CH 4 Part 2

Question 1

What are the properties of globular proteins?

Answer 1

• folding provides structural and functional diversity
• tertiary structures consist of several secondary structures
• examples: enzymes, transport proteins, motor proteins, regulatory proteins, receptors, immunoglobins, etc.

Question 2

Describe motifs

Answer 2

• specific arrangement of secondary structure elements
• motifs can be found as reoccurring structures in numerous proteins
• proteins are made of different motifs folded together

Question 3

Describe intrinsically disordered domains

Answer 3

• contain protein segments that lack definable structure
• composed of amino acids whose higher concentration forces less defined structure
• disordered regions can conform to many different proteins, facilitating interaction with numerous different partner proteins

Question 4

What is quaternary structure?

Answer 4

formed by the assembly of individual polypeptides into a larger functional cluster

Question 5

What is denaturation?

Answer 5

loss of structural integrity with accompanying loss of activity

Question 6

How can proteins be denatured?

Answer 6

• heat or cold
• pH extremes
• organic solvents
• chaotropic agents: urea and guanidinium hydrochloride

Question 7

describe the ribonuclease refolding experiement

Answer 7

• urea in the presence of 2-mercaptoethanol fully denatures ribonuclease
• when urea and 2-mercaptoethanol are removed, the protein spontaneously refolds and the correct disulfide bonds are reformed
• conclusion: the sequence alone determines the native conformation

Question 8

What is Levinthal’s paradox?

Answer 8

it is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest energy one is found

Question 9

describe the thermodynamics of protein folding

Answer 9

• entropy is at its highest at unfolded state and decreases as it folds
• potential energy is highest at unfolded state
• inside the protein, order is increasing
• as the protein folds, water moves out and overall entropy goes up
• the more stable intermediates there are, the more possible ways it could fold

Question 10

What are chaperones?

Answer 10

interact with proteins and aid in folding by preventing aggregation

Question 11

What are chaperonins?

Answer 11

they actively facilitate protein folding

Question 12

What is proteostasis?

Answer 12

maintenance of cellular protein activity is accomplished by the coordination of many different pathways

Question 13

What is autophagy

Answer 13

Autophagy is the natural, conserved degradation of the cell that removes unnecessary or dysfunctional components through a lysosome-dependent regulated mechanism.
“self eating”

Question 14

What is ubiquitin proteasome system?

Answer 14

Through the concerted actions of a series of enzymes, proteins are marked for proteasomal degradation by being linked to the polypeptide co-factor, ubiquitin.