Ch. 9 Flashcards by Rene Galindo

What do the central metabolic pathways do (i.e. what do they provide)?

Provide the precursors for all other pathways

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What are the major carbohydrate pathways? Which are only in prokaryotes?

Glycolysis
Pentose phosphate pathway (PPP)
Entner-Doudoroff (ED) pathway: prokaryotes

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What 2 generalizations can be made about the 3 carbohydrate pathways?

All pathways convert glucose to phosphoglyceraldehyde (PGA)
All PGA to pyruvate (oxidation reaction) via the same reaction

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What happens to pyruvate in respiration vs. fermentation?

Respiration: pyruvate –> oxidized to acetyl-CoA –> oxidized to carbon dioxide in the citric acid cycle
Fermenation: converted to end products (alcohols, organic acids, solvents)

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Give an overview of carbohydrate catabolic pathways:
1. How many SLPs are there and when do they occur?
2. How many oxidation reactions are there and when do they occur?
3. What do the oxidations produce?
4. What happens to the oxidation products?

3 SLPs
- 2 during carbohydrate catabolism
- 1 in citric acid cycle
6 oxidation reactions
- 1 in glycolysis
- 1 in pyruvate dehydrogenase reaction
- 4 in citric acid cycle
NADH and FADH₂
They get reoxidized into NAD⁺ and FAD

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What are the 2 stages of glycolysis? How many ATPs are used or generated per glucose?

Catalyzes the splitting of the glucose molecule into 2 phosphoglyceraldehyde molecules
- 2 ATPs used per glucose
Catalyzes the oxidation of phosphoglyceraldehyde to pyruvate
- 4 ATPs generated

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What is the net yield of ATP in glycolysis?

2 ATP

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What are the equations for the 2 stages of glycolysis? What is their sum?

Stage 1: glucose + 2 ATP –> 2 PGALD + 2 ADP
Stage 2: 2 PGALD + 2P_i + 4 ADP + 2 NAD⁺ –> 2 pyruvate + 4 ATP + 2 NADH + 2 H⁺
Sum: glucose + 2 ADP + 2 P_i + 2 NAD⁺ –> 2 pyruvate + 2 ATP + 2 NADH + 2 H⁺

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What are the major outcomes of glycolysis?

ATP is generated via SLP
Provides precursor metabolites for many other pathways

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What must organisms do when they’re not growing on carbohydrate?

They must synthesize glycolytic intermediates from other carbon sources

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Why can the glycolytic pathway only be reversed from PEP to fructose 1,6-bisphosphate (FBP), and not at all from pyruvate?

Because the high free energy in the phosphoryl donors with respect to the phosphorylated products renders the kinase reactions irreversible
- Therefore, to reverse glycolysis, the kinase reactions are bypassed

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What are the 2 key enzymes in regulating the directionality of carbon flow in glycolysis?

Phosphofructokinase (PFK)
Fructose-1,6-bisphosphate kinase

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In glycolysis, high AMP and ADP concentrations are a signal that ATP levels are low. This is an example of _____ regulation.

allosteric

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What is the result of the glycolysis regulation?

ADP promotes glycolysis, AMP inhibits gluconeogenesis

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_____ is feedback inhibited by PEP. This is an example of _____ inhibition.

phosphofructokinase
end-product

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Consider the isomerization of glucose-6-phosphate to fructose-6-phosphate. What is the rationale for this isomerization?

It creates an electron-attacking keto group at the C2 of the sugar
- Necessary to break the bond between C3 and C4 in the aldolase reaction

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NAD⁺ is reduced during central metabolism. What would happen if it is not reoxidized?

All pathways (including glycolysis) that require NAD⁺ would stop

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What are the 3 NADH reoxidation pathways in bacteria?

Respiration
Fermentation
Hydrogenase reaction

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Why is the PPP important?

It produces the pentose phosphates (precursors to ribose and deoxyribose in nucleic acids)
It provides erythrose phosphate (precursor to aromatic amino acids)
Produces NADPH (source of electrons for biosynthesis)
Several reactions are the same as those in the Calvin cycle

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What are the 3 stages of the PPP? What are the products of each stage?

Oxidation-decarboxylation reactions
- Produces CO₂ and NADPH
Isomerization reactions
- Produces precursors for stage 3
Sugar rearrangements
- Produces phosphoglyceraldehyde

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Stage 1 of the PPP:
- General description
- Steps
- What are the products?
- What enzymes are involved?

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Reactions oxidize the C1 in glucose-6-P to a carboxyl group and remove it as carbon dioxide
Steps
1. Glucose-6-P is oxidized by NADP⁺ to 6-P-gluconolactone by glucose-6-P dehydrogenase
2. Hydrolysis: 6-P-gluconolactone –> 6-P-gluconate by gluconolactonase
3. Oxidation: 6-P-gluconate is oxidaized on the C3 –> keto group β to the carboxyl
4. β-decarboxylation: generates ribulose-5-P
Products: CO₂, NADPH, RuMP
Enzymes: G-6-P dehydrogenase, gluconolactonase

Stage 2 of the PPP:
- What happens in it?
- What are the enzymes involved and what products do they make?

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Some RuMP is isomerized to ribose-5-P and xylulose-5-P
RuMP epimerase makes xylulose-5-P (moves -OH group)
R-5-P isomerase makes ribose-5-P (moves keto group)

Stage 3 of the PPP:
- What are the 2 types of sugar arrangements (i.e. what enzyme)?

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Tranketolase (TK): transfers 2-carbon fragments from a ketose to an aldose
Transaldolase (TA): transfers 3-carbon fragment from a ketose to an aldose

What are isomers?

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Molecules with the same chemical formula but different structural formulas

What is the rule for sugar rearrangements?

The donor is always a ketose and the acceptor is always an aldose

Summarize the PPP (what is each reaction, products).

A. Reactions 1-3: oxidative decarboxylation reactions of stage 1 - Produces 3 moles of ribulose-5-P B. Reactions 4 and 5: isomerization reactions of stage 2 - Produces 1 mole of of ribose-5-P and 2 moles of xylulose-5-P C. Reaction 6-8: sugar rearrangements of stage 3 - Reaction 6: TK reaction - Reaction 7: TA reaction - Reaction 8: TK reaction

Some bacteria rely completely on the PPP for _____.

sugar catabolism

Where do the PPP and glycolysis interconnect?

At phosphoglyceraldehyde and fructose-6-P

What are the reactions of the Entner-Doudoroff (ED) pathway?

2. Oxidation of C1 in glucose-6-P to the carboxyl in 6-P-gluconate 3. Dehydration reaction forms KDPG 4. KDPG is split by KDPG aldolase to pyruvate and phosphoglyceraldehyde 5-9. identical to stage 3 of glycolysis

Why does the ED pathway generate less ATP than glycolysis?

ED pathway only produces 1 phosphoglyceradehyde (glycolysis makes 2 phosphoglyceraldehyde)

Give an example of the use of the ED pathway.

*E. coli* transferred from a medium containing glucose as the carbon source to one with gluconate as the carbon source

What are the 2 fates of pyruvate?

1. Fermentation 2. Oxidation to acetyl-CoA --> citric acid cycle --> oxidized completely to CO₂

The oxidation of pyruvate to acetyl-CoA during aerobic growth is carried out by the enzyme complex _____.

pyruvate dehydrogenase

What are the 3 enzymes of the PDH complex?

1. E1: pyruvate dehydrogenase 2. E2: dihydrolipoate transacetylase 3. E3: dihydrolipoate dehydrogenase

What are the 5 cofactors of the PDH complex?

1. Thiamine pyruphosphate (TPP) 2. FAD 3. α-lipoic acid (RS₂) 4. NAD⁺ 5. Coenzyme A

What are the 5 steps of the PDH complex?

1. E1: Pyruvate decarboxylated --> active acetaldehyde bound to TPP 2. E1: Active acetaldehyde oxidized to a carboxyl by disulfide in lipoic acid; TPP displace 3. E2: Transacetylation (lipoid acid displaced by CoA-SH --> acetyl-CoA) 4. E3: Lipoate electron transferred to FAD 5. E3: Electrons transferred from FADH₂ to NAD⁺

The physiologically irreversible PDH reaction is under allosteric regulation. How is the PDH reaction regulated?

1. Feedback inhibition (end product): **acetyl-CoA and NADH** 2. Positive regulation: **PEP** (signals that more pyruvate is on the way) and **AMP** (signals low ATP)

What is the rationale behind end product inhibition of the PDH reaction?

Ensures that the enzyme only produces as much acetyl-CoA and NADH as can be used immediately

What does the citric acid cycle produce?

- 2 NADH - 1 NADPH - 1 FADH₂ - 1 ATP via SLP

What are the following molecules precursors for and what pathway are they from?

What are the 10 reactions of the citric acid cycle?

1. Addition of acetyl group fro acetyl-CoA to oxaloacetate --> citrate 2. Dehydration of citrate --> *cis*-aconitate 3. Rehydration of *cis*-aconitate --> isocitrate 4. Oxidation of isocitrate --> oxalosuccinate 5. Decarboxylation of oxalosuccinate --> α-ketoglutarate 6. Oxidative decarboxylation of α-ketoglutarate --> succinyl-CoA 7. SLP forms ATP 8. Oxidation of succinate --> fumarate 9. Hydration of fumarate --> malate 10. Oxidation of malate -> oxaloacetate

What are the enzymes for each of the reactions in the citric acid cycle? Which ones are irreversible?

1. Citrate synthase (irreversible) 2. Aconitase 3. Aconitase 4. Isocitrate dehydrogenase 5. Isocitrate dehydrogenase 6. α-ketoglutarate dehydrogenase (irreversible) 7. Succinate thiokinase 8. Succinate dehydrogenase 9. Fumarase 10. Malate dehydrogenase

How is the citric acid cycle regulated in Gram-negative vs. Gram-positive bacteria?

1. Gram-negative bacteria: citrate synthase is alloesterically inhibited by **NADH** (prevent oversynthesis of NADH) - In facultative anaerobes: **α-ketoglutarate** is an additional inhibitor (prevent overprodution of glutamate) 2. Gram-positive bacteria and eukaryotes: citrate synthase inhibited by **ATP**

In what way is the citric acid cycle also an anabolic pathway?

It provides the precursors for 10 or 20 amino acids

What amino acid precursors does the citric acid cycle make?

- Succinuyl-CoA --> L-lysine and L-methionine - Oxaloacetate --> aspartate - α-Ketoglutarate --> glutamate

Because the citric acid cycle intermediates are constantly being removed to provide precursors for biosynthesis, they must be replaced. How are they replaced?

- Growth on amino acids: can use amino acids to replenish oxaloacetate - Growth on sugar: carboxylation of pyruvate or PEP to replenish oxaloacetate

What is the glyoxylate cycle?

A second pathway for the metabolism of acetyl-CoA

When is the glyoxylate cycle required?

Required by aerobic bacteria to grow on fatty acids and acetate

Compare the glyoxylate cycle and the citric acid cycle.

- Pathways diverge at isocitrate - Glyoxylate cycle bypasses 2 decarboxylation reactions - No CO₂ formed

What are the 2 reactions of the glyoxylate cycle?

1. Isocitrate lyase: socitrate is cleaved to succinate and glyoxylate 2. Malate synthase: glyoxylate condenses with acetyl-CoA --> malate --> replenishes oxaloacetate

What are the products of the glyoxylate cycle?

- 1 **succinate** --> oxidized to oxaloacetate --> converted to PEP - 1 **NADH**

What is the net result of the glyoxylate cycle?

Condensation of 2 acetyl-CoA to form succinate

Ch. 9 Flashcards

(52 cards)