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BIO1332 - Biochemistry > Enzyme and Co-Enzymes > Flashcards

Enzyme and Co-Enzymes Flashcards

1
Q

What is the importance of an enzyme?

A
  • Natural catalysts and carry out all the reactions in the cell
  • Many inherited diseases are caused by mutations in key enzymes
  • Measurement of certain enzymes in blood is used to diagnose disease
  • Used commercially in food products and in detergents
  • Used in drug synthesis
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2
Q

What are the 6 classes that enzymes can be split into?

A
  • Oxidoreductase
  • Transferase
  • Hydrolase
  • Hydrolase
  • Lyase
  • Isomerase
  • Ligase
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3
Q

What is the function of an oxidoreductase in a chemical reaction?

A

Oxidation-reduction in which oxygen and hydrogen are gained or lost

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4
Q

What is the function of a transferase in a chemical reaction?

A

Transfer of functional groups

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5
Q

What is the function of a hydrolase in a chemical reaction?

A

Hydrolysis (addition of water)

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6
Q

What is the function of a lypase in a chemical reaction?

A

Removal of groups of atoms without hydrolysis

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7
Q

What is the function of an isomerase in a chemical reaction?

A

Rearrangement of atoms within a molecule

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8
Q

What is the function of a ligase in a chemical reaction?

A

Joining of two molecules (using energy normally derived from the breakdown of ATO)

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9
Q

Give an example of an oxidoreductase enzyme:

A

Cytochrome oxidase, lactate dehydrogenase

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10
Q

Give an example of a transferase enzyme:

A

Acetate kinase, alanine deaminase

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11
Q

Give an example of a hydrolase enzyme:

A

Lipase, sucrase

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12
Q

Give an example of a lyase enzyme:

A

Oxalate decarboxylase, isocitrate lyase

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13
Q

Give an example of an isomerase enzyme:

A

Glucose-phosphate isomerase, alanine racemase

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14
Q

Give an example of a ligase enzyme:

A

DNA ligase, Acetly-CoA synthetase

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15
Q

Arrehenius equation:

A

k = Ae^-DG‡/RT

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16
Q

Should the DGreaction be positive or negative for the reaction to be favourable?

A

Positive

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17
Q

Finish the sentence: The higher the activation energy, the ….

A

slower the reaction

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18
Q

What is the Arrhenius equation showing?

A

The relationship between activation energy and the reaction rate constant

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19
Q

What is the transition state?

A

Transient high-energy species in the conversion of substrate to product

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20
Q

What is the speed of the reaction dependent on?

A

The activation energy

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21
Q

What does the catalyst?

A

Reduce the activation energy

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22
Q

Does a catalyst lower the activation energy?

A

Yes

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23
Q

Does a catalyst change the energy of a reaction?

A

No

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24
Q

Can a catalyst make a thermodynamically unfavourable reaction become more favourable?

A

No

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25
Q

Can a catalyst change the position of equilibrium?

A

No

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26
Q

Can a catalyst speed up how quickly the reaction reached equilibrium?

A

Yes

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27
Q

What is the role of an enzyme as a catalyst?

A
  • Provides a specific environment for substate so reaction is more favourable
  • Has pocket which is know as the active site
  • Lowers the activation energy
  • Enzyme is regenerated
  • ES AND EP are reaction intermediates
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28
Q

Where does the transition state take place?

A

in the intermediate stage of a reaction

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29
Q

What is bad for the catalysis?

A

Tight binding to wither substrate or products

30
Q

When is it important for the catalyst to bind tightly?

A

During transistion state

31
Q

What happens during transition state?

A
  • The same forces that stabilise protein folding also stabilise the ES‡
  • Some enzymes form transient covalent bonds
  • binding energy is formed during complex formation
  • Enzyme is complimentary to transient state
32
Q

Does an acid a donor or accepter to a proton?

A

Donor

33
Q

Define co-enzyme:

A

Non-protein organic molecules required for catalysis

34
Q

Example of a co-enzyme:

A

biotin, NAD+, FAD

35
Q

Define co-factors:

A

Inorganic substances that are required for catalysis

36
Q

Example of co-factors:

A

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

37
Q

Define holoenzyme:

A

Combination of protein and co-enzyme/co-factor

38
Q

Define apoenzyme:

A

The protein alone without the co-enzyme/ co-factor

39
Q

What do co-enzymes and co-factors allow enzymes to access?

A

Chemistries that amino acid side chains cannot access

40
Q

How can disease result from co-enzymes?

A

Due to a deficiency

41
Q

What coenzyme mediated a carboxylation reaction?

A

Biotin

42
Q

What coenzyme mediated an alkylation reaction?

A

B12

43
Q

What coenzyme mediated an acyl transer reaction? (2)

A

Coenzyme A

Lipoic acid

44
Q

What coenzyme mediated an oxidation-reduction reaction? (2)

A

Flavin coenzyme

Nicotinamide coenzyme

45
Q

What coenzyme mediated an amino group transfer reaction?

A

Pyridoxal phosphate

46
Q

What coenzyme mediated a one-carbon transfer reaction?

A

Tetrahydrofolate

47
Q

What coenzyme mediated an aldehyde transer reaction?

A

Thiamine pyrophosphate

48
Q

What are the three enzyme mechanisms?

A
  • General acid-base catalysts
  • Metal ion catalyse
  • Covalent catalysis
49
Q

What is a general acid-base catalysts?

A

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

50
Q

What do amino acid side chains act as in acid-base catalysts?

A

Weak proton donors or acceptors

51
Q

Describe the RNAse mechanism:

A
  • His12 acts as general base = takes proton from RNA 2’-OH making a nucleophile which attacks the phosphoryl group
  • His119 acts as general base = promotes bond scission
  • 2’,3’ cynic intermediate is hydrolysed through revers of first step (water replaces leading group
  • His12 is the acid
  • His199 acts as the base
52
Q

What type of enzyme mechanism is the RNAse mechanism?

A

Acid-base catalyst

53
Q

What is a metal ion catalysis?

A 
Interactions between an enzyme bound metal and substate can:
orient a substate for reaction
or 
stabilise charged reaction states
or
mediate oxidation-reduction reaction
54
Q

What type of enzyme mechanism is the carbonic anhydrase doing?

A

Metal ion catalysis

55
Q

What does the carbonic anhydrase assist in a reaction?

A

Zn2+ forms a bond with an OH- ion in the active site.

56
Q

Why do water molecules readily dissolve?

A

To give protons

57
Q

What is a covalent catalysis?

A

Formation of transient covalent bond between enzyme and substrate

58
Q

Why do covalent complex undergo a reaction?

A

Regenerate the free enzyme

59
Q

Serine protease has a catalytic triad at the active site. What are the amino acids?

A

Aspartate, histidine and serine

60
Q

What type of enzyme is serine protease?

A

endoproteases

61
Q

What is meany by endoprotease enzyme?

A

hydrolyse the peptide bond

62
Q

What is the protease mechanism?

A

A mixture of acid-base catalysis and covalent catalysis

63
Q

Which amino acid is the most important in the serine protease catalytic triad?

A

Serine

64
Q

Which amino acids acts as the nucleophile in the serine protease?

A

Serine

65
Q

What do the histone and aspartic acid provide to serine?

A

Makes serine more nucleophilic

66
Q

What are the 6 steps in protease mechanism?

A
  • ES complex (Michaelis complex)
  • First transition state (Tetrahedral intermediate)
  • Acyl enzyme intermidate
  • Acyl enzyme water complex
  • Second transition state - Tetrahedral intermediate
  • Free enzyme
67
Q

What is meant by serine protease specificity?

A

Each enzyme has different pockets: Trypsin/Chymotrypsin/Elastase

68
Q

What does the trypsin do?

A

Cleaves after Arg and Lys residues and has an Asp residue in the binding pocket

69
Q

What does the chymotrypsin do?

A

cleaves after aromatic residue and has a serine in the binding point

70
Q

What does the elastase fo?

A

cleaves after small hydrophobic residue e.g glycine, alanine or valine

BIO1332 - Biochemistry (19 decks)

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