Protein denaturation and folding

Question 1

proteostasis

Answer 1

• protein homeostasis
• maintenance of an active set of cellular proteins
• misfolded or partially folded proteins can have exposed hydrophobic surfaces

Question 2

comparative genomics

Answer 2

• when you try to compare a gene/protein by comparison to other genes or genes in other organism

Question 3

orthologs

Answer 3

• genes that occur in different species, but have clear sequence and functional relationship
• do similar things

Question 4

paralogs

Answer 4

• genes that occur in the same species, but have a clear sequence and functional relationship

Question 5

synteny

Answer 5

• the conservation of the order of genes on a large segment of a chromosome between two closely related species
• shows evolutionary relationships
• supports gene/protein predictions

Question 6

Levinthal’s paradox

Answer 6

theory: folding is hierarchial
- “nucleus” of folding that starts the folding to native state
1. first, local interactions happen between aa near each other in linear sequence
- segments form secondary structures
2. assembly of local structures is followed by longer-range interaction
- ex: 2 elements of secondary structure coming together
3. more interactions based on what is now nearby from partial folding
overall - as folding occurs, less and less different options become available

Question 7

What does the free energy funnel show?

Answer 7

• shows how folding ooptions decrease leading to a “collapse” into native conformation
• shows semi-stable folding intermediates

Question 8

what are semi-stable intermediate

Answer 8

• can happen on the way to native state
• if barrier is too large, folding will not progress to native state

Question 9

what are the 3 major classes of chaperones

Answer 9

1. Hsp70
2. chaperonins
3. isomerases

Question 10

what are chaperones?

Answer 10

• proteins that interact with partially folded or misfolded polypeptides
• facilitate correct folding
• prevent aggregation
• create microenvironment for folding to occur by shielding from outside influences

Question 11

hsp70

Answer 11

• heat shock protein 70
• don’t actively fold proteins
• bind hydrophobic aa in unfolded or partially folded proteins to:
  
  • prevent aggregation
  • prevent heat denaturation
  • keep proteins unfolded until they cross an organelle membrane

Question 12

chaperonins

Answer 12

• large complexes of proteins that create a microenvironment for folding

Question 13

isomerases

Answer 13

• protein disulfide isomerase (PDI)
  
  • catalyzes interchange of S-S bonds where inappropriate ones have formed
• peptide prolyl cis-trans isomerase (PPI)
  
  • interconverts cis-trans isomers of proline

Question 14

what are three ways a protein can denature?

Answer 14

1. heat - weakens interactions in protein (mostly H-bonds)
2. pH - alters net charge causing electrostatic repulsion and disruption of H bonds
3. detergents, organic solvents, urea - disrupt hydrophobic interactions and H-bonds

Question 15

describe the experiment by Christian Anfisen and its importance

Answer 15

• investigated ribonuclease protein with 8 cystienes linked by 4 disulfide bonds
• should have many ways to refold
• protein unfolded (urea and mercaptoethanol)
• refolded to natural state when unfolding reagents were removed
• shows that the sequence is enough to drive proper folding (used sequence that didn’t need chaperone)