Protein Structure and Function 2 (L4)

Question 1

native state

Answer 1

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

Question 2

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

Answer 2

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

Question 3

purpose of chaperones/chaperonins

Answer 3

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

Question 4

chaperones

Answer 4

HSP

Question 5

chaperonins

Answer 5

GroEL, GroES -> cylindrical macromolecular complex

Question 6

Alzheimer’s disease

Answer 6

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

Question 7

amyloidogenic vs. non-amyloidogenic protein products

Answer 7

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

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

Question 8

A-beta normal vs. pathologic

Answer 8

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

Question 9

two classical pathological hallmarks of Alzheimer’s

Answer 9

neurofibrillary tangles (protein aggregates inside neurons) and amyloid plaques

Question 10

concept of specificity

Answer 10

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

Question 11

concept of affinity

Answer 11

how tightly a protein binds its substrate

Question 12

relationship b/w kd and affinity

Answer 12

high kd -> more dissociation -> low affinity

low kd -> less dissociation -> high affinity

Question 13

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

Answer 13

antibody-antigen (complementarity-determining regions)

Question 14

antibody generation in B cells

Answer 14

somatic recombination then somatic hypermutation

Question 15

somatic recombination

Answer 15

different combinations for binding w/ particular antigens

Question 16

somatic hypermutation

Answer 16

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

Question 17

function of enzymes

Answer 17

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

Question 18

how do chemical reactions change enzymes?

Answer 18

they do not change they permanently

Question 19

active site

Answer 19

mediates biochemical reaction - contains catalytic site + binding pocket

Question 20

Michaelis-Menton equation

Answer 20

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

Question 21

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

Answer 21

Kcat and Km - useful for comparing different enzymes

Question 22

Km

Answer 22

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

= [S] when Vo = Vmax/2

Question 23

relationship b/w Km and affinity

Answer 23

high Km -> more dissociation -> low affinity

low Km -> less dissociation -> high affinity

Question 24

Vmax

Answer 24

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

Question 25

how do serine proteases bind their substrates?

Answer 25

• 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

Question 26

role of His in serine protease active site

Answer 26

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

Question 27

at what pH can serine proteases not function and why?

Answer 27

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

Question 28

pH and enzyme activity/efficiency

Answer 28

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

Question 29

how are proteins involved in maintaining cell structure?

Answer 29

microfilaments - actin
microtubules - alphabeta - tubulin dimer
intermediate filaments

Question 30

how are proteins involved in signal transduction?

Answer 30

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

Question 31

how is Shh signal transduction pathway turned on?

Answer 31

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

Question 32

what are some clinical manifestions of mutations in Shh?

Answer 32

polydactyly, cyclopia

Question 33

non-covalent protein modifications

Answer 33

1. GTP switch

2. calmodulin

Question 34

what regulates GTPase?

Answer 34

GEF and GAP

Question 35

GEF

Answer 35

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

Question 36

GAP

Answer 36

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

Question 37

how do you turn proteins off?

Answer 37

protein degradation by proteolytic cleavage

Question 38

what is proteolytic cleavage mediated by?

Answer 38

proteosome

Question 39

ubiquitination

Answer 39

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

Question 40

proteosome function

Answer 40

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