Biochem Exam 1 part 2

  1. Primary structure
    description of covalent bonds between amino acids
  2. secondary structure
    • local spatial arrangement of main chain atoms
    • rotation around phi and psi bonds
  3. tertiary structure
    polypeptide chain, beta and alpha sheets together
  4. importance of amino acid sequence
    • determines 3-D structure
    • reveals structural and functional relationships between proteins
    • evolutionary relationship
    • provides a partial molecular definition of some genetic disease
  5. Sanger sequencing method for amino acids
    • 1. Determine N terminus
    • 2. Cleave disulfide bonds
    • 3.Cleavage
    • 4. Sequence fragments
    • 5. Line up fragments
  6. How to determine N-Terminus
    • add FDNP-bond to first amino acid
    • strong acid- to remove first amino acid
  7. cleavage methods
    • trypsin-cuts Coo- side of + amino acid residues: lysine and arginine
    • Chymotrpsin: tyrosine, tryptophan phenylalanine
    • CNBr: cuts the carboxyl group of methionine
  8. sequence amino acids
    • Edman Degredation
    • 1.Phenylisothiocyanate + peptide
    • 2.add base to connect
    • 3. add acid to remove first amino acid in the fragment
  9. phi bond
    amino and alpha carbon
  10. psi bond
    alpha carbon and carboxyl carbon
  11. stability factors involved in alpha helix
    • maximum h- bonding
    • rigidity of peptide bonds
    • side chain interactions
    • prolines(creates kink in structure)
  12. stability factors involved in beta sheets
    • inter or intrachain H-bonding
    • small amino acid side chains (in fibrous proteins)
    • parallel and anti parallel
  13. Beta bend
    • 4 amino acids 
    • to types of bends
    • bond between hydrogen(N) and oxygen
  14. alpha keratin
    • hooves, horns, hard and or flexible
    • fibrous structure
    • 2 chain coiled helix-protofilament-protofibril
    • linked by disulfide binds
  15. collagen
    • most abundant protein
    • Gly-Pro-HyPro(hydroxyproline)
    • left hand helix
    • 3 helix, tropocollagen super helix right hand
    • no space in the middle
  16. globular protein structures
    complex structures, marginally stable
  17. stabilization of globular proteins
    • hydrophobic forces (important)
    • disulfide bonds
    • electrostatic forces
    • hydrogen bonds
  18. structural constraints of tertiary structures
    • L-amino acids
    • cis and trans configurations of peptide bonds
    • steric constraints on phi and psi bonds
    • proline is found in 6% if peptide bonds next to proline, at bends
  19. lessons from myoglobin
    • predicted that secondary structure exist
    • very compact
    • hydrophobic residues buried
    • proline often at bends
  20. structural tendencies of beta sheets
    • twist in a right handed fashion
    • often connect 2 antiparallel beta chains
  21. super secondary structures
    • folds/motifs
    • Domains
    • Tertiary structures
  22. folds/motifs
    • simpler structural patterns found repeatedly in globular proteins
    • folding pattern with two or more secondary structures
  23. domains
    • independently stable cluster of amino acids
    • sometimes has a discrete function
    • proteins can have multiple domains
  24. different types of motifs
    • all alpha(serum albumin)
    • alpha/beta (alcohol dehydrogenase)
    • all beta (UDP, collagenase)
    • alpha+ beta (GFP)
  25. protein folding is...
    not a random process
  26. probable steps of protein folding
    • stepwise path (short stretches of secondary structure)
    • formation of loose "molten globule" intermediate (enzymers catalyze some steps)
  27. what is heme
    a porphoryn ring (Pyrole ring)  with a Fe +2
  28. equilibrium association constant
  29. binding sites occupied/total binding sites=
  30. the lower the Kd
    the higher the affinity of the ligand for the protein
  31. where is Kd
    where [O2] binding sites are half occupies
  32. binding equilibirum equation
  33. why does o2 bind to heme in globin strucutre more than CO
    the distal histidine offers h-bonding which increases its stability
  34. myoglobin vs hemoglobin
    • hemoglobin multiple subunits (2 with heme) located in blood for O2 transport
    • myoglobin 1 unit with heme and located in muscle for storage
  35. what conformational change does O2 induce in hemoglobin
    • T state tense low afinity for O2, predominate in the absence of O2
    • R state relaxed high O2 affinity.
    • O2 binding triggers T to R transition and other structural changes
  36. regulation of hemoglobin
    • hemoglobin transports H+ and CO2(binds to amino teminus) stabilize T state
    • binding of 2,3 Biphosphoglycerate stabilize T state
  37. enzymes affect...not
  38. enzymes...
    lower the activation barrier for rxns
  39. enzyme principles
    • accelerate rxn rates not equilibrium
    • catalyzes rxns in both directions
  40. two theories of active site function
    • lock and key: active site complementary to substrate
    • modern: active site complementary to transition state
  41. foces that hold enzyme and substrate together
    • same as the ones that hold proteins together
    • binding energy is substantial (transition state)
  42. binding energy
    the currency used to reduce activation energy
  43. how binding energy is used
    • entropy reduction-hold subtrate in proper orientation to react
    • desolvation-replace H-bonds to H2O
    • strain-facilitate geometric or electrostatic distortion
    • induced fit-bring reactive groups on enzyme into proper orientation for catalysis
Card Set
Biochem Exam 1 part 2
chp 5- idk yet