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Biochem > Unit 11 (2) > Flashcards

Unit 11 (2) Flashcards

1
Q

What is meant by the term gluconeogenesis? Why is this process important to animals? In what tissues does it mainly occur

A
  • The biosynthesis of a carbohydrate from
  • Converts pyruvate and other related 3-4 carbon molecules into glucose.
  • This process is important because some tissues rely almost completely on glucose for their metabolic energy and unfortunately, the supply of glucose from these stores is not always sufficient between meals, from fasting, or from exercise (because glycogen is depleted)
  • Mainly occurs in the liver
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2
Q

Name three carbohydrate precursors of glucose

A
  • Lactate –> Pyruvate
  • Glucogenic amino acids
  • Triacylglycerols –> Glycerol
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3
Q

Why does gluconeogenesis require a pathway different than the reversal of glycolysis

A
  • Because there are three reactions in glycolysis that are essentially irreversible (do to the fact that these steps require so much energy since they release so much). These are known as the bypasses
  • Glucose 6 Phosphate –> Glucose
  • Pyruvate –> Phosphoenolpyruvate
  • Fructose 1,6-Bisphosphate –> Fructose 6 Phosphate
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4
Q

Point out the three steps in glycolysis that are irreversible

A
  • Glucose –> Glucose 6 Phosphate
  • Fructose 6 Phosphate –> Fructose 1,6- Bisphosphate
  • Phosphoenolpyruvate –> pyruvate
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5
Q

Draw the charts for glycolysis and gluconeogenesis to see which areas are opposing

A
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6
Q

Bypass 1: Conversion of pyruvate to phosphoenolpyruvate

Using structures, write balanced equations for the reaction

A

Pyruvate + HCO3- + ATP + GTP –> PEP + ADP + CO2 + GDP + Pi

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7
Q

Write the equation of going from pyruvate to oxaloacetate

A

Pyruvate + HCO3- + ATP –> Oxaloacetate + ADP + Pi

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8
Q

Name the cofactor used by pyruvate carboxylase and describe its function?

A

Biotin. It’s function is to move it from one site to the other with the second site having the pyruvate so it can become oxaloacetate

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9
Q

What is the role of ATP in the conversion of pyruvate to phosphoenolpyruvate?

A

To turn the HCO3- into CO2

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10
Q

*In this series of reactions, pyruvate is first carboxylated to oxaloacetate and then decarboxylated to phosphoenolpyruvate. Why is this series of steps important?

A

Carboxylating it onto the biotin doesn’t require any energy so it can be added to the pyruvate to make oxalate

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11
Q

Discuss two alternative pathways from pyruvate to phosphoenolpyruvate. What is the purpose of the variation in pathways?

A

During gluconeogenesis, the pyruvate to phosphoenolpyruvate can either take place in the mitochondria or the cytosol.

The reason for this is because after PEP is formed, the rest of gluconeogenesis is performed in the cytosol. One important part of gluconeogenesis is NADH. Therefore, NADH must be generated somwhere in the cytosol so it can be available for later use.

If lactate –> pyruvate in the cytosol, the NADH will be made in the cytosol. Therefore, the oxaloacetate and PEP will be made in the mitochondria using mitochondrial pyruvate carboxylase and mitochondrial PEP carboxykinase. After the PEP is formed, it will leave the mitochondria into the cytosol so gluconeogenesis can continue

If you start with pyruvate. You must generate your oxaloacetate in the mitochondria but convert it into malate first. This generates a NAD+ and uses NADH in the mitochondria. This is only done so that we have an NAD+ to bring outside of the mitochondria (into the cytosol), and convert malate back to oxaloacetate just to create the NADH (uses cytosolic malate dehydrogenase) . Then oxaloacetate can react with cytosolic PEP carboxykinase to make PEP.

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12
Q

Write a balanced equation for the reaction of fructose 1,6-bisphosphate. Name the type of reaction

A

Fructose 1,6 bisphosphate + H20 –> Fructose 6 phosphate + Pi

Hydrolysis

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13
Q

Write a balanced equation for the reaction of glucose 6-phosphate. Name the type of reaction

A

Glucose 6 phosphate + H2O –> Glucose + Pi

Hydrolysis

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14
Q

Overall net equation of gluconeogenesis

A

2 pyruvate + 4 ATP + 2 GTP + 2 NADH + 2 H+ + 4H20 + —> Glucose + 4ADP + 2GDP + 6Pi + 2NAD+

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15
Q

How many net ATPs does glycolysis produce?

A

2 ATPs and 2 pryruvate

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16
Q

Where do the 6 ATPs required for gluconeogenesis come from? Energetically, ATP and GTP are equivalent and we are dealing with two moles of pyruvate

A
  • Pyruvate –> Oxaloacetate
  • Oxaloacetate –> PEP
  • 3- Phosphoglycerate –> 1,3-bisphosphoglycerate

Two molecules of pyruvate for 3 ATP x 2 = 6 total ATPs

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16
Q

Which other steps in gluconeogenesis can be described as an energy input?

A

NADH and H being added to go from 1,3- Bisphosphoglycerate to Glyceraldehyde 3 Phosphate

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16
Q

How many net ATPs does gluconeogenesis consume?

A

6 ATPs and produces one glucose

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16
Q

Draw the diagram for the reciprocal regulation of PFK-1 and FBPase-1

A

Draw simrita’s version

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16
Q

Why would it be wasteful for a cell to simultaneously carry out both glycolysis and gluconeogenesis? How is this prevented?

A

It would be wasteful because glycolysis only generates 2 ATPs (net) while gluconeogenesis used 6 ATPs. There would be a -4 ATP with each cycle. To be prevented, there is reciprocal regulation. This means some things that activate glycolysis will inhibit gluconeogenesis

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17
Q

What is a futile cycle? Give an example

A

refers to a pair of opposing metabolic pathways that continuously convert the same substrates back and forth, resulting in a net consumption of ATP or energy without any significant overall change in the concentration of the metabolites involved.

Example is glycolysis and gluconeogensis

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17
Q

Draw the diagram for the regulation of F 2,6-BP by the special enzymes. Make sure to include the proteins that regulate this as well

A

*Remember that F 2,6 BP comes from Fructose 6 phosphate and that it uses PFK2 and FBPase 2

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17
Q

Draw the diagram for how insulin and glucagon regulate PFK2 and FBPase. Make sure to name the enzymes

A

Insulin activates phosphoprotein phosphatase to remove the Pi group from the PFK-2 to activate it

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18
Q

Discuss the reciprocal regulation of pyruvate carboxylase and the enzyme that prepares pyruvate for entry into the citric acid cycle, pyruvate dehydrogenase

A
  • Draw the diagram
  • Pyruvate can either turn into oxaloacetate and enter gluconeogenesis or turn into acetyl CoA (irreversible) and enter the TCA cycle.
  • To convert pyruvate into acetyl CoA, pyruvate dehydrogenase is used. When there is a lot of acetyl CoA (which signifies we don’t need more of it), it will inhibit the pyruvate dehydrogenase (to let it know we are already producing energy, you can try to make glucose instead.
  • Acetyl CoA will activate pyruvate carboxylase so that pyruvate can turn into oxaloacetate and enter the TCA cycle
18
Q

Draw out the complete regulation of PFK1 starting with the insulin glucagon pathway. Show how/when fructose 2,6 BP accumulates in the cell

A
19
Q

What does the FAD do in the PDH complex?

A

Gets reduced and oxidized the lipoate. Removes the two H’s. It also reduces the NAD+ to make it NADH

20
Q

Pyruvate Dehydrogenase Complex (roughly sketch the complex as well)

A
  • Remember TPP, lipoate, and FAD are all catalyzing the reaction but they are not the reaction itself

*The actual reaction is that we are adding a CoASH group while removing a CO2 from the molecule using NAD+

21
Q

What is the name of the enzyme complex that forms acetyl-CoA from pyruvate?

A

The Pyruvate Dehydrogenase Complex

22
Q

Write the net reaction catalyzed by the pyruvate dehydrogenase complex

A
  • Remember TPP, lipoate, and FAD are all catalyzing the reaction but they are not the reaction itself

*The actual reaction is that we are adding a CoASH group while removing a CO2 from the molecule using NAD+

23
Q

What does TPP do in the PDH complex?

A

Removes the CO2 from the pyruvate and passes it to the second enzyme

23
Q

What does the lipoate do in the dehydrogenase complex?

A

Moves the decarboxylated pyruvate to the CoASH so it can be added on

24
Q

How many coenzymes are involved in the conversion of pyruvate to acetyl-CoA? Name them

A

5 coenzymes
- TPP (often used for oxidative decarboxylation)
-lipoate (reduced then oxidized)
- NAD+ (reduced)
- FAD (reduced then oxidized)
- CoASH

24
Q

What does the NAD+ do in the PDH complex?

A

Reduced by the FADH2.

25
Q

How many enzymes are involved in the conversion of pyruvate to acetyl-CoA?

A

3 enzymes - E1, E2, E3

25
Q

*distinction between coenzymes and enzymes

A
26
Q

What is the process of what occurs to pyruvate to become acetyl-CoA

A

Oxidative decarboxylation (then an acetyl group gets added on)

26
Q

Where does the PDH complex occur?

A

In the mitochondrial matrix. Therefore, we have to figure out some way to get the pyruvate teh was made in the cytosol into the mitochondrial matrix

27
Q

Discuss “substrate channeling”. What is the advantage of having these enzymes organized into a complex

A
  • Movement of chemical intermediates in a series of enzyme catalyzed reactions from the active site of one enzyme to that of the next in the pathway. This is advantages because it increases rate (having the intermediates concentrated on the enzymes) and it prevents the loss of intermediates
28
Q

Write the net reaction for the pyruvate dehydrogenase complex

A

Pyruvate + CoASH + NAD+ –> Acetyl-CoA + NADH + H+ + CO2

29
Q

What is the function of FAD and NAD+ in the reaction pathway? Does it seem odd that FADH2 is strong enough to reduce NAD+ to NADH

A

The function is for them to serve as electron carriers to reduce the other coenzymes
- it’s the enzyme dihydrolipoamide dehydrogenase (E3) and the microenvironment within the complex that facilitate the transfer of electrons from FADH2 to NAD+.
Dihydrolipoamide dehydrogenase (E3) plays a crucial role in this process by serving as a bridge between the reduction of FAD to FADH2 and the oxidation of NAD+ to NADH. This enzyme provides the necessary catalytic environment to facilitate the transfer of electrons from FADH2 to NAD+, ultimately leading to the regeneration of NADH.
*Overall, it’s the coordinated action of dihydrolipoamide dehydrogenase (E3) and the specific microenvironment within the PDH complex that makes it possible for FADH2 to effectively reduce NAD+ to NADH in this context.

30
Q

What is the goal of the TCA cycle?

A

To generate the electron carriers, NADH and FADH2 that can be used in the ETC for ATP synthesis
It also generates ATP during the process as well

31
Q

Using the structural formulas, write the reaction catalyzed by citrate synthase to form citroyl-CoA (draw how this works as well and go by Simrita, not the textbook).

Why is the thioester bond in the citroyl-CoA intermediate important?

How is the wasteful hydrolysis of the thioester bond in acetyl-CoA prevented?

A
  • Acetyl-CoA + Oxaloacetate
    (draw the rest)
  • The thioester bond is a high energy bond, so once it’s hydrolyzed it releases a high amount of energy and is essentially irreversible
  • The wasteful hydrolysis of the thioester bond is prevented because:
    1. Acetyl-CoA can’t bind until oxaloacetate is bound to the citrate synthase first
    2. Side chains of citrate synthase are not in place for hydrolysis until citroyl-CoA is formed

*A claisen condensation requires a lot of energy so the energy release from the thioester bond is beneficial

31
Q

Draw out the entire TCA cycle. You can choose to show all the reactions on the side but you just have to draw the circle

A
32
Q

Draw and discuss the mechanism of action of isocitrate dehydrogenase

A

Isocitrate dehydrogenase will facilitate oxidative dehydrogenation. This will result in the formation of alpha ketoglutarate

33
Q

Discuss the mechanism of coupling between high energy thioester cleavage and GTP synthesis by succinyl-CoA synthetase

A
  • In step 1, a phosphoryl group replaces the CoA of succinyl-CoA bound to the enzyme, forming a high energy phosphate
  • In step 2, the succinyl phosphate donates its phosphoryl group to a His residue of the enzyme, forming a high energy phosphatidyl enzyme
  • In step 3, the phosphoryl group is transferred from the His residue to the terminal phosphate of GDP (or ATP) forming GTP (or ATP)
34
Q

Which reactions aren’t reversible in the TCA cycle?

A
  • Citrate synthase (the thioester bond)
  • Isocitrate dehydrogenase (OD)
  • Alpha-ketoglutarate dehydrogenase (OD)
34
Q

What is the name of the enzyme that catalyzes the formation of GTP?

A

Succinyl-CoA synthetase

34
Q

What is the name of the enzyme that catalyzes the formation of citrate?

A

Citrate synthase

34
Q

List the four oxidation reactions in the citric acid cycle and tell which coenzymes picks up the electrons and the H atoms released in each of these reactions

A
  • Isocitrate –> alpha-ketogglutarate (NADH)
  • Alpha-ketoglutarate –> Succinyl-CoA (NADH)
  • Succinate –> Fumarate (FADH2)
  • Malate –> Oxaloacetate (NADH)
34
Q

How can one explain the ability of an enzyme to distinguish between the two ends of a component like citrate?

A

The enzyme aconitase (the one responsible for creating isocitrate) has 3 points to which the citrate must be bound to be attacked. The binding of citrate to these three points can only work in one way, allowing for the formation of only one type of product instead of a mixture of isocitrate or alpha ketoglutarate.

35
Q

Is the carboxyl carbon of citrate randomized between the two ends of the molecule during the conversion of citrate to succinyl-CoA?

A

No

36
Q

Where else can acetyl-CoA come from?

aka. Name three classes of molecules that undergo their final oxidation in the citric acid cycle

A

Carbs, fats, and proteins can undergo their final breakdown in the TCA cycle

37
Q

What eventually happens to these electrons and H atoms

A

Although the TCA cycle only generates one ATP (really GTP) per turn, the 4 oxidation steps provide a large flow of electrons into the respiratory chain via NADH and FADH2

37
Q

Illustrate the anabolic functions of the citric acid cycle

A

Citrate –> fatty acids, sterols
Alpha ketoglutarate –> purines, amino acids
Succinyl CoA –> heme
Oxaloacetate –> pyrimidines, amino acids

37
Q

Write a balanced equation for the anaplerotic reaction catalyzed by pyruvate carboxylase. Why is it analpluerotic?

A

Pryruvate + HCO3- + ATP –> oxaloacetate + ADP + Pi

38
Q

Define anaplerotic reaction and explain the metabolic importance of pyruvate carboxylase reaction

A
  • An enzyme catalyzed reaction that can replenish the supply of intermediates in the citric acid cycle
  • This is important because oxaloacetate can be used to become many things, so this reaction can create some for the TCA cycle. If not, the TCA cycle would not be able to occur
38
Q

Name the prosthetic group used by pyruvate carboxylase and describe its mechanism of action. What is the purpose of ATP?

A
  • Biotin. Helps transport the CO2 from one active site to the other (pyruvate) so they can react.
  • The purpose of ATP is to activate the bicarbonate by making it CO2
38
Q

Discuss how the pyruvate dehydrogenase complex is regulated by both allosteric mechanisms and by covalent mechanisms

A

Allosterically activated:
- ADP
- NAD+
- Ca2+
- CoASH

Allosterically inhibited:
- ATP
- NADH
- Acetyl-CoA

Covalently:
When phosphorylated, the PDH complex is inhibited

When there are high concentrations of ATP, a kinase is activated which will phosphorylate PDH and inhibit it

When there are low concentrations of ATP, a phosphatase (wont have competition with the kinase) and will remove the phosphate from the PDH complex to activate it

38
Q

What are other ways the TCA cycle can be regulated? Where and by what?

A

Can be regulated at the three irreversible steps:

Citrate Synthase:
Inhibitor: NADH, Citrate, ATP, Succinyl CoA
Activator: ADP

Isocitrate dehydrogenase:
Inhibitor: ATP
Activator: Ca2+, ADP

Alpha ketoglutarate dehydrogenase complex:
Inhibitor: Succinyl CoA, NADH
Activator: Ca2+

Biochem (15 decks)

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