Background Assumed for Upper Division Courses

Background Assumed for Upper Division Courses:

(You are expected to know, understand and be able to discuss and apply this material to new circumstances)

1. Hierarchical organization of living systems

SUBATOMIC PARTICLES => ATOMS => SMALL MOLECULES => MACROMOLECULES => MACROMOLECULAR ASSEMBLIES=>CELL ORGANELLES => CELLS => TISSUES => ORGANS => ORGAN SYSTEMS => ORGANISMS

2. Chemical Bonds A. Form so atoms become STABLE = have full outer ELECTRON SHELL B. Strong bonds = COVALENT bonds & IONIC bonds C. Weak bonds = HYDROGEN bonds, HYDROPHOBIC bonds & Van der Waals forces I. POLAR & NONPOLAR covalent bonds II. HYDROPHOBIC and HYDROPHILIC molecules D. STRONG BONDS exist between atoms & small molecules I. CONDENSATION and HYDROLYSIS II. require ENZYMES to form & break inside cells E. WEAK BONDS exist between macromolecules, macromolecular assemblies and within macromolecules I. chemical environment within cell causes these to form and break II. chemical environment acts through EQUILIBRIUM CONSTANT affect concentrations of REACTANTS and PRODUCTS

3. Functional Groups in Biological Molecules A. Acetyl, Amino, Carbonyl, Carboxyl, Hydroxyl, Methyl, Phosphate, Sulfhydryl B. recognize FORMULA, POLARITY C. SULFHYDRYL common covalent crosslinker within/between polypeptide chains

4. Water A. Importance to living systems I. it's everywhere II. HYDROGEN BOND formation => solubility, cohesion, specific heat, surface tension, III. dissociation => two reactive ions = H+ & OH- B. PH = - LOG[H+] I. [H+][OH-] = 10-14M II. appreciate that pH = very important part of chemical environment w/i cell (cf. 2.E.II, above) III. approximate pH ranges for physiological, acid & basic conditions

Small Molecules & Macromolecules of the Cell

1. Small molecules = MONOMERS linked together to form macromolecules = POLYMERS

Background Assumed for Upper Division Course 4/27/2018 2. For each of the four types of macromolecules A. NAME B. nature of MONOMER C. RECOGNIZE STRUCTURE of monomer & of polymer D. general FUNCTION E. general LOCATION w/i cell F. GENERAL NATURE of macromolecule -hydrophobic vs. hydrophilic vs. charged vs. neutral under physiological conditions

3. For CARBOHYDRATES A. general chemical & structural formulae for MONOSACCHARIDES I. HYDROPHILIC & therefore water soluble B. polysaccharides = linear or branched C. FUNCTIONS of polysaccharide I. animal: energy storage = glycogen & structure = chitin II. plant: energy storage = starch & structure = cellulose D. can be COVALENTLY LINKED TO protein or lipid to form GLYCOPROTEINS or GLYCOLIPIDS

4. LIPIDS A. built of FATTY ACID CHAIN I. alkyl (CH2) chains II. very hydrophobic B. glycerol w/ three fatty acids = TRIGLYCERIDE I. long term energy storage C. glycerol w/two fatty acids and a phosphate link to an "R" = PHOSPHOLIPID I. structural component of cell membranes II. AMPHIPATHIC a. molecule w/areas of 2 different properties b. HYDROPHOBIC fatty acid chains c. HYDROPHILIC HEAD (glycerol, phosphate & "R") D. STEROIDS I. Four interconnected carbon rings II. Cholesterol: plasma membrane component III. Hormones

5. PROTEINS A MONOMER = amino acid I. general structure of an AMINO ACID II. 20 common ones III. backbone vs. "R" groups IV. classes of "R" groups: nonpolar, neutral polar, acidic polar, basic polar B. POLYMER = PROTEIN I. amino acids linked by PEPTIDE BONDS

Background Assumed for Upper Division Course 4/27/2018 C. LEVELS OF ORGANIZATION I. PRIMARY = amino acid sequence II. SECONDARY = a-helix, b-sheet & random coil III. TERTIARY = spatial arrangement of regions of secondary structure IV. QUATERNARY = spatial arrangement of polypeptides in multimeric proteins D DOMAINS of proteins I. each domain = piece of polypeptide w/unique function/structure II. each domain from different portion of genome a. evolution of gene/protein by movement of these regions of DNA b. production of multidomain protein by transcript processing

E. IMPORTANT FEATURE is 3D shape & flexibility which => function

F. FUNCTIONS w/i cell = "tools" of the cell I. receptors, transport channels, motors, enzymes, structural elements, carriers

6. NUCLEIC ACIDS A. MONOMER = NUCLEOTIDE I. phosphate, sugar & base II. four kinds of bases in RNA & in DNA III. role of EACH CARBON IN THE SUGAR IV. DEOXYRIBOSE vs. RIBOSE

B. POLYMER = NUCLEIC ACID I. monomers linked by phosphodiester bond between sugar & phosphate II. information "written" in base sequence of the monomers III. DNA a. 2 molecules hydrogen bonded in a double helix b. BASE SEQUENCE of carries genetic information IV. RNA a. several types b. each has specific role in converting genetic information of DNA into amino acid sequence of protein

Energy, Enzymes and Biological Reactions

1. Spontaneous Reactions & The Laws of Thermodynamics A. FIRST LAW & SECOND LAWS OF THERMODYNAMICS I. energy cannot be created or destroyed, but converted from one form to another II. all systems spontaneously move to their lowest free energy condition (most disordered)

B. Reversible reactions & EQUILIBRIUM CONSTANTS I. Keq = [P]/[S] = constant for a given reaction

C. ENDERGONIC and EXERGONIC reactions

Background Assumed for Upper Division Course 4/27/2018 I. ENERGY DIAGRAMS II. REACTION COUPLING: energy released from exergonic drive endergonic

2. ATP = energy currency of the cell

3. Role of ENZYMES in Biological Reactions A. enzymes act on ACTIVATION ENERGY of chemical reactions B. Characteristics: I. BRIEFLY COMBINE w/S II. UNCHANGED after catalyzing reaction of S => P III. each catalyzes a SPECIFIC reaction IV. SATURATED by high [S] e. many contain COFACTORS C. Catalytic Mechanisms I. ACTIVE SITE = location in enzyme at which reaction occurs II. transition state bound best in active site III. SAME ENZYME CATALYZES BOTH DIRECTIONS OF A REVERSIBLE REACTION D. Factors Affecting Enzyme Activity I. SUBSTRATE CONCENTRATION II. INHIBITORS: competitive & noncompetitive III. TEMPERATURE & pH E. ALLOSTERY: allosteric enzymes have >1 binding site F. COVALENT MODIFICATION EXTREMELY IMPORTANT CONCEPT I. minor chemical modification has major effects on protein activity II. common modifiers: Ca+2, PO4, CH3, COCH3 III. KINASES & PHOSPHATASES

4. RNA-BASED CATALYSIS A. RNA splicing & processing B. Peptide bond formation in the ribosome C. Impact on concepts of evolution of life

Nucleic Acid and Protein Synthesis

1. Form of the genetic information = structure of DNA double helix A. Single DNA molecule = nucleotide linked by covalent bonds between sugar of one & phosphate of next B. BACKBONE of DNA I. sugar-phosphate w/base of each nucleotide perpendicular to backbone II. POLARIZED; one end has phosphate & other end has sugar C. Double helix I. two DNA molecules II. ANTIPARALLEL = 3' => 5' on one molecule next to 5' => 3' on other III. hydrogen bonding between COMPLEMENTARY BASE PAIRS D. Knowing sequence of one molecule = TEMPLATE, provides sequence of the other

2. Reproduction of the genetic information = replication of a double helix

Background Assumed for Upper Division Course 4/27/2018 A. SEMICONSERVATIVE B. DNA POLYMERASE C. Role of complementary base pairing D. DISCONTINUOUS on one strand & continuous on the other because 3'=>5' on each molecule

3. Use of the genetic information = protein synthesis A. TRANSCRIPTION I. part of one DNA molecule = template for mRNA synthesis II. 3'=>5' III. complementary base pairing B. TRANSCRIPT PROCESSING I. conversion of TRANSCRIPT into mRNA a. removal of INTRONS b. addition of cap & poly A tail c. transport into cytoplasm C. TRANSLATION I. sequence of events a. mRNA binds to SMALL RIBOSOMAL SUBUNIT b. LARGE RIBOSOMAL SUBUNIT joins complex c. AMINOACYL TRNA SYNTHETASE "charges" each tRNA with amino acid d. charged tRNAs join RIBOSOME e. peptide bond forms as amino acid released from tRNA f. free tRNA leaves ribosome g. TERMINATION CODON binds termination factor, not a charged tRNA h. complex dissociates, releasing polypeptide II. genetic code a. CODON = 3 nucleotide sequence of mRNA b. each codon brings in tRNA bearing only one specific amino acid c. ANTICODON = 3 nucleotide sequence of tRNA that base pairs with the codon

Specific Features of Cell Structure and Function

1. Biological Membranes A. FLUID MOSAIC MODEL 2D phospholipid bilayer with embedded (INTEGRAL) and associated (PERIPHERAL) proteins B. INTEGRAL VS. PERIPHERAL PROTEINS I. operationally defined by extraction with hydrophobic or hydrophilic solvents II. determined by extent & nature of associations with phospholipids of bilayer C. Properties of membranes I. asymmetry: phospholipids, proteins & carbohydrates II. types of mobility: lateral, rotational & flip-flop

Background Assumed for Upper Division Course 4/27/2018