Enzymes and Metabolism

Question 1

What is a holoenzyme and what are its two components?

Answer 1

Complex protein enzyme: Apoenzyme and cofactor

Question 2

What are the two models for enzyme active site functionality? Which is most generally accepted?

Answer 2

• Lock and key model

- Induced fit hypothesis (favoured model)

Question 3

True or false? Increasing substrate concentration increases enzymatic reaction velocity

Answer 3

True!

But this levels off with saturation kinetics, usually involving feedback inhibition.

Question 4

Enzyme inhibitors are categorized reversible and irreversible. What is the biggest difference between these two classes?

Answer 4

Irreversible inhibitors usually react covalently to render the enzyme inactive

reversible inhibitors react instantaneously with an enzyme non-covalently (in general)

Question 5

What is enzyme induction? What is the opposite of this called?

Answer 5

Enhancement of its synthesis in a cell

The opposite is called repression.

Question 6

What are ways enzymatic activity can be regulated? (6)

Answer 6

• Amount of enzyme (induction/repression)
• Covalent modification (eg. phosphorylation)
• pH
• Temperature
• Allosteric mechanisms
• Positive co-operativity

Question 7

What is positive co-operativity (enzymes)

Answer 7

When the binding of one substrate or ligand makes it easier for the second to bind

Question 8

The breakdown of what two macromolecules yields ATP?

Answer 8

• Carbohydrates

- Lipids

Question 9

Contrast anaerobic and aerobic production of ATP from glucose

Answer 9

Anaerobic

• Cytosol
• Glycolysis yields 2 pyruvate and 2 ATP
• Fermentation yields 2 lactate and 2 ATP
• Fast

Aerobic

• Krebs cycle
• Oxidative phosphorylation (Electron transport chain) produces 6 moles carbon dioxide, 6 moles H2O and 36 ATP
• Relatively slow

Question 10

Give all the steps of glycolysis and the enzymes that catalyze each (long - 10 steps)

Answer 10

1. Glucose is phosphorylated with ATP by hexokinase or glucokinase
2. Phosphohexose isomerase converts glucose-6-phosphate to fructose-6-phosphate
3. Phosphofructokinase (PFK) catalyzes the second phosphorylation to produce fructose-1,6-diphosphate (rate limiting step)
4. Aldolase cleaves fructose-1,6-diphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate
5. Triose phosphate isomerase forms glcyeraldehyde-3-phosphate from the previous two compounds
6. Glyceraldhehyde-3-phosphate dehydrogenase triose, NAD+ and Pi to yield 1,3-diphosphoglycerate
7. Phosphoglycerate kinase forms ATP and phosphoglycerate from ADP and 1,3-diphosphoglycerate
8. Phosphoglycerate mutase catalyzes teh transfer of the phosphoryl group from carbon two to yield 2-phosphoglycerate
9. Enolase catalyzes an isogonic dehydration to yield phosphoenolpyruvate
10. Pyruvate kinase yields pyruvate from phosphoenolpyruvate

Question 11

Why is fluoride added to blood samples?

Answer 11

Fluoride inhibits enolase at non-physiological concentrations, actively inhibiting glycolysis.

Question 12

After pyruvate is formed in glycolysis, what happens to it in the presence of oxygen?

Answer 12

Pyruvate is converted to Acetyl CoA, which enters Kreb’s cycle, followed by oxidative phosphorylation to produce a total of 38 ATP per molecule of glucose

Question 13

True or false? Every human cell is equipped for glycolysis?

Answer 13

True

Question 14

After pyruvate is formed in glycolysis, what happens to it in anaerobic conditions?

Answer 14

Pyruvate is quickly reduced by NADH to lactic acid using the enzyme lactate dehydrogenase (fermentation). Only 2 ATP is produced per molecules of glucose.

Question 15

How are negative charges important for glycolysis?

Answer 15

• The phosphorylation of glucose makes it negative and prevents it from leaving the cell
• Then glucose-6-phosphate becomes its isomer, fructose-6-phosphate. F6P is then further phosphorylated to form F-1,6-dP
• This large sugar breaks into two 3 carbon triose phosphates
• A triose phosphate is ultimately converted to 1,3-diphosphoglycerate, which is clearly an unstable compound (two negative phosphate groups). Thus it transfers a high energy phosphate group onto ADP to produce ATP (substrate phosphorylation)

Question 16

What is pyruvate cleaved into in the mitochondria in the Kreb’s cycle?

Answer 16

Water and carbon dioxide

Question 17

True or false? Proteins and fats use the TCA for channeling their metabolic pathways

Answer 17

True, which is why it is often called the final common pathway of metabolism

Question 18

What can feed into Kreb’s cycle?

Answer 18

2 pyruvate (C3) produce 2 CO2 and 2 acetyl CoA (C2). The catabolism of both glucose and fatty acids yield acetyl CoA. Catabolism of amino acids yields acetyl CoA or other TCA cycle intermediates

Question 19

How many turns around the TCA cycle are needed for 1 molecule of glucose?

Answer 19

2, one for each pyruvate produced from 1 molecule of glucose in glycolysis

Question 20

How much CO2 is generated per turn of the TCA cycle?

Answer 20

2 CO2 per turn

Question 21

How many GTP (if any) is produced from one turn of TCA cycle?

Answer 21

1 GTP per turn

Question 22

What is the reducing agent in TCA cycle?

Answer 22

Hydrogen

once a turn from FADH2+ and three times a turn from NADH+.

The hydrogen eventually produces H20 in the last step of the electron transport chain

Question 23

What are the components of the electron transport chain (in the order that electrons travel)? What are the two locations that reducing equivalents (eg. hydrogen) enter the ETC?

Answer 23

• NAD-specific dehydrogenases
• Flavoprotein
• Ubiquinone
• Cytochromes
• Molecular oxygen
• Electrons from NADH can enter at NADH dehydrogenase
• In reactions involving iron, sulphur protein electrons are transferred to coenzyme Q and protons are translocated from the mitochondrial matrix to the exterior of the inner membrane during this process (creating a proton gradient)

Question 24

Describe the flow of electrons in the ETC

Answer 24

• Electrons entering from succinate dehydrogenase (FADH2) are donated directly to coenzyme Q
• Electrons are transported from reduced coenzyme Q to cytochrome b and then cytochrome c
• Electrons are then carried by cytochrome c to cytochrome a (cytochrome oxidase)
• Cytochrome oxidase catalyzes the reaction of electrons and protons with molecular oxygen to produce water

Question 25

What is a powerful inhibitor of cytochrome oxidase?

Answer 25

Cyanide

Question 26

How many ATP are made from the following molecules:

• NADH
• FADH2

Answer 26

1 NADH produces 3 ATP

1 FADH2 produces 2 ATP

Question 27

What is one factor that makes ATP production less efficient?

Answer 27

Heat lost from the system

Less than 40% of the energy generated from glucose metabolism is converted into ATP

Question 28

During vigorous exercise, how much ATP is made available for sodium pumps per molecule of glucose?

Answer 28

2

Vigorous exercise entails anaerobic conditions, where one molecule of glucose produces two molecules of ATP.

Question 29

Suppose that an extract from a muscle cell contains only the following: all the enzymes of the glycolytic pathway, including the enzyme that converts pyruvate to lactate; phosphate and other salts; NAD+ and ADP. When the extract is incubated anaerobically and glucose is introduced, neither pyruvate nor lactate is produced. What must be added in order for pyruvate to be made?

Answer 29

ATP

ATP must be added to kick off the reaction with the phosphorylation of glucose. Once glycolysis is initiated with a small amount of ATP, more ATP is produced and the reaction becomes self sufficient.

(note: ADP and phosphate cannot spontaneously come together, ATP must be present for glycolysis to begin)

Question 30

If someone (such as an athlete) normally has a greater cardiac output than someone else, why would the normal person have a greater buildup of lactic acid in muscle cells than the ‘athlete?’

Answer 30

An athlete is able to pump more blood to muscles, and therefore, more oxygen. The non athlete must resort to using more anaerobic respiration than the athlete because less oxygen is pumped to muscles.

Question 31

An elevation of amino acids has what effect on the secretion of insulin and glucagon?

Answer 31

An increase in amino acids in the blood causes an increased secretion of insulin and glucagon (both!).

High blood sugar causes an increase in insulin, but decrease in glucagon.

Question 32

The peptidyl transferase center on the large ribosomal subunit is altered during the termination reaction. What is it altered to do?

Answer 32

It becomes a esterase, to promote the hydrolysis of the ester bond between the 2’ hydroxyl group in tRNA and the aminoacyl.

Question 33

In some cases, after rat liver enzymes are additionally applied to the culture plate in order to enhance the efficiency of the Ames test; more colonies arise. Why?

Answer 33

Rat liver enzymes metabolize some non-carcinogenic agents into carcinogenic ones.

The liver is the organ responsible for the metabolism of all the compounds in the body, including the metabolism of toxic substances. Many enzymes in the liver are responsible for the break down of chemicals in the circulation.

As a result, in some cases certain chemical reagents which are not carcinogenic at first, may only act as carcinogens after they have been altered by liver enzymes.

Consequently, adding liver enzymes to the culture plate could convert the chemical into the active form and allow the Ames test to be more efficient in identifying a chemical carcinogen.

This is done in practice to more realistically simulate how a real substance would get processed in the body, making the Ames test more accurate and more efficient.

Question 34

What best explains why 97% of oxygen in blood is in the HbO2 form?

Answer 34

There are allosteric interactions between hemoglobin subunits.

Allosteric proteins have different configurations. Hemoglobin has cooperative binding which means that each oxygen facilitates the binding of the next oxygen which occurs as a result of changes in the molecule’s configuration.

Question 35

In a muscle, at what temperature would you expect to find the most saturated hemoglobin, and when would you find the least?

Answer 35

Most saturated: during rest, cold muscles

Most Unsaturated: During exercise, hot muscles

Question 36

What is the difference between fetal and adult hemoglobin?

Answer 36

Fetal hemoglobin binds oxygen at lower partial pressures, competitively ‘taking it’ from adult hemoglobin in the placenta.

Question 37

Which of the following molecules can bind to hemoglobin more readily than oxygen?

A. Carbon monoxide (CO)
B. Carbon dioxide (CO2)
C. Both
D. Neither

Answer 37

A. Carbon monoxide (CO)

Think of someone committing suicide by carbon monoxide poisoning. It binds to hemoglobin more readily than oxygen, resulting in asphyxiation and death.

Question 38

How is a force generated by muscle contraction increased, at the level of actin and myosin?

Answer 38

To increase force, you increase the number of active cross bridges. This can be done by increasing the frequency or voltage of stimulation, or by increasing the number of neurons sending messages.

Cross-bridge formation, improves contractile power of the muscles.

Question 39

Which participant in the electron transport chain has the greatest attraction for electrons?

Answer 39

Oxygen

FAD and NAD+ do not directly donate electrons to the electron transport chain - it is their reduced forms that do.

Electrons move to a slightly more electronegative carrier as the electrons pass through each step in the electron transport chain.