Essentials of Medical Chemistry and Biochemistry

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Essentials of Medical Chemistry and Biochemistry MASARYK UNIVERSITY Faculty of Medicine ESSENTIALS OF MEDICAL CHEMISTRY AND BIOCHEMISTRY Jiří Dostál, Editor Brno 2014 Editor: Doc. RNDr. Jiří Dostál, CSc. Authors: Doc. RNDr. Jiří Dostál, CSc. RNDr. Hana Paulová, CSc. Prof. RNDr. Eva Táborská, CSc. Doc. RNDr. Josef Tomandl, Ph.D. Reviewers: Prof. RNDr. Zdeněk Glatz, CSc. (Department of Biochemistry, Faculty of Science, Masaryk University, Brno) Doc. RNDr. Jitka Vostálová, Ph.D. (Department of Medical Chemistry and Biochemistry, Faculty of Medicine, Palacký University, Olomouc) Content 1 Basic Chemical Definitions ..…………………………………………………………...… 5 2 Chemical Bonds …………………………………………………………………………... 8 3 Energetics of Chemical Reactions ……………………………………………………….. 12 4 Chemical Kinetics ………………………………………………………………………… 17 5 Chemical Equilibrium …………………………………………………………………….. 23 6 Liquid Dispersions ………………………………………………………………………... 26 7 Solubility of Substances ………………………………………………………………….. 27 8 Quantitative Composition of Solutions …………………………………………………… 28 9 Colloidal Solutions …………………………………………….…………………………. 30 10 Osmotic Pressure …………………………………………………………………………. 34 11 Coarse Dispersions ……………………………………………………………………….. 37 12 Adsorption and Adsorbents ………………………………………………………………. 38 13 Surfactants ………………………………………………………………………………... 39 14 Electrolytes ……………………………………………………………………………….. 42 15 Acid-Base Reactions ……………………………………………………………………… 44 16 Buffers ……………………………………………………………………………………. 51 17 Precipitation Reactions. Solubility Product……………………………………………….. 57 18 Complex-Forming Reactions ……………………………………………………………... 60 19 Redox Reactions ………………………………………………………………………….. 62 20 Latin Names ………………………………………………………………………………. 68 21 Essential Macroelements …………………………………………………………………. 70 22 Essential Microelements ………………………………………………………………….. 87 23 Introduction to Organic Compounds ……………………………………………………... 93 24 Alcohols and Phenols …………………………………………………………………….. 96 25 Esters of Inorganic Acids …………………………………………………………………. 101 26 Organic Sulfur Compounds ………………………………………………………………. 104 27 Aldehydes and Ketones …………………………………………………………………... 107 28 Carboxylic Acids and Their Derivatives …………………………………………………. 111 29 Derivatives of Carbonic Acid …………………………………………………………….. 118 30 Hydroxy Acids and Oxo Acids …………………………………………………………… 120 31 Amines ……………………………………………………………………………………. 124 32 Biochemically Important Heterocycles …………………………………………………... 128 33 Toxicologically Important Substances …………………………………………………… 134 34 Monosaccharides …………………………………………………………………………. 140 35 Disaccharides ……………………………………….…………………………………….. 148 36 Polysaccharides …………………………………………………………………………… 150 37 Nucleosides and Nucleotides ……………………………………………………………... 155 38 Nucleic Acids …………………………………………………………………………….. 161 39 Lipids ……………………………………………….…………………………………….. 165 40 Terpenes ………………………………………………….……………………………….. 177 41 Steroids …………………………………………………………………………………… 179 42 Amino Acids …………………………………………………………………………….... 183 43 Peptides …………………………………………………………………………………… 190 44 Proteins …………………………………………………………………………………… 193 45 Glycoproteins ……………………………………………………………………………... 200 46 Vitamins …………………………………………………………………………………... 203 Index ……………………………………………………………………………………… 209 The text has been created and designed for one-semester English program of General medicine and Dentistry studies in the Faculty of Medicine, Masaryk University, Brno. The selection of topics emphasizes the biochemical processes and the metabolic conversions of compounds occurring in the human body. The text describes the most important biomolecules in the human tissues (saccharides, lipids, amino acids, proteins, nucleic acids), however, it also comprises essential facts from general chemistry (energy, equilibrium, kinetics, acids and bases, redox reactions, solutions, etc.), summarizes biologically important elements (macroelements, microelements), and treats main groups of organic compounds (alcohols, aldehydes, amines, carboxylic acids, heterocycles, etc.). Some special topics are also included like colloidal solutions, dispersions, osmotic pressure, Latin nomenclature, steroids, terpenes, glycoproteins, vitamins, selected toxic substances. Some structural formulas, indicated by a side dotted line, are presented just to illustrate the issue; they are not demanded in testing. The authors believe that Essentials of Medical Chemistry and Biochemistry will become a very useful and friendly tool for students to acquire primary knowledge for the following study of Biochemistry I and Biochemistry II. Brno, May 2014 1 Basic Chemical Definitions Elementary Particles of Matter, Substances, Elements, Compounds A substance is a specific kind of matter that exhibits stable physical characteristics at definite condi- tions. All substances contain atoms. An atom is the smallest electrically neutral particle that still keeps the chemical characteristics (quali- ty) of the corresponding element. It consists of a positively charged nucleus and negatively charged electron shell. The arrangement of electrons in the shell influences the chemical characteristics of an atom. A molecule is the smallest part of a pure substance that still keeps the chemical characteristics of this substance. It is electroneutral, characterised by a specific composition (nature and number of the pre- sent atoms) and structure (their mutual arrangement in space, kind of bonds). Di- or polyatomic mole- cules of one type of chemical element have isoatomic composition (they contain one kind of atom e.g. H2, O2, N2, Cl2). Molecules of compounds have heteroatomic composition, e.g. HCl, H2O, etc. In some substances (e.g. solid substances with crystal structure), the individual molecules are not identifiable. In this case, we formally appoint the smallest part of the substance (the smallest numerical ratio of atoms), the composition of which still describes the composition of the whole substance, and we call it formula unit (e.g. a pair of ions Na+ and F− in sodium fluoride, carbon atom in diamond, Si atom and two O atoms in silicon dioxide, etc.). From this formula unit (the repeating part) the name of the sub- stance is derived. According to the composition, chemically pure substances and mixtures (homogeneous, colloid, and heterogeneous) are distinguished. In nature, substances usually occur in the form of mixtures. A chemically pure substance (chemical individual) consists of the same particles with stable charac- teristic properties (boiling point and melting point, density, refractive index, specific rotation). We distinguish two groups of chemically pure substances – elements and compounds. An element is a chemically pure substance consisting of atoms with the same proton/atomic number. If the element is formed by atoms with the same mass number, it is called a nuclide. Atoms of the given element can be non-combined (noble gases), form molecules (gaseous dioxygen O2), or they are combined altogether to form more complex structures (e.g. covalent bonds – diamond, metal bonds in metals, covalent bonds and van der Waals forces – graphite). A compound is a chemically pure substance consisting of two or more different atoms. The atoms can be arranged in isolated molecules (gaseous carbon dioxide) or they can form more complex structures (crystalline structures – sodium chloride). A mixture (dispersion system) consists of several different, chemically pure substances. The proper- ties of mixtures are not stable; they depend on the composition of the mixture. A mixture can be ho- mogeneous (formed by only one phase – air, solutions), colloid (e.g. egg white in water) or heteroge- neous (more phases physically separated from each other – water with sand). 5 Expressing the Amount of Substance and Their Structural Elements The amount of any substance (chemical element, compound, mixture) can be expressed in several ways: mass (m), volume (V) or the number of basic structural particles, atoms, ions, molecules (N). Atomic and Molar Mass Mass (m) is an additive quantity that does not depend on temperature and pressure. The mass of the structural particles can be expressed in common mass units (kg, g). The absolute mass of an atom (the value of its resting mass) is very small, about 10−27–10−25 kg. Thus, the absolute quantities are impractical for everyday use. Mass can be more conveniently expressed by the comparative standard (object with a mass similar to the mass of these particles). This standard was stated during the last correction in 1961 to be the atom of a carbon nuclide 12C. Exactly 1/12 of the rest mass of this atom 12 m0( C) was determined as an accessory unit. It is the unified atomic mass unit (symbol u); in bio- chemistry and molecular biology, it is more often called dalton (symbol Da). The value of its mass is called the atomic mass constant (symbol mu). 12 −27 mu = 1/12 m0( C) = 1.660 54 · 10 kg = 1 u = 1 Da The absolute atomic masses are not as important from the chemical point of view as the ratio (the rela- tive amount), under which the atoms react with each other. Therefore, we most frequently use the rela- tive (proportional) expression of mass (related to 1/12 of the mass of the carbon nuclide 12C). The relative atomic mass (Ar) is a dimensionless number representing how many times the mass of a given atom (X) is higher than the atomic mass constant mu. It is given by the ratio between the (abso- lute) mass of one atom m(X) in kg to the atomic mass constant mu in kg. For the given element X it is accepted that: m(X) Ar (X) mu The relative molecular mass (Mr) is the sum of the relative atomic masses of all atoms present in the mol- ecule. It is
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