Exam 1: Chapter 4 - Protein Structure

Question 1

Describe a-helix in detail

Answer 1

Right handed helix only in nature with 3.6 residues per turn, the side chain points out, the core of the helix is packed due to alignment of peptide bonds, and amino acids does not have adjacent H bonds.

Question 2

Describe B-sheets in detail

Answer 2

There are antiparallel and parallel B-sheets. The H bonds occurs between the adjacent polypeptide chains instead of adjacent amino acids.

Question 3

Are peptide bonds planar?

Answer 3

yes, due to the partial double bond resonance between NH and carbonyl group

Question 4

Is B-sheets completely planar/flat?

Answer 4

No, with a big enough B-sheet, they always have a twist to them which would eventually roll up into a barrel shape

Question 5

What secondary structures are loops and turns made out of?

Answer 5

a combination of a-helixes and B-sheets

Question 6

What are common secondary structures?

Answer 6

a alpha-helix, a B-sheets, or loops and turns

Question 7

What are alpha helix and beta sheets destabilizer?

Answer 7

Pro destabilize both due to its ring structure
Val, Thr, Ile destabilize alpha helix due to branching

Question 8

Ramachandran plot and what it shows

Answer 8

it is the statistical distribution of the dihedral angle phi and psi in most peptide bonds. Which means that α helices and β sheets have repeating values of the torsional angles (out of a small subset of allowed values) which leads to their specific shapes/structures such as a-helixes and beta-sheets

Question 9

What can Cys do?

Answer 9

Form disulfide bonds

Question 10

Explain why the peptide bond is usually in the trans configuration

Answer 10

It is mainly due to steric hinderance that could happen between side chain and especially bulky R groups.

Question 11

What are tertiary protein structures?

Answer 11

1. Globular proteins: water soluble, with nonpolar residues on interior of proteins and charged residues on the surface
2. Combination of secondary structures called motifs, such as Beta hairpins and BaB.

Question 12

What are domains?

Answer 12

different area of a polypeptides that are regions that does a specific function, such as binding to small molecules.

Question 13

Quaternary Structure and example

Answer 13

quaternary structure of a protein refers to the arrangement and interaction of multiple polypeptide chains (also known as subunits) in a multi-subunit protein complex.
Ex. hemoglobin