Protein structure and function

Question 1

What elements do proteins provide?

Answer 1

Structural and functional

Question 2

What functions do proteins provide?

Answer 2

Carrier functions - e.g. trafficking oxygen
Metabolic functions - e.g. Enzymes utilising energy
Form parts of cellular machinery - e.g. ribosomes
Make up structural scaffold - e.g. microtubules
Sensory molecules - e.g. receptors

Question 3

Structure of amino acids

Answer 3

Tetrahedral arrangement of atoms with the alpha carbon at its centre

Carboxyl and amine groups attached to a central carbon

A variable side chain (R) - confers specific physicochemical properties

And a Hydrogen

Question 4

Ionisation of amino acids

Answer 4

Amino and carboxyl groups of amino acids can readily ionise

Low pH: NH2 accepts H+ to form NH3+. (Acts as a base)
Neutral pH: Both NH2 and COOH become ionised to form NH3+ and COO-. (Acts as a zwitterion)
High pH: COOH donates H+ thus becoming COO- . (Acts as an acid).

Question 5

Chirality of amino acids

Answer 5

Central carbon of amino acids is asymmetric/chiral. Exception to this is Glycine as central carbon has 2 H atoms bonded to it.

Question 6

Why do amino acids exist as D and L isomers?

Answer 6

Tetrahedral arrangement of the atoms which make up the amino acids give rise to the D and L isomers.

Question 7

When viewed along axis of the hydrogen-C- alpha bond what do the D and L isomers read?

Answer 7

L (levo) isomer would read CORN in a clockwise direction while the D (dextro) isomer would read CORN in an anticlockwise direction.

Question 8

What does CORN stand for?

Answer 8

CO of COOH group
R (R group or radical side chain)
N of NH2 group

Question 9

Which isomer of an amino acid is incorporated into proteins?

Answer 9

L isomer

Question 10

Where is the D isomer of amino acids found?

Answer 10

D isomer residues comprise cell walls in bacteria, and are often used in therapeutics

Question 11

Why do polypeptides have polarity?

Answer 11

Joining of amino acids to form polypeptide gives it an amino (N) and carboxyl (C) terminus which have differing charges.

Amino terminus = positively charged
Carboxyl terminus = negatively charged

Question 12

Why are polypeptides arranged in a trans conformation?

Answer 12

Trans formation (R groups of amino acids on alternate side of the chain) is the most energetically favourable arrangement

Question 13

What percentage of polypeptides are arranged in a Cis formation and why?

Answer 13

Only 0.1% of polypeptides arranged in Cis formation because it is a less energetically favourable formation.

Question 14

What are the 3 structures that can make up the secondary structure of a protein?

Answer 14

Alpha helices, Beta turns and Beta sheets

Question 15

How are Beta sheets formed and stabilised?

Answer 15

formed from the continuous folded polypeptide chain and are stabilised by intra molecular hydrogen bonds

Question 16

What role do beta turns have within large protein structures?

Answer 16

Help large protein structures to bend into compact structures

Question 17

Which structure is more stable, parallel or anti parallel beta sheets? why is this the case?

Answer 17

Anti parallel beta sheets are more stable. This is because the fact that the beta strands are oppositely orientated means that the loops that connect them are a lot shorter than in a parallel beta sheet.

Question 18

How is an alpha helix stabilised?

Answer 18

stabilised by H-bonds between two amino acids 4 residues apart
e.g. between residue 1 and 5

Question 19

How many residues per turn are there within an alpha helix?

Answer 19

3.6

Question 20

What does the arrangement of the variable side chain provide a protein?

Answer 20

Provides a protein with its specific physiochemical properties

Question 21

What why do the side chains within an alpha helix and a beta sheet face?

Answer 21

Side chains protrude outwards from the structure

Question 22

What is a cofactor?

Answer 22

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme’s activity. e.g. Heme of Haemoglobin

Question 23

What is the structural integrity of a protein determined by?

Answer 23

1. Interactions the protein has with itself: intra-chain and inter-chain bonding
2. Interaction the protein has with other factors such as cofactors