Amino Acids&proteins/protein Structure

Question 1

Features of peptide bonds, and their implications

Answer 1

C-N has shorter than expected bond length-> no rotation

-ve charge on O & +ve on N -> H bonds with other polar groups

Question 2

Names of first and last aa, groups they contain

Answer 2

N-terminal end has NH3+

C-terminal end has COO-

Question 3

4 examples of other covalent linkages in proteins. Examples.

Answer 3

1. Disulfide bridges
   Intra/interchain cys-CYs bridges in insulin
2. Methylation
   NH2 groups of Lys & arg in histones
3. Glycosylation
   O-linked OH of T&S
   N-linked NH2 of N
4. Phosphorylation
   Phosphorylation of Y in insulin receptors

Question 4

Alpha helix structure and implications

Answer 4

Intra H-bonds between c=O & N-H of every 4th peptide
3.6 residues per turn 
R groups outside 
RIGHT handed helix 
Cylinder shape -> architectural support

Question 5

Beta pleated sheets features

Answer 5

Linear
Inter H bonding
Side chains lie above and below alternately

Question 6

Types of beta sheets

Answer 6

Antiparallel

Parallel

Question 7

Collagen triple helix features

Answer 7

H BONDS BETWEEN CHAINS
Left handed helix
3 residues per turn
G-mainly P-mainly hydroxyproline

Question 8

Proteins with high %age of alpha/beta

Alpha vs beta

Answer 8

Alpha- haemoglobin 60%
Beta- silk fibres
Alpha has high elasticity.
Beta has high tensile strength

Question 9

Super secondary vs tertiary vs quaternary structures

Answer 9

Supersecondary: many alpha/beta structures, 1 domain
Tertiary: many domains, folding, 1 subunit
Quaternary: many subunits

Question 10

Forces that stabilise proteins

Answer 10

Covalent: disulfide bridges 
Non-covalent: 
1. H bonds 
2. Van der waals 
3. Electrostatic interactions 
4. Hydrophobic effect

Question 11

How do electrostatic interactions work

Answer 11

Between R groups
GLUTAMIC AND ASPARTIC ACID HAVE IONISED COOH GROUPS

LYSINE AND ARGININE HAVE IONISED NH3 GROUPS

Question 12

How do van der waals forces work

Answer 12

Sum of attractive or repulsive forces between molecules due to unequal distribution of electrons

Question 13

How do hydrophobic effects work

Answer 13

Hydrophobic R groups fold in a way to minimise contact with aqueous environment
PREVENTS H BONDS FROM FORMING

Question 14

3 Diseases associated with misfolded proteins

Answer 14

1. Sickle cell (glu-> Val) hydrophobic HbS
2. Alzheimer’s disease: amyloid proteins form plaques
3. Creutzfeldt jakob disease: prion protein polymerisation

Question 15

What happens in Creutzfeldt-Jakob disease?

Answer 15

Prion protein conversion from PrPc to PrPsc (pathogenic)
PrPc is ALPHA HELICAL -> susceptible to proteolysis
PrPsc is BETA PLEATED -> protease resistant
Polymerisation of PrPsc to fibrils