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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 (EA or DG‡ ) 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 DH or
(and) better DS
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
– Km
– Vmax/kcat
– kcat/Vmax
– Ki
• 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
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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?)
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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
– DG 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 DE ~ neg DG
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 O2 (fermentation)
• TCA cycle
– Start with pyruvate
– Generate acetate (acetyl CoA)
– Generate CO2 and reduced NADH and FADH2
• Electron transport
– Start with NADH/FADH2
– Generate electrochemical H+ gradient
• Oxidative phosphorylation
– Start with H+ gradient and O2 (and ADP + Pi)
– Generate ATP and H2O