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Biochemistry > Enzymes & Coenzymes > Flashcards

Enzymes & Coenzymes Flashcards

1
Q

Why are enzymes important?

A

natures catalysts
carry out all reactions in the cell
inherited diseases caused by mutations in key enzymes
diagnose diseases
food products and detergents
drug synthesis

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2
Q

What are the 6 classes of enzymes?

A

Oxioreductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase

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3
Q

What is an oxioreductase?

A

Catalyses oxidation-reduction in which oxygen and hydrogen are gained or lost

cytochrome oxidase, lactate dehydrogenase

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4
Q

What is a transferase?

A

Catalyses transfer of functional groups
e.g. amino group, acetyl group or phosphate group

acetate kinase, alanine deaminase

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5
Q

What is a hydrolase?

A

Catalyses hydrolysis
addition of water

Lipase, sucrase

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6
Q

What is a lyase?

A

Catalyses removal of groups of atoms within a molecule

oxalate decarboxylase, isocitrate lyase

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7
Q

What is an isomerase?

A

Catalyses rearrangement of atoms within a molecule

Glucose-phosphate isomerase, alanine racemase

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8
Q

What is a ligase?

A

Catalyses joining of two molecules
using energy usually derived from the breakdown of ATP

Acetyl-CoA synthesise, DNA ligase

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9
Q

Reaction energetics

A

For a favourable reaction, delta G is negative
products lower energy than reactants

speed of reaction (kinetics) determined by activation energy
higher activation energy means a slower reaction

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10
Q

What is the Arrhenius equation?

A

Gives relationship between activation energy and reaction rate constant

k = Ae ^-ae/RT

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11
Q

Energy diagram

A

y = energy state
x= reaction coordinate (time)

Equilibrium will lie heavily to R because of products
Higher the graph hump, the higher the activation energy

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12
Q

What is a transition state?

A

A transient high energy species in conversion of substrate to molecule

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13
Q

What affect do catalysts have on activation energy?

A

Lower the ae for reaction, but don’t change the energy of reaction

can’t make a thermodynamically unfavourable reaction become favourable

don’t change equilibrium position

Products and substrates have same energy with to without an enzyme

make an unstable intermediate more stable, lowering the energy barrier to overcome
creating a faster reaction

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14
Q

What are the roles of an enzyme as a catalyst?

A
  1. enzyme provides specific environment for substrate where reaction more favourable
  2. reaction pocket = active site
  3. lowering activation energy
  4. not used up in the process
  5. enzyme-substrate and enzyme-product are reaction intermediates
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15
Q

LOOK AT ENERGETIC PROFILE OF ENZYME CATALYSED REACTION

A

DIAGRAM

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16
Q

What is an enzyme pocket?

A

Designed to complement reaction transition state
bonds are H bonds, hydrophobic, ionic and VdW
(some transient covalent bond formed)

enzyme complementary to the transition state

17
Q

What is binding energy?

A

Energy derived from enzyme pocket complex

18
Q

What is a coenzyme?

A

Non protein organic molecule required for catalysis

biotin, NAD+, FAD and most vitamins

19
Q

What is a cofactor?

A

Inorganic substances that are required for catalysis

metal ions: Fe2+, Zn2+, Cu2+, Mg2+

20
Q

What is the combination of a coenzyme and cofactor called?

A

Holoenzyme

21
Q

What is a protein without a coenzyme?

A

Apoenzyme

22
Q

What is the function of coenzymes and co factors?

A

allow enzymes to access chemistries that amino acid side chain can’t access

allow for further and different reactions

23
Q

coenzymes

A

have a catalytic role, not substrates
some don’t finish reaction same way they started

24
Q

common coenzymes

A

coenzyme A (HSCoA)
adenosine triphosphate (ATP)
S-adenosyl methionine (SAM)
pyridoxal phosphate (PLP)
thiamine diposhphate (TPP)
nicotinamide adenine dinucleotide - oxidised form (NAD+)
lipoate
glutathione
biotin

25
Q

coenzyme disease

A

arise as result of deficiency in these coenzymes:
megaloblastic anaemia - folic acid deficiency
beriberi for thiamine deficiency
pellagra for nicotinamide deficiency

26
Q

how do enzymes act as general acid-base catalysts?

A

stabilise unstable (charged) transition states
transferring protons to and from them
decreasing their free energy

27
Q

what act as weak proton donors or acceptors

A

amino acid side chains
Glu, Asp, Lys, Arg, His, Cis, Tyr

28
Q

Step 1 RNAse mechanism

A

His12 acts as a general base
- takes proton from RNA 2’-OH (accepts as a base)
- makes a nucleophile
- then attacks the phosphoric group

29
Q

Step 2 RNAse mechanism

A

His119 acts as a general acid
- promotes bond scission
ph gains extra bond, breaks the bond and then donate e-

30
Q

Step 3 RNAse mechanism

A

2’,3’ cyclic intermediate is hydrolysed through reverse step 1
- water replaces the leaving group

31
Q

interactions between enzyme bound metal and substrate can

A

anent a substrate for reaction
stabilise charged reaction states
mediate redox reactions

32
Q

carbonic anhydrase

A

Zn2+ forms bond with OH- ion in active site
Zn is stabilising the hydroxyl

33
Q

Enzyme mechanism

A

formation of transient covalent bond between enzyme and substrate
this complex undergoes a reaction to regenerate free enzyme

this formation offers an alternative route to same products that has a lower activation energy

34
Q

Serine Proteases

A

large family of enzymes
include digestive enzymes and blood clotting enzymes

end-proteases that hydrolyse the peptide bond

have a catalytic trip (3 enzymes in active site) all required for catalysis

35
Q

Protease mechanism

A

mixture of acid-base catalysis & covalent catalysis

serine residue acts as nucleophile and made more nucleophilic by histidine and aspartic acid

36
Q

6 steps of protease mechanism

LOOK AT DIAGRAM

A
  1. ES complex - Michaelis complex
  2. First transition state - Tehtrahedral intermediate
  3. Acyl enzyme intermediate
  4. Acyl enzyme water complex
  5. Second transition state - tetrahedral intermediate
  6. Free enzyme
37
Q

Trypsin in serine protease specificity

A

Cleaves after Arg & Lys
Has an Asp residue in binding pocket

38
Q

Chromotrypsin in serine protease specificity

A

Cleaves after aromatic residues
has serine in bonding pocket

39
Q

Elastase in serine protease specificity

A

Cleaves after small hydrophobic residues
Glycine, alanine and valine

Biochemistry (20 decks)

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