Protein Structure

Question 1

List the roles of a protein in Biochem processes.

Answer 1

Catalysts
Transporters
Structural support 
Machines (muscle)
Immune protection
Ion channels
Receptors and ligands

Question 2

Describe the basic chemical 3D structure of an amino acid.

Answer 2

Has a central Carbon atom
Has one H group
Has one amino group (NH2)
Has one carbonyl group (COOH)
Has one R group

Question 3

Define a base.

Answer 3

A proton acceptor

Question 4

Define an acid

Answer 4

A proton donor

Question 5

What is an amino acid residue?

Answer 5

The part that remains of an AA after it is joined by a peptide bond to form a protein.

Question 6

What is the rule in regards to pH vs Pka of an AAs R group (when determining wether it becomes protonated or deprotonated).

Answer 6

If pH < pKa then group is protonated.

If pH > pKa then group is deprotonated.

Question 7

What is the Isoelectric point (pI) of a protein?

Answer 7

The pH at which the protein has no overall NET charge.

Question 8

What is the rule regarding pH and pI of a protein (when protonating or deprotonating a protein)?

Answer 8

If pH < pI then protein is protonated

If pH > pI then protein is deprotonated

Question 9

What is a conjugated protein?

Answer 9

It contains covalently linked components (ie lipids or carbs)

Question 10

Describe the characteristics of an alpha helix.

Answer 10

A right handed helix
3.6 AAs per turn
Every one AA it rises 0.54nm (Pitch)
Stabilised by H bonds (between NH and CO groups that lie 4 AAs away from each other)

Question 11

What residues help/disrupt Alpha Helix formation?

Answer 11

Small hydrophobic (Ala and Leu) form helixes
Pro breaks them as N-C rotation is impossible
Gly breaks them as its small R group supports other conformations

Question 12

Describe the properties of a Beta Sheet.

Answer 12

0.35nm between adjacent AAs
R groups alternate at opposite sides of the chain
Can be antiparallel, parallel or mixed