L7: Protein Folding II

Question 1

prediction of 2ndary structure

Answer 1

using the chou-fasman method

empirical technique for prediction of 2ndary structures

Question 2

protein tertiary structure

Answer 2

spatial arrangement of aa residues that are far apart in the sequence and to the pattern of disulfide bonds

Question 3

quaternary structure

Answer 3

spatial arrangement of subunits and nature of their interaction

Question 4

protein denaturation

Answer 4

unfolding is an all or nothing process

partial loss of structure destabilizes the remainder of the structure

Question 5

PDI

Answer 5

protein disulfide isomerase

rearranges the polypeptide’s non-native S-S bonds

Question 6

protein turnover

Answer 6

lifespan of proteins is highly regulated

Question 7

PPI

Answer 7

peptidyl prolyl cis-trans isomerases

Question 8

HSP 70 and 40

Answer 8

ATP-driven
functions: reverse misfolded proteins

unfold/refold proteins

Question 9

mitochondria contain their own Hsp proteins

Answer 9

60 and 70

are distinct from the heat shock proteins of the cytosol

Question 10

conditions for protein denaturation

Answer 10

heat
extreme pH’s
agitation

Question 11

chemicals for protein denaturation

Answer 11

detergents ex. SDS
chaotropic agents
organic solvents

Question 12

methods of analysis of protein denaturation

Answer 12

turbidity
circular dichroism
uv absorption
fluorescence
biological acitivty

Question 13

define molecular chaperons

Answer 13

essential proteins that bind to unfolded and partially folded polypeptide chains

Question 14

functions of molecular chaperons

Answer 14

prevent improper association of exposed hydrophobic segments of misfolded proteins

allow misfolded proteins to refold or be destroyed

Question 15

what are co-chaperons?

Answer 15

binds to molecular chaperons to activate them

Question 16

what are co-chaperons?

Answer 16

binds to molecular chaperons to activate them

Question 17

Hsp90 family

Answer 17

integrates signaling functions, acting at a late stage of folding of substrates

Question 18

chaperonins

Answer 18

a protein folding container
hsp60, 10

barrel analogy from bittel
*ATP to take top on/off

Question 19

short lived proteins are mostly associated w/ ?

Answer 19

metabolic functions

Question 20

the proteasome

Answer 20

a protein degradation machinery

large protease complex which digest ubiquinated proteins

Question 21

26S proteasome is made of

Answer 21

2 19S regulatory units –exit/entry channels

20S catalytic core

Question 22

functions of 19S

Answer 22

recognizes ubiquintaed proteins

isopeptidase cleaves signal off

protein directed inwards to 20S

Question 23

20S segment

Answer 23

composed of 28 subunits

access controlled by 19S

Question 24

proteasome generates free amino acids

Answer 24

degrades proteins into peptide fragments which can be further digested to yield free amino acids

Question 25

free amino acids can be used for ?

Answer 25

biosynthetic rxns