Cofactors and coenzymes

Question 1

What is a cofactor?

Answer 1

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

Question 2

What is a prosthetic group?

Answer 2

A cofactor permanently bound to a protein

Question 3

What is a coenzyme?

Answer 3

A cofactor that associates reversibly with an enzyme

Question 4

What is often the role of Zn²⁺ in cofactors?

Answer 4

Regulating pKa

Question 5

How do NADP+ and NAD+ differ?

Answer 5

By the phosphorylation of the ribose C2

Question 6

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

Answer 6

To add binding sites

Question 7

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

Answer 7

Hydride transfer

Question 8

What is a hydride ion made up of?

Answer 8

2 electrons and 1 proton

Question 9

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

Answer 9

340nm

Question 10

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

Answer 10

It is no longer planar

Question 11

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

Answer 11

Reduced

Question 12

What does a dehydrogenase do?

Answer 12

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

Question 13

What does a reductase do?

Answer 13

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

Question 14

What does an oxidase do?

Answer 14

Catalyses the oxidation of a substrate and reduction of molecular oxugen

Question 15

Which 2 enzymes are involved in alcohol metabolism?

Answer 15

• alcohol dehydrogenase
• aldehyde dedhydrogenase

Question 16

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

Answer 16

NAD+

Question 17

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

Answer 17

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

Question 18

How can flavins act as transducers?

Answer 18

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

Question 19

What are the 3 states flavins can exist in?

Answer 19

• reduced
• Semiquinone
• oxidised

Question 20

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

Answer 20

NADPH oxidase

Question 21

What is the function of NADPH oxidase?

Answer 21

Catalyses the production of reactive oxygen species using electrons from NADPH

Question 22

What cofactors does NADPH oxidase contain?

Answer 22

FAD and 2 heme groups

Question 23

What does NADPH oxidase react with?

Answer 23

Molecular Oxygen (O₂)

Question 24

In what kind of cells is NADPH oxidase present?

Answer 24

Neutrophils

Question 25

Outline how NADPH oxidase can help kill pathogens

Answer 25

* 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

Question 26

Which 2 enzymes shield the body from reactive oxygen species?

Answer 26

* Superoxide dismutase * Catalase

Question 27

What reaction does superoxide dismutase undergo?

Answer 27

2O₂^-+ 2H⁺ → O₂ + H₂O₂

Question 28

What reaction does catalse catalyse?

Answer 28

2H₂O₂ → 2H₂O + O₂

Question 29

What affects the form of superoxide dismutase present?

Answer 29

The metal ion cofactor

Question 30

What are the 3 forms of superoxide dismutase?

Answer 30

* mitochondrial * cytosolic * prokaryotic

Question 31

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

Answer 31

1st

Question 32

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

Answer 32

Managanese

Question 33

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

Answer 33

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

Question 34

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

Answer 34

* Fe²⁺ * Fe³⁺ * Fe⁴⁺

Question 35

Are B vitamins water soluble?

Answer 35

Yes

Question 36

What is the metabolically active form of vitamin B₆?

Answer 36

Pyridoxal phosphate (PLP)

Question 37

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

Answer 37

Lysine

Question 38

What is the first step in all PLP dependent enzymes?

Answer 38

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

Question 39

What is a racemase?

Answer 39

An enzyme that catalyses the inversion of stereochemistry of a substrate

Question 40

What is the name of B₁₂?

Answer 40

Cobalamin

Question 41

What unusual bond is found in vitamin B₁₂?

Answer 41

Cobalt-carbon

Question 42

Why is cobalamin highly coloured?

Answer 42

Due to the delocalised cyclic ring

Question 43

What kind of cyclic molecule does cobalamin contain?

Answer 43

A macrocycle

Question 44

What is the macrocyclic effect?

Answer 44

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

Question 45

What is the advantage of macrocylic ligands over polydentate ligands?

Answer 45

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

Question 46

What are the 3 states of cobalamin?

Answer 46

* Co(I) * Co(II) * Co(III)

Question 47

What is the resting state of cobalamin?

Answer 47

Co(III)

Question 48

What shape complex does Co(III) form?

Answer 48

Octahedral

Question 49

What are the 2 biologically active forms of cobalamin?

Answer 49

* Adenosylocobalamin * Methylcobalamin

Question 50

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

Answer 50

Radical chemistry

Question 51

Outline how adenosylcobalamin works in an enzyme

Answer 51

* 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

Question 52

What is the function of the enzyme methylmalonyl CoA mutase?

Answer 52

Catalyses the rearrangement of methymalonyl-CoA to succinyl CoA

Question 53

What is methylcobalamin a good donor of?

Answer 53

CH₃⁺

Question 54

Give an example of an enzyme which contains methylcobalamin

Answer 54

Methionine synthase

Question 55

What is the role of methionine sythase?

Answer 55

It catalyses the methylation of homocysteine

Question 56

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

Answer 56

* Deprotonation occurs to produce planar intermediates * Reprotonation of the amino acid occurs at the opposite face from where the intial deprotonation occurred

Question 57

What important compound does PLP-dependent transamination produce?

Answer 57

Urea