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Enzymes Flashcards

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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
Lock and key model
The binding site acts as a rigid lock which is complementary to the substrate
26
Induced fit model
Substrate binding → _Structurally interactive process_ * *The enzyme isn't rigid* * *Binding isn't exactly complimentary*
27
Fluctuation theory
* Confirmation of the enzyme's active site always changes * Binding only occurs if substrate is complimentary
28
What is required to initiate _all_ reactions?
Activation energy
29
Activation energy definition
Ea Free energy between initial and transitional state
30
Mechanism of enzyme action
* Enzymes _only_ speed reaction rates * Enzymes _lower activation energy_
31
Mechanism of enzyme action _when the atoms of the molecules are rearranged_
* Hydrate hull removed * Existing bonds in the reactants broken * New bonds of products formed
32
Which levels of specificity are expressed by enzymes
Specificity of: * Reactants * Susceptible bond * Type of product produced
33
List the degree of specificity each specificity type has
Bond (reaction) specificity: **Broad** Group (reaction) specificity: **Medium** Substrate specificity: **Strict** Stereospecificty: **Very strict**
34
Non-specific factors affecting enzymes
Affect the velocity of each enzymatic reaction * Temp * pH * Denaturation
35
Specific factors affecting enzymes
Affecting only certain enzymes * Conc. of reactants (substrate) * Inorganic effectors * Organic effectors
36
Effect of temperature on enzymatic activity
* The velocity of reaction increases with temperature * High temperature kills cells * Work best between 35-40°C (Mammals)
37
Optimal pH for enzymes
Between 6 - 8
38
Reaction velocities are proportional to...
The concentration of the substrate
39
Michaelis Constant
* [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
Enzyme activity _International unit_
µmol/min Amount of enzyme catalysing _1 µmol substrate in 1 minute_
41
Enzyme activity: Katal
mol/sec Amount of enzyme catalysing _1 mol of the substrate in 1 second_
42
Enzyme activity: Turnover
Substrate/sec _Number of substrate molecules_ converted in _1 second by 1 enzyme molecule_
43
List the units of enzyme activity
* International unit * Katal * Turnover
44
Can enzymes speed up reaction rate in reverse?
Yes
45
Give an example of a reversible enzymatic reaction
46
Give examples of irreversible enzymatic reactions
* ATP Degradation * Protein Degradation * Glycogen Degradation * Fatty Acid Oxidation
47
Denaturation
48
* Acids & Bases * Temp * Alcohol * Heavy Metals * Reducing agents
49
Competitive
50
* Non-competitive feedback * Allosteric feedback
51
Competitive Inhibition
Selective inhibition of enzyme activity * Inhibitors resemble normal substrate molecule * Compete for admission to the active site
52
Give an example of competitive inhibition
Inhibition of _Succinate Dehydrogenase_ by _Malonate_
53
Give an example of competitive inhibition in pathology
Inhibition of folic acid synthesis by sulphonamides ## Footnote *Sulphonamides have a similar structure to PABA*
54
How do non-competitive inhibitors function?
* Inhibitors don't bind to an active binding site * Bind to the enzyme, changing the shape of the active site
55
Irreversible inhibition
* The substrate can no longer bind to the active site * Enzyme becomes inactivated
56
Give examples of irreversible inhibition
* _Cytochrome oxidase_ inhibition by _CN_- (Cyanide ions) * Inhibition of enzymes by heavy metals (Hg2+, As2+, Pb2+)
57
Reversible inhibition
Rapid equilibrium of the enzyme and inhibitor
58
Coarse control of enzyme action
* Regulation of enzyme concentration * Repression/inducing of synthesis
59
Constitutive Enzymes
An enzyme that is permanently produced without regulation of enzyme synthesis ## Footnote *e.g Respiratory chain*
60
Fine control of enzyme action
Activity can be: * Allosteric regulation * Covalent modification * Phosphorylation * Zymogen activation * Isoenzymes * Modulator proteins
61
_Induction_ of enzymes
'Turning on' of transcription
62
Repression of enzymes
'Turning off' of transcription
63
Allosteric regulation
* Molecules bind to the allosteric site (not the active site) * May inhibit or stimulate enzyme activity * Key enzymes used in metabolic pathways
64
Allosteric enzymes are constructed from...
2+ polypeptide chains (Quarternary structure)
65
Allosteric activator
When the binding of an allosteric molecule _promotes a shift to the relaxed state._
66
Allosteric inhibitor
When the binding of an allosteric molecule promotes a shift to the tense state.
67
Describe the plot of Substrate concentration against Velocity What does it indicate?
Sigmoidal plot Indicates cooperative effect and inter-molecular communication
68
Feedback inhibition
Example of Allosteric Regulation * Final product of metabolic pathway is: Allosteric inhibitor of the first enzyme * (A feedback molecule)
69
Give an example of feedback inhibition
_Thr-deaminase_ by the end produce _Ile_
70
Fine tuning by phosphorylation
Addition of a specific functional group
71
Give examples of enzyme phosphorylation as a method of enzyme fine tuning
* Glycogen synthase ⇔ Glycogen phosphorylase * Phosphorylase form is the _active_ enzyme _Converter enzymes_ exist to add/remove functional groups
72
Fine tuning by zymogen activation
* 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
Give an example of Zymogen activation
Chymotrypsinogen → π-Chymotrypsin ## Footnote *Activated by Trypsin*
74
Fine tuning by Isoenzymes
* 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
Fine tuning by modulator proteins: example
Catabolite activator protein (CAP)
76
Enzymes of the Nucleus
* DNA polymerase * DNA Ligase * RNA Polymerase
77
Enzymes of the mitochondrial matrix
* Enzymes of: * Citric acid cycle * Fatty acid oxidation * Urea cycle * L-glutamate dehydrogenase
78
Enzymes of the mitochondrial inner membrane
* Enzymes of: * Respiratory chain * Oxidative phosphorylation * Carnitine-fatty acyltransferase II * β-hydroxy-butyrate dehydrogenase
79
Enzymes of the mitochondrial intermembrane space
* Adenylate kinase
80
Enzymes of the mitochondrial outer membrane
* Fatty acyl CoA synthetase * Carnitine-fatty acyltransferase I
81
Enzymes of the lysosomes
* Acid phosphatase * _Ribonuclease_ * _Deoxyribonuclease_ * Protease * Lipase
82
Enzymes of microsomes ## Footnote *e.g Ribosomes, ER, golgi*
* _Peptidyl transferase_ (Protein synthesis) * CYP450
83
Enzymes of the cytosol
Enzymes of: * Glycolysis * Amino acid activation * Fatty acid synthesis
84
Nomenclature of enzymes decided by...
* Substrate + 'ase' * Substrate + 'chemical reaction'
85
Give the major subclasses of enzymes
* Oxidoreductase * Transferase * Hydrolase * Lyase ↔ Synthase * Isomerase * Ligase ↔ Synthetase (ATP)
86
Give an example of an oxidoreductase
Lactate dehydrogenase
87
Give the sub sub-classes of transferase enzymes
* Aldehydtransferases * Ketotransferases * Acyltransferases * Aminotransferases * Phosphotransferases * C1 fragments
88
Give the sub sub-classes of hydrolase
* Esterases * Glycosidases * Peptidases * Amidase
89
Give an example of an esterase
_Lipase_
90
Give examples of glycosidases
* _Amylase_ * _Maltase_
91
Give examples of peptidases
* Pepsin * Trypsin * Elastase * Renin
92
Function of Lyase ↔ Synthase enzymes
* Elimination/addition * Non-hydrolytic cleavage/synthesis of different bonds * _Without_ _breakdown_ _of ATP_
93
Give an example of a Lyase ↔ Synthase enzyme
Carbonic anhydrase
94
Give an example of an isomerase enzyme
Phosphoglucomutase
95
Give examples of a Ligase ↔ Synthetase enzyme
* Aminoacyl-tRNA synthetase * DNA ligase

Biochemistry (21 decks)

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