Enzyme Regulation

Question 1

What are 3 ways to regulate enzymes?

Answer 1

1. Change the amount of enzyme available
2. Have the enzyme interact with ligands (inhibitors, activators)
3. Have the enzyme covalently bind with modification molecules

Question 2

What is mass action as it relates to enzymatic activity?

Answer 2

Mass action means working through concentration gradients. If you increase the concentration of a competitive inhibitor it will eventually steal interaction opportunities from the more ideally “fit” substrate

Question 3

What are the 3 types of inhibition? Describe and draw

Answer 3

1. Competitive inhibition - substrate homologue sneaks in and interacts in the place of the substrate. Changes Km but not Vmax
2. Noncompetitive inhibition - inhibitor binds to allosteric site and decreases the functionality of the enzyme. Vmax decreases but Km stays the same (usually, except for v-type noncompetitive inhibitors)
3. uncompetitive inhibition - inhibitor AND substrate bind, but inhibitor keeps substrate stuck to enzyme and doesn’t allow the reaction to carry forward.

Question 4

What is enzymatic efficiency?

Answer 4

Kcat/Km

Question 5

What does Km represent?

Answer 5

Binding affinity. How easy it is for substrate to bind to enzyme

Question 6

What does Kcat represent?

Answer 6

Turnover speed. How quickly the enzyme cranks out products

Question 7

What does allosteric mean?

Answer 7

An allosteric enzyme has at least 2 active states (off, inactive, active). Active state binds effectively, inactive state still binds, but just not well.

Question 8

Where does competitive inhibition occur?

Answer 8

At the catalytic site

Question 9

What type of inhibition occurs at the catalytic site?

Answer 9

competitive inhibition

Question 10

Where does noncompetitive inhibition occur?

Answer 10

At the allosteric site

Question 11

What are some examples of covalent modification of a protein?

Answer 11

Phosphorylation, adenylylation. These are usually caused by some hormone-mediated signalling cascade

Question 12

What is the timeframe that enzyme regulation occurs within?

1. modifying quantity of enzyme
2. modifying activity of current enzyme

Answer 12

1. hours to days (you need to decrease gene expression) or minutes (if you induce post-translation protein modification)
2. nearly instantaneously if you’re trying to use binding ligands to affect change

Question 13

What does kinase do?

Answer 13

Adds phosphates

Question 14

What does phosphatase do?

Answer 14

Takes away phosphates

Question 15

Where does the control for signal cascades occur?

Answer 15

Usually at the first signal. If you modify just the first signal you only need to change the concentration of one binding molecule. But if you change later on you might have to make multiple adjustments. First is simplest, and first protein often has surface area exposed to extracellular matrix

Question 16

What type of inhibition increases Km but does not impact Vmax

Answer 16

Competitive (once you outcompete inhibitors the efficiency is the same)

Question 17

What type of inhibition decreases Vmax without impacting Km?

Answer 17

Noncompetitive (substrate concentration doesn’t matter)

Question 18

What does a michaelis menten graph look like? What are its axes? Draw

Answer 18

Velocity vs. substrate concentration, an asymptotic curve.

Question 19

What does a lineweaver burk plot look like? What are its axes? What is its x-intercept? What about the y-intercept?

Answer 19

Lineweaver burk plot is 1/v vs. 1/s. linear. x intercept is -1/km y intercept is 1/vmax

Question 20

How does competitive inhibition change lineweaver burk plot?

Answer 20

y-intercept is constant, slope gets steeper with more inhibitor, x-intercept approaches 0

Question 21

What type of inhibition causes the lineweaver burk plot to have a flatter slope and a change in the y-intercept?

Answer 21

noncompetitive inhibition (changes vmax but not km(

Question 22

How does noncompetitive inhibition change the lineweaver burk plot?

Answer 22

make slope steeper, vmax decreases

Question 23

What constants matter in competitive inhibition?

Answer 23

Km vs. Ki. Ki is basically binding affinity of inhibitor. Km is binding affinity of attacking protein.

Question 24

Which type of inhibition is more efficient?

Answer 24

Noncompetitive. Well actually suicide inhibition is better but super rare. Suicide inhibition is when an inhibitor binds permanently to the enzyme

Question 25

What are positive and/or negative feedback loops for enzyme regulation?

Answer 25

as more product is made, the product is actually used to regulate further production. positive feedback increases production, negative feedback slows production

Question 26

Draw a michaelis menten plot for an allosteric enzyme

Answer 26

changing binding affinities make an S shape (low affinity when low S, high affinity when high S)

Question 27

Draw a normal michaelis menten plot and label axis

Answer 27

Hill looking function (high affinity at top right)

Question 28

Draw a lineweaver burk plot

Answer 28

flat line

Question 29

Draw a lineweaver burk plot for an allosteric enzyme

Answer 29

looks like the right half of a U (high affinity at bottom left)

Question 30

What causes an allosteric enzyme to change its binding affinity?

Answer 30

Something, whether a substrate or supporting molecule, interacts with the enzyme (often at least a dimer) and either induces shape change right away to the whole enzyme or induces shape change wherever the substrate bound.

Question 31

What is concerted binding for enzymes?

Answer 31

Conformational shape change occurs for both dimers at the same time (as soon as first substrate binds), and then second substrate binds to newly changed dimer. concerted means simultaneous shape change. Both dimer halves immediately jump from T (low binding affinity state) to R (high binding affinity state)

Question 32

What does sequential conformation adjustment in enzymes look like?

Answer 32

One half of dimer binds substrate and changes shape, then the next half binds and changes shape. Not simultaneous. Takes both for dimer to get into R (high binding affinity state)

Question 33

What does an allosteric lineweaver burk plot look like?

Answer 33

The lines have curved (upwards) slopes, because as less substrate is present/bound more and more of the enzyme are found in the inefficient conformation

Question 34

What are k-type inhibitors?

Answer 34

K-type inhibitors are allosteric inhibitors that only change Km as they switch conformations (binding affinity increases)

Question 35

What are v-type inhibitors?

Answer 35

V-type inhibitors change vmax and km as they change conformation. V-type enzymes (if meant to be positive) could be rapid response enzymes, maybe for use in tissue damage.

Question 36

What are G proteins used for?

Answer 36

Signalling cascade from extracellular matrix to (usually) gene expression

Question 37

What is an example of a zymogen?

Answer 37

Prothrombin, (turns into thrombin, which is forced into fibrin, which eventually impact pathways. Digestion enzymes in the liver

Question 38

What is an isozyme?

Answer 38

“isomer” of protein enzyme, slightly altered from initial enzyme.

Question 39

What type of enzyme is a blood clotting enzyme?

Answer 39

v-type enzyme: extremely fast response so highly active state means vmax increases and km decreases

Question 40

Are isozymes good or bad?

Answer 40

Some isozymes are great! They represent innovation and diversity in the body. But isozymes can also represent tissue damage.

Question 41

Anabolic vs. Catabolic?

Answer 41

Anabolic means synthesize

Catabolic means breakdown