Enzyme Kinetics

Question 1

Define: Catalyst

Answer 1

Increases the rate of reaction by decreasing the energy barrier

Question 2

Why are enzymes a special type of catalyst?

Answer 2

1. They can increase the rate by 10⁶ to 10¹² greater than non-catalyst reactions, and 10³ increase greater than non-enzymatic catalysts.
2. Can occur in mild conditions (pH 7, >100C°, 1atm)
3. Can be regulated by biologcial molecules

Question 3

Unit (when measuring ezymic activity)

Answer 3

Amount of substrate converted to product in a given time (ex: 1µmol/min)

Question 4

Specific Activity

Answer 4

Number of units per a mg of protein

Question 5

Temperature optimum: definition and average for humans

Answer 5

The temperature at which ezymes perform the best. Typically 37C° for humans

Question 6

pH optimum for pepsin

Answer 6

pH of 2

Question 7

pH optimum of Trypsin

Answer 7

pH of 8

Question 8

Oxidoreductases

Answer 8

Catalyze reduction-oxidation reactions

Question 9

Transferases

Answer 9

Catalyses the transfer of a group (glycosyl, methyl, phosporyl)

Question 10

Hydrolases

Answer 10

Catalyzes hydrolytic cleavage of bonds

(C-C, C-O, C-N, and others)

Question 11

Lyases

Answer 11

Catayzes atom elimination to leave double bonds

(C-C, C-O, C-N, and others)

Question 12

Isomerases

Answer 12

Catalyses geometric/structural changes in a molecule

Question 13

Ligases

Answer 13

Catalyzes the joining of 2 molecules.

Coupled to hydrolysis of ATP

Question 14

Active Site

Answer 14

Specific region on the enzyme where the catalysis occurs. Substrates bind to the active site (plus any required elements) in a specific manor. Enzyme structure determines active site structure, so changes in structure may (or may not) affects the active site.

Question 15

Catalysis by proximity

Answer 15

Molecules must come within bond forming distance. Active sites create a high local concentration of the target molcule by binding it. Substrates are bound in a specific orientation conducive to the reaction.

Question 16

Acid-Base Catalysis

Answer 16

Ionizable functional groups of amino acids may act as an acid or base in the catalysis

Question 17

Catalysis by strain

Answer 17

If catalyzing reaction is to break bonds, the substrates may be bound in such a way that the bonds are destabilized.

Question 18

Covalent Catalysis

Answer 18

The enzyme and substrate covalently bond. The modified enzyme becomes the subtrate for a different reaction.

K_eq of the modified enzyme > K_eq of the inital substrate to the product

Question 19

Prostetic groups

Answer 19

Tightly/stably incorporated into the proteins (sometimes by covalent bonds). Metal ions are the most common.

Question 20

Most common metal prostetic groups

Answer 20

Co, Cu, Mg, Mn, Zn

Question 21

Cofactors

Answer 21

Bind transiently to the substrate or enzyme, but are required for activity

Question 22

Metalloenzymes

Answer 22

Enzymes that contain a metal prostetic group

Question 23

Coenzymes

Answer 23

Accept a group from one reaction, and supplies groups in other reactions

Ex: CoA transfers acyl groups, Folates transfer 1 carbon groups

Question 24

Isoenzymes

Answer 24

Physically different enzymes that catalyze the same reaction. May have different properties like substrate affinities or activity regulation. May be expressed differently by different tissues.

Question 25

Michaelis-Menten equation

Answer 25

V_max is maximum reaction velocity K_m is the substrate concentration when v= 1/2 V_max When [S] = K_m, v=1/2 V_max

Question 26

Significance of the slope, y and x intercept of the Kineweaver-Burk plot

Answer 26

Slope—K_m/V_max Y-intercept — 1/V_max X-Intercept — -1/K_m

Question 27

Competitive Inhibition

Answer 27

Inhibitor competes with the substrate for the active site of the enzyme. Inhibitor is usually structurally similar to the substrate and only binds to the free enzyme.

Question 28

What value do competetive inhibitors increase?

Answer 28

K_m is increased due to the decrease in available enzymes V_max is unaffected because inhibitors can be overcome by the substrates

Question 29

Noncompetitive inhibition

Answer 29

Bind to either the E or ES in a place other than the active site. Heavy metals act via this inhibition.

Question 30

What values do noncompetitive inhibitors affect?

Answer 30

V_max is affects because the inhibitor cannot be displaced by substrates K_m is unaffected

Question 31

Uncompetitive inhibition

Answer 31

Only binds to the ES

Question 32

What values do uncompetitive inhibitiors affect?

Answer 32

K_m and V_max are both affects, creating a parallel line in the Lineweaver-Burk plot

Question 33

When are the top and bottom equations used to calculate K_i?

Answer 33

V^app_max is used to calculated the Ki of noncompetitive and uncompetitive enzymes K^app_m is used to calculate the Ki of uncompetitive enzymes

Question 34

Allosteric Enzymes

Answer 34

The binding of one molecule facilitiates the binding of subsequent molecules to the enzyme. If enzyme has positive cooperativity, will respond quickly to a low amount of S. Binding of S promotes an active conformation

Question 35

What is the Hill equation used for?

Answer 35

To describe the kinetics of allosteric enzymes

Question 36

Homotropic regulation

Answer 36

Binding of S to allosteric enzyme increases the affinity of other catalytic sites for S

Question 37

Heterotropic regulation

Answer 37

Regulatory molecule distinct from the substrate that bonds to a site other than the catalytic sites. Can be positive or negative

Question 38

V-system effectors

Answer 38

Effectors that affect the catalytic rate, thus influencing V_max

Question 39

K-system effectors

Answer 39

Effectors that affect the bonding of the substrate, thus influencing K_0.5. Can be positive or negative.

Question 40

Compartmentalization

Answer 40

Conflicting metabolic pathways are restricted to specific organelles to keep everything physically separate

Question 41

Allosteric regulation

Answer 41

Hormones produce second messengers which are allosteric effectors of various enzymes. Ex: hormones stimulate cAMP production and increase cytosolic [Ca²⁺] that interacts with calmodulin

Question 42

Phosphorylation

Answer 42

Enzymes are affected by phophorylation via a protein kinase (can be specific or general)

Question 43

Proteolytic activation

Answer 43

Some enzymes are synthesized in an inactive form that must be activated via a proteolytic cleavage. (Digestion and coagulation)

Question 44

Name the 3 positive regulators of glycogen phophorylase given in class

Answer 44

1. AMP (allosteric effector) 2. Phophorylation 3. Ca²⁺-calmodulin (Allosteric regulation)