B2.024 Protein Life Cycles

Question 1

when do a large percent of normal proteins misfold?

Answer 1

after translation

Question 2

what is the two fold effect of cytoplasmic crowding?

Answer 2

retards unfolding but enhances aggregation

Question 3

what are protein denaturing conditions?

Answer 3

pH, ionic strength, pressure, temperature, osmotic pressure, urea

Question 4

discuss protein unfolding in digestion

Answer 4

extreme acidity in the stomach unfolds proteins that have been consumed

Question 5

what is a characteristic of pathological protein folding?

Answer 5

B sheet fibers, amyloid

Question 6

how many proteins form amyloid?

Answer 6

> 21

Question 7

what is amyloidosis from dialysis?

Answer 7

proteins sensitive to dialysis form amyloid and deposit in the patient’s body

Question 8

how does ligand binding affect folding?

Answer 8

biases toward folded form in equilibrium

Question 9

what are osmolytes?

Answer 9

nonspecific effect on all encountered proteins, induce solvation effects that increase folding

Question 10

what are examples of osmolytes?

Answer 10

free amino acids, polyols, methylamines

Question 11

how do kidney cells adapt to special stress?

Answer 11

can have high urea and NaCl concentrations, conditions change over time, compensate by changing sorbitol, betaine, inositol, glycerolphosphoryl choline

Question 12

what makes the ER a special environment for protein folding and processing?

Answer 12

synthesis of secreted proteins, some lysosomal enzymes, integral membrane proteins

Question 13

what two factors increase protein stability?

Answer 13

oxidizing w/ disulfide bonds

glycosylation

Question 14

how are covalent osmolytes thought to work?

Answer 14

encourage protein folding bc proteins would rather fold than interact w osmolytes, preferential solvation

Question 15

what is an example of a protein than can survive digestion?

Answer 15

ovomucoid, major egg white allergen

Question 16

what are chaperone proteins?

Answer 16

heat shock proteins that are upregulated in stressful conditions, they fold new proteins, refold misfolded proteins, transport across membranes, and control activities of some proteins

Question 17

what is the chaperonin pathway?

Answer 17

protein binds to chaperonin
ATP allows lid to close on chaperonin w protein inside
protein remodeling occurs inside
remodeled protein emerges

Question 18

how many amino acids can fit in a chaperonin cavity?

Answer 18

450, 50 kD

Question 19

how much protein degradation each day is normal?

Answer 19

1-2% turnover

Question 20

what are 3 primary reasons for protein degradation?

Answer 20

cellular change, functional regulation, adverse conditions

Question 21

what are the two protein degradation pathways and how do they differ?

Answer 21

proteasome: used with short half life proteins with transient functions that are abnormal or damaged
lysosome: used with long half life proteins used for housekeeping functions or in membranes

Question 22

what are the two types of lysosomal degradation?

Answer 22

autophagy and chaperone mediated autophagy

Question 23

characterize autophagy

Answer 23

nonselective, slow, constitutive

Question 24

characterize chaperone mediated autophagy

Answer 24

selective, 30% of cytosolic proteins, hsc73 binding to “KFERQ” motifs, unfolded protein transported into the lysosome

Question 25

what are the functional molecules in the lysosome?

Answer 25

> 12 cathepsin proteases
broad, overlapping substrate specificities
no apparent order to proteolysis

Question 26

what is a proteasome?

Answer 26

large protein complex, not an organelle

Question 27

what is the proteasome pathway?

Answer 27

misfolded protein gets tagged with ubiquitin
protein binds to proteasome
addition of ATP allows proteasome to degrade protein and recycle ubiquitin

Question 28

describe the ubiquitin tagging process

Answer 28

E1- activator protein, ATP required
E2- several carrier isoforms
E3- recognizes both ubiquitin and target protein

Question 29

how does ubiquitin bind to a protein?

Answer 29

peptide/amide bond between Ubq C-terminus and the lysine side chain of the protein

Question 30

how does poly-ubq form?

Answer 30

bind at internal ubq lysines

Question 31

what is the active site on a proteasome?

Answer 31

Asp-Thr-His

Question 32

what is the outcome of protein turnover?

Answer 32

75% of free amino acids recycles
25% amino acids metabolized
-nitrogen excreted as urea
-carbon compounds burned for energy

Question 33

what types of stress occur in the ER?

Answer 33

unfolded proteins in ER
ROS of UV damage
low amino acids
heat
hypoxia
high free fatty acids

Question 34

what is BiP?

Answer 34

a chaperone that senses stress

normally binds sensor proteins, unfolded proteins “soak up” Bip, thus releasing sensor proteins, becoming active

Question 35

what are cellular responses to ER stress?

Answer 35

1. inhibit global translation
2. activate transcription/translation of
   - ERAD proteins
   - chaperones
   - amino acid transporters
   - oxidative stress protection

Question 36

what is an example of protein degradation backfiring?

Answer 36

in cystic fibrosis the F508 deletes one aa in a protein, this causes the protein to fold slowly, the protein is degraded before it can function