Enzyme properties, kinetics and regulation

Question 1

Definition of an enzyme

Answer 1

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

Question 2

Definition of cofactors

Answer 2

Inorganic elements, often transition metals as oxidation state can change

Question 3

Definition of coenzymes

Answer 3

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

Question 4

Definition of isoenzymes

Answer 4

Different protein structures but catalyst same reaction

Question 5

Definition of enzyme kinetics

Answer 5

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

Question 6

Definition Kcat

Answer 6

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)

Question 7

Definition of competitive inhibitors

Answer 7

Block enzyme AS, does not actually bind

Question 8

Definition of non competitive inhibitors

Answer 8

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

Question 9

Process of enzyme catalysis

Answer 9

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

Question 10

Consequences of enzyme specificity in a compartment

Answer 10

Results in complex coordinated metabolic pathways

Question 11

Classification of the enzymes based on catalytic reaction

Answer 11

Further divided into groups according to substrate/source

With 4 digits

Question 12

Classification on enzymes

Answer 12

Oxidoreductase, 
Transferase,
Hydrolase, 
Lyase,
Isomerase, 
Ligase,

Question 13

Oxidoreductase

Answer 13

Oxidation or reduction

Question 14

Transferase

Answer 14

Transfer functional groups from donor to acceptor

Question 15

Hydrolase

Answer 15

Hydrolysis w H2O

Question 16

Lyase

Answer 16

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

Question 17

Isomerase

Answer 17

Isomerisations in same molecule

Question 18

Ligase

Answer 18

Form C-C/C-N w ATP cleavage

Question 19

Naming of enzymes

Answer 19

Substrate reaction type + are

No at front=class

Question 20

Enzyme structure

Answer 20

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

Question 21

Lock and key model assumptions

Answer 21

Assumes enzyme and AS is rigid

Question 22

Modifies lock and key model assumptions

Answer 22

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

Question 23

Induced fit model

Answer 23

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

Question 24

Catalytic triad in chymotrypsin by hydrolysis

Answer 24

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

Question 25

Effects of temperature on enzyme reactions

Answer 25

Increased temp, increased KE, increased collision theory | Increased optimum, AS denatures, no further reactions can take place

Question 26

Effect of pH on enzymes reactions

Answer 26

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

Question 27

Common enzyme cofactors

Answer 27

``` Cu2+ Fe2+/3+ K+ Mg2+ Ni2+ Se Zn2+ ```

Question 28

Enzyme coenzymes

Answer 28

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

Question 29

What makes isoenzymes different to normal enzymes

Answer 29

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

Question 30

Rate of reaction equation

Answer 30

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

Question 31

Rate of reaction to conc of substrate

Answer 31

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

Question 32

Michaelis Menton reaction model

Answer 32

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

Question 33

Michaelis Menton reaction model assumptions

Answer 33

[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

Question 34

Michaelis Menton equation

Answer 34

Vo = Vmax [S] / Km + [S] ``` Vmax = max rate when all AS saturated Km = k-1 +k2 / k1 ```

Question 35

Km values and its significance

Answer 35

Higher Km = lower affinity between E and S

Question 36

Michaelis Menton plot

Answer 36

When Vmax/2 = Km = [S]

Question 37

Kcat, turnover number

Answer 37

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

Question 38

How to compare catalytic efficiency

Answer 38

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

Question 39

What is the ideal value of Kcat/Km?

Answer 39

Be as high as possible!

Question 40

Lineweaver Burke plot equation

Answer 40

MM plot/1 | 1/Vo = Km/Vmax [S] + 1/Vmax

Question 41

What does the x intercept mean on LBP

Answer 41

-1/Km

Question 42

What does the y intercept mean on LBP

Answer 42

1/Vmax

Question 43

Clinical uses of enzyme measurements

Answer 43

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

Question 44

Describe the 5 forms of lactate dehydrogenase isoemzymes

Answer 44

``` 4H 3H1M 2H2M 1H3M 4M ```

Question 45

Why do you have different forms of the isoenzymes

Answer 45

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

Question 46

Use of isoenzymes

Answer 46

Electrophoresis of LDH | Different tissues have different levels of each LDH, diagnostic tool

Question 47

Competitive inhibitors, what changes in MM plots

Answer 47

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

Question 48

Non competitive inhibitors, what changes in MM plots

Answer 48

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

Question 49

Chemical uses of enzyme inhibitor

Answer 49

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 ```

Question 50

How to regulate enzyme activity

Answer 50

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

Question 51

Allosteric regulation and binding

Answer 51

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

Question 52

Covalent modification by phosphorylases/kinases

Answer 52

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

Question 53

Regulating enzyme activity

Answer 53

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

Question 54

When substrate availability changes, what changes and time frame

Answer 54

Rate | Immediate

Question 55

When product inhibition occurs, what changes and time frame

Answer 55

Vm, Km | Immediate

Question 56

When allosteric control occurs, what changes and time frame

Answer 56

Vm, Km | Immediate

Question 57

When covalent modification occurs, what changes and time frame

Answer 57

Vm, Km | Immediate to minutes

Question 58

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

Answer 58

Amount of enzyme | Hours to days

Question 59

What cofactor does carbonic anhydride need

Answer 59

Zn2+

Question 60

What cofactor does glutathione peroxidase need

Answer 60

Se

Question 61

What cofactor does urease need

Answer 61

Ni2+

Question 62

What cofactors does pyruvate kinase need

Answer 62

Mg2+ | K+

Question 63

What cofactors does cytochrome oxidase need

Answer 63

Fe2+/Fe3+ | Cu2+