Enzymes

Question 1

Patient with slurred speech, frequent falls, inability to climb stairs, and difficulty in rising from a supine posture. Low Iq, very weak limb muscles and enlarged, atrophied calf muscles. High levels of enzyme creatine kinase (Ck-total) and its specific isoenzyme CK-MM (CK-3).
1. What is going on with this patient?

Answer 1

his muscles aren’t working. There is muscle breakdown because of creatine kinase.

Question 2

2. What is the significance of CK and Ck-3 levels in the diagnosis?

Answer 2

Creatine kinase is an enzyme that phosphorylates creatine to make phosphocreatine.
More CK3 leads to muscle damage.

Question 3

Where is creatine kinase expressed?

Answer 3

in the skeletal muscle cells, cardiac muscle cells, also in neurons.

Question 4

what are the 3 different isoenzymes of creatine kinase?

Answer 4

Ck1 in the brain, Ck2 in cardiac muscles, Ck3 in the muscles. (creatine-kinase)

Question 5

Can enzymes be a diagnostic indicator of certain diseases?

Answer 5

yes

Question 6

If a patient has high levels of amylase and lipase what can this indicate?

Answer 6

acute pancreatitis.

when pancreatic cells are inflamed they release a lot of these enzymes.

Question 7

What is lactate dehydrogenase?

Answer 7

It converts pyruvate into lactate.
part of glycolysis
Present in all cells.

Question 8

High levels of lactate dehydrogenase indicate what?

Answer 8

There is some kind of cell damage

Question 9

High amounts of alkaline phosphatase indicate?

Answer 9

There are epithelial cells in the liver, this enzyme is also in bone cells.
Could indicate a liver or bone issue.

Question 10

Enzymes enlist 3 features of enzyme activity what are they?

Answer 10

its a protein that catalyzes the reaction.
lowers the activation energy without the cells being changed.
it speeds up the rate of the reaction.

Question 11

Are enzymes specific?

Answer 11

yes, they bind to very specific substrates and catalyze very specific reactions.

Question 12

What is the allosteric site?

Answer 12

it is involved in regulation.

Question 13

Active site?

Answer 13

substrate binds here. promotes the catalyzation.

Question 14

What is the relationship between glucose and galactose?

Answer 14

They are epimers (same chemical formula but differ in one positional group (OH).

Question 15

Glucose (substrate) is bound to the enzyme glucokinase. Can galactose bind to glucokinase?

Answer 15

No, because Galactose has that OH group difference. the binding won’t be a tight fit.

Question 16

What dictates a binding of the substrate in the active site?

Answer 16

The active site of every enzyme is made up of specific amino acids arranged in a specific orientation. They can be hydrophilic, hydrophobic, charged, uncharged.
The arrangement of amino acids made up of the active site, provides the type of substrate specificity.
Spatial orientation and compensation of the amino acid is important for substate specificity.

Question 17

What does lock and key mean?

Answer 17

The enzymes’ active site and substrate fit together.

The active site is premade and matches the shape of the substrate, a very tight fit.

Question 18

What is the induced fit model?

Answer 18

Same specificity but with a little more fluidity. the enzyme is a bit more open.

Question 19

How does the induced fit model work?

Answer 19

In the induced fit model, the substrate binds to the active site. Cofactors help with enzyme activity.
The substrate is trying to change in order to make a better fit. (at this point the bond formation is not tight and rigid yet). It is a loose fit. (enzyme-substrate complex)
Then the transition state complex is where the substrate is fitting a bit better, it is now a closed fit at the active site.

Question 20

What is the transition state complex?

Answer 20

It is the state in which the enzyme is fluid after substrate binding, it is trying to make the substrate fit better.
It is a transient state that is in a hurry to form the product.

In induced fit, enzymes don’t change composition but they can slightly adjust bonds to adopt and bind to the substrate.

Question 21

Glucokinase binds to glucose supports the induced fit, how?

Answer 21

Glucokinase binds to glucose. The glucose is phosphorylated. Converted to G6P and locks it. A phosphate is needed from ATP. The enzyme isn’t as rigid, does its best to promote the reaction.

Question 22

When looking at a graph, energy being the y-axis, and x being the progress of the reaction, what will the graph look like without an enzyme and with an enzyme?

Answer 22

Without an enzyme, the graph will have a higher curve. it has higher activation energy.
With an enzyme, the curve will be lower because it has lower activation energy.
If an enzyme isn’t present, a reaction can still happen but the cell will need to utilize more energy to get it done (uphill battle).

Question 23

What do enzymes do with activation energy?

Answer 23

Enzymes reduce the energy of activation and increase the rate of chemical reaction (formation of product).

Question 24

What is net energy?

Activation energy?

Answer 24

Net energy is the difference between energy and energy released.
Activation energy: energy required to form the transition state complex.

Question 25

What causes the reduction of activation energy by the enzyme?

Answer 25

When looking at a graph, little curves are intermediates that are catalyzed by different kinds of reactions that happen within the site. These could be different kinds of catalysis or cofactor.

Question 26

What else could cause the reduction of activation energy by the enzyme?

Answer 26

proximity catalysis could be occurring. (active site provides closed environment and aligns substrates properly for the reaction to happen). All these things that are happening in the little curves before they actually hit the transition state complex.

Question 27

What are coenzymes?

Answer 27

They are organic compounds like vitamins which help the enzyme in the catalysis of the reaction.
Coenzymes are vitamins, they are essential for functonality of important enzymes for cellular function and reaction.

Question 28

Case: 44-year-old man, has been an alcoholic for the past 5 years, unusually irritable and confused after drinking two bottles of scotch, eat very little. poorly oriented to time, place, and person. Physical exam showed heart rate of 104 bpm and low blood pressure. admitted to the hospital and intravenous thiamin administration was initiated. he was diagnosed with acute thiamin deficiency known as beriberi heart disease. What is thiamine?

Answer 28

Thiamine is a coenzyme. It can be widely classified as vitamin B, vitamin B-1.

Question 29

Case: 44-year-old man, has been an alcoholic for the past 5 years, unusually irritable and confused after drinking two bottles of scotch, eat very little. poorly oriented to time, place, and person. Physical exam showed heart rate of 104 bpm and low blood pressure. admitted to the hospital and intravenous thiamin administration was initiated. he was diagnosed with acute thiamin deficiency known as beriberi heart disease.
What is making the patient thiamine deficient?

Answer 29

He is very alcoholic. high intake of alcohol prevents thiamine absorption. Thiamine acts as a coenzyme of different mitochondrial enzyme like pyruvate dehydrogenase (PDH). PDH converts pyruvate to acetyl-coA.

Question 30

Case: 44-year-old man, has been an alcoholic for the past 5 years, unusually irritable and confused after drinking two bottles of scotch, eat very little. poorly oriented to time, place, and person. Physical exam showed heart rate of 104 bpm and low blood pressure. admitted to the hospital and intravenous thiamin administration was initiated. he was diagnosed with acute thiamin deficiency known as beriberi heart disease.
How will thiamine affect the function of PDH?

Answer 30

Thiamine in the pyrophosphate form is the coenzyme of the mitochondrial dehydrogenases. The thiamine has a very active carbon atom that is ready to give away its proton. PDH extracts proton from thiamine and turns it into a carbanion. It then forms a covalent bond with the keto group of pyruvate.

Without thiamine, the binding of pyruvate will be difficult.

Question 31

Case: 44-year-old man, has been an alcoholic for the past 5 years, unusually irritable and confused after drinking two bottles of scotch, eat very little. poorly oriented to time, place, and person. Physical exam showed heart rate of 104 bpm and low blood pressure. admitted to the hospital and intravenous thiamin administration was initiated. he was diagnosed with acute thiamin deficiency known as beriberi heart disease.
What will be the effect of thiamine deficiency?

Answer 31

The effect would be that the utilization of glucose would be affected. glucose is turned into pyruvate which is then turned into acetyl-coA for the TCA cycle. without pyruvate, this could affect energy production.

Question 32

what is the difference between cofactors and coenzymes?

Answer 32

Coenzymes are vitamins. Cofactors are metal ions. They also bind to the active site of an enzyme and help start enzyme activity.

Question 33

In the case of metal ions in catalysis. How would a cofactor help with the enzyme activity of alcohol dehydrogenase? (enzyme slide of PowerPoint)

Answer 33

Zinc is a cofactor that will help the enzyme Alcohol dehydrogenase. The substrate is ethyl alcohol. It oxidizes ethyl alcohol and gives the H from it to an NAD+. the zinc binds to the unstable oxygen atom of the ethanol.

Question 34

What is the relationship between enzyme activity and temperature?

Answer 34

increase in temperature increases the rate of the enzyme. the optimal temperature for enzyme is 0-37 C.
48-50 enzyme activity will decrease and the enzymes will be denatured.

Question 35

Enzyme X is active at pH 7.4. It forms 2 ionic bonds with the substrate at the catalytic site. What would happen to the functional groups in the active site at a pH of 1.5? a pH of 10.5?

functional groups present are: COO-, NH3+, COO-, NH3+.

Answer 35

At a pH of 1.5, carboxylic acids will be protonated. This will be protonated because the amine group already is protonated. the pH of 1.5 is acidic so protonation will occur.
At a pH of 10.5 the amine group will be deprotonated and lose its ionic bond.

Question 36

How does penicillin kill bacteria?

Answer 36

it punches holes in the cell wall. penicillin mimics transition state of glycopeptide transpeptidase. the penicillin mimics tetrapeptide chains that bond the cell wall of the bacteria. the enzyme glycopeptide transpeptidase will accidentally bind with the penicillin. This will disable cross-linking of peptide chains in the cell wall of the bacteria. So the wall will be weak and unstable. Bacteria attempts to divide, the cell wall collapses.

Question 37

Why is Allopurinol a transition state analog?

Answer 37

It inhibits xanthina oxidase. Xanthina oxidase turns allopurinol into oxpurional. this is what tightly binds to the xanthina oxidase and inhibits it. It is called a suicide inhibitor.

Question 38

What limits penicillin activity?

Answer 38

Beta lactamase inhibits it. its an enzyme produced by bacteria that cleaves the penicillin beta lactam ring and deactivates it.

Question 39

Organophosphate poisoning: What is the normal process for acetylcholinesterase?

Answer 39

Acetylcholinesterase is trying to break down acetylcholine. We don’t want too much acetylcholine. we want to be able to control it in the synapse.

Question 40

What happens to acetylcholinesterase in the presence of an organophosphate or a pesticide?

Answer 40

The acetylcholinesterase is going to be inhibited by the organophosphate, it inactivates it by forming a covalent complex. Acetylcholine will then build up.

Question 41

Enzyme kinetics: when the km is high what is the enzyme affinity?

Answer 41

The enzyme affinity is low. (takes more substrate to get to 1/2 vmax).

Question 42

Enzyme kinetics: when the Km is low what is the enzyme affinity?

Answer 42

Lower Km means higher enzyme affinity. (takes less substrate to get 1/2 vmax).

Question 43

Hexokinase and glucokinase has different Km values for glucose. Why?

Answer 43

Hexokinase has a low Km and a high affinity for glucose. (takes less substrate to get to 1/2 vmax). So when we have that low level of glucose, they can still use the glucose for energy production.
Glucokinase (in pancreas and beta cells), shouldn’t be active because the Km is higher with a lower affinity. (you need more substrate to reach 1/2 vmax).

Question 44

Ann R’s jogging. her skeletal muscles are using glucose as the energy source. As she jogs, her blood glucose level falls. How will this affect the activity of the enzymes hexokinase and glucokinase? Which is more likely to remain active?

Answer 44

Glucokinase has a high km and a low affinity. So that means it will need more substrate. it won’t be active because there won’t be enough glucose.
Hexokinase has a low km and a high affinity. this means that it doesn’t need that much substrate to reach 1/2 vmax. Therefore under low glucose levels it should still be able to produce energy.

Question 45

Ann eats a high carbohydrate meal, her blood glucose rises to approximately 20 mM in the portal vein. how will this increase her blood glucose levels affect the activity of glucokinase?

Answer 45

she will have excess glucose in her body. A lot of glucose will be stored as glycogen in the liver. there will be a lot more substrate so glucokinase will be active and helping to store that glucose in the liver.

Question 46

After eating the carbohydrate meal, which will be more active the glucokinase or the hexokinase.

Answer 46

The hexokinase will still be more active.

Question 47

Explain Lineweaver Burk Plots

Answer 47

They are the inverse of Michaelis-Menten plot. It is inversed in order to get a linear curve. it is more accurate.
intercept of x-axis is (-1/Km) (when the line crosses the x-axis).
y-intercept is 1/vmax.
as you go up the y axis, the value of Km will decrease.
as you get closer to 0 the value of Km will increase.

Question 48

Explain competitive inhibition using Lineweaver Burk plots.

Answer 48

Competitive inhibition shares structural similarities with a substrate. It is competing to bind to the substrate-binding part of the active site. It competes with the substrate.

Question 49

explain competitive inhibition using Lineweaver Burk plots.

how can a competitive inhibitor outcompete the substrate? How will this affect the affinity?

Answer 49

If you increase the inhibitor concentration from the substrate concentration.

The Km will increase so it will decrease the affinity of the enzyme with the substrate. (it will not change velocity). (low affinity means it needs more substrate.)

Question 50

Explain non-competitive inhibition using Lineweaver Burk plots.

Answer 50

Noncompetitive inhibition binds to the catalytic site of the active site. It will affect the structure of the catalytic site. This will affect the Vmax.
A substrate enzyme complex forms, but it will be slowed down. The Km will remain the same. substrate binding is not affected and it does not look like the enzyme.
Prevents formation of product.

Question 51

The antibiotic penicillin acts on?

Answer 51

glycopeptide transpeptidase

Question 52

Occasional resistance to penicllin is due to bacterial production of beta-lactamases which bind to ____ (substrate) and cleaves the ___ to inactivate it.

Answer 52

Penicillin. beta-lactam ring.

Question 53

Beta-lactamase inhibitors can combat penicillin resistance by?

Answer 53

competitive inhibition

Question 54

the mechanism of inhibition exhibited by beta-lactamase inhibitors (structural analogs of penicillin) can be defined as competitive inhibition. Justify and discuss.

Answer 54

If you have a higher concentration of the inhibitors they are going to bind to the beta-lactamase and inhibit it. Penicillin can then go in.
Penicillinase (b-lactamases) share homology with penicillin. they have a beta-lactam ring-like penicillin.

Question 55

How do allosteric regulators affect enzyme activity?

Answer 55

Allosteric sites are totally separate from the active site. it plays a role in enzyme regulation.
There are allosteric inhibitors and activators.

Question 56

What will happen if an inhibitor binds to the site? How will it affect the activity of the enzyme?

Answer 56

It will decrease the Vmax. it changes the enzyme in which it is locked in the inactive state.
It will affect binding site and will decrease the affinity of the enzyme.
There will be less affinity of the substrate and Km increases.

Question 57

What if an activator binds to the allosteric site?

Answer 57

It decreases the Km so it increases the affinity of the enzyme. It will lock the enzyme in the R state (active state).
Km goes low, so higher affinity for enzyme. Vmax will remain the same.