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Biological Chemistry 1A > Cofactors and coenzymes > Flashcards

Cofactors and coenzymes Flashcards

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1
Q

What is a cofactor?

A

A non-protein chemical molecule required for the biological activity of a protein

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2
Q

What is a prosthetic group?

A

A cofactor permanently bound to a protein

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3
Q

What is a coenzyme?

A

A cofactor that associates reversibly with an enzyme

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4
Q

What is often the role of Zn2+ in cofactors?

A

Regulating pKa

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5
Q

How do NADP+ and NAD+ differ?

A

By the phosphorylation of the ribose C2

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6
Q

What is the purpose of most of the NAD(P)H molecule?

A

To add binding sites

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7
Q

What is the fundamental reaction that NAD(P)H undergoes?

A

Hydride transfer

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8
Q

What is a hydride ion made up of?

A

2 electrons and 1 proton

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9
Q

At what wavelength does the reduced form of NADH absorb light?

A

340nm

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10
Q

What happens to the geometry of the NAD(P)+ molecule once it has accepted a hydride?

A

It is no longer planar

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11
Q

Does the reduced or oxidised form of NAD(P)H fluoresce at 340nm?

A

Reduced

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12
Q

What does a dehydrogenase do?

A

Catalyses the oxidation of a substrate by NAD(P)+ to form NAD(P)H

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13
Q

What does a reductase do?

A

Catalyses the reduction of a substrate by NAD(P)H to form NAD(P)+

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14
Q

What does an oxidase do?

A

Catalyses the oxidation of a substrate and reduction of molecular oxugen

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15
Q

Which 2 enzymes are involved in alcohol metabolism?

A
  • alcohol dehydrogenase
  • aldehyde dedhydrogenase
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16
Q

What do both ADH and ALDH (aldehyde dehydrogenase) depend on?

A

NAD+

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17
Q

What is the role of zinc in the alcohol dehydrogenase mechanism?

A

It acts as a Lewis acid and weakens the OH bond (reduced pKa)

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18
Q

How can flavins act as transducers?

A

They can convert a 2 electron donor (hydride) into single electrons

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19
Q

What are the 3 states flavins can exist in?

A
  • reduced
  • Semiquinone
  • oxidised
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20
Q

Give an example of an enzyme which uses FAD (flavin adenine dinucleotide) as a transducer

A

NADPH oxidase

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21
Q

What is the function of NADPH oxidase?

A

Catalyses the production of reactive oxygen species using electrons from NADPH

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22
Q

What cofactors does NADPH oxidase contain?

A

FAD and 2 heme groups

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23
Q

What does NADPH oxidase react with?

A

Molecular Oxygen (O2)

24
Q

In what kind of cells is NADPH oxidase present?

A

Neutrophils

25
Q

Outline how NADPH oxidase can help kill pathogens

A
  • FAD accepts a H- from NADPH
  • Then gives one e- to each heme
  • When the 2nd heme receives an e- it can react with O2
  • O2 picks up an electron and forms superoxide which goes on to produce hypochlorous acid
26
Q

Which 2 enzymes shield the body from reactive oxygen species?

A
  • Superoxide dismutase
  • Catalase
27
Q

What reaction does superoxide dismutase undergo?

A

2O2-+ 2H+ → O2 + H2O2

28
Q

What reaction does catalse catalyse?

A

2H2O2 → 2H2O + O2

29
Q

What affects the form of superoxide dismutase present?

A

The metal ion cofactor

30
Q

What are the 3 forms of superoxide dismutase?

A
  • mitochondrial
  • cytosolic
  • prokaryotic
31
Q

What order is the reaction which superoxide dismutase undergoes with respect to superoxide?

A

1st

32
Q

Which metal is the cofactor in the mitchondrial form of superoxide dismutase?

A

Managanese

33
Q

How is the manganese ion held in place in mitochondrial superoxide dismutase?

A

By coordination bonds to 4 ligands (3 histidine and 1 aspartic acid residues)

34
Q

What are the 3 most common oxidation states for iron under physiological conditions?

A
  • Fe2+
  • Fe3+
  • Fe4+
35
Q

Are B vitamins water soluble?

A

Yes

36
Q

What is the metabolically active form of vitamin B6?

A

Pyridoxal phosphate (PLP)

37
Q

Which amino acid is involved in the activation step of PLP dependent enzymes?

A

Lysine

38
Q

What is the first step in all PLP dependent enzymes?

A

Imine exchange, the active site lysine is displaced by the amino acid substrate

39
Q

What is a racemase?

A

An enzyme that catalyses the inversion of stereochemistry of a substrate

40
Q

What is the name of B12?

A

Cobalamin

41
Q

What unusual bond is found in vitamin B12?

A

Cobalt-carbon

42
Q

Why is cobalamin highly coloured?

A

Due to the delocalised cyclic ring

43
Q

What kind of cyclic molecule does cobalamin contain?

A

A macrocycle

44
Q

What is the macrocyclic effect?

A

The ligand (in this case cobalamin) is cyclic and has mutiple coordination bonds to the metal ion which has the effect of kinetically and thermodynamically stabilising the complex

45
Q

What is the advantage of macrocylic ligands over polydentate ligands?

A

With macrocycles even if a coordinate bond is broken the metal ion is still held firmly in place. They do not release metal ions easily

46
Q

What are the 3 states of cobalamin?

A
  • Co(I)
  • Co(II)
  • Co(III)
47
Q

What is the resting state of cobalamin?

A

Co(III)

48
Q

What shape complex does Co(III) form?

A

Octahedral

49
Q

What are the 2 biologically active forms of cobalamin?

A
  • Adenosylocobalamin
  • Methylcobalamin
50
Q

What is the prescence of adenosylcobalamin in an enzyme indicative of?

A

Radical chemistry

51
Q

Outline how adenosylcobalamin works in an enzyme

A
  • Subrate binds and prompts homolytic cleavage of the carbon-cobalt bond which produces radicals
  • Radical is transferred to substrate which rearranges to form product radical
  • radical is transferred back to CH3Ad
52
Q

What is the function of the enzyme methylmalonyl CoA mutase?

A

Catalyses the rearrangement of methymalonyl-CoA to succinyl CoA

53
Q

What is methylcobalamin a good donor of?

A

CH3+

54
Q

Give an example of an enzyme which contains methylcobalamin

A

Methionine synthase

55
Q

What is the role of methionine sythase?

A

It catalyses the methylation of homocysteine

56
Q

How does PLP-dependent L-amino acid racemase work?

A
  • Deprotonation occurs to produce planar intermediates
  • Reprotonation of the amino acid occurs at the opposite face from where the intial deprotonation occurred
57
Q

What important compound does PLP-dependent transamination produce?

A

Urea

Biological Chemistry 1A (10 decks)

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