Chapter 6- Tertiary and Quaternary Structures

Question 1

the tertiary structure consists of

Answer 1

multiple secondary structure elements

Question 2

protein is folded when it adopts ___ _____ ____

Answer 2

biologically relevant structure

Question 3

main driving force for protein folding

Answer 3

hydrophobic interaction

Question 4

main stabilizing forces of protein folding

Answer 4

• formation of a large number of H bonds
• hydrophobic interactions
• Van der Waals forces

Question 5

The surface of the proteins is ______ _____

Answer 5

predominantly polar

Question 6

The core of a protein is _____ ______ and is made via _____ ______

Answer 6

predominantly hydrophobic, hydrophobic interactions

Question 7

N-H and C=O of the backbone must be ___ in the hydrophobic core

Answer 7

neutralized

Question 8

Water on the surface of the protein _____ the structure

Answer 8

stabilize

Question 9

Side chains on the surface make _____ with solvent water –> ______ __ ______

Answer 9

H-bonds, Layer of water

Question 10

Alpha helices on the surface of a protein are typically ______

Answer 10

Amphipathic

Question 11

Hydrophobic helices are found in the protein _____

Answer 11

interior

Question 12

Polar helices are found _____ to the solvent

Answer 12

completely exposed

Question 13

domains are _________ _____ _____ and are typically connected by _____ ________ _______

Answer 13

structurally independent units, one polypeptide segment

Question 14

Identical subunits are called

Answer 14

homo-multimers

Question 15

Non-identical subunits are called

Answer 15

hetero-multimers

Question 16

Van der Waals interactions contribute to _____ _______

Answer 16

oligomer stability

Question 17

oligomerization is accomplished by

Answer 17

• unfavorable energy changes (entropy loss due to association)
• Favorable energy changes (van der waals, H-bonds, and hydrophobic interactions)

Question 18

Forces driving quaternary association

Answer 18

1. van der waals interaction
2. hydrophobic interactions ‘
3. Disulfide bonds

Question 19

Hydrophobic interactions in quaternary structure have a ____ _____ ____ and provide enough to _____- _______ _____

Answer 19

main stabilization effect, counterbalance unfavorable entropy

Question 20

Structural and functional advantages driving quaternary association

Answer 20

1. stability
2. genetic economy and efficiency
3. bringing catalytic sites together
4. cooperativity

Question 21

A functional protein is a ____ protein

Answer 21

stable

Question 22

Proteins are only ______ _____ under physiological conditions

Answer 22

marginally stable

Question 23

Protein structures arise from a delicate ____ ____ ____

Answer 23

balance between forces

Question 24

The free energy of proteins is ____ which means it is ____ to go from one form to the other

Answer 24

low, easy

Question 25

Denaturing forces

Answer 25

sidechain conformational entropy (proteins do not want to be constrained)

Question 26

Hydrophobic interaction drives the folding of proteins through the clustering of _____ ____ ___

Answer 26

hydrophobic amino acids

Question 27

Loss of protein structure results in loss of protein _____

Answer 27

function

Question 28

proteins denature by altering the weak _____ _____

Answer 28

nonbonding forces

Question 29

Denaturation methods

Answer 29

1. high temperature 2. high or low pH 3. Chaotropic agents 4. detergents

Question 30

When protein is unfolded via heat it is _____

Answer 30

irreversible

Question 31

when protein is denatured via chaotropic agents, the process is _____

Answer 31

reversible

Question 32

The melting temperature is when the protein is ____ folded and ____ unfolded

Answer 32

50%, 50%

Question 33

Alpha helices monitors CD signals at

Answer 33

222 nm

Question 34

Proteins fold in _____ ________

Answer 34

prearranged pathways (Levinthal paradox)

Question 35

The probability of forming contact C2 is much higher if ___ is formed than in the absence of ___

Answer 35

C1

Question 36

Protein folding occurs on an ___ _____

Answer 36

energy surface (landscape theory)

Question 37

Unfolding/ improper folding can lead to protein _____

Answer 37

aggregation

Question 38

Chaperone proteins guide proteins along the proper folding pathways by

Answer 38

providing a protective environment

Question 39

Chaperone proteins are often called

Answer 39

heat shock proteins

Question 40

What residue pairs confer flexibility and rigidity to a peptide

Answer 40

Gly and Pro

Question 41

Why is there little allowable rotation around the peptide bond?

Answer 41

the partial double bond character makes the peptide bond planar

Question 42

For beta sheets, the terms parallel and anti-parallel refer to

Answer 42

the direction of the associated peptide strands

Question 43

tertiary structure is defined as

Answer 43

the folding of a single polypeptide chain in three-dimensional space

Question 44

Why should the core of most globular and membrane proteins consist almost entirely of alpha helix and beta sheets (not loops)

Answer 44

Highly polar N-H and C=O bonds of the peptide backbone must be neutralized in the hydrophobic core of the protein

Question 45

How does protein affect protein stability

Answer 45

alters ionization states