Proteins

Question 1

Define genome.

Answer 1

Full set of genes

Question 2

Define proteome.

Answer 2

Full set of proteins encoded by the genome

Question 3

Amino acids differ from one another because of the different chemical properties of their R groups. Identify 5 ways in which these R groups can differ.

Answer 3

Size
Shape (aliphatic/aromatic)
Hydophobicity
Charge (acid/base)
Sulphur
Imino (proline is not an AA)

Question 4

Are all amino acids optically active?

Answer 4

All except glycine

Question 5

Identify 8 different protein functions.

Answer 5

1. Enzymes - catalyse metabolic reactions
2. Transport/storage - e.g. Hb
3. Motion - muscle proteins
4. Communication - receptors
5. Structure - keratin, collagen
6. Channels/transporters
7. Regulation - cell division, protein synthesis, hormones
8. Immunity - antibodies, self-recognition

Question 6

Why are peptide bonds quite rigid?

Answer 6

They have partial double bond characteristics, resonating between single & double bonds.
Rotation around the bond is also very limited.

Question 7

What is the primary structure of a protein?

Answer 7

Sequence of amino acids

Question 8

What is the secondary structure of a protein?

Answer 8

The local spatial arrangements of amino acids in the chain

Question 9

What is the tertiary structure of a protein?

Answer 9

3D shape of the folded protein chain

Question 10

What is the quaternary structure of a protein?

Answer 10

The spatial arrangement of different folded chains in relation to each other

Question 11

Polypeptide chains have direction because amino acids have different ends.
When writing a sequence down, it is convention to start with which end?

Answer 11

N-terminus (the amino)

written on the left

Question 12

How is the a-helix structure formed?

Answer 12

Side chains stick outwards.
H bonds between N-H and C=O 4 residues ahead.
These are intrachain H-bonds.
Helix has some elasticity.

Question 13

How is the B-pleated sheet structure formed?

Answer 13

Fully extended polypeptide chains run alongside one another.
Can be parallel or antiparallel.
H-bonding between adjacent strands.
May be intrachain or interchain.
Side chains lie above & below the plane of the sheet.

Question 14

What is the function of molecular chaperones?

Answer 14

They bind to short segments of a protein to facilitate correct folding of that area.

Question 15

What is the function of chaperonins?

Answer 15

They form protein chambers which provide a stable space where the protein can fold correctly.

Question 16

What is thought to be the biochemical basis for Alzheimer’s Disease? (how it occurs)

Answer 16

Fragments from a normal membrane protein amyloid precursor protein (APP) accumulate and aggregate to form insoluble fibrils of amyloid B.
This forms plaques which destroy neurones.

Question 17

What is the biochemical basis for Creutzfeldt Jacob Disease (CJD)? (how it occurs)

Answer 17

The normal membrane protein PrPc has an identical primary sequence to the abnormal PrPSc which has more B-pleated sheets.
Contact with this abnormal form (usually through ingestion) causes the PrP*c protein to acquire the abnormal structure.
Thus forming insoluble aggregates.

Question 18

The exterior of soluble proteins is mostly hydrophobic.

True or False?

Answer 18

FALSE
Interior of soluble proteins is hydrophobic.
Exterior is hydrophilic.

Question 19

Give 2 examples of the advantages of multi-subunit proteins.

Answer 19

1. Structural proteins - multiple chains provide strength and rigidity e.g. collagen.
2. Multi-enzyme complexes - multiple sites catalysing the same reaction or several different active sites close together to maximise efficiency.

Question 20

What is the strongest type of interaction which stabilises protein structures? and how does this occur?

Answer 20

Disulphide bonds.

Oxidation occurs between 2 Cys residues which come close together to form a disulphide bond.

Question 21

How does a salt bridge interaction occur in proteins?

Answer 21

Electrostatic attraction between oppositely charged amino acids, called an ‘ion pair’.

Question 22

What is the Hydrophobic effect?

Answer 22

In order to minimise contact with water, non-polar amino acids are buried in the core of proteins.
Polar amino acids are found on the surfaces of proteins.