biochem: mark's medical biochem chapter 39- synthesis and degradation of amino acids

this chapter looked at the synthesis and degradation of different amino acids (put in bold). first it introduced the cofactors involved in these reactions: transamination reactions (such as the reaction involving glutamate introduced in chapter 38) require pyridoxal phosphate (PLP), which bonds its aldehyde carbon to the amino nitrogen and allows for different reactions to occur. FH4 is another cofactor that is involved in one carbon exchanges. BH4 is a cofactor that is involved in ring hydroxylations.

there are several amino acids that can be derived from the glycolytic intermediate, 3-phosphoglycerate. these include serine, cysteine, and glycine. serine is formed by oxidation, transamination to phosphoserine, then removal of the phosphate to form serine. it degrades in a separate pathway to form pyruvate. serine can then be converted to glycine in a reaction that involves both PLP and FH4. cysteine is also derived from serine- serine combines with homocysteine to form cystathione, which forms cysteine (and also succinyl CoA by way of alpha-keto butyrate- to be explained later).

amino acids can also be synthesized to TCA cycle intermediates. in particular, oxaloacetate and alpha-ketoglutarate. as we saw in the urea cycle, oxaloacetate can be transaminated to aspartate, which can be further converted into asparagate. alpha-ketoglutarate can be converted to glutamate in the glutamate dehydrogenase reaction. glutamate can then be converted to glutamine, or it can be converted to glutamate 5-semialdehyde. this compound can be converted to proline, or ornithine. ornithine can then be used to fuel the urea cycle, which produces arginine.

there are also several amino acids that can supply TCA cycle intermediates (an anaplerotic reaction); in particular, the intermediate succinyl CoA. the first was mentioned above- the homocysteine that reacts with serine to form cysteine actually is derived from methionine. in the last step of the cysteine synthesis pathway, the intermediate cystathione cleaves into cysteine and alpha-ketobutyrate, which is converted into propionyl CoA, and ultimately succinyl CoA.

valine and isoleucine are two branched chain amino acids that can replenish succinyl CoA. they are both transaminated into keto acids, then oxidatively decarboxylated into acyl CoA. these are oxidized in a way similar to fatty acid beta oxidation, ultimately producing FADH2, NADH, and propionyl CoA, which is converted to succinyl CoA.

finally, there are amino acids which are "ketogenic"- they produce ketone bodies, either acetyl CoA or acetoacetate, in their degradation. this includes leucine, isoleucine, tyrosine, phenylalanine, threonine, and tryptophan. isoleucine, as mentioned above, produces both succinyl CoA and acetyl CoA in its degradation, whereas leucine only produces acetyl CoA. phenylalanine is converted to tyrosine, which then produces acetoacetate and fumarate in its degradation. finally, tryptophan is an amino acid that produces formate, acetyl CoA, and alanine in its degradation.


questions
cofactors...
1. what are the three cofactors involved in amino acid metabolism?
2. how does pyridoxal phosphate aid in amino acid reactions?
3. how is FH4 involved in amino acid reactions? what is it derived from?
4. how is BH4 involved in amino acid reactions?

amino acids derived from glycolysis...
5. what are the amino acids derived from intermediates of glycolysis?
6. describe the synthesis of serine from glycolytic intermediates.
7. describe the degradation of serine.
8. how is serine synthesis regulated?
9. how is glycine synthesized?
10. how does glycine relate to kidney stones?

cysteine...
11. describe the synthesis of cysteine.
12. describe the regulation of the synthesis of cysteine.
13. how is methionine involved in cysteine synthesis?
14. describe the degradation of cysteine.
15. how is alanine synthesized?

amino acids related to TCA cycle intermediates...
16. which TCA cycle intermediates can be used to synthesize amino acids?
17. which TCA intermediates can be replenished by anaplerotic reactions via amino acids?
18. explain the statement "glutamate can be both derived from glucose and converted to glucose".
19. what are the three enzymes in the body that can "fix" free ammonia?
20. why is glutaminase important in the kidney?

alpha keto glutarate derived amino acids...
21. describe the synthesis of proline.
22. how is arginine synthesized?
23. what is the enzyme that transaminates glutamate 5-semialdehyde into ornithine?
24. describe the synthesis of aspartate and asparagine.

amino acids that supply succinyl CoA...
25. which amino acids degrade to form succinyl CoA?
26. describe the degradation of methionine to succinyl CoA.
27. describe the degradation of threonine to succinyl CoA.
28. where does most branched chain amino acid oxidation occur?
29. how are the degradations of valine and isoleucine both anaplerotic and energy producing?
30. what does degradation of leucine form?

ketogenic amino acids...
31. what are the main ketogenic amino acids?
32. describe how phenylalanine can produce ketone bodies.
33. what does tryptophan degradation produce?
34. what does degradation of lysine form?

answers
1. pyridoxal phosphate (PLP) (see chapter 38), FH4, and BH4.
2. the N on the amino acids bind to the aldehyde carbon of the PLP and pulls electrons away from the alpha carbon on the amino acid, allowing for different reactions to occur.
3. FH4 is required to donate or accept one carbon groups. it is derived from the vitamin folate.
4. BH4 is important for ring hydroxylation reactions.

5. serine, glycine, cysteine, and alanine.
6. 3-phosphoglycerate is oxidized to 3-phosphohydroxypyruvate, by 3-pg dehydrogenase. 3-phosphohydroxypyruvate is then transaminated to phosphoserine. the phosphate from phosphoserine is then removed to form serine.
7. serine is transaminated to hydroxypyruvate. hydroxypyruvate is reduced and phosphorylated to form 2-phosphoglycerate, which then forms PEP and pyruvate.
8. when serine levels fall, higher levels of 3-phosphoglycerate dehydrogenase are induced, and inhibition of phosphoserine phosphatase by serine is relaxed.
9. the major pathway of glycine synthesis is a conversion of serine, involving FH4 and PLP. the minor pathway is through the degradation of threonine in an aldolase-like reaction.

10. glycine can be converted to glyoxalate, which can be oxidized to oxalate- the accumulation of which can cause kidney stones.
11. homocysteine combines with serine to form cystathione. cystathione is cleaved to form propionyl CoA (which is converted to succinyl CoA) and cysteine.
12. cysteine inhibits the cystathione synthase; thereby inhibiting its own production.
13. methionine, an essential amino acid, provides the sulfur for cysteine synthesis. if methionine is in short supply, cysteine can not be synthesized de novo and becomes an essential amino acid.
14. degradation of cysteine produces pyruvate, NH4, and sulfate.
15. alanine is synthesized from the transamination of pyruvate via alanine aminotransferase (ALT).

16. oxaloacetate, alpha-keto glutarate.
17. oxaloacetate, alpha-keto glutarate, succinyl CoA, fumarate.
18. glutamate is derived from alpha-ketoglutarate, which is derived from glucose via the TCA cycle. in the liver, it can be degraded back into alpha-ketoglutarate, which leads to the formation of malate, which produces glucose via gluconeogenesis.
19. carbamoyl phosphate synthetase I (first reaction from the urea cycle), glutamate dehydrogenase, and glutamine synthetase.
20. glutaminase catalyzes the release of NH3 from glutamine, which then is secreted into the renal tubules and is the basis of the ammonia buffer system which aids in the excretion of H+.

21. glutamate is reduced to glutamate 5-semialdehyde, which then spontaneously forms a cyclical structure. this is then reduced to proline.
22. glutamate 5-semialdehyde can be converted to ornithine via a transamination reaction. ornithine can then be used to fuel the urea cycle, which produces arginine.
23. ornithine aminotransferase.
24. aspartate is transaminated from oxaloacetate (see chapter 38 notes). aspartate can be converted to asparagine by aspargine synthetase.

25. methionine, valine, isoleucine, threonine.
26. see question 13. methionine is converted to S-adenhosylhomocysteine, which is converted to homocysteine, which combines with serine to form cystathione. cystathione cleaves to produce cysteine and alpha-keto butyrate, which can be converted to propionyl CoA and ultimately succinyl CoA.
27. threonine is converted to alpha-keto butyrate by a hydratase, using PLP as a cofactor. alpha-keto butyrate is converted to succinyl CoA in the same path as for methionine degradation to succinyl CoA.
28. in muscle.
29. in both degradation pathways, they are transaminated to the alpha keto acids, then oxidatively decarboxylated to acyl CoA's. at this point they are oxidized just like fatty acyl CoA's using beta oxidation, producing NADH, FADH2, and propionyl CoA, which can be converted to succinyl CoA. thus the NADH and FADH2 provides energy while the succinyl CoA replenishes the TCA cycle.
30. leucine, the third branched chain amino acid, does not form succinyl CoA- instead it just produces acetoacetate and acetyl CoA (and thus is "ketogenic")

31. phenylalanine, tyrosine, isoleucine, threonine, tryptophan.
32. phenylalanine is converted to tyrosine, which is ultimately converted into acetoacetate (a ketone body) and fumarate.
33. alanine, formate, and acetyl CoA.
34. acetyl CoA, and NADH, FADH2.

biochem: mark's medical biochem chapter 22- glycolysis

this chapter introduces glycolysis and its role in cellular energy production. glycolysis is basically the first step in breaking down glucose for use in energy production. in aerobic glycolysis, one molecule of glucose is broken down into two molecules of pyruvate, in the process forming 2 molecules of NADH and 2 molecules of ATP. in anaerobic glycolysis, one molecules of glucose produces lactate and 2 molecules of ATP. the reactions for aerobic glycolysis are as follows:

1. glucose is phophorylated to glucose-6-phosphate via hexokinase.
2. glucose 6-phophate is isomerized to fructose 6-phosphate via phosphoglucose isomerase.
3. fructose 6-phosphate is phosphorylated to fructose 1,6 bisphosphate via phosphofructokinase-1.
4. fructose 1,6 bisphosphate is cleaved into two triose phosphates via an aldolase.
5. the triose phophates isomerize into glyceraldehyde 3-phosphate (G3P).
6. G3P is oxidized by G3P dehydrogenase, which reduces NAD+ to NADH2 and transfers a high energy acyl phosphate bond onto G3P, forming 1,3 bisphophoglycerate.
7. 1,3 bisphosphoglycerate phosphorylates ADP via phosphoglycerate kinase and becomes 3 phosphoglycerate.
8. 3-phosphoglycerate is isomerized to 2-phosphoglycerate via phosphoglyceromutase.
9. 2-phosphoglycerate loses an H2O and becomes phosphoenolpyruvate (PEP) via enolase.
10. PEP phosphorylates another ADP via pyruvate kinase and becomes pyruvate.

reactions 1 through 4 are known as the preparative phase, in which glucose is basically phosphorylated twice and cleaved into two 3 carbon molecules. reactions 5-10 are known as the ATP generating phase, because the phosphate groups from the 3 carbon molecules are then transferred onto ADP. after the first phosphate group is transferred in reaction 7, reactions 8 and 9 basically transform the remaining phosphate group from a low energy to a high energy one so that it can also be transferred to ADP.

in reaction 6, NAD+ is used as an electron acceptor during the oxidation of G3P. thus, the NADH2 must be constantly reoxidized to NAD+ in order to maintain a source for transferring electrons. in aerobic glycolysis, this problem is solved by shuttling NADH2's electrons across the mitochondrial membrane (shuttling is needed because the membrane is impermeable to NAD), where they can be used to power oxidative phosphorylation. the most common shuttle is the G3P shuttle: NADH2 reduces DHAP to G3P via G3P dehydrogenase. G3P then diffuses across the mitochondrial membrane and transfers the electrons to FAD, forming FADH2, which can then donate its electrons to coenzyme Q in the electron transport chain. the other shuttle mechanism is the malate aspartate shuttle, in which NADH2 reduces oxaloacetate to malate, which is then shuttled across the mitochondrial membrane via a translocase, and then donates its electrons to mitochondrial NAD+, reforming oxaloacetate. oxaloacetate is then transaminated to aspartate, which can then be shuttled back out the mitochondria via another translocase, and once it is back, transaminated back into oxaloacetate and ready to accept electrons from NADH2 again.

the net ATP production from the G3P shuttle is 3 moles of ATP per mole of glucose, whereas the malate aspartate shuttle produces 5 moles of ATP. combining this with the ATP produced in the ATP-generating phase of glycolysis (2 ATP per glucose), and taking into account the pyruvate, which can be further oxidized in the mitochondria to produce an additional 12.5 ATP (25 ATP per glucose): this means in aerobic glycolysis, total ATP production for each molecule of glucose is either 3+2+25=30 when the G3P is in use or 5+2+25=32 when the malate aspartate shuttle is in use.

when oxygen is not readily available or mitochondria are not present (as in red blood cells, where oxidative metabolism might interfere with hemoglobin's interaction with oxygen, or in the eye, where mitochondria would deflect incoming light), or if cellular demands for energy exceeds that which is produced via aerobic processes, then anaerobic glycolysis is used. in order to regenerate the NAD+ to serve as the electron acceptor in reaction 6, NADH2 reduces pyruvate into lactic acid, which dissociates into lactate and proton (which has the potential to decease body pH). pyruvate therefore cannot be further oxidized and therefore the energy production in anaerobic glycolysis is quite lower, requiring tissues to work 15 times as fast to produce the same energy output. whereas in aerobic glycolysis the total energy production can be up to 32 moles of ATP per mole of glucose, in anaerobic glycolysis, the total energy production is only 2 moles of ATP (from the ATP-generating phase of glycolysis)

questions
1. describe the process of glycolysis and what it produces.
2. what are the two phases of glycolysis and what happens in each?

3. what is the first step in glycolysis and what does it produce?
4. what are the next steps in the preparative phase of glycolysis?
5. describe the oxidation of G3P.
6. what is substrate level phosphorylation?
7. where is the first phosphorylation of ADP?
8. how is the low energy phosphate bond in 3 phosphoglycerate transformed into a high energy phosphate bond that can be transferred to ADP?
9. what is the final reaction of glycolysis?
10. what is the total free energy change from glycolysis?
11. why does NADH need to be reoxidized and what are the two pathways in which this is accomplished?
12. what are the two fates for pyruvate?

13. why are reducing equivalent shuttles required?
14. describe the G3P shuttle.
15. describe the malate-aspartate shuttle.
16. describe anaerobic glycolysis.
17. what is the ATP production of the G3P vs. the malate-aspartate shuttle?
18. describe the difference of ATP production possible in aerobic vs. anaerobic glycolysis.
19. how is anaerobic glycolysis related to body pH?
20. when do cells or tissues use anaerobic glycolysis vs. aerobic?


answers
1. glycolysis is the splitting of glucose into pyruvate and production of 4 ATP molecules per molecule of glucose.
2. the preparative phase, in which glucose is phosphorylated twice by ATP and cleaved into two triose phosphates, and the ATP-generating phase, in which the triose phosphates produce 2 ATP each.

3. phosphorylation of glucose yields glucose-6-phosphate via hexokinases.
4. isomerization of glucose 6-phosphate via phosphoglucose isomerase to fructose 6-phosphate, phosphorylation to fructose 1,6 bisphosphate via phosphofructokinase-1 (PFK-1), and cleavage into two triose molecules (glyceraldehyde 3-phosphate) via aldolase.
5. G3P is oxidized by glyceraldehyde-3-phosphate dehydrogenase, which has a cysteine residue near the active site which accepts a high energy acyl phosphate and transfers it to G3P. in this process, NADH and a high energy phosphate bond are formed.
6. the formation of a high energy phosphate bond without oxygen via direct transfer of a phosphate bond from a high energy intermediate.
7. 1,3 bisphosphoglycerate transfers its phosphate group to ADP via phosphoglycerate kinase, forming 3 phosphoglycerate.
8. the low energy phosphate bond in 3-phosphoglycerate is first shifted to the middle carbon via phosphoglyceromutase, and then transformed into a higher energy phosphate bond via enolase, which removes a water molecule and turns the compound into phosphoenolasepyruvate.
9. transfer of the high energy phosphate bond phospho enol pyruvate to ADP, turning the compound into pyruvate.
10. -22kcal
11. NADH needs to be reoxidized in order to continually accept electrons during the oxidation of G3P via G3P dehydrogenase. when oxygen is available, reducing equivalents are shuttled across the mitochondrial membrane to the electron chain. when oxygen is not available, NADH transfers its electrons to pyruvate, which is then reduced to lactate.
12. pyruvate can be reduced to lactate in anaerobic glycolysis, or can be converted into acetyl coenzyme A and further oxidized in aerobic glycolysis.

13. because the mitochondrial membrane is impermeable to NADH.
14. the G3P shuttle is the main shuttle mechanism in which cytosolic NAD+ is regenerated by G3P dehydrogenase, which transfers the electrons from NADH2 to DHAP, forming G3P. G3P then diffuses across the mitochondrial membrane and donates its electrons to FAD, forming FADH2 and reforming DHAP, which can then diffuse back and be reused in the reaction.
15. the malate-aspartate shuttle is the other way that NAD+ is regenerated: NADH transfers its electrons to oxaloacetate, reducing it to malate, which is then transported across the mitochondrial membrane via a translocase. in the membrane, the malate reduces NAD to NADH2, which can then be used in the electron transport chain. the oxaloacetate that is formed is transaminated to aspartate, which is transported back across the mitochondrial membrane via another translocase, and transaminated back into oxaloacetate in the cytosol.
16. anaerobic glycolysis occurs when the the oxidative capacity of a cell is limited. in this reaction, the electrons from NADH2 are donated to pyruvate, creating lactic acid, catalyzed by the enzyme lactate dehydrogenase.
17. the G3P shuttle produces 1.5 moles of ATP per NADH2, whereas the malate-asparate shuttle produces 2.5 moles of ATP per NADH2.
18. in anaerobic glycolysis, pyruvate is reduced to lactate and thus cannot produce any more ATP besides the two moles (per glucose) that is produced during glycolysis. in aerobic glycolysis, in addition to these two ATP's, the pyruvate is oxidized and used in the mitochondria to produce 25 ATP (per glucose), and the NADH produced can add another 3 (if using the G3P pathway) or 5 (if using the malate aspartate pathway) ATP molecules.
19. lactic acid is produced from the reduction of pyruvate in anaerobic glycolysis via lactate dehydrogenase. at the normal intracellular pH of 7.35, lactic acid dissociates into lactate and H+, which is then transferred out of the cell and eventually into the blood, where it can influence body pH.
20. tissues that have a low ATP demand and low O2 availability. also, blood cells have undergo anaerobic glycolysis because aerobic metabolism might interfere with the loading and unloading of O2 from hemoglobin. also, in other tissues with mitochondria and O2 availability, anaerobic glycolysis is used when the cell's energetic demands are not met by aerobic processes.