Protein Structure and Function 2 (L4) Flashcards

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1
Q

native state

A

protein folds into the most stable position (lowest free energy)

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2
Q

why are proteins not always in their native states inside the cell?

A
  • multiple stable conformations
  • pH
  • need chaperones for folding
  • not enough space inside cell
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3
Q

purpose of chaperones/chaperonins

A

assist in protein folding - creates isolated compartment for protein to fold properly

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4
Q

chaperones

A

HSP

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5
Q

chaperonins

A

GroEL, GroES -> cylindrical macromolecular complex

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6
Q

Alzheimer’s disease

A

abnormal protein folding -> amyloid plaques that are insoluble protein aggregates

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7
Q

amyloidogenic vs. non-amyloidogenic protein products

A

amyloidogenic: A-beta-42 pieces aggregate w/ each other

non-amyloidogenic: A-beta-40 pieces that are relatively soluble (not a problem)

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8
Q

A-beta normal vs. pathologic

A

normal: usually have alpha helices
path: more beta sheets that are more hydrophobic - fall out of solution and aggregate -> amyloid plaque

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9
Q

two classical pathological hallmarks of Alzheimer’s

A

neurofibrillary tangles (protein aggregates inside neurons) and amyloid plaques

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10
Q

concept of specificity

A

does protein bind only one thing or does it bind many things

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11
Q

concept of affinity

A

how tightly a protein binds its substrate

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12
Q

relationship b/w kd and affinity

A

high kd -> more dissociation -> low affinity

low kd -> less dissociation -> high affinity

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13
Q

what is an example of binding that is usually very tight and specific?

A

antibody-antigen (complementarity-determining regions)

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14
Q

antibody generation in B cells

A

somatic recombination then somatic hypermutation

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15
Q

somatic recombination

A

different combinations for binding w/ particular antigens

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16
Q

somatic hypermutation

A

evolved a way to create new mutations:

  • deamination
  • mismatch w/ error prone DNA pol -> more new lesions
  • activation-induced deaminase: base-excision repair w/ low fidelity DNA pol delta -> create more mutations that generate variety in antibodies to bind more antigens
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17
Q

function of enzymes

A

molecular catalysts - increase rxn rate by lowering Ea of transition state

18
Q

how do chemical reactions change enzymes?

A

they do not change they permanently

19
Q

active site

A

mediates biochemical reaction - contains catalytic site + binding pocket

20
Q

Michaelis-Menton equation

A

Vo = (Vmax x [S]) / ([S] + Km)

21
Q

what are two characteristics of enzymes by which they can be described?

A

Kcat and Km - useful for comparing different enzymes

22
Q

Km

A

measure of the affinity of an E for it’s S

= [S] when Vo = Vmax/2

23
Q

relationship b/w Km and affinity

A

high Km -> more dissociation -> low affinity

low Km -> less dissociation -> high affinity

24
Q

Vmax

A

the fastest rate that a specific unit of enzyme can work theoretically

25
Q

how do serine proteases bind their substrates?

A
  • binding site has beta sheets to H-bond w/ peptide to be broken
  • specificity binding pocket to recognize specific S
  • catalytic triad: Ser, His, Asp
  • utilizes Ser in active site for nucleophilic attack on S
26
Q

role of His in serine protease active site

A

imidazole ring can pick up H and have positive charge (is pH dependent) so it pulls H off of hydroxyl of Ser

27
Q

at what pH can serine proteases not function and why?

A

low pH because at these pH levels, the active site His cannot pull the proton from Ser

28
Q

pH and enzyme activity/efficiency

A

due to specific aa’s in active site - if they have the wrong charge, rxn cannot proceed

29
Q

how are proteins involved in maintaining cell structure?

A

microfilaments - actin
microtubules - alphabeta - tubulin dimer
intermediate filaments

30
Q

how are proteins involved in signal transduction?

A
  • act as molecular switches - active vs. inactive
  • channel proteins
  • can be receptors, ligands, and/or signal transducers
31
Q

how is Shh signal transduction pathway turned on?

A

ligand binds receptor -> active form -> triggers events -> transcription occurs

32
Q

what are some clinical manifestions of mutations in Shh?

A

polydactyly, cyclopia

33
Q

non-covalent protein modifications

A
  1. GTP switch

2. calmodulin

34
Q

what regulates GTPase?

A

GEF and GAP

35
Q

GEF

A

guanine nucleotide exchange factor - activates GTPases by stimulating release of GDP to allow binding of GTP

36
Q

GAP

A

GTPase activating protein - bind activated G proteins and stimulates GTPase activity - terminates signaling event

37
Q

how do you turn proteins off?

A

protein degradation by proteolytic cleavage

38
Q

what is proteolytic cleavage mediated by?

A

proteosome

39
Q

ubiquitination

A

labels proteins to be degraded with a protein tag (ubiquitin) put onto a Lys residue

40
Q

proteosome function

A

recognizes ubiquitin labels, binds to protein, hydrolyzes ATP to release ubiquitin, then core of proteosome chops protein into pieces