Ch. 5

1
Ch. 5

• Reversible interactions
• Simple binding (myoglobin)
• Constant affinity (Kd)
• Cooperative binding
• Allostery

2
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

3
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 (dont change DG or
  the equilibrium constant)
• Create a new reaction pathway with better DH or
  (and) better DS

4
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

5
Chapter 6

• Quantification of catalysis
• Km
• Vmax/kcat
• kcat/Vmax
• Ki
• Michaelis-Menten kinetics
• Lineweaver-Burk plots

6
Chapter 6

• Enzyme regulation
• Why?
• How?

7
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

8
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/polymerizatio
n Disaccharide/polysaccharides
9
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

10
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)

11

• 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

12
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

13
Ch.10 114/23, 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

14
Ch. 1011

• 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)

15
Ch. 1011

• 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

16
Ch.1011

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

17
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

18
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

19
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