Protein Structure

Question 1

A protein’s 3 dimensional conformation is called :

Answer 1

The native fold

Question 2

What are some favorable interactions in proteins?

Answer 2

• Hydrophobic effect
• Hydrogen bonds
• London dispersion
• Electrostatic interactions

Question 3

The structure of the protein is partially dictated by the properties of the peptide bond. The resonance causes the peptide bonds to be :

Answer 3

Less reactive compared to esters, for example
– to be quite rigid and nearly planar
– to exhibit a large dipole moment in the favored trans configuration

Question 4

What are phi and psi angles ?

Answer 4

• f (phi): angle around the a-carbon—amide nitrogen bond
• y (psi): angle around the a-carbon—carbonyl carbon bond
• In a fully extended polypeptide, both y and f are 180

Question 5

What does a Ramachandran plot show ?

Answer 5

• A Ramachandran plot shows the distribution of f and y dihedral angles that are found in a protein
➔ shows the common secondary structure elements
➔ reveals regions with unusual backbone structure

Question 6

Why does glycine fall out of the Ramachandran plot ?

Answer 6

it is too small and flexible

Question 7

Describe 2 regular and 1 irregular arrangement in protein secondary structure

Answer 7

• The a helix – stabilized by hydrogen bonds between nearby residues
• The b sheet – stabilized by hydrogen bonds between adjacent segments that may not be nearby
• Irregular arrangement of the polypeptide chain is called the random coil

Question 8

Which AAs are strong helix formers ?

Answer 8

Small hydrophobic residues such as Ala and Leu

Question 9

Which AAs break the alpha helix and why ?

Answer 9

• Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible
• Gly acts as a helix breaker because the tiny R-group supports other conformations

Question 10

Does the helix have a charge ?

Answer 10

• The a helix has a large macroscopic dipole moment
• Negatively charged residues often occur near the positive end of the helix dipole

( the peptide bond has a strong dipole moment – Carbonyl O negative – Amide H positive)

Question 11

What’s the difference between parallel and antiparallel beta sheets ?

Answer 11

• In parallel b sheets the Hbonded strands run in the same direction resulting in bent H-bonds (weaker) (> 5 residues)
• In antiparallel b sheets the H-bonded strands run in opposite directions resulting in linear H-bonds (stronger)

Question 12

When do beta turns occur ?

Answer 12

whenever strands in b sheets change the direction

Question 13

What are the 2 major classes for protein tertiary structure ?

Answer 13

Fibrous and globular (water or lipid soluble)

Question 14

When does quarternary structure occur ?

Answer 14

It results from interactions between two or more polypeptide chains.

Question 15

What is protein denaturation?

Answer 15

Loss of structural integrity with accompanying loss of activity

Question 16

What is the basis of numerous human diseases?

Answer 16

Protein misfolding (prions)

Question 17

How do prion and amyloid proteins escape the proteases and chaperones of the quality control systems?

Answer 17

• Alternatively folded precursor proteins have surface structures that are not recognized by the chaperones and proteases.
• A second possibility is that amyloids forms aggregate more quickly than they can be degraded or refolded.
• Most abundant chaperones and proteases in cells do not appear to act on aggregates, fibril formation will not be easily reversed once initiated.

Question 18

In an a-helix, the R groups on the amino acid residues are found where?

Answer 18

on the outside of the helix spiral.