Chapter 14

Question 1

1. What are the 4 functions of metabolic pathways?

Answer 1

1. Functions:
   
   1. Obtain chemical energy from capturing solar energy or from degradation of energy rich nutrients.
   2. Conversion of nutrient molecules into cellular precursors.
   3. Polymerization of monomeric precursors into macromolecules.
   4. Synthesis and degradation of specialized cellular biomolecules (e.g., intracellular messengers, pigments).

Question 2

General Principles of Metabolic Pathways:

1. Metabolic Pathways are Irreversable
   
   1. What happens when the reaction is highly exergonic?
   2. What happens if the highly exergonic reaction is part of a multistep pathway?

Answer 2

1. Metabolic Pathways are Irreversable
   
   1. A highly exergonic reaction (large negative free energy change) is irreversible - it goes to completion.
   2. If a highly exergonic reaction is part of a multistep pathway the entire pathway is irreversible.

Question 3

General Principles of Metabolic Pathways:

1. Catabolic and Anabolic Processes Must Differ
   
   1. If two metabolites are metabolically inter-convertible what must they be?
   2. In the picture conversion of 1 to 2 is highly exergonic and therefore irreversible; what does this mean?
      
      1. What is an example?

Answer 3

1. Catabolic and Anabolic Processes Must Differ
   
   1. If two metabolites are metabolically inter-convertible, the pathway from the first to the second must differ from the pathway from the second to the first.
   2. Conversion of 1 to 2 is highly exergonic and therefore irreversible; a different route is required that provides the energy to get 2 back to 1.
      
      1. Glycolysis-Gluconeogenesis

Question 4

General Principles of Metabolic Pathways:

1. Every metabolic pathway has a committed step.
   
   1. Explain
   2. What step in glycolysis is the committed step?

Answer 4

1. Every metabolic pathway has a committed step.
   
   1. Early in each pathway, there is an irreversible reaction, which “commits” the intermediate that it produces to continue down the pathway (usually the one, which is heavily regulated).
   2. The 3^rd step is the committed step.

Question 5

General Principles of Metabolic Pathways:

1. All metabolic pathways are heavily regulated
   
   1. What are methabolic pathways regulated by?
   2. What step is usually the regulated step?
   3. What is usually the “committed step”?

Answer 5

1. All metabolic pathways are heavily regulated
   
   1. Regulated by the law of supply and demands.
   2. Usually the rate limiting step.
   3. The committed step is the usually the rate limiting step.

Question 6

General Principles of Metabolic Pathways:

1. Metabolic pathways in eukaryotic cells occur in specific compartments:
   
   1. What is the reason for this?
   2. What are some examples of this?
2. Specific metabolic pathways in specific compartments in eukaryotic cells:
   
   1. What occurs in the Mitochondrion?
   2. What occurs in the Cytosol?
   3. What occurs in the ER (rough)?
   4. What occurs in the ER (smooth)?
3. In multicelluar organisms:
   
   1. What occurs in the liver
   2. What occurs in the adipose tissue?

Answer 6

1. Metabolic pathways in eukaryotic cells occur in specific compartments:
   
   1. Different metabolites can operate in different locations and in different pathways.
   2. ATP is synthesized in mitochondrion but used in cytosol. Acetyl-CoA is produced in mitochondrion but utilized in cytosol.
2. In eukaryotic cells:
   
   1. Citric acid cycle, electron transport oxidative phosphorylation, fatty acid oxidation, amino acid breakdown.
   2. Glycolosis, pentose phosphate pathway fatty acid biosynthesis, gluconeogenesis.
   3. Protein synthesis
   4. Lipid and steroid biosynthesis.
3. In multicellular organisms
   
   1. Glconeogenesis
   2. Storage of Fats

Question 7

1. Why is glucose an excellent fuel?
2. Glucose is a….?
   
   1. What can Bacteria use glucose to do?

Answer 7

1. Why glucose is an excellent fuel:
   
   1. Yields good amount of energy upon oxidation.
   2. Can be efficiently stored in the polymeric form.
   3. Many organisms and tissues can meet their energy needs on glucose only.
2. Versatile chemical compound
   
   1. Bacteria can use glucose to build the carbon skeletons of:
      
      1. Amino Acids
      2. Membrane lipids
      3. Nucleotides in DNA and RNA
      4. Cofactors needed for the metabolism

Question 8

1. What is the digestion pathway of starch, glycogen, and sucrose?
2. What happens when a person is lactose intolerant?

Answer 8

1. Pathway:
   
   1. 1st: glycogen⇒oligosaccharides, di and tri. (salivary amylase)
   2. 2nd: oligosaccharides, di and tri.⇒ oligosaccharides, di and tri. (Chyme) (acid hydrolysis in the stomach).
   3. 3rd: oligosaccharides, di and tri. ⇒ lactose (α-amylase in small intestine)
   4. 4th: lactose ⇒ fructose (lactase)
2. Person will not be able to break down lactose because they are unable to synthesize lactase.

Question 9

Four Major Pathways of Glucose Utilization:

1. Storage?
2. Glycolysis?
3. Pentose Phosphate Pathway?
4. Synthesis of Structural Polysaccharides?

Answer 9

1. Storage:
   
   1. Can be stored in the polymeric form (starch, glycogen).
   2. When there’s plenty of excess energy.
2. Glycolysis:
   
   1. Generates energy via oxidation of glucose.
   2. Short-term energy needs.
3. Pentose Phosphate Pathway:
   
   1. Generates NADPH via oxidation of glucose.
   2. For detoxification and the biosynthesis of lipids and nucleotides.
4. Synthesis of Structural Polysaccharides
   
   1. For example, in cell walls of bacteria, fungi, and plants.

Question 10

1. When was glycolysis developed?
2. How is energy extracted from glucose anaerobically?
3. What is glucose converted to in glycolysis?
4. What is SLP?
5. What is oxidative phosphorylation?
6. What drives ATP synthesis?
7. What is the general chemical strategy for glycolysis?

Answer 10

1. Devolped before photosynthesis, when the atmosphere was still anaerobic.
2. First: Activate it by phosphorylation. Second: Collect energy from the high-energy metabolites.
3. Converted to pyruvate via enzyme-catalyzed reaction. Pyruvate can be further aerbobically oxidized. Pyruvate can be used as a precursor in biosynthesis.
4. S-P + ADP ⇒ S + ATP
5. NADH ⇒ NAD⁺ + H⁺
6. A proton gradient across the mitochondrial membrane. (about 2.5 ATP/NADH).
7. Strategy:
   
   1. Add phosphoryl-group(s) to glucose.
   2. Convert phosphorylated glucose into intermediates with high phosphoryl-group transfer potential.
   3. Couple hydrolysis with ATP synthesis.

Question 11

Step 1: Phosphorylation of Glucose

1. What is glucose coverted into?
2. What is the rationale behind this step?
3. What enzyme do prokayotes use?
4. Why is Mg²⁺ used in this reaction?
5. How is this step regulated?

Answer 11

1. Glucose ⇒ Glucose 6-phosphate
   
   1. By Hexokinase, uses ATP, irreversible reaction.
2. Rationale:
   
   1. Traps glucose inside the cell.
   2. Lower intracellular glucose concentration to allow further uptake.
3. Glucokinase
4. ATP-bound Mg²⁺ facilitates this process by shielding the negative charges on ATP.
5. Regulated by substrate inhibition.

Question 12

1. H₂O is just as reactive as Glucose and can freely move into the active site of hexokinase. How did nature prevent Hexokinase from being a useless ATPase?

Answer 12

1. Induced Fit!!! In the absence of glucose: Hexokinase is almost inactive because active site residues are not in correct position. Binding of glucose and Mg·ATP induces large conformational changes, which are required to bring the active site residues together.

Question 13

Step 2: Phosphohexose Isomerization

1. What is the reaction? What is the enzyme?
2. What is the rationale behind the reaction?
3. What is aldose glucose converted to?
4. Is this reaction thermodynamically favorable, or unfavorable?

Answer 13

1. Glucose 6-phosphate ⇔ Fructose 6-phosphate
   
   1. Enzyme: phosphohexose isomerase
   2. Mg²⁺ is still present
   3. ΔG^‘o = 1.7 kJ/mol
2. Rationale:
   
   1. C1 of fructose is easier to phosphorylate by PFK.
   2. Allows for symmetrical cleave by aldolase.
3. Coverted into ketose fructose
4. Thermodynamically unfavorable/reversible. Product concentration kept low to drive forward.

Question 14

Step 3: 2nd Priming Phosphorylation

1. What is the reaction? What enzyme is used? What is the ΔG^‘o?
2. What is the rationale behind this step?
3. What is special about this reaction?
4. Is this reaction thermodynamically favorable, or unfavorable?

Answer 14

1. Fructose 6-phosphate ⇒ Fructose 1,6-bisphosphate
   
   1. Phosphofructokinase-1
   2. ATP used, along with Mg²⁺. ADP is generated.
   3. ΔG^‘o = -14.2 kJ/mol
2. Futher activation of glucose. Allows for 1 phosphate/3-carbon sugar after step 4.
3. First committed Step of Glycolysis. Fructose 1,6-bisphosphate is committed to become pyruvate and yield energy.
4. Highly thermodynamically favorable/irreversible. Phosphofructokinase-1 is highly regulated.
   
   1. By ATP, fructose-2,6-bisphosphate, and other metabolites.
   2. Do not burn glucose if there is plenty of ATP.

Question 15

Step 4: Aldol Cleavage of F-1,6-bP

1. What is the reaction? What enzyme is used? What is the ΔG^‘o for this reaction?
2. What is the rationale?
3. What kind of reaction is the reverse reaction?
4. Is the reaction thermodynamically favorable, or unfavorable?
5. What product concentration is kept low to pull the reaction forward?

Answer 15

1. Fructose 1,6-bisphosphate ⇔ Dihydroxyacetone phosphate + Glyceraldhyde 3-phosphate.
   
   1. Aldolase
   2. 23.8 kJ/mol
2. Cleavage of a six-carbon sugar into two three-carbon sugars. High-energy phosphate sugars are three-carbon sugars.
3. An aldol condensation
4. Thermodynamically favorable
5. GAP

Question 16

Step 5: Triose Phosphate Interconversion

1. What is the reaction? What enzyme is used? What is the ΔG’^o?
2. What is the rationale behind the reaction?
3. What are the two triose phosphates created?
4. Which of the triose phosphates is the subtrate for the next enzyme?
5. What does this reaction signify?

Answer 16

1. Dihydroxyacetone phosphate ⇔ Glyceraldhyde 3-phosphate
   
   1. triose phosphate isomerase
   2. 7.5 kJ/mol
2. Allows glycolysis to proceed by one pathway.
3. DHAP and GAP
4. GAP is the substrate used in the next reaction
5. Brings an end to the preparatory phase of glycolysis.

Question 17

The second stage of glycolysis: the payoff stage

1. What two steps in this phase generate ATP?
2. Which step generates NADH?
3. What nuclotide must be recovered to keep glycolysis going?
4. Which steps are reversible?

Answer 17

1. Steps 7 & 10 generate ATP.
2. Step 6 generates ATP
3. NAD⁺ must be recovered for glycolysis to continue (oxidative phosphorylation, fermentation).
4. All steps are reversible except 10.

Question 18

Step 6: Oxidation of GAP

1. What is the reaction? What enzyme is used? What is the ΔG’o? What does it yield?
2. What is the rationale behind the reaction?
3. What is special about this step?
4. How do we make NADH?
5. What does the active site of cysteine form? What is it subjected to?
6. Is this reaction thermodynamically favorable, or unfavorable?

Answer 18

1. Glyceraldehyde 3-phosphate + inorganic phosphate ⇔ 1,3-Bisphosphoglycerate
   
   1. glyceraldehyde 3-phosphate dehydrogenase
   2. 6.3 kJ/mol
   3. 2 NADH + H⁺
2. Rationale:
   
   1. Generation of a high-energy phosphate compound.
   2. Incorporates inorganic phosphate.
   3. Which allows for net production of ATP via glycolysis!
3. First energy-yielding step.
4. Via the oxidation of the aldehyde.
5. Forms high-energy thioester intermediate. Subject to inactivation by oxidative stress.
6. Unfavorable, coupled to the next reaction to pull it forward.

Question 19

Step 7: 1st Production of ATP

1. What is the reaction? What is the enzyme? What is the ΔG’o? What does it yield?
2. What is the rationale behind the reaction?
3. What is makes 1,3-Bisphosphoglycerate a unique compound?
4. Is this reaction thermodynamically favorable, or unfavorable?

Answer 19

1. 1,3-Bisphosphoglycerate + ADP ⇔ 3-Phosphoglycerate + ATP
   
   1. phosphoglycerate kinase
   2. -18.5 kJ/mol
   3. Yields 2 ATP
   4. Mg²⁺ is also used in this reaction
2. Rationale:
   
   1. SLP to make ATP
3. 1,3-Bisphosphoglycerate is a high-energy compound. Can donate the phosphate group to ADP to make ATP.
4. Highly themodyamically favorable. Is reversible because of coupling to GAPDH reaction.

Question 20

1. What is unique about multienzyme complexes?

Answer 20

Question 21

Step 8: Migration of the Phosphate

1. What is the reaction? What enzyme is used? What is the ΔG’o?
2. What is the rationale behind the reaction?
3. What catalyzes the migration?
4. Is this reaction thermodynamically favorable, or unfavorable?

Answer 21

1. 3-Phosphoglycerate ⇔ 2-Phosphoglycerate
   
   1. Phosphoglycerate mutase
   2. 4.4 kJ/mol
   3. Mg²⁺ is also available
2. Be able to form a high-energy phosphate compund.
3. Mutases catalyze the (apparent) migration of functional groups.
4. Unfavorable/reversible! Reactant concentration kept high by PGK to push forward.

Question 22

Step 9: Dehydration of 2-PG to PEP

1. What is the reaction? What enzyme is used? What is the ΔG’o?
2. What is the rationale behind the reaction?
3. Why do we need to convert 2-phosphoglycerate?
4. Is this reaction thermodynamically favorable, or unfavorable?

Answer 22

1. 2-phosphoglycerate ⇔ phosphoenolpyruvate
   
   1. enolase
   2. 7.5 kJ/mol
   3. Yields 2 water molecules
2. To generate a high-energy phosphate compound
3. 2-PG is not a good enough phosphate donor. Two negative charges in 2-PG are fairly close. But loss of phosphate from 2-PG would give a secondary alcohol with no further stabilization.
4. Slightly thermodynamically unfavorable/reversible. Product concentration kept low to pull forward.

Question 23

Step 10: Phosphotransfer from PEP

1. What is the reaction? What enzyme is used? What is the ΔG’o?
2. What is the rationale behind the reaction?
3. What does the loss of phosphate from PEP yield?
4. What does tautomerization do?
5. What does pyruvate kinase require?
6. Is this reaction thermodynamically favorable, or unfavorable?

Answer 23

1. Phosphoenolpyruvate ⇒ Pyruvate
   
   1. pyruvate kinase
   2. -31.4 kJ/mol
   3. Yields 2 ATP
   4. Second SLP: Generates more ATP. Dispite ATP production highly exergonic (irreversible)
2. SLP to make ATP. Net production of 2 ATP/glucose
3. Loss of phosphate from PEP yields an enol that tautomerizes into ketone.
4. Effectively lowers the concentration of the reaction product. Drives the reaction toward ATP formation.
5. Pyruvate kinase requires divalent metals (Mg++ or Mn++) for activity.
6. Highly thermodynamically favorable/irreversible.
   
   1. Regulated by ATP, divalent metals, and other metabolites

Question 24

Cancer cells and glycolysis:

1. What are cancer cells usually not connected to? What do they contain less of?
2. What induces the expression of glycolytic enzymes?
3. What do they depend on for energy production?
4. What method is used to detect cancer?

Answer 24

1. Usually not connected to capillary systems (hypoxia). Fewer mitochondria (less extensive respiration linked phosphorylation).
2. Hypoxia-inducible transcription factors.
3. Depends on anaerobic glycolysis for energy production. 10x faster
4. PET Scan: isotope-labeled glucose that is taken up but not metabolized – can be detected in heavily metabolizing tissue, such as brain but also in CANCER.

Question 25

1. What are the three fates of Pyruvate?
2. Fermentation:
   
   1. What does it generate?
   2. What is reduced?
   3. What does it regenerate?
   4. In lactic acid fermentation what is produced?

Answer 25

1. Fates:
   
   1. Converted to 2 Lactate, under hypoxic or anaerobic conditions
   2. Converted to 2 Ethanol + 2 CO₂, under hypoxic or anaerobic conditions.
   3. Converted to 2 Acetyl-CoA under aerobic conditions.
2. Fermentation:
   
   1. Generation of energy without consuming NAD⁺. No net change in oxidation state of the sugars.
   2. Reduction of pyruvate to another product.
   3. Regenerates NAD⁺ for further glycolysis under anaerobic conditions.

Question 26

Lactic Acid Fermentation:

1. What is the reaction?
2. What is regenerated?
3. What causes lactic acid build up?
4. What does the acidification of the muscle prevent?
5. Where can the lactate be transported?
6. What is required for the release of this lactic acid?

Answer 26

1. Pyruvate ⇔ Lactate
   
   1. NADH is converted to NAD⁺
   2. Lactate dehydrogenase
   3. -25 kJ/mol
2. NAD⁺ is regenerated by transferring e- to pyruvate and reducing it to lactate.
3. Dangerous strenuous exercise, lactate builds up in the muscle. Generally less than 1 minute.
4. The acidification of muscle prevents its continuous strenuous work.
5. The lactate can be transported to the liver and converted to glucose (Cori cycle).
6. Recovery Time:
   
   1. High amount of oxygen consumption to fuel gluconeogenesis.
   2. Restores muscle glycogen stores.

Question 27

Ethano Fermentation:

1. What is the reaction?
2. What do humans lack?
3. What is CO₂ in the first step responsible for?

Answer 27

1. Pyruvate ⇔ Acetaldehyde ⇔ Ethanol
   
   1. Enzymes: pyruvate decarboxylase, alcohol dehydrogenase
   2. Two-step reduction of pyruvate to ethanol, irreversible.
   3. First step releases CO₂, second step regenerates NAD⁺.
2. Lack pyruvate decarboxylase. Also, we do not express alcohol dehydrogenase.
3. Carbonation in beer, dough rising when baking bread.