Lecture 3: Central Metabolism, The Citric Acid Cycle and the Glyoxylate Cycle - Exam 4

Question 1

In the ED pathway, when is there NO NADPH created in the ED pathway?

Answer 1

When organisms are growing on gluconate (not glucose), the first two steps are bypassed. Instead, gluconate is phosphorylated to 6-P-gluconate by another enzyme, glucokinase, and NO NADPH is created.

Question 2

What are the three possible fates of Acetyl-CoA?

Answer 2

Aerobic respiration, anaerobic respiration, and fermentation.

Question 3

What is the TCA cycle? Who has it? What is the starting product and where does it come from?

Answer 3

The TCA cycle is a central driver of cellular respiration used by all aerobic organisms. The TCA cycle takes acetyl CoA – produced by the oxidation of pyruvate and originally derived from glucose – as its starting material and, in a series of redox reactions, harvests much of its bond energy in the form of NADH, FADH2, and GTP (or ATP).

Question 4

Why is the TCA cycle so important to respiring organisms?

Answer 4

The TCA cycle (and other central metabolic pathways) are important for oxidation of acetyl CoA to CO2 but also for generation of precursors and intermediates for biosynthesis of other macromolecules including amino acids.

Question 5

What are the reduced electron carriers generated in the TCA cycle? What will they do?

Answer 5

NADH and FADH2 will pass their electrons into the electron transport chain and, through oxidative phosphorylation, will generate most of the ATP produced in cellular respiration.

Question 6

How many oxidations occur in the TCA cycle? How many NADH and FADH2 are produced as a result? How many substrate level phosphorylations? How many irreversible reactions?

Answer 6

4 oxidations –> 3 NADH & FADH2
1 substrate level phosphorylation –> 1 GTP (or ATP in some cases)
3 irreversible reactions:
Citrate synthase (step 1)
Isocitrate dehydrogenase (step 3)
alpha-ketoglutarate dehydrogenase (step 4)

Question 7

What happens in the first step of the TCA cycle?

Answer 7

The enzyme citrate synthase catalyzes the formation of citrate (6 Carbon) from acetyl CoA and a four carbon acceptor molecule oxaloacetate.
-This step is IRREVERSIBLE

Question 8

What happens in the second step of the TCA cycle?

Answer 8

A quick rearrangement converts citrate to isocitrate.

Question 9

What happens in steps 3&4 of the TCA cycle?

Answer 9

Isocitrate releases two of its carbons as CO2 in two oxidation reactions, each one producing a molecule of NADH.
The enzymes that catalyze these reactions are isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase. These are key regulators of the citric acid cycle, speeding it up or slowing it down based on the cell’s energy needs.

Question 10

What happens in steps 5-8 in the TCA cycle?

Answer 10

The succinyl CoA undergoes a series of additional reactions.
Step 5: Succinyl CoA -> Succinate
a GTP is produced.
Step 6: Succinate -> Fumarate
-The electron carrier FAD is reduced to FADH2
Step 7: Fumarate -> Malate
Step 8: Malate -> Oxaloacetate

Question 11

The final step of the TCA cycle generates…?
What does this set of reactions generate?

Answer 11

The final steps generates another ATP.
This set of reactions regenerates the starting molecule of the TCA cycle, oxaloacetate, so the cycle can repeat.

Question 12

For every glucose molecule, how many times does the TCA cycle run?
What is the total yield per mol glucose?

Answer 12

Twice
2 ATP (GTP), 2 FADH2, and 6 NADH

Question 13

During respiratory growth, TCA cycle is coupled to..?

Answer 13

PMF generation and ATP synthesis via ATP Synthase.

Question 14

The TCA cycle provides precursors for ____ of the 20 amino acids found in proteins.

Answer 14

10

Question 15

Because the TCA cycle intermediates are constantly being removed to provide precursors for biosynthesis, they must be replaced. If not, what happens?

Answer 15

If not, the decrease in oxaloacetate level that is required for the citrate synthase reaction would result in stoppage of the cycle.

Question 16

So, how is oxaloacetate replenished?

Answer 16

If the organism is growing on amino acids or organic acids, then this can be easily replenished by the conversion of these molecules to OAA directly.
If the carbon source is sugar (ex. glucose), the carboxylation of pyruvate or PEP replenishes OAA.

Question 17

Who uses the reductive TCA cycle?

Answer 17

Fermenting bacteria
Since fermenting organisms are not carrying out respiration, it is best under fermenting conditions not to have an oxidative pathway that produces so much NADH and FADH2.

Question 18

Reductive TCA pathway:
Which enzyme is not expressed under anaerobic conditions?

Answer 18

alpha-ketoglutarate dehydrogenase

Question 19

How does the Reductive TCA pathway work?

Answer 19

Instead of succinyl-CoA being oxidized to oxaloacetate, oxaloacetate is reduced to succinyl-CoA by fumarate reductase.
Some organisms can completely reverse TCA cycle to fix carbon from CO2 using alternative enzymes.

Question 20

What does the Reductive TCA pathway yield?

Answer 20

1 NADPH and oxidizes
1 NADH –> NAD+, and
1 FADH2 –> FAD+

Question 21

What is the primary function of the Glyoxylate Pathway?

Answer 21

Is to mediate the conversion of acetyl-CoA to succinate for the production of carbohydrates.

Question 22

Which bacteria have the Glyoxylate Pathway and when is it used?

Answer 22

It is required by aerobic bacteria to grow on fatty acids or acetate. Plants and some protozoans also have the pathway, but it is absent in animals.

Question 23

What does the Glyoxylate Pathway allow bacteria growing on fatty acids to do?

Answer 23

Allows them to synthesize glucose from acetyl-CoA.

Question 24

How does the Glyoxylate Cycle differ from the TCA cycle? What are the two unique enzymes and what do they do?

Answer 24

The Glyoxylate Pathway resembles the TCA cycle except it bypasses the two decarboxylation reactions.
The two pathway specific enzymes:
Isocitrate (6C) is then converted directly to succinate (4C) and glyoxylate (2C) by the Glyoxylate pathway-specific enzyme, Isocitrate lyase.
The second enzyme is Malate synthase, which catalyzes the reaction between glyoxylate and acetyl-CoA to produce malate. Malate is then converted to oxaloacetate (this is an extra malate, so there is extra OAA) which can begin a new round of TCA or glyoxylate pathway, or begin gluconeogenesis.
***This allows the isocitrate to bypass the decarboxylation reactions of the TCA cycle. The carbons of acetyl-CoA are not lost as CO2 in glyoxylate pathway (these carbons can be used in the synthesis of macromolecules)

Question 25

The succinate produced in the Glyoxylate pathway can be used for what?

Answer 25

Can be used for energy by ultimately converting it to PEP.

Question 26

What is the yield of the Glyoxylate pathway?

Answer 26

Because the Glyoxylate Pathway skips the two oxidation reactions of the TCA cycle, less energy and fewer reducing agents.
Each turn of the Glyoxylate cycle yields 1 NADH and 1 FADH2 (versus 3 NADH, 1 FADH2, and 1 ATP (GTP) in the TCA cycle).
Also, where the TCA cycle has no net production of oxaloacetate, in the glyoxylate pathway, each acetyl-CoA produces two molecules of oxaloacetate, resulting in a net of 1 OAA molecules (b/c one is used to start the cycle).

Question 27

How is the Glyoxylate pathway regulated?

Answer 27

When cells are grown on acetate, the high acetate inactivates isocitrate dehydrogenase and induces isocitrate lyase

Question 27

How are the central metabolic pathways and the TCA cycle coupled to oxidative phosphorylation? Explain the connection of
these pathways and the creation of ATP during cellular respiration. Make sure to discuss the importance of the ETC as a
pathway for both oxidation and reduction, and the central metabolic pathways/TCA cycle in anabolism and catabolism. This
will be an important question on your exam, so be able to pull all of this information together.

Answer 27

Look over!

Question 27

Despite diversity of energy, electron and carbon sources used by organisms, they all have the same basic needs. What are they?

Answer 27

-ATP as an energy currency
-Reducing power to supply electrons for chemical reactions
-Precursor metabolites for biosynthesis
Many complex pathways exist to generate these building blocks.

Question 28

Describe Autotrophic metabolism.

Answer 28

Autotrophic bacteria synthesize their cell constituents using carbon dioxide as the carbon source.
The most common pathways for synthesizing organic compounds from CO2 are the Calvin cycle, the reductive TCA cycle, and the acetyl-CoA pathway.

Question 29

The Calvin Cycle operates in which organisms?

Answer 29

Plants, algae, photosynthetic bacteria, and most aerobic lithoautotrophic bacteria.

Question 30

What is the purpose of the calvin cycle?

Answer 30

CB Cycle = CO2 fixation to make carbohydrates. Organisms that fix carbon are autotrophic. It takes energy to fix carbon.

Question 31

Calvin Cycle:
Each CO2 molecule contributes __________ to build a _________.

Answer 31

One carbon ; 6-carbon glucose molecule.

Question 32

Calvin Cycle:
Other than CO2 molecules, what is does building a six carbon glucose molecule take?

Answer 32

Two 3-phosphoglycerate (3-PGA) molecules because one 3-PGA molecule contains three fixed carbon atoms.

Question 33

How many turns of the calvin cycle does it take to produce 1 glucose molecule?

Answer 33

It takes six turns and it takes 6CO2, 18 ATP, and 12 NADPH molecules.

Question 34

What are the three phases of the calvin cycle?

Answer 34

1. Carbon fixation: Carbon fixation from CO2 to 3-Phosphoglycerate by RuBisCO enzyme. RuBisCO catalyzes the addition of CO2 to a 5-C ribulose biphosphate molecule (from the PPP). This is a carboxylation reaction.
2. Reduction: Reduction of 3-PGA to 3-phosphoglyceraldehyde (PGALD or G3P).
3. Regeneration: Generate Ribulose 1,5-biphosphate to continue the cycle.

Although associated commonly with photosynthetic organisms, some non-photosynthetic organics (nitrifying bacteria) can use this cycle to fix CO2.

Question 35

Describe the RuBisCO enzyme.

Answer 35

-It is the first step in the calvin-bensen cycle.
-Is the most abundant enzyme one earth since it is present in photosynthetic bacteria, algae, plants, and other autotrophic organisms.
-The RuBisCO enzyme in chloroplast is the same type as in Cyanobacteria.