Ch. 5 Reversible interactions Simple binding (myoglobin) –Constant affinity (Kd) Cooperative binding –Allostery

Ch. 5 Cooperativity –Multiple binding sites –Two states: high affinity (R for Hb) & low (T) –Different factors influence the R↔T equil Oxygen: allosteric activator (positive) BPG, H +, etc.: allosteric inhibitors

Chapter 6 3/16, 19, 21, 26, 27, 28 Catalysis in general –Activation energy (E A or  G ‡ ) is a kinetic barrier to reaction –Enzymes lower this barrier (don’t change DG or the equilibrium constant) Create a new reaction pathway with better  H or (and) better  S

Chapter 6 General types of catalysis (how do enzymes change the reaction pathway?) –General acid/base Donate/accept protons from a substrate (substrates) –Many times water (activation of water) –Covalent catalysis –Metal ion catalysis Stabilize (slightly) negatively charged intermediates (ie. lower H of transition state) Oxidation/reduction

Chapter 6 Quantification of catalysis –K m –V max /k cat –k cat /V max –K i Michaelis-Menten kinetics Lineweaver-Burk plots

Chapter 6 Enzyme regulation –Why? –How?

Ch.7 4/13, 16 Carbohydrates (sugars) –Polyhydroxy + ketone OR aldehyde –Named –ose –Typically a ring structure -OH attack on carbonyl carbon creates a hemiacetal or hemiketal Makes an anomeric carbon: new stereocenter –Capable of mutarotation

Ch.7 Cyclic sugars: chair form, not flat Hemiacetal/ketal can be attacked by another hydroxyl group: full ace-/ke-tal Often another sugar: glycosidic bond/polymerization Disaccharide/polysaccharides

Ch.7 Sugars as energy sources –Highly polymerized, starch/glycogen Structural sugars –Cellulose, chitin Sugar/peptide conjugates –Peptido/proteoglycans Mainly sugar: biological activity modified by protein attachment –Glycoproteins Mainly proteins: bio activity modified by sugars

Ch.8 4/17, 18 Nucleotides/nucleic acids –Different functions ATP, etc Signal transduction (cAMP, etc) Coenzymes (NADH, etc) Information transfer, storage Components of proteins (RNA-containing proteins)

Structure of nucleotides Structure of nuc acids –Base pairing: weak interactions Hbonding/stacking (vdW) –Antiparallel –“Melting point”: determined by? –RNA: ss, but still base pairs Secondary structure

Ch.8 Consequences of covalent modification of DNA (RNA?): mutation –Base deamination –Depurination (removal of the base) –Dimerization of pyrimidines –Oxidative damage Other functions of nucleotides

Ch.10 & 11 4/23, 24, 25, 30 Fatty acids –Melting points? –Modification of the carboxylic acid Lipid structure, esp glycophospholipids Fluid mosaic model Roles of lipids (why different types/dynamics?) Membrane fluidity Activity of integral membrane proteins Attraction of peripheral memb proteins Precursors to other molecules: vitamins, signaling molecules, hormones

Ch. 10&11 Cholesterol –Membrane component, precursor to steroids Fat-soluble vitamins –D (derived from cholesterol: regulates Ca2+ uptake, etc) –A (retinol; visual pigment, regulates gene expression (skin plasticity)) –E (antioxidant, protects membrane lipids from free radical damage) –K (coenzyme, processing of blood clotting proteins)

Ch. 10&11 Membranes –Lipid bilayer: fluid mosaic –Lateral diffusion is easy (in general) –Transverse diffusion (flip-flop) is slow (sans catalysis) –Integral/peripheral membrane proteins –Membrane asymmetry/modification of fluidity Inner/outer leaflets different lipids Lipid rafts: keep multiprotein complexes together Intracellular ‘anchoring’ of memb proteins

Ch.10&11 Concept of hydropathy plots to predict integral membrane proteins Membrane fusion –Regulated exocytosis Problems? Solute movement through membranes –Diffusion Simple vs. facilitated –Active transport

Ch.13 Bioenergetics –  G stuff –ATP as a good energy storage molecule Other energy storage molecules Creation of ATP –Slow (ie. respiration) –Fast (eg. creatine kinase) Use of ATP (not just ‘parallel’ hydrolysis) –Redox Terminology (oxidation/reduction/oxidizing agt/etc) Pos  E ~ neg  G

Aerobic respiration of glucose Glycolysis: –Start with glucose (6 carbon) –Generate some ATP, some NADH, pyruvate (2 x 3 carbon) –Regeneration of NAD+ in absence of O 2 (fermentation) TCA cycle –Start with pyruvate –Generate acetate (acetyl CoA) –Generate CO 2 and reduced NADH and FADH 2 Electron transport –Start with NADH/FADH 2 –Generate electrochemical H + gradient Oxidative phosphorylation –Start with H+ gradient and O 2 (and ADP + P i ) –Generate ATP and H 2 O