protein biochemistry and enzymology

Question 1

What is the function of B-galactosidase?

Answer 1

• hydrolyse lactose
• can also hydrolyse nitrophenylgalactose

Question 2

What is the michaelis-menten equation?

Answer 2

v=Vmax x [S]/Km + [S]

Question 3

Write an equation for Vmax

Answer 3

Vmax = Kcat [Etot]

Question 4

What does Kcat and Km refer to?

Answer 4

Kcat - how fast it works
Km- describes its substrate conc dependence

Question 5

Write an equation for specificity constant

Answer 5

Kcat/Km

For a good enzyme:
Kcat –> high
Km –> low
Kcat/Km —> high

Question 6

Describe the lineweaver-burke plot

Answer 6

y axis –> 1/V
x axis –> 1/[S]
gradient = Km/Vmax
intercept = 1/Vmax

Question 7

What happens during to Vmax during competitive inhibition

Answer 7

stays the same

Question 8

Write the equation for specific irreversible inhibition

Answer 8

E+I –> EI + EI’

Question 9

What is myasthaenia gravis?

Answer 9

• acetylcholine receptors become progressively blocked by antibodies
• condition can be relieved by raising conc of acetylcholine

Question 10

What is edrophonium?

Answer 10

a competitive inhibitor of acetylcholinesterase –> used to diagnose myasthaenia gravis

Question 11

What is neostigmine

Answer 11

a cholinesterase inhibitor

Question 12

What are the features of a zwitterion?

Answer 12

+H3N- group
-COO- group

Question 13

List the side chains of amino acids

Answer 13

Alanine –> R=CH3
Serine –> R=CH2OH
Cysteine –> R=CH2SH
Histidine

Question 14

What are good hydrogen bond donors and acceptors?

Answer 14

N –> good donor
O —> good receptor

Question 15

How many residues per turn in a right handed helix?

Answer 15

3.6

Question 16

List some helix formers

Answer 16

• glutamate
• glutamine
• alanine
• histadine
• methionine
• leucine
• lysine
• arginine

Question 17

Give an example of a helix destabiliser

Answer 17

tyrosine

Question 18

Give an example of a helix breaker

Answer 18

proline –> side chain makes bond with N on Ca so bond cannot rotate

Question 19

What R chains does silk fibroin contain?

Answer 19

glycine, alanine

Question 20

What are structural motifs?

Answer 20

• arrangement of tertiary structures
• arrangements occur repeatedly

Question 21

Give some examples of structural motifs

Answer 21

• myaglobin
• IgG
• triose phosphateisomerase

Question 22

List some hydrophobic side chains

Answer 22

• valine
• leucine
• phenylamine

Question 23

List some hydrophilic sidechains

Answer 23

• aspartate
• lysine
• serine

Question 24

What is meant by the entropic effect

Answer 24

• hydrophobic molecule makes water molecules form a cage
• water molecules more ordered

Question 25

What are disulphide bonds?

Answer 25

covalent bonds between two cysteine side-chains

Question 26

Write an equation for pH

Answer 26

pH = pKa + log10[COO-]/[COOH]

Question 27

What is the henderson-hasselbach equation?

Answer 27

pH = pKa +log [base]/[acid]

Question 28

What is meant by the domain?

Answer 28

globular unit formed from part of a polypeptide --> large domain binds ATP

Question 29

What is domain movement governed by?

Answer 29

dGTPase

Question 30

What is the function of SDS

Answer 30

unfolds protein by coating unfolded chain

Question 31

What is the isoelectric point?

Answer 31

pH where a molecule has no net charge

Question 32

Describe the process of isolelectric focusing

Answer 32

- proteins move either towards + or - depending on net charge - as they move along the pH gradient their net charges are reduced - stop moving at the isolelectric point - gel stained with either coomassie blue or silver nitrate

Question 33

What is the difference between SDS PAGE and SEC

Answer 33

SDS PAGE - gives monomer size SEC - gives native size combinations of the two indicates quaternary structure