The Three Dimensional Structure of Proteins

Question 1

what drives protein structure

Answer 1

the hydrophobic effect

Question 2

what are the four levels of protein structure

Answer 2

primary, secondary, tertiary and quaternary structure

Question 3

describe the favorable interactions in proteins and what they do for protein structure

Answer 3

1. hydrophobic effect - release of water from solvation layer (area between solvent and solute) when the protein is folding increases the net entropy
2. hydrogen bonds - interaction of N-H and C=O of peptide bonds leads to formation of a helices and B sheets
3. london dispersion - weak attraction between all atoms, contributes to the stability of the interior of the protein
4. electrostatic interactions - include long range strong interactions between permanently charged groups. salt bridges i.e in the hydrophobic environment strongly stabilize the proteins

Question 4

what is the primary structure of protein

Answer 4

the peptide bond

Question 5

what is the constant triple repeat (backbone) of the amino chain

Answer 5

N-C-C repeats through the amino chain

Question 6

are peptide bonds polar or non polar

Answer 6

polar since the O2 and N atoms have partial pos and neg charges

Question 7

why is there restriction around the C-N bond

Answer 7

due to the double bond in the resonance form - the molecule switches back and forth from the resonance structure and in turn it cannot rotate around the C-N bond as it exists somewhere between its two forms

Question 8

explain where there is rotation in the peptide bond

Answer 8

there is rotation around the alpha carbons (phi and psi) where phi = the amide nitrogen and psi = the carbonyl carbon

Question 9

when fully extended what degrees are psi and phi

Answer 9

180 degrees

Question 10

what is the effect of steric crowding on psi and phi

Answer 10

means that certain psi and phi combinations are very unfavorable

Question 11

what may occur with favourable psi and phi combinations

Answer 11

favorable H bonding interactions may form

Question 12

what does secondary structure refer to

Answer 12

local spatial arrangement within the polypeptide backbone resulting in two regular arrangements - a helix and B sheets

Question 13

what is a random coil

Answer 13

occurs when irregular arrangement of the polypeptide chain happens

Question 14

describe the structure of the a helix

Answer 14

held together by hydrogen bonds at n and n+ 4 amino acids. is a right handed helix and has 3.6 residues per turn. peptide bonds are aligned roughly parallel and the side chains point out and are roughly perpendicular with the helicial axis

Question 15

give examples of strong helix formers

Answer 15

Ala and Leu

Question 16

which residues are typically found in the turn of the helix

Answer 16

Pro and Gly