Enzymes

Question 1

Not all enzymes exhibit these specificities

Answer 1

Substrate specificity: only bind & react a single substrate/group of substrates

Reaction specificity: only catalyze one type of reaction

Tissue specificity, others are ubiquitous

Question 2

How do enzymes cause reactions to reach quilibrium more quickly?

Answer 2

they accelerate the rate without changing the thermodynamics

Question 3

How do enzymes accelerate rxn rates?

Answer 3

They form weak bonds (hydrogen, hydrophobic, ionic, vdw) between the enzymes and the substrate that puts the substrate in a favorable position for hte reaction

Question 4

If a reaction is to proceed from substrate to product, it’s thermodynamically favorable and the ground state of the ___ is lower than that of the ___.

Answer 4

Product’s ground state is lower than that of the substrate

Question 5

Enzymes lower

Answer 5

the energy required to achieve the transition state

Question 6

Change in free energy of activation(delta G*)- what is it and how do enzymes impact it?

Answer 6

The change in E required to reach the transition state

Enzymes lower it

Question 7

deltaG^‘o is the total change in the reaction from substrate, through transition state, and to product.

Favorable reactions have a

Answer 7

negative deltaG^o’

Question 8

Transition state analogues as pharmacological agents- how do they work _{and what are 2 examples}?

Answer 8

May bind the enzyme more tightly than the actual substrate o product –> can act as competitive inhibitors

_{<strong>HIV protease inhibitors</strong>}

_{<strong>Tamiflu</strong> on neuraminidase}

Question 9

The most important reaction for metabolism is done by what class of enzymes? What does it do?

Answer 9

Oxidoreductases transfer electrons (H- or H atoms)

Question 10

Oxidation-reduction

Answer 10

change in electron density around carbon, nitrogen, and sulfur

Question 11

An atom that gained electrons is

Answer 11

reduced

OIL RIG

Question 12

An atom that lost electrons is

Answer 12

oxidized

OIL RIG

Question 13

Name some electron carriers

Answer 13

Question 14

Velocity

Answer 14

The RATE (unit per time) of appearance of P or disappearance of S

Question 15

Initial velocity (v₀ or v_i)

Answer 15

velocity at the beginning of an enzyme-catalyzed reaction at time zero

This exhibits the “true” rate of reaction before the substrate becomes limiting

Question 16

Describe the relationship between V₀ and [enzyme]

Answer 16

V₀ increases linearly with enzyme concentration

note: Reaction rate decreases (curves on the graph) once the enzyme depletes the substrate pool

Question 17

Why does the left graph flatten out? Why does the right graph flatten out?

Answer 17

The left graph plots velocity - it’s reaching equilibrium.

The right graph plots initial velocity - enzymes are becoming saturated with substrate, so you’ve already reached Vmax

Question 18

Vmax

Answer 18

The velocity at infinitely high [substrate], when all enzymes are occupiied in the E-S complex

Question 19

Km

Answer 19

the [substrate] at which velocity is 1/2 maximal.

Thus if [S]=Km, then V₀=1/2V_max

Question 20

this is the michaelis menten equation. How does it change at low [substrate]? At high [substrate]?

Answer 20

At low substrate, the “+[S]” disappears. –> V₀ = (V_max/K_m)[S]

At high substrate, V₀=V_max

Question 21

Relationship between Km and affinity

Answer 21

Lower Km = high enzyme affinity

Question 22

Hexokinase I in the brain/muscle

vs

Hexokianse IV in the liver

Answer 22

Hexokinase I has a much lower Km for glucose –> high affinity for glucose –> readily saturated with glucose to phosphorylate it.

Question 23

K_cat/turnover number

Answer 23

k_cat = V_max/[total enzyme]

It is a rate constant = the number of substrate converted to product each second on a single enzyme when the enzyme is saturated with substrate

in sec^-1

Question 24

Competitive inhibition

Answer 24

Inhibitor binds the active site, thus blocking the substrate from binding so catalysis can’t occur

Reverse by simply increasing [S]

Question 25

Mixed inhibition

Answer 25

Inhibitor binds to a site on either the **enzyme** or **E-S**, distant from the active site

Question 26

Uncompetitive inhibition

Answer 26

Inhibitor binds to a site distance from the active site on the **ES** **complex** only

Question 27

The lineweaver burke double reciprocal plot is just an extrapolation of the mcihaelis menten. What does the **y-intercept** mean? What does the **x-intercept** mean? What does the **slope** mean?

Answer 27

Question 28

What kind of inhibition is this?

Answer 28

**Competitive inhibition.** * **K_m increases** as **[I]** increases - the more inhibitor, the more substrate needed to reach 1/2 V_max * **V_max** **stays the same** - infinitely high [S] will outcompete the inhibitor

Question 29

What kind of inhibition is this?

Answer 29

Mixed inhibition * **Km** **increases** as you increase [I] * **Vmax** **decreases** as you increase [I]

Question 30

Allosteric inhibitors often display what kind of inhibition\>

Answer 30

Mixed Mixed inhibition is the msot common type of inhibition

Question 31

What kind of inhibition is this?

Answer 31

**Noncompetitive inhibition (**a type of mixed inhibition) : both E and ES have the same affinity for binding the inhibitor Super rare * **No effect on Km** * **Decreases Vmax**

Question 32

What kind of inhibition is this?

Answer 32

**Uncompetitive inhibition** parallel lines * Both **Km** and **Vmax** decrease as inhibitor increases

Question 33

**Irreversible inhibitors** work by

Answer 33

forming a covalent bond with a specific active site residue; may resemble the substrate or transition state for the reaciton

Question 34

**Mechanism-based / suicide inhibitors**

Answer 34

An irreversible inhibitor that is inactive until it's acted upon by the enzyme and converted to a reactive intermediate that can then form a covalent bond with the enzyme --\> enzyme kills itself by activating the inhibitor

Question 35

**Serpins**

Answer 35

suicide inhibitors of cellular proteases Ex) **Alpha 1-antitrypsin, Antithrombin III**

Question 36

**A****lpha 1-antitrypsin****deficiency****(A1AD)** can result in

Answer 36

emphysema and liver failure Because A1A inhibits inflammatory cells' enzymes to protect tissues

Question 37

**Antithrombin III deficiency**

Answer 37

Can cause excessive clotting Beccause antithrombin III inhibits coagulation by neutralizing thrombin

Question 38

Oxygen is a __ for hemoglobin

Answer 38

Allosteric activator - it changes the structure of hemoglobin to bind more oxygen

Question 39

Negative feedback inhibition

Answer 39

The product of a pathway accumulates and turns that pathway off

Question 40

Would transition state analogues be stronger or weaker inhibitors than substrate analogues?

Answer 40

**TS analogues** **are stronger** because they make more molecular contacts with the enzyme

Question 41

At what point of a metabolic pathway is it most important to control enzyme activity?

Answer 41

The first committed step in the pathway, after which it can't funnel into any other alternative metabolic pathway in the cell

Question 42

Answer 42

Transferase

Question 43

Answer 43

Lyase

Question 44

Answer 44

Ligase

Question 45

Answer 45

Enzyme conc

Question 46

Answer 46

0.4mM

Question 47

Answer 47

0.4 umoles/min

Question 48

What enzyme modifications are associated with the process of angiogenesis?

Answer 48

**Prolyl** and **asparaginyl hydroxylation**

Question 49

What enzyme modifications are associated with cholera toxin and how does it cause cholera symptoms?

Answer 49

**ADP ribosylation of G_a in intestinal epithelial cells** --\> constitutive cAMP production --\> Na & K production --\> Cl- and HCO_3^- into the lumen of the small intestine

Question 50

Loss of Ras prenylation is a

Answer 50

cancer therapy

Question 51

Cleavage of a peptide bond is

Answer 51

irreversible