1. Protein composition and Structure

Question 1

What is a standard/common AA?

Answer 1

Those which have a genetic code and corresponding tRNA

Question 2

Peptide bond

Answer 2

Forms from elimination of water between alpha carboxyl and alpha amino group of 2 different AA
Trans/cis (O of CO and H of NH)
More stable and short than CN sg bond as partial db
Factors limiting spatial config =
- planar, semi-rigid (no free rotation around CN bond)
- e density unequal (CO=partial -ve, N= partial +)
- adj AA residues usually trans

Question 3

What is the difference between peptides and proteins?

Answer 3

peptides have molecular weight <5000Ds (insulin =5000)

Question 4

How can you determine the no. aa?

Answer 4

Mr/110

Question 5

Primary Structure

Answer 5

AA seq

Question 6

Secondary structure

Answer 6

Local Spatial arrangement of polypeptide backbone - stabilised by H bonds betwen atoms of peptide groups (side chain take no part) as well as Van der Walls
Example beta pleated sheet and alpha helix and beta bend

Question 7

A helix

Answer 7

Most abundant and most stable conformation (Max H bonds)
Average 12 residues (4-50)
3.6(13) a helix - 3.6 residues/turn with 13 atoms in backbone
Also pi helix (4.4(16))=looser and 3(10) helix

Question 8

Beta sheet

Answer 8

Major element in globular proteins
Parallel variety - chains in same direction to carboxyl end. NH > COOH
Antiparallel - chain going in opposite direction, more stable
Pleated as C atoms above and below plane of sheet

Question 9

Beta bend

Answer 9

B bend - 3(10) helix reversal in polypept chain direction inv -> loop ( CO H bond w/ Amide group 3 positions farther)
Common in collagens

Question 10

Tertiary structure

Answer 10

3D structure from spatial relationships between secondary elements
Stabilised by weak interaction between AA side chains inc ionic interactions, H bond, disulf bond (oxidation of bond -> loss of bio properties) and hydrophobic interactions.
+ nonpolar AA assoc w/ interior of globular (stabilise cpre via VdW), if on surface -> clattrates w/ quasi-crystal structure
+Charged polar - surface (most form salt bridges) - not signif contribute to stailisation, some on interior (active site/bind metals but not energetically favourable)
+ noncharged polar - mainly surface (high solvated)/interior(stabilise molecule + neutralise polarity)
+ pro and gly - disturb normal a helix. Proline always -> bend

Question 11

Supersecondary structure

Answer 11

Compact 3D structure of several adjacent elements of a secondary structure that is smaller than a protein domain or a subunit. Can be part of 3o sructure allowing ligand binding, active site etc
act as nucleations in the process of protein folding.
Inc:
B hairpin (antiparallel sheets)
B-a-B motif
a - helix-turn-a helix
Leucine zipper
zinc finger - reg DNA-receptor interaction
helix-turn-helix & helix-loop-helix

Question 12

Quaternary structure

Answer 12

2/2+ pp chains (subunits) [dimeric, tri, tetra etc)
Subunits stabilise each other VdW, ionic interactions, H bond, disulf bond hydrophobic interactions
Each subunit has distinct fct
Example a2b2