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Biochemistry > Enzymes > Flashcards

Enzymes Flashcards

1
Q

Enzyme definition

A

Proteins that speed up a chemical reaction in a living organism

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2
Q

The term ‘enzyme’ was created by…

A

Wilhelm Kühne

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3
Q

Eduard Büchner discovered…

A

Cell-free fermentation

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4
Q

Who showed that enzymes are pure proteins?

Who verified this?

A

James B. Sumner

Verified by Northrop and Stanley

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5
Q

What are the roles of enzymes in vet med?

A
  • Speed chemical reactions in the intermediary metabolism
  • Speed degradation during digestion
  • Measure elevation of enzyme/substrate/product concentration in blood
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6
Q

Enzymes which don’t require cofactors to show full activity

A

Ser-proteases

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7
Q

Examples of cofactors

A
  • Metal ions
  • Water-soluble vitamin derivatives (coenzymes)
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8
Q

Example of an enzyme containing a metal cofactor (4 x Zn)

A

Carbonic anhydrase

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9
Q

Role of coenzymes

A

Intermediary carriers of:

  • Electrons
  • Specific atoms
  • Functional groups in biochemical reactions
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10
Q

Enzyme + Coenzyme

A

Holoenzyme

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11
Q

Enzyme - Coenzyme

A

Apoenzyme

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12
Q

Annotate the figure

A

Grey: Apoenzyme

Green: Cofactor

Yellow: Substrate

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13
Q

Tightly bound organic cofactors

A

Prosthetic groups

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14
Q

How big a portion of the enzyme is the active site?

A

3-4 amino acids (relatively small portion)

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15
Q

The components of the active site

A
  • Substrate binding site
  • Catalytic site

Making it highly specific

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16
Q

After catalysing a reaction, enzymes are…

A

Unchanged

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17
Q

Give examples of Serine-proteases

A
  • Chymotrypsin
  • Trypsin
  • Elastase
  • Acetylcholinesterase
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18
Q

Chymotrypsin has a large pocket which can accommodate the side chains of…

A
  • Phenylalanine
  • Tyrosine
  • Tryptophan
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19
Q

Give the substrate binding sites of Chymotrypsin

A
  • Ser-189
  • Gly-216
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20
Q

Give the substrate binding sites of Elastase

A
  • Ser-189
  • Val-216
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21
Q

Elastase accommodates which side chains?

A
  • Phe
  • Leu
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22
Q

The catalytic site of Ser-proteases

A

Ser-195

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23
Q

Ser-195 can be inhibited by…

A

diisopropylphospho-fluridate

(DIPF)

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24
Q

Give the models of enzyme binding

A
  • Lock and Key
  • Induced Fit
  • Fluctuation theory
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25
Q

Lock and key model

A

The binding site acts as a rigid lock which is complementary to the substrate

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26
Q

Induced fit model

A

Substrate binding → Structurally interactive process

  • The enzyme isn’t rigid
  • Binding isn’t exactly complimentary
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27
Q

Fluctuation theory

A
  • Confirmation of the enzyme’s active site always changes
  • Binding only occurs if substrate is complimentary
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28
Q

What is required to initiate all reactions?

A

Activation energy

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29
Q

Activation energy definition

A

Ea

Free energy between initial and transitional state

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30
Q

Mechanism of enzyme action

A
  • Enzymes only speed reaction rates
  • Enzymes lower activation energy
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31
Q

Mechanism of enzyme action when the atoms of the molecules are rearranged

A
  • Hydrate hull removed
  • Existing bonds in the reactants broken
  • New bonds of products formed
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32
Q

Which levels of specificity are expressed by enzymes

A

Specificity of:

  • Reactants
  • Susceptible bond
  • Type of product produced
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33
Q

List the degree of specificity each specificity type has

A

Bond (reaction) specificity: Broad

Group (reaction) specificity: Medium

Substrate specificity: Strict

Stereospecificty: Very strict

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34
Q

Non-specific factors affecting enzymes

A

Affect the velocity of each enzymatic reaction

  • Temp
  • pH
  • Denaturation
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35
Q

Specific factors affecting enzymes

A

Affecting only certain enzymes

  • Conc. of reactants (substrate)
  • Inorganic effectors
  • Organic effectors
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36
Q

Effect of temperature on enzymatic activity

A
  • The velocity of reaction increases with temperature
  • High temperature kills cells
  • Work best between 35-40°C (Mammals)
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37
Q

Optimal pH for enzymes

A

Between 6 - 8

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38
Q

Reaction velocities are proportional to…

A

The concentration of the substrate

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39
Q

Michaelis Constant

A
  • [S] = Km
  • Substrate concentration where velocity is half of the max value
  • _(_Enzyme is 50% saturated by the substrate)
  • Active enzymes have a lower Km
40
Q

Enzyme activity International unit

A

µmol/min

Amount of enzyme catalysing 1 µmol substrate in 1 minute

41
Q

Enzyme activity: Katal

A

mol/sec

Amount of enzyme catalysing 1 mol of the substrate in 1 second

42
Q

Enzyme activity: Turnover

A

Substrate/sec

Number of substrate molecules converted in 1 second by 1 enzyme molecule

43
Q

List the units of enzyme activity

A
  • International unit
  • Katal
  • Turnover
44
Q

Can enzymes speed up reaction rate in reverse?

45
Q

Give an example of a reversible enzymatic reaction

46
Q

Give examples of irreversible enzymatic reactions

A
  • ATP Degradation
  • Protein Degradation
  • Glycogen Degradation
  • Fatty Acid Oxidation
47
Q
A

Denaturation

48
Q
A
  • Acids & Bases
  • Temp
  • Alcohol
  • Heavy Metals
  • Reducing agents
49
Q
A

Competitive

50
Q
A
  • Non-competitive feedback
  • Allosteric feedback
51
Q

Competitive Inhibition

A

Selective inhibition of enzyme activity

  • Inhibitors resemble normal substrate molecule
  • Compete for admission to the active site
52
Q

Give an example of competitive inhibition

A

Inhibition of Succinate Dehydrogenase by Malonate

53
Q

Give an example of competitive inhibition in pathology

A

Inhibition of folic acid synthesis by sulphonamides

Sulphonamides have a similar structure to PABA

54
Q

How do non-competitive inhibitors function?

A
  • Inhibitors don’t bind to an active binding site
  • Bind to the enzyme, changing the shape of the active site
55
Q

Irreversible inhibition

A
  • The substrate can no longer bind to the active site
  • Enzyme becomes inactivated
56
Q

Give examples of irreversible inhibition

A
  • Cytochrome oxidase inhibition by CN- (Cyanide ions)
  • Inhibition of enzymes by heavy metals (Hg2+, As2+, Pb2+)
57
Q

Reversible inhibition

A

Rapid equilibrium of the enzyme and inhibitor

58
Q

Coarse control of enzyme action

A
  • Regulation of enzyme concentration
  • Repression/inducing of synthesis
59
Q

Constitutive Enzymes

A

An enzyme that is permanently produced without regulation of enzyme synthesis

e.g Respiratory chain

60
Q

Fine control of enzyme action

A

Activity can be:

  • Allosteric regulation
  • Covalent modification
    • Phosphorylation
    • Zymogen activation
  • Isoenzymes
  • Modulator proteins
61
Q

Induction of enzymes

A

‘Turning on’ of transcription

62
Q

Repression of enzymes

A

‘Turning off’ of transcription

63
Q

Allosteric regulation

A
  • Molecules bind to the allosteric site (not the active site)
  • May inhibit or stimulate enzyme activity
  • Key enzymes used in metabolic pathways
64
Q

Allosteric enzymes are constructed from…

A

2+ polypeptide chains (Quarternary structure)

65
Q

Allosteric activator

A

When the binding of an allosteric molecule promotes a shift to the relaxed state.

66
Q

Allosteric inhibitor

A

When the binding of an allosteric molecule promotes a shift to the tense state.

67
Q

Describe the plot of Substrate concentration against Velocity

What does it indicate?

A

Sigmoidal plot

Indicates cooperative effect and inter-molecular communication

68
Q

Feedback inhibition

A

Example of Allosteric Regulation

  • Final product of metabolic pathway is: Allosteric inhibitor of the first enzyme
  • (A feedback molecule)
69
Q

Give an example of feedback inhibition

A

Thr-deaminase by the end produce Ile

70
Q

Fine tuning by phosphorylation

A

Addition of a specific functional group

71
Q

Give examples of enzyme phosphorylation as a method of enzyme fine tuning

A
  • Glycogen synthase ⇔ Glycogen phosphorylase
  • Phosphorylase form is the active enzyme

Converter enzymes exist to add/remove functional groups

72
Q

Fine tuning by zymogen activation

A
  • Zymogen = Inactive enzyme precursor
  • Longer polypeptide to be hydrolysed
  • Cleavage of the polypeptide active site by protease(s)
  • ‘Pro-sequence’ release and enzyme activation
73
Q

Give an example of Zymogen activation

A

Chymotrypsinogen → π-Chymotrypsin

Activated by Trypsin

74
Q

Fine tuning by Isoenzymes

A
  • An isoform of an enzyme
  • Differ slightly in the amino acid sequence
  • Therefore differ in catalytic properties
  • Catalytic properties can be tailored to suit a certain tissue
75
Q

Fine tuning by modulator proteins: example

A

Catabolite activator protein (CAP)

76
Q

Enzymes of the Nucleus

A
  • DNA polymerase
  • DNA Ligase
  • RNA Polymerase
77
Q

Enzymes of the mitochondrial matrix

A
  • Enzymes of:
    • Citric acid cycle
    • Fatty acid oxidation
    • Urea cycle
  • L-glutamate dehydrogenase
78
Q

Enzymes of the mitochondrial inner membrane

A
  • Enzymes of:
    • Respiratory chain
    • Oxidative phosphorylation
  • Carnitine-fatty acyltransferase II
  • β-hydroxy-butyrate dehydrogenase
79
Q

Enzymes of the mitochondrial intermembrane space

A
  • Adenylate kinase
80
Q

Enzymes of the mitochondrial outer membrane

A
  • Fatty acyl CoA synthetase
  • Carnitine-fatty acyltransferase I
81
Q

Enzymes of the lysosomes

A
  • Acid phosphatase
  • Ribonuclease
  • Deoxyribonuclease
  • Protease
  • Lipase
82
Q

Enzymes of microsomes

e.g Ribosomes, ER, golgi

A
  • Peptidyl transferase (Protein synthesis)
  • CYP450
83
Q

Enzymes of the cytosol

A

Enzymes of:

  • Glycolysis
  • Amino acid activation
  • Fatty acid synthesis
84
Q

Nomenclature of enzymes decided by…

A
  • Substrate + ‘ase’
  • Substrate + ‘chemical reaction’
85
Q

Give the major subclasses of enzymes

A
  • Oxidoreductase
  • Transferase
  • Hydrolase
  • Lyase ↔ Synthase
  • Isomerase
  • Ligase ↔ Synthetase (ATP)
86
Q

Give an example of an oxidoreductase

A

Lactate dehydrogenase

87
Q

Give the sub sub-classes of transferase enzymes

A
  • Aldehydtransferases
  • Ketotransferases
  • Acyltransferases
  • Aminotransferases
  • Phosphotransferases
  • C1 fragments
88
Q

Give the sub sub-classes of hydrolase

A
  • Esterases
  • Glycosidases
  • Peptidases
  • Amidase
89
Q

Give an example of an esterase

90
Q

Give examples of glycosidases

A
  • Amylase
  • Maltase
91
Q

Give examples of peptidases

A
  • Pepsin
  • Trypsin
  • Elastase
  • Renin
92
Q

Function of Lyase ↔ Synthase enzymes

A
  • Elimination/addition
  • Non-hydrolytic cleavage/synthesis of different bonds
  • Without breakdown of ATP
93
Q

Give an example of a Lyase ↔ Synthase enzyme

A

Carbonic anhydrase

94
Q

Give an example of an isomerase enzyme

A

Phosphoglucomutase

95
Q

Give examples of a Ligase ↔ Synthetase enzyme

A
  • Aminoacyl-tRNA synthetase
  • DNA ligase

Biochemistry (21 decks)

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