Proteins 3

Question 1

Name some hydrophobic side chains

Answer 1

1. Valine
2. Leucine
3. Phenylamine

Question 2

Name some hydrophilic side chains

Answer 2

1. Aspartate
2. Lysine
3. Serine

Question 3

What is the hydrophobic effect ?

Answer 3

The main determinant that pushes proteins to fold into the tertiary structure
Hydrophobic residues to cluster together in the middle of the protein and hydrophilic ones are on the outside- hydrophobic collapse

Question 4

What is hydrophobic collapse ?

Answer 4

An entropic effect

Question 5

What bonds are found between side chains?

Answer 5

1. Wan der walls
2. Hydrogen bonds
3. Disulphide bonds
4. Ion paid bond (salt bridge)

Question 6

What are disulphide bonds ?

Answer 6

Covalent bonds between two cysteine side-chains

Question 7

What is pKa ?

Answer 7

pKa = -log10Ka
It is the PH where the pair is 50% ionised

Question 8

What is the Henderson- hasselbacg equation ?

Answer 8

PH = pKa + log([base] / [acid])

Question 9

What is a domain ?

Answer 9

Globular unit formed from part of a polypeptide
Often associated with particular functions

Question 10

What is the quaternary structure ?

Answer 10

Assembly of more than one polypeptide chain
Eg. Haemoglobin, collagen
Important in enzyme activity

Question 11

What does SDS page stand for ?

Answer 11

Sodium Dodecyl Sulphate (a detergent) , PolyAcrylamide Gel Electrophoresis

Question 12

What is SDS page ?

Answer 12

A technique used to separate proteins by size
SDS unfolds protein by coating the unfolded chain and then it is separated by gel electrophoresis

Question 13

How can proteins be purified ?

Answer 13

Use methods to exploit different properties
1. Solubility:
Precipitation by ammonium sulphate- insoluble proteins sediment
2. Isoelectric focusing- looks at isoeletric points, they stop at this point
3. Column chromatography

Question 14

What is an isoelectric point (PI) ?

Answer 14

PH where a molecule has no net charge

Question 15

What is size exclusion chromatography?

Answer 15

Separation according to size
Larger molecules come out first, smaller molecules last

Question 16

What is ion exchange chromatography?

Answer 16

Separates molecules according to their charge by using a charged resin that binds molecules with opposite charge
The. Molecules are eluded by increasing salt concentration

Question 17

What is affinity chromatography ?

Answer 17

Separates molecules base on a specific interaction between a target molecule and a binding partner attatched to the resin/beads
Only the target molecule sticks to the column

Question 18

What is the matrix in the column made of ?

Answer 18

Ni-Nitrilotriacetate agarose