BMP: Enzymes 4

Question 1

Enzyme naming

Answer 1

• Most commonly used enzyme names have the suffix “-ase” attached to the name of the substrate of the reaction. Eg: urease (urea), sucrase (sucrose), lactase (lactose).
• Or to a description of the action performed. Eg: lactate dehydrogenase, adenylate cyclase.
• Some enzymes retain trivial historic names which give no clues as to the associated enzyme reaction. Eg: Papain, pepsin, trypsin.

Question 2

What are the 6 major classifications of enzymes? Examples of each

Answer 2

1. Oxidoreductases: catalyse oxidation - reduction reactions e.g. LDH
2. Transferases: Catalyse the transfer of C-, N-, P- containing groups e.g. Kinases, methyltransferases
3. Hydrolases: catalyse bond cleave by the addition of water e.g. phosphatases
4. Lyases: Catalyse bond cleavage of C-C, C-O, C-S and some C-N bonds e.g. pyruvate decarboxylases
5. Isomerases: Catalyse the racemisation of optical or geometric isomers e.g. racemases, isomerases
6. Ligases: Catalyse the formation of bonds between C and O, S or N bonds coupled with the hydrolyses of high energy phosphates e.g. carboxylases

Question 3

What are enzymes?

Answer 3

Protein catalysts that increase th velocity of a reaction without being used up themselves

Question 4

What is the Active site? what happens here?

Answer 4

A 3D complex which is complementray ti the substrate molecule.

The substrate binds to the AS to form a Ezyme-substrate complex (ES). This forms Enzyme-product (EP) which dissociates into E and P

E + S –> ES –> EP –> E + P

Question 5

What is turn over?

Answer 5

The number of substrate molecules converted to product by one enzyme molecule per second

Question 6

Discuss specicity in terms of enzymes

Answer 6

Enzymes are very specific and only interact with a small number of similarly shaped substrates and can only catalyse one type of reaction

Absolute specificity - Only interacts with one substrate molecule

Group specificity - catalyses a family of related compounds

stereospecificity - most enzymes can distinguish between enatimers

Question 7

What are cofactors?

Answer 7

Non-protein cofactors which associate with enzymes and are essential for enzymatic activity

Question 8

What are examples of cofactors?

Answer 8

• metal ions
• non-protein organic molecules called coenzymes e.g. vitamins or vitamin dervivatives

Question 9

What does:

1. Holoenyme
2. Apoenzyme
3. Prosthetic group mean?

Answer 9

1. Refers to the enyzme and its cofactor
2. refers to the enzyme portion of the holoenzyme
3. A tightly bound coenzyme which does not dissocate from the enzyme

Question 10

What are the 2 ways of viewing enzyme mechanism of action?

Answer 10

1. Treats catalysis in terms of energy changes that occur during the reaction; enzymes provide an alternate, energetically favourable reaction pathway different from the non-catalysed reaction.
2. Describes how the active site chemically facilitates catalysis.

Question 11

What is activation energy?

Answer 11

Activation energy is the barrier between substrates and products. It is the difference between reactants (A) and a high energy transition state intermediate (T*) when forming product (B).

A <-> T* <-> B

The minimum energy required by the reacting species in order for a reaction to occur

Question 12

What is reaction velocity?

Answer 12

The number of substrate molecules converted to product per unit time

Question 13

What factors effect reaction velocity?

Answer 13

1. Substrate concentration:
   
   • Increasing [S] increases ROR as more enzyme active sites are bound. This begins to level off as enzyme becomes saturated and further increase has no effec t
2. Temperature:
   
   • Increasing temperature increases ROR, this is because more molecules have sufficent energy to overcome the energy barrier to form products. Too much heat can denature
3. pH
   
   • Different enzymes have optimum pHs. Extremeties of pH can lead to denaturing of enzymes. For enzyme-substrate interaction to occur there require specific groups to be ionised/ unionized

*

Question 14

What i the reaction model?

Answer 14

Enzyme and substrate bind reversibilty to form ES complex whihc subsequently breaks down to form product and enzyme

E + S –(k1)–> E + P

km = k-1 + k2 / k1

Question 15

What is the michealis-menten equation?

Answer 15

Vo = Vmax / Km + [S]

Question 16

What assumptions is there?

Answer 16

1. [S] is small is much greater than [E], so that the amount of substrate bound by the enzyme at any one time is small.
2. [ES] does not change with time as it is in ‘steady state’.
3. Only initial velocities are used in analysis of enzyme reactions as it is only at this time when the reaction is linear with time.

Question 17

What does a low anf high km mean?

Answer 17

•The Michaelis constant (Km) is characteristic for of an enzyme and its substrate, and reflects the affinity of the enzyme for that substrate. Km is numerically equal to [S] at which the reaction velocity is at ½Vmax. Km does not vary with the concentration of enzyme.

–Small Km: A numerically small (low) Km reflects a high affinity of the enzyme for substrate because a low concentration of substrate is needed to half-saturate the enzyme i.e. to reach ½Vmax

–High Km: A numerically large (high) Km reflects a low affinity for the substrate because a high concentration is required to half-saturate the enzyme.

Question 18

What is ROR related too?

Answer 18

Directly proportional to enzyme conc at all [S]

Question 19

What is the order of reaction during michealis-menten plot?

Answer 19

1. When [S] much lower than km the reaction velocity is roughly proportional to [S]. First order
2. When [S] is much greater than km the reaction is equal to Vm and velocity constant. Zero order

Question 20

What is the lineweaver burk equation?

Answer 20

Question 21

What is an inhibitor?

Answer 21

Any substance that can dimish the velocity of an enxyme catalysed reaction

Question 22

How do reversible inhibitors bind to enzymes?

How is this reversd?

Answer 22

1. Non-covaently
2. •Dilution of the enzyme-inhibitor complex results in dissociation of the reversibly-bound inhibitor and recovery of enzyme activity.

Question 23

What are irreversbile inhibitors? How do they bind?

Answer 23

• Irreversible inhibition occurs when aninhibited enzyme does not regain activity upon dilution of the enzyme-inhibitor complex.
• Some irreversible inhibitors act by forming covalent bonds with specific groups of enzymes

Question 24

What happens during competitive inhibition?

What happens to km and vmax?

Answer 24

1. •Occurs when the inhibitor binds reversibly to the same site that the substrate would normally occupy and, therefore competes with the substrate for that site.

Question 25

Effect of CI on Vmax, Km and LWBP

Answer 25

1. Effect on Vmax: The effect of a competitive inhibitor is reversed by increasing [S]. At a sufficiently high substrate concentration, the reaction velocity reaches the Vmax observed in the absence of inhibitor.
2. Effect on Km: A competitive inhibitor increases the apparent Km for a given substrate. This means that in the presence of a competitive inhibitor more substrate is needed to achieve ½Vmax.
3. Effect on Lineweaver-Burke plot: Competitive inhibition shows a characteristic Lineweaver-Burke plot in which the plots of the inhibited and non-inhibited reactions intersect on the y-axis. The inhibited and non-inhibited reactions show different x-axis intercepts, indicating that the apparent Km is increased in the presence of the competitive inhibitor.

Question 26

What is an example of a competivie inhibitor?

Answer 26

Malonate

Question 27

Describe non-competive inhibition

Answer 27

• This type of inhibition is recognised by its characteristic effect on Vmax.
• Noncompetitive inhibition occurs when the substrate and inhibitor bind at different sites on the enzyme.
• The noncompetitive inhibitor can bind either free enzyme or the ES complex and prevents the reaction from occurring.

Question 28

Effects of CI on Vmax, km, LWBP

Answer 28

1. Effect on Vmax: Noncompetitive inhibitioncannot be overcome by increasing the concentration of substrate. Thus, noncompetitive inhibitors decrease the Vmax of the reaction.
2. Effect on Km: Noncompetitive inhibitors do not interfere with the binding of substrate to enzyme. Thus, the enzyme shows the same Km in the presence or absence of the noncompetitive inhibitor.
3. Effect on Lineweaver-Burke plot: Noncompetitive inhibition is readily differentiated from competitive inhibition as Vmax decreases and Km remains unchanged.

Question 29

What is an example of a noncompetivie inhibitor?

Answer 29

lead