogenic strains Tuberculin hypersensitivity Cell‐mediated of Escherichia coli. hypersensitivity reaction that occurs in Trench fever Rickettsial disease, caused sensitized individuals when they are ex- by Rochalimaea quintana, resembling posed to tuberculin. 1190 Appendix C: Micro‐organisms, biochemistry, and nomenclature
Tuberculin skin test An immunological Typhus fever Rickettsial disease that oc- test for tuberculosis in which a purified curs in a variety of forms including protein derivative from the Mycobacterium epidemic, endemic (murine), and scrub tuberculosis is injected subcutaneously, typhus. resulting in an induration if there was pre- Tyrocidin An antibacterial agent that dis- vious exposure to the bacterium. rupts cell membranes. Tuberculoid Referring to the anesthetic Ulceroglandular Referring to the form of form of Hansen’s disease leprosy in which tularemia caused by entry of Francisella areas of skin lose pigment and sensation. tularensis through the skin and character- Tuberculosis Disease caused mainly by ized by ulcers on the skin and enlarged Mycobacterium tuberculosis. regional lymph nodes. Tularemia Zoonosis caused by Francisella Ultrafiltration The technique of filtering tularensis, most often associated with cot- a solution under pressure through a tontail rabbits. Semipermeable membrane, which allows Tumor An uncontrolled division of cells, water and small solutes to pass through often caused by viral infection. but retains macromolecules. Turbidity A cloudy appearance in a culture Ultra‐high temperature (UHT) processing A tube indicating the presence of organisms. method of sterilizing milk and dairy Turnover number With respect to an en- products by raising the temperature to zyme‐catalyzed reaction, the number of 87.8 C for 3 s. substrate molecules one enzyme molecule Uncoating Process in which protein coats can process (turn over) per second when of animal viruses that have entered ells are saturated with substrate. It is equivalent to removed by proteolytic enzymes.
the catalytic rate constant, kcat. Undulant fever See brucellosis. Twist (T) With respect to a DNA double Universal precautions A set of guidelines helix, the total number of times the two established by the CDC to reduce the strands of the helix cross over each other, risks of disease transmission in hospital excluding writhing. It is a measure of how and medical laboratory settings. tightly the helix is wound. Unsaturated fatty acid A fatty acid that See also linking number, writhe. contains at least one double bond between Tympanic membrane Membrane separat- adjacent carbon atoms. ing the outer and middle ear. Upper respiratory tract The nasal cavity, Known also as the eardrum. pharynx, larynx, trachea, bronchi, and Type strain Original reference strain of a larger bronchioles. bacterial species, descendants of a single Ureaplasmas Bacteria with unusual cell isolation in pure culture. walls, require sterols as a nutrient. Typhoidal tularemia Septicemia that resem- Ureter Tube that carries urine from the bles typhoid fever, caused by bacteremia kidney to the urinary bladder. from tularemia lesions. Urethra Tube through which urine passes Typhoid fever An epidemic enteric infec- from the bladder to the outside during tion caused by Salmonella typhi, uncom- micturition (urination) mon in areas with good sanitation. Urethritis Inflammation of the urethra. Appendix C: Micro‐organisms, biochemistry, and nomenclature 1191
Urethrocystitis Common term used to de- close other atoms or molecules can ap- scribe urinary tract infections involving the proach; it is thus the effective radius for urethra and the bladder. closest molecular packing. Urinalysis The laboratory analysis of urine Variable Anything that can change in an specimens. experiment. Urinary bladder Storage area for urine. Varicella–Zoster virus A herpesvirus that Urinary system Body system that regulates causes both chickenpox and shingles. the composition of body fluids and Vasodilation Dilation of the capillary and removes nitrogenous and other wastes venule walls during an acute inflammation. from the body. Vector (1) A self‐replicating carrier of Urinary tract infection (UTI) A bacterial uro- DNA; usually a plasmid, bacteriophage, genital infection that causes urethritis or or eukaryotic virus. (2) An organism that cystitis. transmits a disease‐causing organism from Urine Water collected in the kidney tubules. one host to another. (3) In genetic engi- Urogenital system Body system that neering, a DNA molecule that can be (1) regulates the composition of body used to introduce a DNA sequence into a fluids and removes certain wastes from cell where it will be replicated and main- the body and (2) enables the body to par- tained. Usually a plasmid or a viral ticipate in sexual reproduction. genome. Use‐dilution test A method of evaluating Vegetation A growth that forms on dam- the antimicrobial properties of a chemical aged heart valve surfaces in bacterial endo- agent using standard preparations of cer- carditis, exposed collagen fibers elicit fibrin tain test bacteria. deposits, and transient bacteria attach to Uterine tube A tube that conveys ova from the fibrin. the ovaries to the uterus. Vegetative cell A cell that is actively meta- Known also as fallopian tubes or oviducts. bolizing nutrients. Uterus The pear‐shaped organ in which a Vehicle A non‐living carrier of an infec- fertilized ovum implants and develops. tious agent from its reservoir to a suscepti- Vaccine A substance that contains an anti- ble host. gen to which the immune system responds. Venezuelan equine encephalitis Type of See also immunization, specific types of viral encephalitis seen in Florida, Texas, vaccines. Mexico, and South America; infects horses Vacuole A membrane‐bound structure that more frequently than humans. stores materials such as food or gas in the Verminous intoxication An allergic reaction cytoplasm or eukaryotic cells. to toxins in the metabolic wastes of liver Vagina The female genital canal, extending flukes. from the cervix to the outside of the body. Verruga peruana One form of bartonello- Vaginitis Vaginal infection, often caused by sis; a chronic non‐fatal skin disease. opportunistic organisms that multiply Vertical gene transfer Genes that pass from when the normal vaginal microflora are parents to offspring. disturbed by antibiotics or other factors. Vertical transmission Direct contact trans- van der Waals radius (r) The effective radius mission of disease in which pathogens are of an atom or a molecule that defines how passed from parent to offspring in an egg 1192 Appendix C: Micro‐organisms, biochemistry, and nomenclature
or sperm, across the placenta, or while hemolysis of red blood cells in laboratory traversing the birth canal. cultures. Very low‐density lipoprotein (VLDL) Atype Virion A complete virus particle, including of lipoprotein particle that is manufac- its envelope if it has one. tured in the liver and functions mainly Viroid An infectious RNA particle, smaller to carry triacylglycerols from the liver to than a virus and lacking a capsid, that adipose and other tissues. causes various plant diseases. Vesicle A membrane‐bound inclusion in Virulence The degree of intensity of the cells. disease produced by a pathogen. Vibrio A comma‐shaped bacterium. Virulence factor A structural or physiologi- Vibriosis An enteritis caused by Vibrio cal characteristic that helps a pathogen parahaemolyticus, acquired from eating cause infection and disease. contaminated fish and shellfish that have Virulent phage A bacteriophage that enters not been thoroughly cooked. the lytic cycle when it infects a bacterial Virion A single virus particle. cell, causing eventual lysis and death of Villus (plural: villi). A multicellular projec- the host cell. tion from the surface of a mucous mem- Known also as lytic phage. brane, functioning in absorption. Virus A submicroscopic, parasitic, acellular Viral enteritis Gastrointestinal disease caused micro‐organism composed of a nucleic by rotaviruses, characterized by diarrhea. acid (DNA or RNA) core inside a protein Viral hemagglutination Hemagglutination coat. caused by binding of viruses, such as Viruses Infectious entities that contain the those that cause measles and influenza, to nucleic acid to code for their own structure red blood cells. but that lack the enzymatic machinery of a Viral meningitis Usually self‐lining and cell; they replicate by invading a cell and non‐fatal form of meningitis. using its machinery to express the viral ge- Viral neutralization The binding of antibo- nome. Most viruses consist of little but dies to viruses, which is used in an immu- nucleic acid enclosed in a protein coat; nological test to determine if a patient’s some viruses also have an outer lipid‐bilayer serum contains viruses. envelope. Viral pneumonia Disease caused by viruses Visceral larva migrans The migration of such as respiratory syncytial virus. larvae of Toxocara species in human tis- Viral specificity Refers to the specific types sues, where they cause damage and allergic of cells within an organism that a virus can reactions. infect. Vitamin A substance required for growth Viral yield See burst size. that the organism cannot make. Viremia An infection in which viruses are Volutin Polyphosphate granules. transported in the blood but do not multi- Known also as metachromatic granule. ply in transit. Walking pneumonia See primary atypical Viridans group A group of streptococci that pneumonia. often infect the valves and lining of Wandering macrophages Phagocytic cells the heart and cause incomplete (alpha) that circulate in the blood or move into Appendix C: Micro‐organisms, biochemistry, and nomenclature 1193
tissues when microbes and other foreign Whipworm Trichuris trichiura, a worm that material are present. causes trichuriasis infestation of the Wart A growth on the skin and mucous intestine. membranes caused by infection with Whitlow A herpetic lesion on a finger that human papillonavirus. can result from exposure to oral, ocular Known also as papilloma. and probably genital herpes. Water cycle Process by which water is Whooping cough A highly contagious re- recycled through precipitation, ingestion spiratory disease caused primarily by Bor- by organisms, respiration, and evaporation. detella pertussis. Known also as the hydrologic cCycle. Known also as pertussis. Water mold A funguslike protist that pro- Wild‐type Refers to the normal genotype duces flagellated asexual spores (zoospores) found in free‐living, natural members of a and large, motile gametes. group of organisms. Known also as oomycota. Wort The liquid extract from mash. Wavelength The distance between succes- Wound botulism Rare form of botulism sive crests or troughs of a light wave. that occurs in deep wounds when tissue Western blotting A technique for identify- damage impairs circulation and creates ing proteins or protein fragments in a mix- anerobic conditions in which Clostridium ture that react with a particular antibody. botulinum can multiply. The mixture is first resolved into bands by Writhe (W) With respect to a supercoiled one‐dimensional denaturing gel electro- DNA helix, the number of times the helix phoresis. The protein bands are then ‘‘blot- as a whole crosses over itself – that is, ted’’ onto a nitrocellulose sheet, the sheet is the number of superhelical turns that are treated with the antibody and any bands present. that bind the antibody are identified. More See also linking number, twist. accurately called immunoblotting. Xenobiotic An organic compound that is Western equine encephalitis Type of viral not produced by the organism in which it encephalitis seen most often in the western is found. United States; infects horses more fre- Xenograph A graft between individuals of quently than humans. different species. West nile fever Emerging viral disease new X‐ray diffraction A technique that is used to to the USA, transmitted by mosquitoes, determine the three‐dimensional structure causing seizures and encephalitis; lethal to of molecules, including macromolecules. A crows. crystal or fiber of the substance is illumi- Wet mount Microscopy technique in which nated with a beam of X‐rays, and the re- a drop of fluid containing the organisms peating elements of the structure scatter (often living) is placed on a slide. the X‐rays to form a diffraction pattern Wetting agent A detergent solution often that gives information on the molecule’s used with other chemical agents to pene- structure. trate fatty substances. See also diffraction pattern. Whey The liquid portion (waste product) Yeast artificial chromosomes (YACs) Artifi- of milk resulting from bacterial enzyme cial chromosomes used for cloning and addition. maintaining large fragments of genomic 1194 Appendix C: Micro‐organisms, biochemistry, and nomenclature
DNA for investigational purposes. A YAC Ziehl–Neelsen acid‐fast stain A differential is constructed by recombinant DNA tech- stain for organisms that are not decolor- niques from a year centromere, two telo- ized by acid in alcohol, such as the bacteria meres (chromosome ends), selectable that cause Hansen’s disease (leprosy) and markers, and cloned DNA in the megabase tuberculosis. range. Zone of inhibition A clear area that appears Yeast extract Substance from yeast contain- on agar in the disk diffusion method, indi- ing vitamins, coenzymes, and nucleosides; cating where the agent has inhibited used to enrich media. growth of the organism. Yellow fever Viral systemic disease found in Zoonosis (plural: zoomoses). A disease that tropical areas, carried by the mosquito can be transmitted from animals to humans. Aedes aegypti. Zygomycosis Disease in which certain fungi Yersiniosis Severe enteritis caused by Yersi- of the genera Mucor and Rhizopus invade nia enterocolitica. lungs, the central nervous system, and tis- Z‐DNA A DNA duplex with a specific left‐ sues of the eye orbit. hand helical structure. In vitro, it tends to Zygomycota See bread mold. be the most stable form from DNA Zygospore In bread molds, a thick‐walled, duplexes that have alternating purines resistant, spore‐producing structure enclo- and pyrimidines, especially under condi- sing a zygote. tions of cytosine methylation or negative Zygote A cell formed by the union of supercoiling. gametes (egg and sperm). Appendix C: Micro-organisms, biochemistry, and nomenclature 1195
2. Bacteria II. Gram‐negative bacteria, excluding photosynthetic forms The classification below is based on that in the 3rd edition of Microbiology (Bernard D Cell shape: Cocci David, Harper & Row, New York, pp. 27–28). Motility: Permanently immotile The extent of classification is to the genus Other distinguishing and, in selected cases families, but the species characteristics Genera Families are listed in the text. Aerobic Neisseria Neisseriaceae Veillonella Brucella Bordetella a. Main groups of bacteria* Pasteurella Anerobic Hamophilus Brucellacease I. Gram‐positive eubacteria Cell shape: Straight rods Motility: Motile with peritrichous flagella, Motility: Nearly all permanently immotile and related immotile forms Cell shape: Straight rods
Other Other Genera distinguishing distinguishing characteristics Genera Families characteristics Aerobic Bacillus Families Escherichia Cell shape: cocci Sarcina Erwinia Cells in cubical Micrococcaceae Shigella packets Mixed acid Salmonella Micrococus Fermentation Proteus Enterobacteriaceae Cells irregularly Staphylooccus of sugars Yersinia arranged Facultative— Butylene glycol Enterobacter Azotobacteraceae Cells in chains Streptoccoccus Streptococcaceae anerobic fermentation Serrati Lactic fermentation Leuconostoc Free‐living Azotobacter of sugars nitrogen Cell shape: straight fixers rods Aerobic Symbiotic Rhizobium Rhizobiaceae Lactic fermentation Lactobacillus Lactobacillaceae nitrogen of sugars fixers Propionic fermentation Propionibacterium Propionibacteriaceae of sugars Corynebacterium Listeria Oxidative, Erysipelothrix weakly fermentative Cell shape: Straight rods Motility: Motile with polar flagella Cell shape: Curved rods Motility: Motile with pertrichous flagella, Other Genera and related immotile forms distinguishing characteristics Aerobic Bacillus Families
Oxide Nitrosomonas Nitrobacteraceae inorganic Nitrobacter Thiobacillus compounds Other Genera Aerobic Oxidize Pseudomonas Pseudomonadaceae distinguishing organic Acetobacter characteristics Aerobic Bacillus Families compounds Facultative Photobacterium Endorspores Anaerobic Clostridum Bacillaceae aneobic Zymomonas produced Aeromonas 1196 Appendix C: Micro-organisms, biochemistry, and nomenclature
Motility: Motile with polar flagella 2. The web page ‘‘www/bacterio.cict.fr/’’ is a source for the complete identification of all bacteria and viruses using Bergey’s classifica- Other Genera distinguishing tion of bacteria. characteristics Aerobic Bacillus Families
Comma‐shaped Aerobic Vibro Spirllaceae Desulfovibrio Spiral Anaerobic Spirillum b. Classification of bacteria
Domain ‘‘Archaea’’ III. Other major groups Phylum A1. Crenarchaeota phy. nov. Class I. Thermoprotei class. mov. Other distinguishing characteristics Genera Families Order I. Thermoproteales Family I. Thermoproteaceae Acid‐fast rods Mycobacterium Actinomycetales Nocardia Genus I. Thermoproteus Ray‐forming rods Streptomyces Actinomyces (actinomycetes) Treponema Genus II. Caldivirga Borrelia Genus III. Pyrobaculum Leptospira Spiral organisms, motile Spirocheta Spirochetales Genus IV. Thermocladium Small, pleomorphic; lack Mycoplasma Mycoplasmataceae rigid wall Rickettsia Family II. Thermofilaceae Small intracellular Coxiella Rickettsiaceae Genus I. Thermofilum parasites Small intracellular parasites, Chlamydia Chlamydiaceae Order II. Desulfurococcales ord. nov. readily filterable Intracellular parasites; Bartonella Bartonellaceae Family I. Desulfurococcaceae borderline with protoza Genus I. Desulfurococcus
*Some of these traditional names have been officially replaced. (Modified Genus II. Acidolobus from Stanier RY et al: The microbial world. Prentice Hall, Englewood Genus III. Aeropyrum Clifffs, NJ, 1963). Genus IV. Ignicoccus Genus V. Staphylothermus Genus VI. Stetteria Bacteria are classified as follows: Genus VII. Sulfophobococcus Kingdom: Monera (Prokaryotae) Genus VIII. Thermodiscus gen. nov. Division/Phylum: Gracillcutes Genus IX. Thermosphaera Subphylum: Family II. Pyrodictiaceae Class: Scotobacteria Genus I. Pyrodictium Order: Spirochaetales Genus II. Hyperthermus Family: Spirochaetaceae Genus III. Pyrolobus Genus: Treonema Order III. Sulfolobales Specific Epithet: pallidum Family I. Sulfolobaceae Subspecies(strain): Genus I. Sulfolobus Genus II. Acidianus Genus III. Metallosphaera Sources Genus IV. Stygiolobus 1. Bergey’s manual of systematic bacteriology, 2nd Genus V. Sulfurisphaera edn. Springer‐Verlag, New York, April 2001. Genus VI. Sulfurococcus Appendix C: Micro-organisms, biochemistry, and nomenclature 1197
Phylum AII. Euryarchaeota phy. nov. Genus V. Methanolobus Class I. Methanobacteria class. nov. Genus VI. Methanomicrococcus Order I. Methanobacteriales Genus VII. Methanosalsum gen. Family I. Methanobacteriaceae nov. Genus I. Methanobacterium Family II. Methanosaetaceae fam. Genus II. Methanobrevibacter nov. Genus III. Methanosphaera Genus I. Methanosaeta Genus IV. Methanothermobacter Class III. Halobacteria class. nov. Family II. Methanothermaceae Order I. Halobacteriales Genus I. Methanothermus Family I. Halobacteriaceae Class II. Methanococci class. nov. Genus I. Halobacterium Order I. Methanococcales Genus II. Haloarcula Family I. Methanococcaceae Genus III. Halobaculum Genus I. Methanococcus Genus IV. Halococcus Genus II. Methanothermococcus gen. Genus V. Haloferax nov. Genus VI. Halogeometricum Family II. Methanocaldococcacae fam. Genus VII. Halorhabdus nov. Genus VIII. Halorubrum Genus I. Methanocaldococus gen. Genus IX. Haloterrigena nov. Genus X. Natrialba Genus II. Methanotorris gen. nov. Genus XI. Natrinema Order II. Methanomicrobiales Genus XII. Natronobacterium Family I. Methanomicrobiaceae Genus XIII. Natronococcus Genus I. Methanomicrobium Genus XIV. Natronomonas Genus II. Methanoculleus Genus XV. Natronorubrum Genus III. Methanofollis Class IV. Thermoplasmata class. nov. Genus IV. Methanogenium Order I. Thermoplasmatales ord. nov. Genus V. Methanolacinia Family I. Thermoplasmataceae fam. Genus VI. Methanoplanus nov. Family II. Methanocorpusculaceae Genus I. Thermoplasma Genus I. Methanocorpusculum Family II. Picrophilaceae Family III. Methanospirillaceae fam. Genus I. Picrophilus nov. Family III. Ferroplasmatacaea Genus I. Methanospirillum Genus I. Ferroplasma Genera incertae sedis Class V. Thermococci class. nov. Genus I. Methanocalculus Order I. Thermococcales Order III. Methanosarcinales ord. nov. Family I. Thermococcaceae Family I. Methanosarcinaceae Genus I. Thermococcus Genus I. Methanosarcina Genus II. Palaeococcus Genus II. Methanococcoides Genus III. Pyrococcus Genus III. Methanohalobium Class VI. Archaeoglobi class. nov. Genus IV. Methanohalophilus Order I. Archaeoglobales ord. nov. 1198 Appendix C: Micro-organisms, biochemistry, and nomenclature
Family I. Archaeoglobaceae fam. nov. Genus I. Thermus Genus I. Archaeoglobus Genus II. Meiothermus Genus II. Ferroglobus Phylum BV. Chrysiogenetes phy. nov. Methanopyri class. nov. Class VII. Class I. Chrysiogenetes class. nov. Methanopyrales ord. nov. Order I. Order I. Chrysiogenales ord. nov. Family I. Methanopyraceae fam. nov. Family I. Chrysiogenaceae fam. Genus I. Methanopyrus nov. Domain ‘‘Bacteria’’ Genus I. Chrysiogenes Chloroflexi phy. nov. Aquificae phy. nov. Phylum BVI. Phylum BI. ‘‘Chloroflexi’’ Aquificae class. nov. Class I. Class I. ‘‘Chloroflexales’’ Aquificales ord. nov. Order I. Order I. Family I. ‘‘Chloroflexaceae’’ Family I. Aquificaceae fam. nov. Genus I. Chloroflexus Genus I. Aquifex Genus II. Chloronema Genus II. Calderobacterium Genus III. Heliothrix Genus III. Hydrogenobacter Family II. Oscillochloridaceae Genus IV. Thermocrinis Genus I. Oscillochloris (moved) Genera incertae sedis ‘‘Herpetosiphonales’’ Genus I. Desulfurobacterium Order II. Family I. ‘‘Herpetosiphonaceae’’ Phylum BII. Thermotogae phy. nov. Genus I. Herpetosiphon Thermotogae class. nov. Class I. Phylum BVII. Thermomicrobia phy. nov. Thermotogales ord. nov. Order I. Class I. Thermomicrobia class. nov. Family I. Thermotogaceae fam. nov. Order I. Thermomicrobiales ord. Genus I. Thermotoga nov. Genus II. Fervidobacterium Family I. Thermomicrobiaceae fam. Genus III. Geotoga nov. Genus IV. Petrotoga Genus I. Thermomicrobium Genus V. Thermosipho Phylum BVIII. Nitrospira phy. nov. Phylum BIII. Thermodesulfobacteria phy. nov. Class I. ‘‘Nitrospira’’ Class I. Thermodesulfobacteria class. nov. Order I. ‘‘Nitrospirales’’ Order I. Thermodesulfobacteriales ord. Family I. ‘‘Nitrospiraceae’’ nov. Genus I. Nitrospira Family I. Thermodesulfobacteriaceae Genus II. Leptospirillum fam. nov. Genus III. Magnetobacterium Genus I. Thermodesulfobacterium Genus IV. Thermodesulfovibrio Phylum BIV. ‘‘Deinococcus‐Thermus’’ Phylum BIX. Deferribacteres phy. nov. Class I. Deinococci class. nov. Class I. Deferribacteres class. nov. Order I. Deionococcales Order I. Deferribacterales ord. nov. Family I. Deinococcaceae Family I. Deferribacteraceae fam. Genus I. Deinococcus nov. Order II. Thermales ord. nov. Genus I. Deferribacter Family I. Thermaceae fam. nov. Genus II. Denitrovibrio Appendix C: Micro-organisms, biochemistry, and nomenclature 1199
Genus III. Flexistipes Form genus VIII. Lyngbya Genus IV. Geovibrio Form genus IX. Microcoleus Genera incertae sedis Form genus X. Oscillatoria Genus I. Synergistes Form genus XI. Planktothrix Form genus XII. Prochlorothrix Phylum BX. Cyanobacteria Form genus XIII. Psuedanabaena Class I. ‘‘Cyanobacteria’’ Form genus XIV. Spirulina Subsection I. Family I. Form genus XV. Starria Form genus I. Chamaesiphon Form genus XVI. Symploca Form genus II. Chroococcus Genus XVII. Trichodesmium Form genus III. Cyanobacterium Form genus XVIII. Tychonema Form genus IV. Cyanobium Subsection IV. Form genus V. Cyanothece Family I. Form genus VI. Dactylococcopsis Form genus I. Anabaena Form genus VII. Gloeobacter Form genus II. Anabaenopsis Form genus VIII. Gloeocapsa Form genus III. Aphanizomenon Form genus IX. Gloeothece Form genus IV. Cyanospira Form genus X. Microcystis Form genus V. Cylindrospermopsis Form genus XI. Prochlorococcus Form genus VI. Cylindrospermum Form genus XII. Prochloron Form genus VII. Nodularia Form genus XIII. Synechococcus Form genus VIII. Nostoc Form genus XIV. Synechocystis Form genus IX. Scytonema Family II. Subsection II. Family I. Form genus I. Calothrix Form genus I. Cyanocystis Form genus II. Rivularia Form genus II. Dermocarpella Form genus III. Tolypothrix Form genus III. Stanieria Subsection V. Form genus IV. Xenococcus Family I. Family II. Form genus I. Chlorogloeopsis Form genus I. Chroococcidiopsis Form genus II. Fischerella Form genus II. Myxosarcina Form genus III. Geitleria Form genus III. Pleurocapsa Form genus IV. Iyengariella Form genus V. Nostochopsis Subsection III. Family I. Form genus VI. Stigonema Form genus I. Arthrospira Phylum BXI. Chlorobi phy. nov. Form genus II. Borzia Class I. ‘‘Chlorobia’’ Form genus III. Crinalium Order I. Chlorobiales Form genus IV. Geitlerinema Family I. Chlorobiaceae Genus V. Halospirulina Genus I. Chlorobium Form genus VI. Leptolyngbya Genus II. Ancalochloris Form genus VII. Limnothrix Genus III. Chloroherpeton 1200 Appendix C: Micro-organisms, biochemistry, and nomenclature
Genus IV. Pelodictyon Genus VI. Xenohaliotis Genus V. Prosthecochloris Family III. ‘‘Holosporaceae’’ Genus I. Holospora Proteobacteria phy. nov. Phylum BXII. Genus II. Caedibacter ‘‘Alphaproteobacteria’’ Class I. Genus III. Lyticum Rhodospirillales Order I. Genus IV. Polynucleobacter Family I. Rhodospirillaceae Genus V. Pseudocaedibacter Genus I. Rhodospirillum Genus VI. Symbiotes Genus II. Azospirillum Genus VII. Tectibacter Genus III. Magnetospirillum Genus VIII. Odyssella Genus IV. Phaeospirillum ‘‘Rhodobacterales’’ Genus V. Rhodocista Order III. Family I. ‘‘Rhodobacteraceae’’ Genus VI. Rhodospira Genus I. Rhodobacter Genus VII. Rhodothalassium Genus II. Ahrensia Genus VIII. Rhodovibrio Genus III. Amaricoccus Genus IX. Roseospira Genus IV. Antarctobacter Genus X. Skermanella Genus V. Gemmobacter Family II. Acetobacteraceae Genus VI. Hirschia Genus I. Acetobacter Genus VII. Hyphomonas Genus II. Acidiphilium Genus VIII. Maricaulis Genus III. Acidisphaera Genus IX. Methylarcula Genus IV. Acidocella Genus X. Octadecabacter Genus V. Acidomonas Genus XI. Paracoccus Genus VI. Asaia Genus XII. Rhodovulum Genus VII. Craurococcus Genus XIII. Roseibium Genus VIII. Gluconacetobacter Genus XIV. Roseinatronobacter Genus IX. Gluconobacter Genus XV. Roseivivax Genus X. Paracraurococcus Genus XVI. Roseobacter Genus XI. Rhodopila Genus XVII. Roseovarius Genus XII. Roseococcus Genus XVIII. Rubrimonas Genus XIII. Stella Genus XIX. Ruegaria Genus XIV. Zavarzinia Genus XX. Sagittula Rickettsiales Order II. Genus XXI. Staleya Family I. Rickettsiaceae Genus XXII. Stappia Genus I. Rickettsia Genus XXIII. Sulfitobacter Genus II. Orientia ‘‘Sphingomonadales’’ Genus III. Wolbachia Order IV. Family I. Sphingomonadaceae Family II. Ehrlichiaceae Genus I. Sphingomonas Genus I. Ehrlichia Genus II. Blastomonas Genus II. Aegyptianella Genus III. Erythrobacter Genus III. Anaplasma Genus IV. Erythromicrobium Genus IV. Cowdria Genus V. Erythromonas Genus V. Neorickettsia Genus VI. Porphyrobacter Appendix C: Micro-organisms, biochemistry, and nomenclature 1201
Genus VII. Rhizomonas Genus III. Agromonas Genus VIII. Sandaracinobacter Genus IV. Blastobacter Genus IX. Zymomonas Genus V. Bosea Order V. Caulobacterales Genus VI. Nitrobacter Family I. Caulobacteraceae Genus VII. Oligotropha Genus I. Caulobacter Genus VIII. Rhodopseudomonas Genus II. Asticcacaulis Family VIII. Hyphomicrobiaceae Genus III. Brevundimonas Genus I. Hyphomicrobium Genus IV. Phenylobacterium Genus II. Ancalomicrobium Order VI. ‘‘Rhizobiales’’ Genus III. Ancylobacter Family I. Rhizobiaceae Genus IV. Angulomicrobium Genus I. Rhizobium Genus V. Aquabacter Genus II. Agrobacterium Genus VI. Azorhizobium Genus III. Carbophilus Genus VII. Blastochloris Genus IV. Chelatobacter Genus VIII. Devosia Genus V. Ensifer Genus IX. Dichotomicrobium Genus VI. Sinorhizobium Genus X. Filomicrobium Family II. Bartonellaceae Genus XI. Gemmiger Genus I. Bartonella Genus XII. Labrys Family III. Brucellaceae Genus XIII. Methylorhabdus Genus I. Brucella Genus XIV. Pedomicrobium Genus II. Mycoplana Genus XV. Prosthecomicrobium Genus III. Ochrobactrum Genus XVI. Rhodomicrobium Family IV. ‘‘Phyllobacteriaceae’’ Genus XVII. Rhodoplanes Genus I. Phyllobacterium Genus XVIII. Seliberia Genus II. Allorhizobium Genus XIX. Starkeya Genus III. Aminobacter Genus XX. Xanthobacter Genus IV. Aquamicrobium Family IX. ‘‘Methylobacteriaceae’’ Genus V. Defluvibacter Genus I. Methylobacterium Genus VI. Mesorhizobium Genus II. Protomonas Genus VII. Pseudaminobacter Genus III. Roseomonas Family V. ‘‘Methylocystaceae’’ Family X. ‘‘Rhodobiaceae’’ Genus I. Methylocystis Genus I. Rhodobium Genus II. Methylopila Class II. ‘‘Betaproteobacteria’’ Genus III. Methylosinus Order I. ‘‘Burkholderiales’’ Family VI. ‘‘Beijerinckiaceae’’ Family I. ‘‘Burkholderiaceae’’ Genus I. Beijerinckia Genus I. Burkholderia Genus II. Chelatococcus Genus II. Cupriavidus Genus III. Derxia Genus III. Lautropia Genus IV. Methylocella Genus IV. Pandoraea Family VII. ‘‘Bradyrhizobiaceae’’ Genus V. Thermothrix Genus I. Bradyrhizobium Family II. ‘‘Ralstoniaceae’’ Genus II. Afipia Genus I. Ralstonia 1202 Appendix C: Micro-organisms, biochemistry, and nomenclature
Family III. ‘‘Oxalobacteraceae’’ Genus II. Alysiella Genus I. Oxalobacter Genus III. Aquaspirillum Genus II. Duganella Genus IV. Catenococcus Genus III. Herbaspirillum Genus V. Chromobacterium Genus IV. Janthinobacterium Genus VI. Eikenella Genus V. Massilia Genus VII. Formivibrio Genus VI. Telluria Genus VIII. Iodobacter Family IV. Alcaligenaceae Genus IX. Kingella Genus I. Alcaligenes Genus X. Microvirgula Genus II. Achromobacter Genus XI. Prolinoborus Genus III. Bordetella Genus XII. Simonsiella Genus IV. Pelistega Genus XIII. Vitreoscilla Genus V. Sutterella Genus XIV. Vogesella Genus VI. Taylorella Order V. ‘‘Nitrosomonadales’’ Family V. Comamonadaceae Family I. ‘‘Nitrosomonadaceae’’ Genus I. Comamonas Genus I. Nitrosomonas Genus II. Acidovorax Genus II. Nitrosospira Genus III. Aquabacterium Family II. Spirillaceae Genus IV. Brachymonas Genus I. Spirillum Genus V. Delftia Family III. Gallionellaceae Genus VI. Hydrogenophaga Genus I. Gallionella Genus VII. Ideonella Order VI. ‘‘Rhodocyclales’’ Genus VIII. Leptothrix Family I. ‘‘Rhodocyclaceae’’ Genus IX. Polaromonas Genus I. Rhodocyclus Genus X. Rhodoferax Genus II. Azoarcus Genus XI. Roseateles Genus III. Azonexus Genus XII. Rubrivivax Genus IV. Azospira Genus XIII. Sphaerotilus Genus V. Azovibrio Genus XIV. Tepidimonas Genus VI. Ferribacterium Genus XV. Thiomonas Genus VII. Propionibacter Genus XVI. Variovorax Genus VIII. Propionivibrio Order II. ‘‘Hydrogenophilales’’ Genus IX. Thauera Family I. ‘‘Hydrogenophilaceae’’ Genus X. Zoogloea Genus I. Hydrogenophilus Class III. ‘‘Gammaproteobacteria’’ Genus II. Thiobacillus Order I. ‘‘Chromatiales’’ Order III. ‘‘Methylophilales’’ Family I. Chromatiaceae Family I. ‘‘Methylophilaceae’’ Genus I. Chromatium Genus I. Methylophilus Genus II. Allochromatium Genus II. Methylobacillus Genus III. Amoebobacter Genus III. Methylovorus Genus IV. Halochromatium Order IV. ‘‘Neisseriales’’ Genus V. Halothiobacillus Family I. Neisseriaceae Genus VI. Isochromatium Genus I. Neisseria Genus VII. Lamprobacter Appendix C: Micro-organisms, biochemistry, and nomenclature 1203
Genus VIII. Lamprocystis Genus II. Dichelobacter Genus IX. Marichromatium Genus III. Suttonella Genus X. Nitrosococcus Order V. ‘‘Thiotrichales’’ Genus XI. Pfennigia Family I. ‘‘Thiotrichaceae’’ Genus XII. Rhabdochromatium Genus I. Thiothrix Genus XIII. Thermochromatium Genus II. Achromatium Genus XIV. Thioalkalicoccus Genus III. Beggiatoa Genus XV. Thiocapsa Genus IV. Leucothrix Genus XVI. Thiococcus Genus V. Macromonas Genus XVII. Thiocystis Genus VI. Thiobacterium Genus XVIII. Thiodictyon Genus VII. Thiomargarita Genus XIX. Genus VIII. Thioploca Genus XX. Thiohalocapsa Genus IX. Thiospira Genus XXI. Thiolamprovum Family II. ‘‘Piscirickettsiaceae’’ Genus XXII. Thiopedia Genus I. Piscirickettsia Genus XXIII. Thiorhodococcus Genus II. Cycloclasticus Genus XXIV. Thiorhodovibrio Genus III. Hydrogenovibrio Genus XXV. Thiospirillum Genus IV. Methylophaga Family II. Ectothiorhodospiraceae Genus V. Thiomicrospira Genus I. Ectothiorhodospira Family III. ‘‘Francisellaceae’’ Genus II. Arhodomonas Genus I. Francisella Genus III. Halorhodospira Order VI. ‘‘Legionellales’’ Genus IV. Nitrococcus Family I. Legionellaceae Genus V. Thiorhodospira Genus I. Leionella Order II. Acidithiobacillales Family II. ‘‘Coxiellaceae’’ Family I. Acidithiobacillaceae Genus I. Coxiella Genus I. Acidithiobacillus Genus II. Rickettsiella Family II. Thermithiobacillaceae Order VII. ‘‘Methylococcales’’ Genus I. Thermithiobacillus Family I. Methylocaccaceae Order III. ‘‘Xanthomonadales’’ Genus I. Methylococcus Family I. ‘‘Xanthomonadaceae’’ Genus II. Methylobacter Genus I. Xanthomonas Genus III. Methylocaldum Genus II. Frateuria Genus IV. Methylomicrobium Genus III. Luteimonas Genus V. Methylomonas Genus IV. Lysobacter Genus VI. Methylosphaera Genus V. Nevskia Order VIII. ‘‘Oceanspirillales’’ Genus VI. Pseudoxanthomonas Family I. ‘‘Oceanospirillaceae’’ Genus VII. Rhodanobacter Genus I. Oceanospirillum Genus VIII. Stenotrophomonas Genus II. Balneatrix Genus IX. Xylella Genus III. Fundibacter Order IV. ‘‘Cardiobacteriales’’ Genus IV. Marinomonas Family I. Cardiobacteriaceae Genus V. Marinospirillum Genus I. Cardiobacterium Genus VI. Neptunomonas 1204 Appendix C: Micro-organisms, biochemistry, and nomenclature
Family II. Halomonadaceae Family I. Vibrionaceae Genus I. Halomonas Genus I. Vibrio Genus II. Alcanivorax Genus II. Allomonas Genus III. Carnimonas Genus III. Enhydrobacter Genus IV. Chromohalobacter Genus IV. Listonella Genus V. Deleya Genus V. Photobacterium Genus VI. Zymobacter Genus VI. Salinivibrio Order IX. Pseudomonadales Order XII. ‘‘Aeromonadales’’ Family I. Pseudomonadaceae Family I. Aeromonadaceae Genus I. Pseudomonas Genus I. Aeromonas Genus II. Azomonas Genus II. Oceanomonas Genus III. Azotobacter Genus III. Tolumonas Genus IV. Cellvibrio Family II. Succinivibrionaeae Genus V. Chryseomonas Genus I. Succinivibrio Genus VI. Flaviomonas Genus II. Anaerobiospirillum Genus VII. Lampropedia Genus III. Ruminobacter Genus VIII. Mesophilobacter Genus IV. Succinimonas Genus IX. Morococcus Order XIII. ‘‘Enterobacteriales’’ Genus X. Oligella Family I. Enterobacteriaceae ‘Genus XI. Rhizobacter Genus I. Enterobacter Genus XII. Rugamonas Genus II. Alterococcus Genus XIII. Serpens Genus III. Arsenophonus Genus XIV. Thermoleophilum Genus IV. Brenneria Genus XV. Xylophilus Genus V. Buchnera Family II. Moraxellaceae Genus VI. Budvicia Genus I. Moraxella Genus VII. Buttiauxella Genus II. Acinetobacter Genus VIII. Calymmatobacterium Genus III. Psychrobacter Genus IX. Cedecea Order X. ‘‘Alteromonadales’’ Genus X. Citrobacter Family I. ‘‘Alteromonadaceae’’ Genus XI. Edwardsiella Genus I. Alteromonas Genus XII. Erwinia Genus II. Allishewanella Genus XIII. Escherichia Genus III. Colwellia Genus XIV. Ewingella Genus IV. Ferrimonas Genus XV. Hafnia Genus V. Glaciecola Genus XVI. Klebsiella Genus VI. Idiomarina Genus XVII. Kluyvera Genus VII. Marinobacter Genus XVIII. Leclercia Genus VIII. Marinobacterium Genus XIX. Leminorela Genus IX. Microbulbifer Genus XX. Moellerella Genus X. Moritella Genus XXI. Morganella Genus XI. Pseudoalteromonas Genus XXII. Obesumbacterium Genus XII. Shewanella Genus XXIII. Pantoea Order XI. ‘‘Vibrionales’’ Genus XXIV. Pectobacterium Appendix C: Micro-organisms, biochemistry, and nomenclature 1205
Genus XXV. Photorhabdus Order III. ‘‘Desulfobacterales’’ Genus XXVI. Plesiomonas Family I. ‘‘Desulfobacteraceae’’ Genus XXVII. Pragia Genus I. Desulfobacter Genus XXVIII. Proteus Genus II. Desulfobacerium Genus XXIX. Providencia Genus III. Desulfobacula Genus XXX. Rahnella Genus IV. Desulfocella Genus XXXI. Saccharobacter Genus V. Desulfococcus Genus XXXII. Salmonella Genus VI. Desulfofaba Genus XXXIII. Serratia Genus VII. Desulfofrigus Genus XXXIV. Shigella Genus VIII. Desulfonema Genus XXXV. Sodalis Genus IX. Desulfosarcina Genus XXXVI. Tatumella Genus X. Desulfospira Genus XXXVII. Trabulsiella Genus XI. Desullfotalea Genus XXXVIII. Wigglesworthia Genus XII. Desulfotignum Genus XXXIX. Xenorhabdus Family II. ‘‘Desulfobulbaceae’’ Genus XL. Yersinia Genus I. Desulfobulbus Genus XLI. Yokenella Genus II. Desulfocapsa Order XIV. ‘‘Pasteurellales’’ Genus III. Desulfofustus Family I. Pasteurellaceae Genus IV. Desulforhopalus Genus I. Pasteurella Family III. ‘‘Nitrospinaceae’’ Genus II. Actinobacillus Genus I. Nitrospina Genus III. Hamemorphilus Genus II. Desulfobacca Genus IV. Lonepinella Genus III. Desulfomonile Genus V. Mannheimia Order IV. ‘‘Desulfuromonadales’’ Genus VI. Phocoenobacter Family I. ‘‘Desulfuromonadaceae’’ Class IV. ‘‘Deltaproteobacteria’’ Genus I. Desulfuromonas Order I. ‘‘Desulfurellales’’ Genus II. Desulfuromusa Family I. ‘‘Desulfurellaceae’’ Family II. ‘‘Geobacteraceae’’ Genus I. Desulfurella Genus I. Geobacter Genus II. Hippea Family III. ‘‘Pelobacteraceae’’ Order II. ‘‘Desulfovibrionales’’ Genus I. Pelobacter Family I. ‘‘Desulfovibrionacea’’ Genus II. Malonomonas Genus I. Desulfovibrio Genus III. Trichlorobacter Genus II. Bilophila Order V. ‘‘Syntrohobacterales’’ Genus III. Lawsonia Family I. ‘‘Syntrophobacteraceae’’ Family II. ‘‘Desulfomicrobiacea’’ Genus I. Syntrophobacter Genus I. Desulfomicrobium Genus II. Desulfacinum Family III. ‘‘Desullfohalobiaceae’’ Genus III. Desulforhabdus Genus I. Desulfohalobium Genus IV. Desulfovirga Genus II. Desulfomonas Genus V. Thermodesulforhabdus Genus III. Desulfonatronovibrio Family II. ‘‘Syntrophaceae’’ Family IV. ‘‘Desulfonatronumaceae’’ Genus I. Syntroiphus Genus I. Desullfonatronum Genus II. Smithella 1206 Appendix C: Micro-organisms, biochemistry, and nomenclature
Order VI. ‘‘Bdelloovibrionales’’ Genus IX. Sarcina Family I. ‘‘Bdellovibrionaceae’’ Genus X. Sporobacter Genus I. Bdellovibrio Genus XI. Thermobrachium Genus II. Bacteriovorax Genus XII. Thermohalobacter Genus III. Micavibrio Genus XIII. Tindallia Genus IV. Vampirovibrio Family II. ‘‘Lachnospiraceae’’ Order VII. Myxococcales Genus I. Lachnospira Family I. Myxococcaceae Genus II. Acetitomaculum Genus I. Myxococccus Genus III. Anaerofilum Genus II. Angiococcus Genus IV. Butyrivibrio Family II. Archangiaceae Genus V. Catenibacterium Genus Archangium Genus VI. Catonella Family III. Cystobacteraceae Genus VII. Coprococcus Genus I. Cystobacter Genus VIII. Johnsonella Genus II. Melittangium Genus IX. Pseudobutyrivibrio Genus III. Stigmatella Genus X. Roseburia Family IV. Polyangiaceae Genus XI. Ruminococcus Genus I. Polyangium Genus XII. Sporobacterium Genus II. Chondromyces Family III. ‘‘Peptostreptococcaceae’’ Genus III. Nannocystis Genus I. Peptostreptococcus Class V. ‘‘Epsilonproteobacteria’’ Genus II. Filifactor Order I. ‘‘Campylobacterales’’ Genus III. Finegoldia Family I. Campylobacteraceae Genus IV. Fusibacter Genus I. Campylobacter Genus V. Helcococcus Genus II. Arobacter Genus VI. Micromonas Genus III. Sulfurospirillum Genus VII. Tissierella Genus IV. Thiovulum Family IV. ‘‘Eubacteriaceae’’ Family II. ‘‘Helicobavteraceae’’ Genus I. Eubacterium Genus I. Helicobacter Genus II. Acetobacterium Genus II. Wolinella Genus III. Anaerovorax Genus IV. Mogibacterium Phylum BXIII. Firmicutes Genus V. Pseudoramibacter Class I. ‘‘Clostridia’’ Family V. Peptococcaceae Order I. Clostridiales Genus I. Peptococcus Family I. Clostridiaceae Genus II. Anaeroarcus Genus I. Clostridium Genus III. Anaerosinus Genus II. Acetivibrio Genus IV. Anaerovibrio Genus III. Acidaminobacter Genus V. Carboxydothermus Genus IV. Anaerobacter Genus VI. Centipeda Genus V. Caloramator Genus VII. Dehalobacter Genus VI. Coprobacillus Genus VIII. Dendrosporobacter Genus VII. Natronincola Genus IX. Desulfitobacterium Genus VIII. Oxobacter Genus X. Desulfonispora Appendix C: Micro-organisms, biochemistry, and nomenclature 1207
Genus XI. Desulfosporosinus Genus XIII. Thermanaerovibrio Genus XII. Desulfotomaculum Genus XIV. Thermohydrogenium Genus XIII. Mitsuokella Genus XV. Thermosyntropha Genus XIV. Propionispira Order II. ‘‘Thermoanaerobacteriales’’ Genus XV. Succinispira Family I. Genus XVI. Syntrophobotulus ‘‘Thermoanaerobacteriacea’’ Genus XVII. Genus I. Thermoanerobacterium Thermoterrabacterium Genus II. Ammonifex Family VI. ‘‘Heliobacteriaceae’’ Genus III. Carboxydobrachium Genus I. Heliobacterium Genus IV. Coprothermobacter Genus II. Heliobacillus Genus V. Moorella Genus III. Heliophilum Genus VI. Sporotomaculum Genus IV. Heliorestis Genus VII. Thermacetogenium Family VII. ‘‘Acidaminococcaceae’’ Genus VIII. Thermoanaerobacter Genus I. Acidaminococcus Genus IX. Theremoanaerobium Genus II. Acetonema Order III. Haloanaerobiales Genus III. Anaeromusa Family I. Haloanaerobiaceae Genus IV. Dialister Genus I. Haloanaerobium Genus V. Megasphaera Genus II. Halocella Genus VI. Papillibacter Genus III. Halothermothrix Genus VII. Pectinatus Genus IV. Natroniella Genus VIII. Family II. Halobacteroidaceae Phascolarctobacterium Genus I. Halobacteroides Genus IX. Quinella Genus II. Acetohalobium Genus X. Schwartzia Genus III. Haloanaerobacter Genus XI. Selenomonas Genus IV. Orenia Genus XII. Sporomusa Genus V. Sporohalobacter Genus XIII. Succiniclasticum Class II. Mollicutes Genus XIV. Veillonella Order I. Mycoplasmatales Genus XV. Zymophilus Family I. Mycoplasmataceae Family VIII. Syntrophomonadaceae Genus I. Mycoplasma Genus I. Syntrophomonas Genus II. Eperythrozoon Genus II. Acetogenium Genus III. Haemobartonella Genus III. Aminobacterium Genus IV. Ureaplasma Genus IV. Aminomonas Order II. Entomoplasmatales Genus V. Anaerobaculum Family I. Entomoplasmataceae Genus VI. Anaerobranca Genus I. Entomoplasma Genus VII. Caldicellulosiruptor Genus II. Mesoplasma Genus VIII. Dethiosulfovibrio Family II. Spiroplasmataceae Genus IX. Pelospora Genus I. Spiroplasma Genus X. Syntrophospora Order III. Acholeplasmatales Genus XI. Syntrophothermus Family I. Acholeplasmataceae Genus XII. Thermaerobacter Genus I. Acholeplasma 1208 Appendix C: Micro-organisms, biochemistry, and nomenclature
Order IV. Anaeroplasmatales Genus III. Aneurinibacillus Family I. Anaeroplasmataceae Genus IV. Brevibacillus Genus I. Anaeroplasma Genus V. Oxalophagus Genus II. Asteroleplasma Genus VI. Thermicanus Order V. Incertae sedis Genus VII. Thermobacillus Family I. ‘‘Erysipelotrichaceae’’ Family VIII. ‘‘Alicyclobacillaceae’’ Genus I. Erysipelothrix Genus I. Alicyclobacillus Genus II. Bulleidia Genus II. Pasteuria Genus III. Holdermania Genus III. Sulfobacillus Genus IV. Solobacterium Family IX. Class III. ‘‘Bacilli’’ ‘‘Thermoactinomycetaceae’’ Order I. Bacillales Genus I. Thermoactinomyces Family I. Bacillaceae Order II. ‘‘Lactobacillales’’ Genus I. Bacillus Family I. Lactobacillaceae Genus II. Amphibacillus Genus I. Lactobacillus Genus III. Anoxybacillus Genus II. Paralactobacillus Genus IV. Exiguobacterium Genus III. Pediococcus Genus V. Gracilibacillus Family II. ‘‘Aerococcaceae’’ Genus VI. Halobacillus Genus I. Aerococcus Genus VII. Saccharococus Genus II. Abiotrophia Genus VIII. Salibacillus Genus III. Dolosicoccus Genus IX. Virgibacillus Genus IV. Eremococcus Family II. Planococcaceae Genus V. Facklamia Genus I. Planococcus Genus VI. Globicatella Genus II. Filibacter Genus VII. Ignavigranum Genus III. Kurthia Family III. ‘‘Carnobacteriaceae’’ Genus IV. Sporosarcina Genus I. Carnobacterium Family III. Caryophanaceae Genus II. Agitococcus Genus I. Caryophanon Genus III. Alloiococcus Family IV. ‘‘Listeriaceae’’ Genus IV. Desemzia Genus I. Listeria Genus V. Dolosigranulum Genus II. Brochothrix Genus VI. Granulicatella Family V. ‘‘Staphylococcaceae’’ Genus VII. Lactosphaera Genus I. Staphylococcus Genus VIII. Trichococcus Genus II. Gemella Family IV. ‘‘Enterococcaceae’’ Genus III. Macrococcus Genus I. Enterococcus Genus IV. Salinicoccus Genus II. Atopobacter Family VI. ‘‘Sporolactobacillaceae’’ Genus III. Melissococcus Genus I. Sporolactobacillus Genus IV. Tetragenococcus Genus II. Marinococcus Genus V. Vagococcus Family VII. ‘‘Paenibacillaceae’’ Family V. ‘‘Leuconostocaceae’’ Genus I. Paenibacillus Genus I. Leuconostoc Genus II. Ammoniphilus Genus II. Oenococcus Appendix C: Micro-organisms, biochemistry, and nomenclature 1209
Genus III. Weissella Genus III. Arcanobacterium Family VI. Streptococcaceae Genus IV. Mobiluncus Genus I. Streptococcus Suborder VI. Micrococcineae Genus II. Lactococcus Family I. Micrococcanceae Family VII. Incertae sedis Genus I. Micrococcus Genus I. Acetoanaerobium Genus II. Arthrobacter Genus II. Oscillospira Genus III. Kocuria Genus III. Syntrophococcus Genus IV. Nesterenkonia Genus V. Renibacterium (moved) Phylum BXIV. Actinobacteria phy. nov. Genus VI. Rothia Class I. Actinobacteria Genus VII. Stomatococcus Subclass I. Acidimicrobidae Family II. Bogoriellaceae Order I. Acidimicrobiales Genus I. Bogoriella (moved) Suborder I. ‘‘Acidimicrobineae’’ Family III. Rarobacteraceae Family I. Acidimicrobiaceae Genus I. Rarobacter (moved) Genus I. Acidimicrobium Family IV. Sanguibacteraceae Subclass II. Rubrobacteridae Genus I. Sanguibacter Order I. Rubrobacterales Family V. Brevibacteriaceae Suborder II. ‘‘Rubrobacterineae’’ Genus I. Brevibacterium Family I. Rubrobacteraceae Family VI. Cellulomonadaceae Genus I. Rubrobacter Genus I. Cellulomonas Subclass III. Coriobacteridae Genus II. Oerskovia Order I. Coriobacteriales Family VII. Dermabacteraceae Suborder III. ‘‘Coriobacterineae’’ Genus I. Dermabacter Family I. Coriobacteriaceae Genus II. Brachybacterium Genus I. Coriobacterium Family VIII. Dermatophilaceae Genus II. Atopobium Genus I. Dermatophilus Genus III. Collinsella Family IX. Dermacoccaceae Genus IV. Cryptobacterium Genus I. Dermacoccus (moved) Genus V. Denitrobacterium Genus II. Demetria (moved) Genus VI. Eggerthella Genus III, Kytococcus (moved) Genus VII. Slackia Family X. Intrasporangiaceae Subclass IV. Sphaerobacteridae Genus I. Intrasporangiun Order I. Sphaerobacterales Genus II. Janibacter Suborder IV. ‘‘Sphaerobacterineae’’ Genus III. Ornithinicoccus Family I. Sphaerobacteraceae Genus IV. Ornithinimicrobium Genus I. Sphaerobacter Genus V. Nostocoidia Subclass V. Actinobacteridae Genus VI. Terrabacter Order I. Actinomycetales Genus VII. Terracoccus Suborder V. Actinomycineae Genus VIII. Tetrasphaera Family I. Actinomycetaceae Family XI. Jonesiaceae Genus I. Actinomyces Genus I. Jonesia Genus II. Actinobaculum Family XII. Microbacteriaceae 1210 Appendix C: Micro-organisms, biochemistry, and nomenclature
Genus I. Microbacterium Genus IX. Verrucosispora Genus II. Agrococcus Suborder IX. Propionibacterineae Genus III. Agromyces Family I. Propionibacteriaceae Genus IV. Aureobacterium Genus I. Propionibacterium Genus V. Clavibacter Genus II. Luteococcus Genus VI. Cryobacterium Genus III. Microlunatus Genus VII. Curtobacterium Genus IV. Propioniferax Genus VIII. Frigoribavterium Genus V. Tessaracoccus Genus IX. Leifsonia Family II. Nocardioidaceae Genus X. Leucobacter (moved) Genus I. Nocardioides Genus XI. Rathayibacter Genus II. Aeromicrobium Genus XII. Subtercola Genus III. Friedmanniella Family XIII. ‘‘Beutenbergiaceae’’ Genus IV. Hongia Genus I. Beutenbergia Genus V. Kribella Family XIV. Promicromonosporaceae Genus VI. Micropruina Genus I. Promicromonospora Genus VII. Marmoricola Suborder VII. Corynebacterineae Suborder X. Pseudonocardineae Family I. Corynebacteriaceae Family I. Pseudonocardiaceae Genus I. Corynebacterium Genus I. Pseudonocardia Family II. Dietziaceae Genus II. Actinoalloteichus Genus I. Dietzia Genus III. Actinopolyspora Family III. Gordoniaceae Genus IV. Amycolatopsis Genus I. Gordonia Genus V. Kibdelosporangium Genus II. Skermania ‘Genus VI. Kutzneria Family IV. Mycobacteriaceae Genus VII. Prauserella Genus I. Mycobacterium Genus VIII. Saccharomonospora Family V. Nocardiaceae Genus IX. Saccharopolyspora Genus I. Nocardia Genus X. Streptoalloteichus Genus II. Rhodococcus Genus XI. Thermobispora Family VI. Tsukamurellaceae Genus XII. Thermocrispum Genus I. Tsukamurella Family II. Actinosynnemataceae Family VII. ‘‘Williamsiaceae’’ Genus I. Actinosynnema Genus I. Williamsia Genus II. Actinokineospora Suborder VIII. MKicromonosporineae Genus III. Lentzea Family I. Micromonosporaceae Genus IV. Saccharothrix Genus I. Micromonospora Suborder XI. Streptomycineae Genus II. Acinoplanes Family I. Streptomycetaceae Genus III. Catallatospora Genus I. Strepstomyces Genus IV. Catenuloplanes Genus II. Kitasatospora Genus V. Couchinoplanes Genus III. Streptoverticillium Genus VI. Dactylosporangium Suborder XII. Streptosporangineae Genus VII. Pilimelia Family I. Streptosporangiaceae Genus VIII. Spirilliplanes Genus I. Streptosporangium Appendix C: Micro-organisms, biochemistry, and nomenclature 1211
Genus II. Acrocarpospora Genus II. Actinocorallia Genus III. Herbidospora Genus III. Excellospora Genus IV. Microbispora Genus IV. Pelczaria Genus V. Microtetraspora Genus V. Turicella Genus VI. Nonomuraea Planctomycetes phy. nov. Genus VII. Planobispora Phylum BXV. ‘‘Planctomycetacia’’ Genus VIII. Planomonospora Class I. Planctomycetales Genus IX. Planopolyspora Order I. Family I. Planctomycetaceae Genus X. Planotetraspora Genus I. Planctomyces Family II. Nocardiopsaceae Genus II. Gemmata Genus I. Nocardiopsis Genus III. Isophaera Genus II. Thermobifida Genus IV. Pirellula Family III. Thermomonosporaceae Genus I. Thermomonospora Phylum BXVI. Chlamydiae phy. nov. Genus II. Actinomadura Class I. ‘‘Chlamydiae’’ Genus III. Spirillospora Order I. Chlamydiales Suborder XIII. Frankineae Family I. Chlamydiaceae Family I. Frankiaceae Genus I. Chlamydia Genus I. Frankia Genus II. Chlamydophila Family II. Geodermatophilaceae Family II. Parachlamydiaceae Genus I. Geodermatophilus Genus I. Parachlamydia Genus II. Blastococcus Family III. Simkaniaceae Genus III. Modestobacter Genus I. Simkania Family III. Microsp0haeraceae Family IV. Waddliaceae Genus I. Microsphaera Genus I. Waddlia Family IV. Sporichthyaceae Phylum BXVII. Spirochaetes phy. nov. Genus I. Sporichthya Class I. ‘‘Spirochaetes’’ Family V. Acidothermaceae Order I. Spirochaetales Genus I. Acidothermus Family I. Spirochaetaceae Family VI. ‘‘Kineosporiaceae’’ Genus I. Spirochaeta Genus I. Kineosporia Genus II. Borrelia Genus II. Cryptosporangium Genus III. Brevinema Genus III. Kineococcus Genus IV. Clevelandina Suborder XIV. Glycomycineae Genus V. Cristispira Family I. Glycomycetaceae Genus VI. Diplocalyx Genus I. Glycomyes Genus VII. Hollandina Order II. Bifidobacteriales Genus VIII. Pillotina Family I. Bifidobacteriaceae Genus IX. Treponema Genus I. Bifidobacterium Family II. ‘‘Serpulinaceae’’ Genus II. Falcivibrio Genus I. Serpulina Genus III. Gardnerella Genus II. Brachyspira Family II. Unknown Affiliation Family III. Leptospiraceae Genus I. Actinobispora 1212 Appendix C: Micro-organisms, biochemistry, and nomenclature
Genus I. Leptonema Genus VIII. Gelidibacter Genus II. Leptospira Genus IX. Ornithobacterium Genus X. Polaribacter Phylum BXVIII. Fibrobacteres phy. nov. Genus XI. Psychroflexus Class I. ‘‘Fibrobacteres’’ Genus XII. Psychroserpens Order I. ‘‘Fibrobacterales’’ Family I. ‘‘Fibrobacteraceae’’ Genus XIII. Riemerella Genus I. Fibrobacter Genus XIV. Saligentibacter Genus XV. Weeksella Acidobacteria phy. nov. Phylum BXIX. Family II. ‘‘Myroidaceae’’ ‘‘Acidobacteria’’ Class I. Genus I. Myroides ‘‘Acidobacteriales’’ Order I. Genus II. Psychromonas Family I. ‘‘Acidobacteriaceae’’ Family III. ‘‘Blattabacteriaceae’’ Genus I. Acidobacterium Genus I. Blattabacterium Genus II. Geothrix ‘‘Sphingobacteria’’ Genus III. Holophaga Class III. Order I. ‘‘Sphingobacteriales’’ Phylum BXX. Bacteroidetes phy. nov. Family I. Sphingobacteriaceae Class I. ‘‘Bacteroidetes’’ Genus I. Sphingobacterium Order I. ‘‘Bacteroidales’’ Genus II. Pedobacter Family I. Bacteroidaceae Family II. ‘‘Saprospiraceae’’ Genus I. Bacteroides Genus I. Saprospira Genus II. Acetofilamentum Genus II. Haliscomenobacter Genus III. Acetomicrobium Genus III. Lewinella Genus IV. Acetothermus Family III. ‘‘Flexibacteraceae’’ Genus V. Anaerorhabdus Genus I. Flexibacter Genus VI. Megamonas Genus II. Cyclobacterium Family II. ‘‘Rikenellaceae’’ Genus III. Cytophaga Genus I. Rikenella Genus IV. Dyadobacter Genus II. Marinilabilia Genus V. Flectobacillus Family III. ‘‘Porphyromonadaceae’’ Genus VI. Hymenobacter Genus I. Porphyromonas Genus VII. Meniscus Genus II. Dysgonomonas Genus VIII. Microscilla Family IV. ‘‘Prevotellaceae’’ Genus IX. Runella Genus I. Prevotella Genus X. Spirosoma Class II. ‘‘Flavobacteria’’ Genus XI. Sporocytophaga Order I. ‘‘Flavobacteriales’’ Family IV. ‘‘Flammeovirgaceae’’ Family I. Flavobacteriaceae Genus I. Flammeovirga Genus I. Flavobacterium Genus II. Flexithrix Genus II. Bergeyella Genus III. Persicobacter Genus III. Capnocytophaga Genus IV. Thermonema Genus IV. Cellulophaga Family V. Crenotrichaceae Genus V. Chryseobacterium Genus I. Crenothrix Genus VI. Coenonia Genus II. Chitinophaga Genus VII. Empedobacter Appendix C: Micro-organisms, biochemistry, and nomenclature 1213
Genus III. Rhodothermus bacteriology, 2nd edn. Springer‐Verlag, New Genus IV. Toxothrix York. Information can also be found in L Collier, J Oxford (1993) Human virology: a Phylum BXXI. Fusobacteria phy. nov. test for students of medicine, dentistry, and Class I. ‘‘Fusobacteria’’ ‘‘Fusobacteriales’’ microbiology. Oxford University Press, Ox- Order I. ‐ Family I. ‘‘Fusobacteriaceae’’ ford, and in J Levy, H Fraenkel Conrat, R ‐ Genus I. Fusobacterium Owens (1994) Virology, 2nd edn. Prentice Genus II. Ilyobacter Hall, NJ. Genus III. Leptrotrichia The 21 families of viruses listed here are Genus IV. Propionigenium primarily those that infect vertebrates. Genus V. Sebaldella Thus, these families represent only a small Genus VI. Streptobacillus part of the 71 families and more than 3000 Virus Taxonomy: Sev- Family II. Incertae sedis viruses recognized in enth Report of the International Committee on Genus I. Cetobacterium Taxonomy of Viruses, Van Regenmortel HV, Phylum BXXII. Verrucomicrobia phy. nov. Bishop DHL, Van Reenmortel MH, and Class I. Verrucomicrobiae Fauquet CM eds., Academic Press, San Order I. Verrucomicrobiales Diego, CA 2000 (ISBN 0123702003). Family I. Verrucomicrobiaceae Genus I. Verrucomicrobium 1. Family: Picornaviridae Genus II. Prosthecobacter Family II. ‘‘Xipinematobacteriaceae’’ Genera Genus I. Xiphinematobacter Enterovirus (gastrointestinal viruses, Phylum BXXIII. Dictyoglomus phy. nov. poliovirus, coxsackie viruses A and Class I. ‘‘Dictyoglomi’’ B, and echoviruses. Order I. ‘‘Dictyoglomales’’ Hapatovirus (hepatitis A virus). Family I. ‘‘Dictyoglomaceae’’ Cardiovirus (encephalomyocarditis virus Genus I. Dictyoglomus of mice and other rodents). Rhinovirus (upper respiratory tract c. Classification of viruses viruses, common cold viruses). Aphthovirus (foot‐and‐mouth disease The classification of viruses has undergone virus). great change, as has bacterial taxonomy. Naked, polyhedral, positive‐sense, and Most viruses have not even been classified ssRNA. Synthesis and maturation take place due to a lack of data concerning their repro- in the host cell cytoplasm. Viruses are re- duction and molecular biology. Estimates leased via cell lysis. suggest that more than 30,000 viruses are being studies in laboratories and reference 2. Family: Caliciviridae centers worldwide. The classification and viral information presented here follows the Genus outline given in Chapter 10 (Tables 10.1 and Calicivirus (Norwalk viruses and similar 10.2) of G Garrity, M Winters, D Searles viruses causing gastroenteritis, hepa- 1 (2001) Bergey’s Manual of systematic titis E virus). 1214 Appendix C: Micro-organisms, biochemistry, and nomenclature
Naked, polyhedral, positive‐sense, and line infectious peritonitis virus, and ssRNA. Synthesis and maturation takes mouse hepatitis virus). place in the host cell cytoplasm. Viruses are Enveloped, helical, positive‐sense, and ssRNA. released via cell lysis. Synthesis occurs in the host cell cytoplasm; mat- uration involves budding through membranes 3. Family: Togaviridae and the endoplasmic reticulum, and Golgi ap- paratus. Viruses are released via cell lysis. Genera Alphavirus (eastern, western, and Vene- 6. Family: Rhabdoviridae zuelan equine encephalitis viruses, and Semliki forest virus). Genera Rubivirus (rubella virus). Vesiculovirus (vesicular stomatitis‐like Arterivirus (equine arteritis virus and virus). simian hemorrhagic fever virus). Lyssavirus (rabies and rabieslike viruses). Enveloped, polyhedral, positive‐sense, and [Unnamed] (proposed, for bovine ssRNA. Synthesis occurs in the host cell ephemeral feverlike viruses). cytoplasm; maturation involves budding of Enveloped, helical, negative‐sense, and nucleocapsids through the host cell plasma ssRNA. Synthesis occurs in the host cell nu- membrane. Viruses are released via cell lysis cleus; maturation occurs via budding from (Arterivirus). Many replicates in arthropods the host cell plasma membrane. Many repli- and vertebrates. cate in arthropods.
4. Family: Flaviviridae 7. Family: Filoviridae
Genera Genus Flavivirus (yellow‐fever virus, dengue Filovirus (Marburg and Ebola viruses). fever virus, St. Louis and Japanese Enveloped; long, filamentous forms, some- encephalitis viruses, and tickborne times with branching, and sometimes encephalitis virus). U‐shaped, 6‐shaped, or circular; negative‐ Pestivirus (bovine diarrhea virus, hop sense, and ssRNA. Synthesis occurs in the cholera virus) Hapatitis C virus. host cell cytoplasm; maturation involves Enveloped, polyhedral, positive‐sense, and budding from the host cell plasma mem- ssRNA. Synthesis occurs in the host cell cyto- brane. Viruses are released via cell lysis. plasm; maturation involves budding through These viruses are ‘‘Biosafety Level 4’’ patho- host cell endoplasmic reticulum and Golgi gens – they must be handled in the laborato- apparatus membranes. Most replicate in ry under maximum containment conditions. arthropods. 8. Family: Paramyxoviridae 5. Family: Coronavirdae Genera Genus Paramyxovirus (parainfluenza viruses 1‐ Coronavirus (common cold viruses, 4, mumps virus, and Newcastle dis- avian infectious bronchitis virus, fe- ease virus). Appendix C: Micro-organisms, biochemistry, and nomenclature 1215
Morbillivirus (measles and measleslike 11. Family: Arenaviridae viruses, canine distemper virus). Pneumovirus (respiratory syncytial Genus virus). Arenavirus (Lassa fever virus, lympho- Enveloped, helical, negative‐sense, and cytic choriomeningitis virus, ssRNA. Synthesis occurs in the host cell cyto- Machupo virus, and Junin virus). plasm; maturation involves budding through Enveloped, helical, ambisense, and ssRNA the host cell plasma membrane. viruses are (two segments). Synthesis occurs in the host released via cell lysis. Morbilliviruses can cell cytoplasm; maturation involves budding cause persistent infections. from the host cell plasma membrane. Virions contain ribosomes. The human pathogens 9. Family: Orthomyxoviridae Lassa, Machuppo, and Junin viruses are ‘‘Biosafety Level 4’’ pathogens – they must Genera be handled in the laboratory under maxi- Influenzavirus A and B (influenza viruses mum containment conditions. A and B). Influenzavirus C (influenza C virus). 12. Family: Reoviridae Enveloped, helical, negative‐sense, and ssRNA (eight segments). Synthesis occurs in Genera the host cell nucleus; maturation takes place Orthoreovirus (reoviruses 1–3). in the host cell cytoplasm. Viruses are re- Orbivirus (Orungo virus). leased through budding from the host cell’s Rotavirus (human rotaviruses). plasma membrane. These viruses can reas- Cypovirus (cytoplasmic polyhidrosis vi- sort genes curing mixed infections. ruses). Coltivirus (Colorado tick fever virus). 10. Family Bunyaviridae Plant Reovirus 1/3 (plant reoviruses Genera subgroups 1–3). Each genus differs in morphology and phy- Bunyavirus (Bunyamwera supergroup). siochemical details. In general, virions are Phlebovirus (sandfly fever viruses). naked, polyhedral, dsRNA (10–12 segments). Nairovirus (Nairobi sheep diseaselike Synthesis and maturation take place in the viruses). host cell cytoplasm. Viruses are released via Uukuvirus (Uukuniemi‐like viruses). cell lysis. Virions contain ribosomes. Hantavirus (hemorrhagic fever viruses, Korean hemorrhagic fever, Sin Nom- bre hantavirus). 13. Family: Birnaviridae Enveloped, spherical, negative‐sense, and ssRNA (three segments; Phlebovirus ambi- Genera sense ssRNA). Synthesis occurs in the host Birnavirus (infectious pancreatic necro- cell cytoplasm; maturation occurs within the sis virus of fish and infections bursal Golgi apparatus. Viruses are released via cell disease virus of fowl). lysis. Closely related viruses can reassort Naked, polyhedral, dsRNA (two segments). genes during mixed infections. Synthesis and maturation take place in the 1216 Appendix C: Micro-organisms, biochemistry, and nomenclature
host cell cytoplasm. Viruses are released via 16. Family: Parvoviridae cell lysis. Genera Parvovirus (feline leucopenia virus, 14. Family: Retroviridae canine parvovirus). Dependovirus ‐ Genera (adeno associatedviruses). Densovirus (insect parvoviruses). MLV‐related virus (spleen necrosis Erythrovirus (human erythrovirus B19). virus, mouse, and feline leukemia vi- Naked, polyhedral, negative‐sense, and ssDNA ruses). (Parvovirus) or positive‐sense and negative‐ Mammalian type‐B (mouse mammary sense, and ssDNA (other genera). Synthesis tumor virus). and maturation occur in rapidly dividing Type D (squirrel monkey retrovirus). host cells, specifically in the host cell nucleus. ALV‐related virus (avian leukemia Viruses are released via cell lysis. virus, rous sarcoma virus). HTL‐BLV group (human T‐cell leuke- 17. Family: Papovaviridae mia virus HTLV‐1, HTLV‐II, and bo- vine leukemia virus). Genera Spumavirus (the foamy viruses) Papillomarirus (wart viruses, genital con- Lentivirus (human, feline, simian, and dylomas, and DNA tumor viruses). bovine immunodeficiency viruses). Polyomavirus (human polyoma‐like vi- Enveloped, spherical, negative‐sense, and ruses, SV‐40). ssRNA (two identical strands). Synthesis Naked, polyhedral, and dsDNA. Synthesis occurs in the host cell cytoplasm; maturation and maturation take place in the host cell involves budding through the host cell plas- nucleus. Viruses are released via cell lysis. ma membrane. These viruses contain the enzyme reverse transcriptase. The retro- 18. Family: Adenoviridae viruses (except the Spumavirus and Lentivi- rus genera) represent the RNA tumor viruses, Genera causing leukemias, carcinomas, and Mastadenovirus (human adenoviruses sarcomas. A‐F, infectious canine hepatitis virus). Aviadenovirus (avian adenoviruses). 15. Family: Hepadnaviridae Naked, polyhedral, and dsDNA. Synthesis and maturation take place in the host cell Genera nucleus. Viruses are released via cell lysis. Orthohepadnavirus (hepatitis B virus). Avihepadnavirus (duck hepatitis virus). 19. Family: Herpesviridae Enveloped, polyhedral, and partially dsDNA. Synthesis and maturation take place in the Subfamily: Alphaherpesvirinae host cell nucleus. Surface antigen production Genera occurs in the cytoplasm. Persistence is com- Simplexvirus (herpes simplex viruses 1 mon and is associated with chronic disease and 2). and neoplasia. Varicellovirus (varicella‐zoster virus). Appendix C: Micro-organisms, biochemistry, and nomenclature 1217
Subfamily: Betaherpesvirinae 21. Family: Irdoviridae Genera Cytomegalovirus (human cytomegalovi- Genera rus). Iridovirus (small iridescent insect viruses). Muromegalovirus (murine cytomegalo- Chloriridovirus (large iridescent insect virus). viruses). Subfamily: Gammaherpesvirinae Ranavirus (frog viruses). Genera Lymphocystivirus (lymphocystis viruses Lymphocryptovirus (Epstein‐Barr viruses). of fish). Rhadinovirus (saimiri‐ateles‐like virus). Enveloped (missing on some insect viruses), Enveloped, polyhedral, and dsDNA. Synthe- polyhedral, dsDNA. Synthesis occurs in both sis and maturation occur in the host cell the host cell nucleus and cytoplasm. Most nucleus, with budding through the nuclear virions remain cell‐associated. envelope. Although most herpesviruses cause persistent infections, virions can be released by rupture of the host cell plasma d. Word roots commonly membrane. encountered in microbiology 20. Family: Poxviridae a‐,annot, without absence abiotic, not living; Subfamily: Chordopoxvirinae anaerobic, in the absence of air. Genera acantho thorn or spinelike Acanthamoeba,an Orthopoxvirus (vaccinia and variola vi- amoeba with spinelike projections. ruses, cowpox virus). action having rays Actinomyces, a bacterium Parapoxvirus (orf virus, pseudocowpox forming colonies that look like sunbursts. virus). aero air. aerobic, in the presence of air. Avipoxvirus (fowlpox virus). agglutino clumping or sticking together Capripoxvirus (sheep pox virus). hemagglutinatin, clumping of blood cells. Leporipoxvirus (myxoma virus). albo white Candida albicans, a white fungus. Suipoxvirus (swinepox virus). amphi around, doubly, both Amphitrichous Yatapoxvirus (yabapox virus and tana- describes flagella found at both ends of a pox virus). bacterial cell. Molluscipoxvirus (mollescum contagio- ant‐, anti‐ against, versus Antibacterial com- sum virus). pounds kill bacteria. Subfamily: Entomopoxvirinae archaeo‐ ancient. Archaeobacteria are Genus thought to resemble ancient forms of life. Entomopoxvirus A/B/C (poxviruses of artho‐ joint arthritis, inflammation of joints. insects). asco‐ sac, bag Ascospores are held in a saclike External envelope, large, brick‐shaped (or container, the ascus. ovoid), and dsDNA. Synthesis and matura- ‐ase denotes enzyme lipase, an enzyme attack- tion take place in the portion of the host cell ing lipids. cytoplasm called viroplasm (‘‘viral fac- aureo‐ golden Staphylococcus aureus has gold‐ tories’’). Viruses are released via cell lysis. colored colonies. 1218 Appendix C: Micro-organisms, biochemistry, and nomenclature
Auto‐ self. Autotrophs, self‐feeding organ- coryne‐ club Corynebacterium diphtheriae, isms. club‐shaped bacterium bacillo‐ rod. bacillus, rod‐shaped bacterium. ‐cul little, tiny molecule, a tiny mass. basid‐ base, foundation basidium, fungal cell cut‐, ‐cut skin cutaneous, of the skin. bearing spores at its end. cyan‐ blue cyanobacteria, formerly called the bio‐ life biology, the study of living things. blue‐green algae. blast‐ bud bladstospore, spore formed by cyst, ‐cyst bladder cystitis, inflammation of budding. the urinary bladder. bovi‐ cow Mycobacterium bovis, bacterium cyt, ‐cyte cell leukocyte, white blood cell. causing tuberculosis in cattle. de‐ lack of removal decolorize, to remove brevi‐ short Lactobacillus brevis, a bacterium color. with short rod‐shaped cells. dermato‐ skin dermatitis, inflammation of butyr‐ butter Butyric acid gives rancid but- the skin. ters its unpleasant odor. di‐, diplo‐ two, double. diplocci, pairs of campylo‐ curved Campylobaccter, a curved spherical cells. bacterium. dys‐ bad, faulty, painful dysentery, a disease carcino‐ cancer a carcinogen causes cancer. of the enteric system. caryo‐, karyo‐ center, kernel Prokaryotic cells ec‐, ecto‐,exoutside, outer Ectoparasite, lack a true, discrete nucleus. found on the outside of the body. caseo‐ cheese caseous, cheeselike lesions. em‐,en‐ in, inside encapsulated, inside a caul‐ stalk, stem Caulobacter, a stalked capsule. bacterium. ‐emia of the blood pyemia, pus in the ceph‐, cephalo‐ of the head or brain enceph- blood. alitis, inflammation of the brain. endo‐ inside endospore, spore found inside a chlamydo‐ cloaked hidden Chlamydia are dif- cell. ficult bacteria to detect. entero‐ intestine enteric, bacteria found in chloro‐ green chlorophyll, a green pigment. the intestine. chromo‐ colored Metachromatic granules epi‐ atop, over epidemic, a disease spreading stain various colors within a cell. over an entire population at one time. chryso‐ golden Streptomyces chryseus, a bac- erythro‐ red lupus erythematosus, disease terium forming golden colonies. with a red rash. ‐cide to kill fungicide kills fungi. etio‐ cause etiology, study of the causes of co‐,con‐ with, together. congenital, existing disease. from birth. eu‐ true, good, normal eukaryote cell with a cocc‐ berry Streptococcus, spherical bacteria true nucleus. in chains. exo‐ outside exotoxion, toxin released outside coeno‐. shared in common coenocytic, many of a cell. nuclei not separated by septa. extra‐ outside, beyond extracellular, outside col‐,colo‐ colon coliform bacteria, found in of a cell. the colon large intestine. fil‐ thread filament, thin chain of cells. conidio‐ dust conidiam tiny dustlike spores flav‐ yellow flavivirus, cause of yellow fever. produced by fungi. ‐fy to become, make solidify, to become solid. Appendix C: Micro-organisms, biochemistry, and nomenclature 1219 galacto‐ milk galactose, monosaccharide lip‐. lipo‐ fat, lipid lipoprotein, molecule from milk sugar. having both fatty and proteinaceous parts. gamet‐ marriage gamete, a reproductive cell, ‐logy, ‐ology study of microbiology, study of such as egg or sperm. microbes. gastro‐ stomach gastroenteritis, inflamma- lopho‐ tuft lophotrihous, having a tuft or tion of the stomach and intestines. group of flagella. gel‐ to stiffen, congeal gelatinous, jellylike. luc‐, luci‐ light luciferase, enzyme that cata- gen‐, ‐gen to give rise to pathogen, microbe lyzes a light‐producing reaction. that causes disease. luteo‐ yellow Micrococcus luteus, bacterium ‐genesis origin, development pathogenesis, producing yellow colonies. development of disease. lys‐, lysis slitting cytolysis, rupture of a cell . germ, germin‐ bud germination, process of macro‐ large macroconidia, large spores. growing from a spore. meningo‐ membrane meninges, membranes ‐globulin protein immunoglobulins, pro- of the brain. teins of the immune system. meso‐ middle Mesophile, organism growing haem‐, hem‐ blood hemmagglutinatin, best a medium temperatures. clumping of blood cells. micro‐ small, tiny microbiology, study of tiny halo‐ salt halophilic, organisms that thrive in forms of life. salty environments. mono‐ one, single monosaccharide, a single hepat‐ liver hepatitis, inflammation of the sugar unit. liver. morph‐ shape, form pleionorphic, having hetero‐ different, other heterotroph, organ- many different shapes. ism deriving nutrition from other sources. multi‐ many mutticellular, having many histo‐ tissue histology, the study of tissues. cells. homo‐ same homologous, having the same mur‐ wall muramic acid, a component of cell structure. walls. hydro‐ water hydrologic cycle, water cycle. muri‐, mus‐ mouse murine, in or of mice. hyper‐ over, above hyperbaric oxygen, higher mut‐, mute to change mutagen, agent that than atmospheric pressure oxygen. causes genetic change. hypo‐ under, below hypodermic, going be- myc‐, myces fungus Actinomyces, a bacterium neath the skin. that resembles a fungus. im‐,in‐ not insoluble, cannot be dissolved. myxo‐ slime, mucus myxomycetes, slime inter‐ between intercellular, between cells. molds. intra‐ inside intracellular, inside a cell. necro‐ dead, corpse necrotizing toxin, causes io‐ violet iodine, element that is purple in death of tissue. gaseous state. nema‐, ‐nema thread Treponema, nematode, iso‐ same, equal isotonic, having the same threadlike organisms. osmotic pressure. nigr‐ black Rhizopus nigricans, a black ‐it is inflammation of meningitis, inflamma- mold. tion of the meninges. oculo‐ eye binocular, microscope with two kin‐ moving kinetic energy, energy of move- eyepieces. ment. ‐oid like, resembling Toxoid, harmless mole- leuko‐ white leukocyte, white blood cell. cule that resembles a toxin. 1220 Appendix C: Micro-organisms, biochemistry, and nomenclature
‐oma tumor carcinoma, tumor of opithelial rhizo‐ root mycorrhiza, symbiotic growth of cells. fungi and roots. onco‐ mass, tumor oncogenes, genes that rhodo‐ red Rhodospirillum, a large red spiral cause tumors. bacterium. ‐osis condition of brucellosis, condition of ‐rrhea flow diarrhea, abnormal flow of liquid being infected with Brucella. feces. patho‐ abnormal pathology, study of abnor- rubric‐ red Rhodospirillum rubrum, a large mal diseased states. red spiral bacterium. peri‐ around peritrichous flagella located all saccharo‐ sugar polysaccharide, many sugar around an organism. units linked together. phago‐ eating phagocytosis, cell eating by sapro‐ rotten, decaying saprophyte, organism engulfing. living on dead matter. philo‐, ‐phil, ‐phile loving, preferring Capno- sarco‐ flesh sarcoma, tumor made up of mus- phile, organism needing higher than normal cle or connective tissue. levels of carbon dioxide. schizo‐ to split schizogony, a type of fission in ‐phob, ‐phobe hating, fearing hydrophobic, malarial parasites. water‐repelling. ‐scope, ‐scopy to see, examine microscopy, ‐phore bearing, carrying electrophoresis, use of the microscope to examine small technique in which ions are carried by an things. electric current. sept‐, septo‐ partition, wall septum, wall be- ‐phyte plant Dermatophyte, fungus that tween cells. attacks skin. septi‐ rotting septic, exhibiting decomposi- pil‐ hair pilus, hairlike tube on bacterial sur- tion due to bacteria. face. soma‐, ‐some body chromosome, colored ‐plast formed part chloroplast, green body body (when stained). inside plant cell. spiro‐ coil spirochete, spiral‐shaped bacteri- pod‐, ‐pod foot podocyte, foot cell of kidney. um. poly‐ many polyribosomes, many ribosomes sporo‐ spore sporocidal, spore killing. on the same piece of messenger RNA. staphylo‐ in bunches, like grapes staphylo- post‐ afterward, behind post‐streptoccal glo- cocci, spherical bacteria growing in clusters. merulonephritis, kidney damage following a ‐stasism stat‐ stopping, not changing bacteri- streptococcal infection. ostatic, able to stop the growth of bacteria. pre‐, pro‐ before, toward prepubertal, before strepto‐ twisted Streptobacillus, twisted puberty. chains of bacilli. pseudo‐ false pseudopod, projection resem- sub‐ under, below Subclinical, signs and bling a foot, false foot. symptoms not clinically apparent. psychro‐ cold psychrophilic, preferring ex- super‐ above, more than superficial mycosis, treme cold. fungal infection of the surface tissues. pyo‐ pus pyogenic, producing pus. sym‐, syn‐together symbiosis, living together. pyro‐ fire, heat pyrogen, fever‐producing tact‐, ‐taxis touch chemotaxis, orientation or compound. movement in response to chemicals. rhin‐ nose rhinitis, inflammation of nasal tax‐, taxon‐ arrangement taxonomy, the clas- membranes. sification of organisms. Appendix C: Micro-organisms, biochemistry, and nomenclature 1221 thermo‐ heat thermophile, organism prefer- vacu‐ empty vacuole, empty‐appearing struc- ring or needing high temperatures. ture in cytoplasm. thio‐ sulfur Thiobacillus, organism that oxi- vesic‐ blister, bladder vesicle, small blisterlike dizes hydrogen sulfide to sulfates. lesions. tox‐ poison toxin, a harmful compound. vitr‐ glass in vitro, grown in laboratory glass- trans‐ through, across transduction, move- ware. ment of genetic information from one cell xantho‐ yellow Xanthomonas oryzae, bacteri- to another. um producing yellow colonies. trich‐ hair Monotrichous, having a single, zeno‐ strange, foreign xenograft, graft from a hairlike flagellum. different species. ‐troph feeding, nutrition phototroph, organ- zoo‐ animal protozoan, first animal. ism that makes its on food, using energy zygo‐ yoke, joining zygote, fertilized egg. from light. ‐zyme ferment enzymes, biological catalysts, uni‐ one, singular unicellular, composed of some of which are involved in fermentation. one cell. Garrity GM, Winters M, and Searles DB undul‐ waving undulant fever disease in (2001) Taxonomic outline of the procar- which fever rises and falls. yotic genera, bergey’s manual of systemat- vac‐, vaccine‐ cow vaccine, disease‐prevent- ic bacteriology, 2nd edn. Springer‐Verlag, ing product originally produced by inoculat- New York. ing it onto skin of calves. References
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