Lec 1 - Fatty acid biosynthesis 1

Question 1

Why, in biological applications, can borohydride (BH4-) not be used as a reductant? What alternative is used for biological systems?

Answer 1

v powerful reductant B is toxic to the cells - NAD(P)H

Question 2

Give the full name of NADP

Answer 2

nicotinamide adenine dinucleotide (P)

Question 3

Draw a rough outline of the NADP structure

Answer 3

Question 4

In which form, NADH or NAD+, do we get a planar e- ring structure and why?

Answer 4

NAD+ - only 1 H at C4 therefore planar 2 Hs @ C4 means that 1 H is pointing above the plane and one is pointing below

Question 5

Draw a generalised mechanism of an NADH cofactor and an acyl group being reduced

Answer 5

Question 6

What are the 2 key things that correct H- transfer has to have in order to achieve perfect stereospecificity?

Answer 6

cofactor and substrate have to be at correct angle and distance for H- efficent transfer

Question 7

What is the normal distance between NADH and its substrate for H- transfer to occur?

Answer 7

VDW distance (3.5A)

Question 8

Regarding the orbitals of the C in a C=O bond, which direction/angle are they in in order for nucleophilic attack to occur?

Answer 8

orbitals are pointing away from the node

Question 9

Name the enzyme system that carries out fatty acid (FA) biosynthesis

Answer 9

Fatty acid synthetase enzyme (FAS)

Question 10

Name the types of FAS and state which organisms they are present in

Answer 10

FAS I - vertebrates, yeast, some bacteria FAS II - plants, most bacteria (eg E. coli, M. tuberculosis)

Question 11

Describe Type I / II FAS systems

Answer 11

Type I - one/two polypeptides w/ catalytic domains Type II - multiple polypeptides each catalysing a single step

Question 12

Draw the fatty acid elongation cycle

Answer 12

Question 13

Describe the FA elongation cycle (in general terms)

Answer 13

addition of 2C units to an S-acyl primed ACYL CARRIER PROTEIN

Question 14

Describe the structure of an E. coli ACP

Answer 14

ACP - phosphopantetheine arm - Ser - covalently linked acyl groups

Question 15

What happens to the binding pocket of ACP during FA elongation? What also happens to the phospopantetheine arm and and FA chain?

Answer 15

the binding pocket expands to accommodate the growing peptide chain - adopt a number of different binding modes and configurations

Question 16

Draw out the reaction mechanism that is catalysed by Beta Keto ACP reductase (BKR)

Answer 16

Question 17

What 2 key residues are in the AS of BKR?

Answer 17

Lys and Tyr

Question 18

Describe the BKR structure

Answer 18

• tetramer
• NADPH dependent
• Rossman fold