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Cell Biology And Signaling > Enzyme properties, kinetics and regulation > Flashcards

Enzyme properties, kinetics and regulation Flashcards

1
Q

Definition of an enzyme

A

Biological catalyst, increase R of R without altering final equilibrium between reactants and products, v efficient

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2
Q

Definition of cofactors

A

Inorganic elements, often transition metals as oxidation state can change

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3
Q

Definition of coenzymes

A

Not enzymes or inorganic ions but are still vital to enzyme function

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4
Q

Definition of isoenzymes

A

Different protein structures but catalyst same reaction

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5
Q

Definition of enzyme kinetics

A

The study of the rate of an enzyme catalyses reaction and how that rate varies with different substrate concs, amount of inhibitors, metal ions and cofactors, pH

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6
Q

Definition Kcat

A

Turnover number is equivalent to no of substrate molecules => product in a given unit of time on a single enzyme molecule when enzyme is saturated (s-1)

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7
Q

Definition of competitive inhibitors

A

Block enzyme AS, does not actually bind

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8
Q

Definition of non competitive inhibitors

A

Interfere in some other way, can be reversible or irreversible
Doesn’t actually change shape of AS, changes bonds within AS

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9
Q

Process of enzyme catalysis

A 
S complementary to AS 
Greater affinity between S and AS to form ESC
Catalysis
Lower affinity between S and AS in EPC
Product released from AS
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10
Q

Consequences of enzyme specificity in a compartment

A

Results in complex coordinated metabolic pathways

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11
Q

Classification of the enzymes based on catalytic reaction

A

Further divided into groups according to substrate/source

With 4 digits

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12
Q

Classification on enzymes

A 
Oxidoreductase, 
Transferase,
Hydrolase, 
Lyase,
Isomerase, 
Ligase,
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13
Q

Oxidoreductase

A

Oxidation or reduction

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14
Q

Transferase

A

Transfer functional groups from donor to acceptor

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15
Q

Hydrolase

A

Hydrolysis w H2O

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16
Q

Lyase

A

Groups to C=C, cleavage of C-C, C-O, C-N

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17
Q

Isomerase

A

Isomerisations in same molecule

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18
Q

Ligase

A

Form C-C/C-N w ATP cleavage

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19
Q

Naming of enzymes

A

Substrate reaction type + are

No at front=class

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20
Q

Enzyme structure

A

Proteins, 1+ polypeptide chains w 3D structures
Stabilized by weak HB, ionic bonds, hydrophobic interactions, easy to break
Sensitive to environmental changes, can denature
AS has functional groups that stabilize transition state of reaction
Bonds maintain 3D structures of AS

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21
Q

Lock and key model assumptions

A

Assumes enzyme and AS is rigid

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22
Q

Modifies lock and key model assumptions

A

AS does not have to be completely complementary to S
As S moves into AS, S distorted so it is complementary
Increase in energy level of S, decrease in free energy of product

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23
Q

Induced fit model

A

Shape of AS and S changes, less competition from other molecules
As will only bind to specific functional groups

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24
Q

Catalytic triad in chymotrypsin by hydrolysis

A

Enzyme creates nucleophile from serine side chain
Nucleophile attacks substrate
Covalent intermediate is formed with second product bonded to serine and first product released
Enzyme creates a nucleophile from water molecule
Nucleophile attacks covalent intermediate, breaking covalent bond to serine
Second product is released

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25
Q

Effects of temperature on enzyme reactions

A

Increased temp, increased KE, increased collision theory

Increased optimum, AS denatures, no further reactions can take place

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26
Q

Effect of pH on enzymes reactions

A

Optimum pH can cary depending on the physiological compartment it works in

27
Q

Common enzyme cofactors

A 
Cu2+
Fe2+/3+
K+
Mg2+
Ni2+
Se
Zn2+
28
Q

Enzyme coenzymes

A

NaD+ => NADH + H+
FAD => FADH2
ATP => ADP + Pi

29
Q

What makes isoenzymes different to normal enzymes

A

Different genetic code, catalyses same reaction with different protein structures
Often found in different cellular compartments or different amounts in different tissues
Have distinct biochemical roles

30
Q

Rate of reaction equation

A

change in product/change in time = rate (v)

31
Q

Rate of reaction to conc of substrate

A

Starts linear, rate proportional to substrate conc
Increases substrate conc, rate plateaus out
Ends asymptotically, will never work at max rate

32
Q

Michaelis Menton reaction model

A

k1 k2
E + S <=> ES => E + P
k-1

33
Q

Michaelis Menton reaction model assumptions

A

[S] > [E] so amount of substrate bound to enzyme at 1 time is small
[ES] does not change with time
Initial rates used
E + S <=> ES

34
Q

Michaelis Menton equation

A

Vo = Vmax [S] / Km + [S]

Vmax = max rate when all AS saturated
Km = k-1 +k2 / k1
35
Q

Km values and its significance

A

Higher Km = lower affinity between E and S

36
Q

Michaelis Menton plot

A

When Vmax/2 = Km = [S]

37
Q

Kcat, turnover number

A

Equivalent to no of substrate molecules converted to product in given unit of time on a single saturated enzymes (s-1)

38
Q

How to compare catalytic efficiency

A

Neither Km, Kcat are alone sufficient to compare catalytic efficiency of 2 enzymes
Kcat/Km, specificity constant, provides best method

39
Q

What is the ideal value of Kcat/Km?

A

Be as high as possible!

40
Q

Lineweaver Burke plot equation

A

MM plot/1

1/Vo = Km/Vmax [S] + 1/Vmax

41
Q

What does the x intercept mean on LBP

A

-1/Km

42
Q

What does the y intercept mean on LBP

A

1/Vmax

43
Q

Clinical uses of enzyme measurements

A

Differential diagnoses of disease (investigating plasma levels of escape enzymes)
Lab estimations of metabolites (glucose in body fluids)

44
Q

Describe the 5 forms of lactate dehydrogenase isoemzymes

A 
4H
3H1M
2H2M
1H3M
4M
45
Q

Why do you have different forms of the isoenzymes

A

Need different monomers for operating in different compartments
Low Kcat, low Km or vice versa, depends on conditions

46
Q

Use of isoenzymes

A

Electrophoresis of LDH

Different tissues have different levels of each LDH, diagnostic tool

47
Q

Competitive inhibitors, what changes in MM plots

A

Km altered as affinity of S changes
As [I] increases, affinity decrease
As [s] increases, affinity increases
Vmax/2 does not change

48
Q

Non competitive inhibitors, what changes in MM plots

A

Vmax altered as maximum rate cannot be reached
Km does not change
No effect on Km as AS not affected
Vmax/2 decreases with inhibition

49
Q

Chemical uses of enzyme inhibitor

A

ACE is an enzyme that converts angiotensin I => II
Captopril inhibits ACE, treats heart failure, causes vasodilation and BP falls

Increased acetylcholine, increase cognitive impairment
Acetylcholine esterase (reversible/irreversible) can breakdown ACh
50
Q

How to regulate enzyme activity

A

Allosteric binding sites
Covalent modification by other enzymes
Induction, supression of enzyme synthesis

51
Q

Allosteric regulation and binding

A

Results in sigmoid curve due to cooperative binding
Can be positive, increase chance that S binds to AS
Can be negative, decrease chance that S binds to AS

52
Q

Covalent modification by phosphorylases/kinases

A

Can both activate and deactivate enzymes
Can also result in catalysis of a different reaction
Can also involved other molecules (adenine, methyl, acetyl)

53
Q

Regulating enzyme activity

A

High levels of substrate => high levels of substrate that increase rate of synthesis of key enzymes

54
Q

When substrate availability changes, what changes and time frame

A

Rate

Immediate

55
Q

When product inhibition occurs, what changes and time frame

A

Vm, Km

Immediate

56
Q

When allosteric control occurs, what changes and time frame

A

Vm, Km

Immediate

57
Q

When covalent modification occurs, what changes and time frame

A

Vm, Km

Immediate to minutes

58
Q

When synthesis/degredation of an enzyme occurs, what changes and time frame

A

Amount of enzyme

Hours to days

59
Q

What cofactor does carbonic anhydride need

A

Zn2+

60
Q

What cofactor does glutathione peroxidase need

A

Se

61
Q

What cofactor does urease need

A

Ni2+

62
Q

What cofactors does pyruvate kinase need

A

Mg2+

K+

63
Q

What cofactors does cytochrome oxidase need

A

Fe2+/Fe3+

Cu2+

Cell Biology And Signaling (11 decks)

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