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Biochemistry II > Rafferty > Flashcards

Rafferty Flashcards

1
Q

what ions are used in oxidation and reduction

A

hydride ions = H- or H+ + 2e-

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2
Q

what is the structure of NAD

A

Nicotinamide adenine dinucleotide (phosphate) NAD(P)
dinucleotide 2 ribose rings connected by 2 phosphates
1st ribose is connected to a nicotinamide ring, where the chemistry occurs
2n ribose is connected to an adenine ring

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3
Q

where does hydride transfer occur in NADH

A

C4 of nicotinamide ring (one opposite to bond with ribose)

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4
Q

what is the difference between NAD+ and NADH

A

NAD+ is the oxidised form it has 1H on the C4 of the nicotinamide ring - the +ve charge is distributed over the ring
NADH is the reduced form it has 2H on the C4 of the nicotinamide ring - it has lost the charge and the plane is disrupted, N has a lone pair

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5
Q

what is the mechanism of hydride transfer of NADH

A

the lone pair from the N moves around the ring to the bond to the 2nd H on the C4 of the nicotinamide ring which leaves a hydride ion, attacking a C breaking a carbonyl (C=O)

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6
Q

what is the difference between NADPH and NADP+

A

an extra P on the 2’ of ribose of adenine
eg. indicates biosynthesis

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7
Q

what is critical to the hydride transfer in NADH

A

the angle of approach due to stereospecificity
distance ~ 3-3.3A

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8
Q

what is acp

A

acyl carrier protein
attached via phosphopantetheine arm
covalently linked to Ser residue on ACP

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9
Q

beta-ketoacyl reductase BKR

A

1st reductive step
Rossman fold
NADPH dependant
tetrameric

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10
Q

what is Rossman fold important for

A

substrate binding

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11
Q

active site of BKR

A

conserved lysine (stabilised -ve O on enolate anion) and tyrosine (4 residues apart) near NAD nic ring

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12
Q

active site of ENR and difference between BKR (and why)

A

conserved lysine and tyrosine are 8 residues apart - the substrate is different

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13
Q

ENR enoyl reductase

A

final reductive step
NADH dependant
also tetrameric

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14
Q

why is ENR a good drug target

A

it is in bac. but differnet in euk. so it is a possible anti-biotic

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15
Q

how to draw ENR mechanism

A

arrow starts from bond between NADH and H (hydride ion)

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16
Q

what is tricolsan

A

substrate intermediate mimic for ENR (Enolate anion)

17
Q

tautomers

A

e- swap between c=c-o and c-c=o
constantly swap
balance changes depending on condition

18
Q

what happens when ENR is inhibited

A

fatty acid synthesis is not completed
membrane disrupted
cell lysed

19
Q

ENR inhibitors how do they work

A

diazaborine - competitive inhibitor, forms covalent bond for nic ring, resistance developed quickly (single base change needed), boron toxic
tricolsan - competitive inhibitor, substrate intermediate mimic (enolate anion)

20
Q

beta hydroxyl dehydratase BHD

A

removes H2O forms double bond

21
Q

how does fatty acid chain elongation occur

A

via successive addition of 2C unites the S-acyl primed acyl carrier protein

22
Q

what is the difference between tautomers and resonance structure

A

tautomers are 2 distinct structures which are in an equilibrium
they convert rapidly between each other (tautomerisation) often involved the movement of a H+ and its accompanying electrons

resonance is 2 representations of the configuration of e- in one structure
the 2 structures do not exist individually

23
Q

what kind of reaction is the breakage of the phosphodiester bond (2 answers)

A

hydrolysis - breaking with water
SN2 - substitution, nucleophile, bimolecular

24
Q

how does the OH- (derived from a water molecule) nucleophile attack the phosphodiester bond

A

attacks the phosphorus of the phosphate ion
attacks from the bottom with the leaving group at the top because it is going to invert the configuration around the phosphorus (means careful arrangement of substrate is needed)

25
Q

how can the RNA phosphodiester bond be self cleaved
what does this result in

A

in alkaline conditions - a base can abstract the proton from the 2’ -OH making a O- nucleophile which can attack the phosphorus
results in a breakage of the 5’ phosphodiester bond using a 3’-2’ cyclic intermediate in which one bond is broken to give a 3’ or 2’ phosphodiester bond (random)

26
Q

how does a restriction endonuclease couple to DNA

A

non-specific binding to stand
linear diffusion - moves along strand like train tracks
specifically binds
couples (bends DNA) –> catalysis

27
Q

structure of EcoRV and EcoR1

A

cup shape for substrate
proline, Asp, Asp/Glu, Lys - split into 2 motifs PD and D/ExK

28
Q

how do RNases utilise metal ions to enable the catalytic process

A

they stabilise the negative charges on the pentavalent intermediate

29
Q

what metal ions are used in RNases

A

Mg2+ and Mn2+
MN more effective but low abundance

Ca2+ seems to have an inhibitory effect

Biochemistry II (8 decks)

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