Enzymes pt. 2 and 3

Question 1

What is the reaction rate of a unimolecular irreversible first order reaction?

A -> P

Answer 1

v = k[A]

Thus the rate of P formation is directly proportional (rate constant k) to the concentration of A

Question 2

What makes a reaction ‘first order’?

Answer 2

An exponent of 1

Question 3

What is the reaction rate of a bimolecular irreversible second order reaction?

A + B ->

Answer 3

Rate of P formation is directly proportional (rate constant k) to the concentration of reactants

v = k[A][B]

Question 4

What is the unit of the rate constant for a first order reaction?

Answer 4

s-1

reciprocal second

Question 5

What is the unit of the rate constant for a second order reaction?

Answer 5

M-1 s-1

reciprocal molarity, reciprocal second

Question 6

What is the rate of formation for a unimolecular reversible reaction?

A -> P k1 and P -> A k2

Answer 6

Rate of formation of P equals rate of P gain minus rate of P gain

v = k1[A] - k2[P]

Question 7

Keq = ?

Answer 7

k1/k2 = [P]/[A]

Question 8

What does a large Keq indicate?

Answer 8

Reaction favors products

Question 9

What does a small Keq indicate?

Answer 9

Reaction favors reactants

Question 10

What is the basic michaelis-menten equation?

Answer 10

E + S -> ES > E + P

and the reverse for rxn 1

ES = enzyme substrate complex

Question 11

What are the units of the Michaelis constant?

Answer 11

M

Question 12

What assumptions are made to simplify Michaelis-Menten?

Answer 12

[S]&raquo_space;> [E]

and [ES] is relatively unchanging

No back reaction from pdt build up (k4 = 0)

Question 13

Maximal velocity (rate of rxn) occurs when __________.

Answer 13

Enzyme is totally saturated with enzyme

Question 14

Vmax = ?

Answer 14

= k3[E]total

Question 15

What is the Michaelis-Menten equation?

Answer 15

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

Question 16

What is Michaelis-Menten plotting?

Answer 16

Vo (rate) versus [S]

Question 17

Km = ?

Answer 17

[S] at 1/2 Vmax

Question 18

Filled sites = ?

Answer 18

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

Question 19

What is Km indicative of?

Answer 19

Enzyme-substrate affinity (higher Km, lower affinity)

Question 20

In the special condition of k2&raquo_space;> k3, what does that mean?

Answer 20

Making the product is the slowest reaction

Km = Kd ~ [E][S]/[ES]

Question 21

A low Km means what?

Answer 21

High binding affinity

Question 22

A high Km means what?

Answer 22

Low binding affinity

Question 23

To judge affinity, what must be true?

Answer 23

k2 must be much greater than k3

Question 24

Increasing your enzyme concentration will ________ your maximum velocity (reaction rate)

Answer 24

Increase

Question 25

Turnover number = ? = ?

Answer 25

= k3 = kcat "Catalytic ability" Typically 1-10^4 Higher value = higher catalytic ability

Question 26

What is catalytic ability?

Answer 26

Number of S molecules converted to P by one E molecule in unit time under saturation conditions (the best your enzyme can be functioning)

Question 27

What does kcat / Km indicate?

Answer 27

The catalytic efficiency of how well an enzyme reacts with dilute amount of substrate

Question 28

What type of enzymes have the higher kcat / Km values?

Answer 28

"Perfect" enzymes

Question 29

What is the equation of a Lineweaver-Burk plot?

Answer 29

1/Vo = ( Km/Vm * 1/[S] ) + 1/Vm

Question 30

What is the slope of a lineweaver-burk plot?

Answer 30

Km/Vm

Question 31

The value of the slope in a lineweaver-burk plot is ______ proportional to the catalytic efficiency.

Answer 31

Inversely

Question 32

What is the y intercept of a lineweaver-burk plot?

Answer 32

1/Vm

Question 33

What is the x intercept of a lineweaver-burk plot?

Answer 33

-1/Km

Question 34

What is the advantage of lineweaber-burk?

Answer 34

Provides easy-to-interpret visual display

Question 35

What is the disadvantage of lineweaver-burk?

Answer 35

Distorts errors at low [S], compresses data at high [S]

Question 36

What are the two main classes of two-substrate (or bi-substrate) reactions?

Answer 36

Sequential (ternary) | Ping-pong (double-displacement)

Question 37

What is a sequential two substrate reaction? What are the kinds?

Answer 37

All substrates bind (ternary complex) before any product releases Essentially, both come down before both come off. Can be ordered (specific) or Random order

Question 38

What is a ping-pong or double replacement mechanism?

Answer 38

For two-substrate reactions, this describe when one substrate binds and released product before the second substrate binds and releases product.

Question 39

What enzyme is a classic ping pong enzyme?

Answer 39

Chymotrypsin - peptide bonds and releases product before water binds and releases water

Question 40

What is an enzyme inhibitor?

Answer 40

A small molecule or ion that binds an enzyme and decreases its activity.

Question 41

What are the two types of inhibitors?

Answer 41

1. Reversible inhibitors | 2. Irreversible inhibitors

Question 42

What are the features of reversible inhibitors?

Answer 42

Bind the enzyme with noncovalent interactions Dissociate rapidly Allow the enzyme to recover its original activity

Question 43

What are the features of irreversible inhibitors?

Answer 43

Bind the enzyme with covalent interactions | Result in permanent inactivation of the enzyme

Question 44

What are competitive inhibitors?

Answer 44

Binds only to free enzyme and competes with the active site - thus usually resembles the shape and structure of the substrate - reduces number of ES complexes by taking up enzymes as part of their EI complexes

Question 45

How do competitive inhibitors affect Vm?

Answer 45

They don't!

Question 46

How do competitive inhibitors affect Km?

Answer 46

Increases it! (i.e. decreases the apaprent binding affinity)

Question 47

How do competitive inhibitors affect the catalytic efficiency?

Answer 47

Decrease!

Question 48

Can the effects of competitive inhibitors be overcome?

Answer 48

Yes! By increasing the amount of substrate

Question 49

When are competitive inhibitors most effective?

Answer 49

When substrate concentration is low

Question 50

Many drugs are ______ or ________ analogs

Answer 50

Substrate or transition-state

Question 51

Are substrate or transition-state analogs more potent inhibitors?

Answer 51

Transition-state because they bind more tightly

Question 52

How do uncompetitive inhibitors work?

Answer 52

Bind to the ES complex NOT at the active site/enzyme alone

Question 53

How do uncompetitive inhibitors affect Vm?

Answer 53

Decreases

Question 54

How do uncompetitive inhibitors affect Km?

Answer 54

Decreases

Question 55

How do uncompetitive inhibitors affect catalytic efficiency (kcat)?

Answer 55

No change

Question 56

Can increasing substrate concentration overcome the effects of uncompetitive inhibition?

Answer 56

No

Question 57

Do rate constants change in the presence of inhibitors?

Answer 57

NO! They just APPEAR to change (hence the term "apparent Km/Vm etc.")

Question 58

At very low substrate concentrations, are uncompetitive inhibitors successful?

Answer 58

No, but it becomes more and more powerful as you increase your substrate concentration

Question 59

What is a noncompetitive inhibitor?

Answer 59

Binds to free enzymes or ES complex at a site different than the active site. Hinders the reaction by distorting enzyme structure and preventing alignment of the catalytic center

Question 60

How do noncompetitive inhibitors affect Vmax?

Answer 60

Decrease

Question 61

How do noncompetitive inhibitors affect Km?

Answer 61

No change...the substrate doesnt really care if the inhibitor is there or not. Itll bind fine regardless

Question 62

How do noncompetitive inhibitors affect catalytic efficiency (Kcat)?

Answer 62

Decrease

Question 63

Does increasing the substrate concentration overcome the effects of noncompetitive inhibitors?

Answer 63

No

Question 64

What common antibiotic is an example of a noncompetitive inhibitor?

Answer 64

Doxycycline

Question 65

What type of inhibitor decreases both Vm AND Km?

Answer 65

Uncompetitive

Question 66

How does allosteric control work?

Answer 66

Allosteric enzymes operate by positive cooperativity: binding of substrate to one active site increases activity of other active sites.

Question 67

What effect do allosetic enzymes have on Km?

Answer 67

Usually decreases with increasing substrate concentration

Question 68

How do binding curves of allosteric enzymes appear?

Answer 68

S-shaped

Question 69

Allosteric enzymes are typically ______-______ enzymes

Answer 69

Rate-determining

Question 70

What is allosteric control?

Answer 70

Noncovalent binding of a ligand (effector) to a site other than the active site, thereby affecting the activity of the active site

Question 71

What is a homotropic effector?

Answer 71

Effector is the same as the substrate Site is usually adjacent to active site Interaction almost always increases activity

Question 72

What is heterotropic effector?

Answer 72

An effector that is the different than the substrate Usually distant from the active site Can increase or decrease activity

Question 73

Allosteric control operates by effector- induced conformational changes that alter activity by changing ___, ____, or both.

Answer 73

Km (K class) or Vm (V class)

Question 74

Are allosteric enzymes generally oligomers with multiple subunits and active sites?

Answer 74

Yes

Question 75

How is ATCase affected by allosteric control?

Answer 75

Aspartate will bind to the enzyme when in the tense state, pushing it into the relaxed state and increasing the reaction rate in an exponential way (S-shaped curve) OR CTP can also bind and stabilize the tense state, pushing the curve to the right

Question 76

How is PKA an example of allosteric regulation?

Answer 76

Examples of protein binding increasing or decreasing activity: 2 subunits are regulatory 2 subunits are catalytic cAMP binds to the active sites and pulls the regulator units away, allowing PKA to become active

Question 77

How do reversible covalent modifications affect enzyme activity?

Answer 77

Charged groups such as phosphate, sulfate, or acetate, can bind enzymes and cause conformational changes that alter function.

Question 78

What is the most common form of reversible covalent modifications to regulate enzyme activity?

Answer 78

Phosphorylation/dephosphorylation via kinases and phosphatases Each step is considered IRREVERSIBLE even if the process as a whole is reversible (i.e. there are 2 different enzymes/2 different reactions to complete the cycle).