Protein primary, secondary, tertiary and quaternary structures

Question 1

Primary structure

Answer 1

amino acid in linear sequence

Question 2

secondary structure

Answer 2

regions of regularly repeating conformations of the peptide chain, such as α-helices and β-strands (local folding)

Question 3

tertiary structure

Answer 3

describes the shape of the fully folded polypeptide chain

Question 4

Quaternary structure

Answer 4

arrangement of two or more polypeptide chains into multisubunit molecule

Question 5

3 ways to represent a protein structure

Answer 5

(a) Space-filling model
(b) Cartoon ribbon model (shows secondary structure)
(c) Substrate-binding site view

Question 6

factors contributing to protein structure

Answer 6

allowable bond rotations define the possible conformations of the polypeptide chain

weak non-covalent interactions between backbone and sidechain groups (e.g., hydrophobic, H-bonding, electrostatic)

Question 7

The C—N peptide bond has double bond character (due to resonance) resulting in ?

Answer 7

no bond rotation around C—N bond and

6 atoms all lying in the same plane (= peptide group)

Question 8

WHich conformation is more favorable - trans or cis and why?

Answer 8

Cis conformation is less favorable than trans due to steric interference of α-carbon side chains

Question 9

which conformation is more common- trans or cis?

Answer 9

Nearly all peptide groups in proteins are in the trans conformation

Question 10

what is phi rotation?

Answer 10

rotation about N- C alpha bond

Question 11

what is psi rotation?

Answer 11

rotation about C alpha-C bond

Question 12

why is phi rotation in proline restricted?

Answer 12

because of its ring structure

Question 13

properties of alpha helix in terms of rise and pitch

Answer 13

rise - each
residue
advances by 0.15 nm along the long axis of the helix

pitch - the advance
along the helix long
axis per turn =
0.54 nm

Question 14

how many amino acids per turn in alpha helix?

Answer 14

3.6

Question 15

is alpha helix left or right handed?

Answer 15

right handed - backbone turns clockwise when viewed from n terminus

Question 16

how is the helix stabilised?

Answer 16

by hydrogen bonds which are nearly parallel to long axis of the helix

Question 17

why are alpha helices ampipathic?

Answer 17

Hydrophobic residues directed inward, hydrophilic outward

Question 18

what are beta strands and beta sheets?

Answer 18

β Strands - polypeptide chains that are almost fully extended
β Sheets - multiple b strands arranged side-by-side
- stabilized by hydrogen bonds between C=O and -NH on adjacent

Question 19

types of beta sheets

Answer 19

Parallel β sheets - strands run in the same N- to C- terminal direction

Antiparallel β sheets - strands run in opposite N- to C- terminal directions

Question 20

what are loops and turns?

Answer 20

Loops and turns connect α helices and β strands and allow a peptide chain to fold back on itself to make a compact structure

Loops - often contain hydrophilic residues and are found on protein surfaces

Turns - loops containing 5 residues or less

Question 21

how are tertiary structures stabilized?

Answer 21

Protein tertiary structures are stabilised primarily by non-covalent interactions between side chains.

Disulfide bridges can also stabilise tertiary structure