BiochemEval6 -Compre

SUBJECT: BIOCHEMISTRY

 

TOPIC: EVALUATION #6 Set L (Amino Acid Metabolism) LECTURER: DR. CHIONGLO-SY DATE: MARCH 2011 I. Multiple Choice 1. The term amino acid pool refers to: a. Amino acids from degraded proteins b. Circulating amino acids

c. Synthesized non-essential amino acids d. A mixture of them

Correct answer: D, a mixture of them. This is because “amino acid pool” refers to the mixture of the amino acids available in the cell. These may come from the diet (the food we take in), or from the degradation of body proteins. We must remember that there is a turnover of proteins in our body, in such that while some are being synthesized, there are also some that are being degraded. So lahat ng amino acids galing doon sa mga processes na yun, they make up the amino acid pool. Hindi pwedeng isa lang sa kanila (sa choices above). BTW. There are no storage sites for amino acids! 2. A newborn began to hyperventilate 3 days after a full term normal delivery. He developed hypothermia and cerebral edema & became comatose. Urinalysis revelead high levels of glutamine and orotic acid (a metabolite in pyrimidine synthesis). The blood urea nitrogen value was below normal. Which of the following enzymes is most likely to be deficient in the neonate? a. Arginase b. Mitochondrial Carbamoyl phosphate synthetase c. Mitochondrial ornithine transcarbamoylase d. Argininosuccinic acid lyase Correct answer: C, Mitochondrial Ornithine Transcarbamoylase In the Urea Cycle (aka Krebs-Henseleit Cycle), the (mitochondrial) Ornithine Transcarbamoylase (OTC) is responsible for the conversion of ornithine and carbamoyl phosphate into citrulline. A lack in OTC will lead to the accumulation of the metabolites ornithine and carbamoyl phosphate. (Syempre, since hindi sila magagamit kasi kulang nga yung OTC enzyme na dapat gagamit sa kanila)  It was mentioned in the question above that there are high levels of orotic acid. This is because excess carbamoyl phosphate is converted to orotic acid.  The blood urea nitrogen value will naturally be lower than normal since the Urea Cycle is not able to “proceed smoothly” because of the lack of OTC.  The answer cannot be arginase If it were a deficiency in arginase, it is arginine that would accumulate (but there will also be a low amount of urea in the urine because arginase is needed to “cleave” arginine to become urea and ornithine).  If the enzyme deficient was mitochondrial carbamoyl phosphate synthetase (CPS-I), there will be an accumulation of ammonia since CPS-I uses ammonia as nitrogen donor in “producing” carbamoyl phosphate.  If it were a deficiency in argininosuccinic acid lyase, there also won’t be an accumulation of orotic acid but an accumulation of argininosuccinate, and perhaps a low amount of fumarate and arginine. (Since there will be no enzyme to convert the argininosuccinate into fumarate and arginine). 3. Disposal of amino groups of these amino acids thru transamination occurs mainly in the muscle. a. gly, ser, thr b. pro, his, OHpro c. Trp, phe, tyr d. leu, ile, val Correct answer: D, leu, ile, val The keyword for this question is “muscle”. Most of the transamination reactions that we discussed take place in the liver. However, for these 3 amino acids (leu, ile, val), the transamination occurs in the muscle. (It was mentioned by Doc Sy that these are the amino acids given by the doctor if the patient has a liver disease).

Remember that valine, isoleucine and leucine are collectively known as branched-chain amino acids. The final products of their catabolism in the muscle can be fully oxidized via the citric acid cycle.  What gly, ser, thr have in common is that they are all small and glucogenic amino acids that have pyruvate as their degradation product.  Pro, his, and OHpro has alpha-ketoglutarate as their degradation product

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 What trp, phe, tyr have in common is that all three of them are BOTH glucogenic and ketogenic amino acids and they are all neutral amino acids with aromatic side chains. 4. A 50-yr old male with a family history of genetic disease underwent replacement surgery for arthritis. During the operation, the surgeon observed pigmentation in the man’s cartilage. His ochronosis is most likely caused by oxidation & polymerization of this compound: (answer question #4 and 5) a. orotic acid b. uric acid c. methylmalonic acid d. homogentisic acid Correct answer: D, homogentisic acid The above case actually describes ALKAPTONURIA. A condition due to lack of homongentisate oxidase, thus causing accumulation of homogentisate or homogentisic acid. The urine darkens upon exposure to air due to oxidation of excreted homogentisic acid There is also arthritis and connective tissue pigementation (called ochronosis) due, again, to the oxidation of homogentisic acid (leading to formation of benzoquinone acetate which polymerizes and binds to connective tissue). Check p. 254 of Harper’s 28th edition if you don’t believe me :p (See pathway on p. 253) 5.The above case, is an inborn error disease involving which amino acid? a. methionine b. proline c. tryptophan

d. tyrosine

Correct answer: D, tyrosine Homogentisate oxidase is an enzyme involved in Tyrosine metabolism. (Wherein tyrosine is eventually degraded to Acetyl CoA + Acetate).  Methionine does not use homogentisate oxidase in its catabolism, nor does it involve homogentisic acid. Instead it involves L-Methionine adenosyltransferase and SAM (S-Adenosylmethionine)  Proline catabolism has 2 metabolic disorders (but not alkaptonuria): Type I Hyperprolinemia o A defect or lack or “metabolic block” at proline dehydrogenase (first enzyme used in catabolism of proline) Type II Hyperprolinemia o Metabolic block at glutamate-gamma-semialdehyde dehydrogenase  This enzyme also functions in hydroxyproline catabolism  A disorder associated with tryptophan is Hartnup disease - Hartnup reflects impaired intestinal and renal transport of tryptophan and other neutral amino acids *** Answer question nos. 6 – 9 *** 6. Reduced capacity to oxidize the following amino acids is found in maple syrup urine disease resulting in their presence in the urine: a. aromatic amino acids c. branched chain amino acids b. acid amino acids d. basic amino acids Correct answer: C, branched chain amino acids 7. Enzyme most commonly defective in maple syrup urine disease: a. isobutyryl CoA dehydrogenase c. Keto acid dehydrogenase complex b. Aminotransferase d. hydroxybutyryl coA hydrolase Correct answer: C, keto acid dehydrogenase complex Maple Syrup Urine disease is also known as branched-chain ketonuria, wherein there is a defect lies in the alphaketo acid decarboxylase complex. Because of this, the plasma and urinary levels of leucine, valine, isoleucine, α-keto acids and α-hydroxy acids are ELEVATED. 8. What observations in the patient aside from the above will conform the in-born error disease? a. hyperventilation of affected person c. urine smells of burnt sugar b. acidosis especially in the newborn d. all these may be observed Correct answer: D, all these may be observed Letter C is a very obvious answer, since this is the primary characteristic of maple syrup urine disease (urine smells like maple syrup or burnt sugar). This condition leads to a buildup of the branched chain amino acids in the body (ketonuria). Because of the buildup: Ketonuria = acidic = “acidosis” may occur = must blow off the excess CO2 = hyperventilation

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9. What recommendation of the attending physician will be of great help and should be immediately carried out in this case? a. Milk should be low in phenylalanine b. Make patient comfortable c. Give bicarbonates for acidosis d. Diet given should have no leu, ile and val Correct answer: D, diet given should have no leu, ile and val Since the body is having trouble breaking down the branched chain amino acids, the best recommendation is to avoid taking in food with leu, ile and val. The less branched chain amino acids taken in the diet, the less of these will build up = less of the symptoms/manifestations.  Giving milk low in Phe still won’t help much. Phe will still be metabolized by the body, but there will still be build up of ile, vale and leu from the diet. Giving bicarbonates does not directly address the problem, and making the patient comfortable is the least that a physician can do, frankly. :| 10. An amino acid is referred to as glucogenic if its final catabolic product fulfills this: a. can be used for glucose synthesis c. can enter mainstream of metabolism b. forms pyruvic acid d. is glucose itself Correct answer: A, can be used for glucose synthesis Glucogenic amino acids are those with a carbon skeleton that can be converted to metabolites that can be used for the synthesis of glucose, such as: These products can enter the Pyruvate formation of glucose via entry Intermediates of TCA cycle points in the TCA cycle: o Ex. OXAA, α-ketoglutarate, Succinyl-CoA, OXAA, α-KG, succinyl-CoA, Fumarate fumarate, pyruvate  These include: Pyruvate as ‘end-product’ : Ala, Cys, Ser, Gly, Thr OXAA: Asparagine, Aspartate Fumarate: Aspartate, Tyr, Phe Succinyl CoA: Val, Ile, Met α-KG: Arg, Glutamine, His, Pro, Glutamate  Therefore, saying that glucogenic AAs are only those that form pyruvic acid, or only those that enter glucose itself or only those that can enter mainstream of metabolism (if I remember correctly, this refers to the TCA cycle) is not enough. Letter A in a sense is like an “all of the above” because the B, C, D are qualities that can be used for glucose synthesis. 11. One knows that amino acids are ketogenic if their catabolic product is: a. acetyl coenzyme A c. OXAA b. a ketone d. α-KG Correct answer: A, Acetyl CoA  Basically, according to Harper, amino acids that give rise to acetyl CoA are referred to as ketogenic, because in prolonged fasting and starvation, much of the acetyl-coA is used for synthesis of ketone bodies in the liver.  OXAA cannot be the answer because yielding a catabolic product of OXAA would mean that the amino acid is glucogenic and not ketogenic. The same reasoning goes for alpha-ketoglutarate. Ketogenic AAs are those whose carbon skeleton can be converted to KETONE BODIES (and therefore can also be converted to lipids).

12. Only these amino acids are purely ketogenic: a. leu, lys b. ile, leu, val

c. phe, tyr d. leu, trp

Correct answer: A, leu, lys Glucogenic AAs Pyruvate as entry point: • Ala • Cys • Ser • Gly • Thr

OXAA as entry points: • Asn • Asp

Fumarate: • Asp • Tyr • Phe

Ketogenic and Glucogenic Succinyl CoA: • Val • Ile • Met

α-KG: • • • • •

Arg Gln Glu His Pro

• • • • •

Phe Tyr Trp Ile Thr (sometimes )

Purely Ketogenic • •

Leucine Lysine

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 Leucine and Lysine yield ONLY acetyl CoA when they undergo oxidation. Therefore, they cannot undergo gluconeogenesis (they are NOT glucogenic). Phe, Tyr, Trp, Ile (and sometimes Thr) can give rise to both Acetyl CoA and TCA intermediates kaya they fall under the “both” category!! **”Entry Point: This is their “end-product”/what becomes of their carbon skeleton when they are catabolized. This is also the one that determines whether they are ketogenic or glucogenic or both. For example, transmaination/catabolism of Histidine yields α-KG. That α-KG

can now enter the TCA cycle. 13. In which of the following conditions is there negative nitrogen balance? a. In Kwashiorkor c. In major injury and trauma b. Advanced cancer d. In all of the above conditions Correct answer: D, all of the above  Recall: Normal Nitrogen Balance

Positive Nitrogen Balance

Negative Nitrogen Balance

Nitrogen intake = nitrogen excreted

Nitrogen intake > nitrogen excreted

Nitrogen intake < nitrogen excreted

Observed in normal conditions

There is an “excess”, therefore proteins will go somewhere else. They may be used somewhere else in the body (ex. source of energy, like Atkin’s Diet). The proteins are not just for growth and repair now.

Nitrogen is lacking, therefore it may pose some problems for the body.

Occurs in: pregnancy (mom takes in more protein)

Occurs in: Starvation, surgery (post-operation/recovery) Medyo “nagkukulang” yung nitrogen kasi masyadong maraming nagagamit na protein. Starvation uses up proteins/amino acids due to processes such as gluconeogenesis. Post-op/Recovery from trauma will also use up a lot of proteins since the body will be using the amino acids in the healing process (i.e. to “repair” the wounds, etc.)

14. Which of the following is/are true about proteases? a. Degrade the peptide bond b. Normally in inactive zymogen forms

c. Are endopeptidases d. All are true statements

Correct answer: D, all are true  Proteases are enzymes that hydrolyze proteins (peptide bonds). There are several categories such as gastric, pancreatic, or carboxypeptidases. Among pancreatic enzymes, trypsin, chymotrypsin and elastase are the endopeptidases because they hydrolyze the bond “within” the molecule.  They are normally in inactive zymogen forms so that they will not irritate the gastrointestinal tract. They are only activated once secreted. Diba kailangan inactive sila kapag hindi sila kailangan, kasi they can damage the GI tract. Kaya they are normally in inactive zymogen forms. 15. Which of the following enzymes starts the degradation of proteins? a. chymotrypsin b. pepsin c. trypsin d. elastase Correct answer: B, Pepsin Pepsin is secreted and works in the stomach, while the other 3 choices are secreted by the pancreas. This means that in terms of action, it is the pepsin that gets to act on the (ingested) proteins first. 16. All these statements are true about the Meister Cycle except one. Which one is the exception? a. Also known as the γ-Glutathione Cycle b. Concerned with transport of amino acids across the membrane c. All amino acids utilize this transport system d. Uses the tripeptide γ-glutamylcysteinylglycine as transporter of amino acids Correct answer: C, all amino acids utilize this transport system  Okay, there is a slight discrepancy in the first choice because the Meister Cycle is actually otherwise known as the γ-Glutamyl Cycle, BUT it DOES involve Glutathione.

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 It is true that it’s concerned with the transport of amino acids across the membrane. It actually makes use of a γ-Glutamyl Transpeptidase (GGT) that catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor (which may be an amino acid, peptide, or water. This leads to glutamate formation) The Meister Cycle is a way in which the amino acids from food are taken up into the body A proposed pathway for the glutathione-dependent transport of certain amino acids (most notably L-cystine, L-methionine, and L-glutamine) and dipeptides into certain cells. o This cycle requires the formation of gamma-glutamyl amino acids and dipeptides, as well as a protein for the translocation of these di- and triisopeptides into the cells. (taken from http://www.mondofacto.com/facts/dictionary?gamma-glutamyl+cycle)

 Yes, it uses the tripeptide γ-glutamylcysteinylglycine (GSH), because GSH is just another term for Glutathione.

 However, we cannot say that ALL amino acids use this transport system, because there are a number of amino acid transport systems. Letter C therefore is the least correct among the choices, making it the correct answer. 17. Important in the digestive processes of infants, this enzyme clots milk and is absent in adults: a. pepsin b. renin c. rennin d. dipeptidase Correct answer: C, rennin Rennin is also known as chymosin. It is a proteolytic enzyme and its role in digestion is to curdle or coagulate milk in the stomach.  Pepsin cannot be the answer basically because it is NOT absent in adults.  Renin (aka angiotensinogenase) that functions in the Renin-Angiotensin System and is important in mediating the body’s extracellular volume. It is also NOT absent in adults and has nothing to do with clotting milk.  Dipeptidases are enzymes secreted in the small intestine and works hydrolyzing dipeptides. It is also NOT absent in adults. 18. A person suffering from Hartnup disease will exhibit symptoms of Vitamin B 3 deficiency because: a. Vit B3 is derived from Trp b. Intestinal absorption of tryptophan is defective in Hartnup c. There is decreased availability of tryptophan for conversion to niacin d. All of the above are reasons. Correct answer: D, all of the above As mentioned earlier, Hartnup reflects impaired intestinal and renal transport of tryptophan and other neutral amino acids. Impaired transport = defective trp absorption = excessive amount excreted in kidneys. The failure to absorb them means there is of course LESS tryptophan available for the production of niacin (Tryptophan is needed for the production of Niacin aka Vit. B 3 ).

19. In catabolism of amino acids, sequential action of these 2 enzymes deaminate amino acids liberating ammonia that will enter the Urea Cycle: a. Amino transferase & glutamate dehydrogenase b. Transaminase & Asparaginase c. Glutamate OXAA transaminase & glutamate pyruvate transaminase d. Glutaminase and Asparaginase Correct answer: A, amino transf & glu dehydrogenase Aminotransferase is an enzyme that catalyzes the transfer of an amino group (donor is usually amino acid) to a recipient (usually an alpha-keto acid), while glutamate dehydrogenase is an enzyme that reversibly converts glutamate to alpha-KG. Their sequential action works on the degradation of glutamine (glutamine  glutamate + NH4): 1. Glutamine reacts with glutaminase (an aminotransferase)  yields glutamate and NH4 2. Glutamate then reacts with glutamate dehydrogenase  forming α-KG ** The NH4 enters the urea cycle  Glutamate OXAA transaminase and Glu pyruvate transaminase do not act sequentially to liberate ammonia.  Glutaminase and Asparaginase have the same function (deamination) but they do not act sequentially as well. Glutaminase deamidates glutamine, forming glutamate; whereas, asparaginase deamidates asparagine, forming aspartate. 20. Ammonia, coming from most tissues except the muscle, is transported in the blood in the form of: a. glycine b. alanine c. asparagine d. glutamine Correct answer: D, glutamine Glutamine IS the transport form for non-toxic ammonia!!

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Glutamine synthase/glutaminase system works in the transport of NH3 from different tissues to kidney and liver. -

In the liver, glutamate is converted to glutamine by adding ammonia (via glutamine synthetase). So it may be considered that the formation of glutamine also somewhat acts like a form of ammonia detoxification. Once glutamine reaches the kidney, the enzyme glutaminase acts on glutamine. This will lead to formation of glutamate and the excretion of the NH4+ ion in the urine.

 Alanine is the transport form of ammonium ion from the MUSCLE cells to the liver. (Recall the glucosealanine cycle) 21. Primary role of the amino acids in the body? a. Serves as building blocks for synthesis of body proteins b. An alternate source of glucose c. Source of energy d. For lipid synthesis Correct answer: A, building blocks for protein synthesis Without amino acids, the body will not be able to synthesize proteins (polypeptides made up of amino acids, primarily used for structures in our body) Though amino acids may also be a source of energy [in part because it CAN be an alternate source of glucose (e.g. gluconeogenesis) and used in lipid synthesis (ketogenic amino acids; gluconeogen)], these only take place once the primary sources of glucose and fats have run out. So letters B, C and D are just secondary functions of amino acids that help us survive when other processes in the body go wrong. 22. Chymotrypsin cleaves peptide bonds where the carboxyl group is provided by all these amino acids except one. Which is the exception? a. tyrosine b. histidine c. tryptophan d. phenylalanine Correct answer: B, histidine Chymotrypsin acts upon Phe, Tyr, and Trp, because of the aromatic ring in their sidechain that fits into the hydrophobic pocket of the chymotrypsin. It also acts on methionine and leucine, though in a slower manner. 23. Transamination reactions of diff. amino acids are designed to collect amino groups in the form of Lglutamate because: a. Amino groups are toxic b. Transaminations is readily reversible c. Transamination is utilized in both degradation and synthesis d. Glu is the only amino acid that undergoes oxidative deamination at a high rate Correct answer: D, glu is the only … For transamination, the general acceptor is our alpha-KG acid, which accepts the amino group from ALL amino acids. This is because the enzyme that acts on glutamate has a very HIGH activity (glutamate dehydrogenase ata), therefore liberating the ammonia. Other dehydrogenases are NOT as active. 24. Serum levels of these 2 transaminases are useful in the diagnosis of heart and liver damage: a. GDH & GOT b. AST & ALT c. AST & GPT d. ALT&GOT Correct answer: C, AST & GPT  AST is Aspartate Transaminase, whose old name used to be Glutamic Oxaloacetate Transaminase (GOT) While GPT is Glutamic Pyruvate Transaminase. GOT occurs in large concentrations in the heart and liver (but also with moderate amts in skeletal muscle etc.); If elevated can imply diseases of the heart and liver (e.g. arrhythmias, liver damage) GPT is found in significant quantities in liver, kidney, and skeletal muscle, in decreasing order. o GOT and GPT levels increase in liver damage. For instance, levels may rise a few days before the onset of jaundice. 25. Coenzyme form of Vit B6 that is important in transamination reactions: a. pyridoxine b. pyridine c. pyridoxol

d. pyridoxal phosphate

Correct answer: D, pyridoxal phosphate Recall that the “–phosphate” versions of pyridoxine etc are their active forms, wherein pyridoxal phosphate is the principal coenzyme form and is very important in human metabolism. In transamination, it functions as a carrier of the amino group that will be transferred.

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26. Major transport form & temporary non-toxic storage of ammonia in the body: a. urea b. glutamine c. glutamate d. ketoglutarate Correct answer: B, glutamine For reasons that was already described earlier. Urea is the form by which the ammonia is excreted (through the urine). Glutamate and ketoglutarate play a role in the formation or “work” of glutamine but again, are not the major transport form and storage of ammonia in the body. 27. The most commonly encountered defect in phenylketonurias is: a. defect in phenylalanine hydroxylase b. mutation in dihydrobiopterin reductase c. mutation in the homogentisic acid oxidase d. absence of gene coding for hydroxyphenylpyruvate oxidase Correct answer: A, defect in phe hydroxylase The deficiency in this enzyme causes an inability to process phenylalanine. This leads to accumulation of phenylalanine, leading to phenylketonuria.  Dihydrobiopterin is produced in the synthesis of dopamine, norepineph and epinephrine. Dihydrobiopterine reductase is needed to convert dihydrobiopterin and water back to tetrahydrobiopterin (see the pathway of catecholamine synthesis for more info). It is SOMETIMES defective in patients with phenylketonuria, but it is NOT the most commonly encountered defect.  Mutation in homogentisic acid oxidase leads to ALKAPTONURIA which was already described earlier. 28. Phenylketonurics often times have lighter skin color, fair hair & blue eyes because: a. of low tyrosine production resulting in less melanin formation b. accumulation of phenylalanine c. of the acidity of keto acids d. effect of the accumulated phenylalanine metabolites. Correct answer, A. low tyr production = less melanin  Recall the formation of catecholamines from tyrosine. The DOPA is an intermediate in the formation of melanin. Therefore, a low amount of tyrosine will mean that there won’t be enough Dopa and thus, also not enough melanin formed. Low melanin = low pigmentation = light skin color, fair hair and light colored eyes. 

Hi, friends. Sorry kung hindi ko ittype ang questions from here onwards. :D 29. Correct answer: B, arginine is regenerated  Arginine is NOT regenerated in the Urea Cycle. It is ORNITHINE that is regenerated. Arginine is acted on by arginase (parang na-ccleave siya) to yield urea and ornithine.  As for the other choices: Yes, it is true that one urea molecule is formed for every 2 ammonia removed (see structure of urea) Pathway needs ATP and is endergonic. In fact, it already requires 2 ATP just for the first step alone. CPS-I needs N-acetylglutamate to be activated (helps enhance affinity for ATP) 30. Correct answer: C. Donor of the second amino group in the urea molecule.  The aspartic acid donates its amino group, and it is initially added to the citrulline (which already has 1 amino group). This forms argininosuccinate. And THEN, galing kay argininosuccinate, matatanggal lang yung fumarate, maiiwan si arginine, tapos maccleave nga si arginine para maging ornithine at UREA! :D (See STD Amino Acid Metabolism 1 Part 2 of 5 to see the structures!) 31. Correct answer: D, all of the above  Tetrahydrobiopterin is a cofactor that carries electrons for REDOX reactions by using OXYGEN as acceptor. This can be seen in the oxidation of phenylalanine to tyrosine. It is formed from dihydrobiopterin through the action of the enzyme dihydrofolate reductase, or from the quinonoid form of dihydrobiopterin through the action of dihydropteridine reductase. (taken from http://www.uic.edu/classes/phar/phar332/Clinical_Cases/aa%20metab%20cases/PKU%20Cases/bioh4.htm)

32. Correct answer: A, ammonia intoxication  ANY defect in the Urea Cycle that will hinder it from proceedingly correctly/smoothly will of course lead to problems in excreting ammonia. (There might even be problems in metabolizing ammonia to form urea.)  As for the other choices, these will only take place depending on the enzyme that is defective. For example, there will be no accumulation of arginine if it is OTC that is defective. Kasi, if OTC is defective, it will be

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carbamoyl phosphate and ornithine that will accumulate. Hindi na siya aabot sa part na may arginine, kasi hindi na nga makaproceed yung process. 33. A. Glutamate- alpha-KG  This is the star couple for transamination reactions. If you’ll notice, a lot of reactions with different amino acids involve glutamate and alpha-KG. (See catabolism of proline, arginine, histidine, aspartate, asparagine, etc.)  The other choices (alanine & pyruvate, etc) are a bit more specific or limited as to the reactions that they are involved in, thus making choice A as the best answer. 34. B, fumarate.  The keyword is that it is COMMON to both the Urea Cycle & Krebs. Fumarate in the Urea Cycle comes from the carbon skeleton of Aspartate, and we all know that it is one of the metabolites of the TCA cycle (aka Krebs). Through the fumarate, the Urea Cycle becomes linked to the TCA cycle because the fumarate can proceed to “join” the TCA cycle after it is formed sa Urea Cycle.  As for the other choices: Choices A, C and D are all present in the TCA cycle too, BUT they are not involved in the Urea Cycle. 35. A, phenacetin  Hyperphenylalaninemias are caused by defects in the enzymes involved in the phenylalanine catabolism. In PKU, there are alternative pathways for Phe that take place, thus forming other rmetabolites. Among them are phenylacetate, phenyllactate, and phenylacetylglutamine. (See p. 254 Harper’s, figure 29-14).  So by studying this alternative pathway in PKU, we can see that phenacetin is NOT involved as a metabolite.  Phenacetin is actually an analgesic. Ahehe. Gulat ka no? 36. D, all of the above  Of course, cellular reactions are always in disequilibrium because it the product of one reaction can be the substrate of the next reaction. An example of this is glycolysis, or how fumarate links the Urea Cycle with Krebs. So as one product is produced, another product is probably being degraded.  There is also a continuous use and/or production of the metabolite, otherwise we might be dead, since a lot of metabolites are constantly required by the body. Also, reactions occur in series and are NOT freely reversible. If they were reversible, it’s possible na ma-cancel out lang yung processes. Parang nag see-saw lang yung reaction, without really producing anything useful. 37. B. 5’deoxyadenosylcobalamin  This is the active coenzyme form of Vit B12 (aka Cobalamin), and like what the question asks, it is the one that enables the entry of propionyl coA into the TCA cycle  Cobalamin can’t be the answer because it is basically just Vitamin B12 and not its coenzyme form. Methylcobalamin is the one used by 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) (aka methionine synthase).  Cyanocobalamin has a cyanide instead of a methyl group, and it “usually does not even occur in nature, and is not one of the forms of the vitamin that are directly used in the human body (or that of any other animal). However, animals and humans can convert cyanocobalamin to active (cofactor) forms of the vitamin, such as methylcobalamin…” (ty Wikipedia) Basta, hindi si cyanocobalamin. Hindi rin si methylcobalamin kasi sa methionine synthase yun.

38. Correct: C, SAM..  First, recall that cysteine is synthesized from methionine. 1. Met will first be converted to SAM (via Met adenosyltransferase) 2. SAM will then help remove the methyl (CH3) group from methionine 3. Homocysteine is formed, it reacts with Serine with cystathionine synthase  Yield cystathionine 4. Cystathionine lyase will act on it, removing NH4 ion and yielding CYSTEINE + alpha-ketobutyrate  So in effect, SAM does NOT donate the methyl group, but just facilitates its removal from methionine. (SAM is involved in METHYL GROUP TRANSFERS)  The S IS from methionine, while the rest of the cysteine moleculel is actually derived from SERINE. 39. Correct: C, N-formiminoglutamic acid  The transformation of formiminoglutamic acid to glutamic acid is dependent on both vitamin B-12 and

tetrahydrofolate. Tetrahydrofolate is a form of folic acid! If there is a low amount of tetrahydrofolate, the body will have trouble transforming formiminoglutamic acid to glutamic acid. Thus, it will accumulate and can find its way into the urine.

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40. Correct answer: A, OXAA  If you’ll recall the synthesis of Aspartic Acid (aspartate), it is basically a transamination of OXAA. Pathway: As you can see from this rxn, glutamate serves as the amino acid donor. Transamination (transfer of NH2 from Glu to OXAA) leads to the formation of aspartate, also w/ “production” of alpha-KG (which is basically glu except that there’s an O where the NH2 originally was. Recall that α-KG is formed when Glutamate is transaminated ).

 Though it is an intermediate of the TCA cycle, Alpha-KG is NOT the one that is acted on by the aminotransferase to form Aspartate. Remember that α-KG is the general acceptor of amino groups (partly because it can be converted to glutamate. Then, this glutamate can be acted upon by the glutamate dehydrogenase enzyme in the liver so that the ammonia can be liberated and sent to the Urea Cycle.) 41. C, Decarboxylation

Decarboxylation means the removal of the carboxylic acid group (COOH). In the formation of histamine, the COOH is removed from histidine. 

 Hydroxylation is the process of “adding” an OH. This is the type of reaction that happens in the conversion of tyrosine to DOPA.  Transamination – Transferring of amino group; Ex. Glutamate + OXAA = Asp (NH3 transferred to OXAA)  Reduction – Process of gaining an electron (think LEORA-GEROA) 42. C, Lysine  Lysine CANNOT undergo transamination. Most amino acids need to undergo transamination first before they can be fully metabolized, but lysine, threonine, proline and OHproline are exceptions to the rule. 43. A, Dopamine  Dopamine is NOT derived from tryptophan. It is derived from tyrosine, just like all the other catecholamines.  Recall Tryptophan Metab:

Figure for number 44.

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44, Correct answer: B, Xanthurenic acid  Hydroxykynurenine is dependent on the enzyme kynureninase, which is the enzyme dependent on Vit B6 (specifically pyridoxal phosphate). Failure to completely metabolize (or oxidize) hydroxykynurenin will lead to its accumulation. From there, it will follow an alternate route/pathway where it will become xanthurenic acid with the help of the enzyme kynurenine aminotransferase. (This is therefore a transamination reaction.) (See image above) 45. A, Folic acid & B12  Conversion of homocysteine to methionine makes use of N 5 -methyl-THF as a carrier, and the enzyme methionine synthase. THF or tetrahydrofolate, as we all know, is a form of folic acid. Methionine synthase, on the other hand, is a Vit. B12-dependent enzyme. (Recall water-soluble vitamins!) 46. C, Valine and Isoleucine  After a series of reactions, the branched-chain amino acids (namely Leu, Val, Ile) give rise to PROPIONYLand Acetyl CoA.  In branched-chain AA metab, the end-product of the first 3 reactions are: - Leucine  Methylcrotonyl-CoA  further metabolized  Acetoacetate & Acetyl CoA - Isoleucine  Tiglyl CoA  further metabolized  Propionyl CoA & Acetyl CoA - Valine  Methacryl CoA  further metabolized  Aminoisobutyrate & Propionyl CoA**

This Propionyl CoA from Valine will undergo further processing that will link it to the TCA: Propionyl CoA  Methylmalonyl CoA  Succinyl CoA **enzyme used: methylmalonyl mutase + coenzyme Vit B12 (deoxyadenosylcobalamin)

47. C, Compartmentation of CPS-I/OTC & rest of enzymes  This form of regulation can be observed well in the Urea Cycle. In that cycle, you have a set of reactions that first happen in the mitochondria (e.g. reactions by CPS-I & OTC), and then another set or series of reactions that follow in the cytosol. Compartmentation occurs as a way of preventing the reactions from becoming “reversible.” For ex, if the enzymes responsible for phosphorylation and dephosphorylation of the same protein, edi baka wala lang mangyari and parang naglokohan lang sila. Not efficient. :| 48. B, Cystathionine β-synthase  Based on the Methionine metab (check the pathway! NOW! Joke lang :D), the absence of this enzyme will hinder the reaction of homocysteine with serine (para magform ng cystathionine).Therefore, the homocysteine will accumulate and thus find its way to the urine. (Syempre, di kasi siya magamit kasi walang enzyme. So tulad ng kahit sinong taken for granted, magwwalk out na lang siya… Aww. Haha! Joke.) 49. C, Action of kidney glutaminase on glutamine.  We mentioned earlier how glutamine acts like a carrier, then the glutaminase will act on it so that the NH3 can be “cleaved” out and can be excreted through the urine. Dibaaa? There :P  The “keyword” in this question is the NH 4 +. 50. B, Serotonin  Genetic defect in tyrosine hydroxylase will naturally affect its metabolism, and thus affect the substances that are derived from tyrosine. And by now we all know that the catecholamines are all derivatives of tyrosine! So sila ang maaapektuhan. On the other hand, serotonin is from tryptophan, so kahit masira si tyrosine, di affected si serotonin because it came from tryptophan, NOT tyrosine. 51. D, all of the above.

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(from STD, AA metab3)

Creatine is formed in the muscle from creatine phosphate by irreversible, nonenzymatic dehydration and loss of phosphate. Glycine, arginine, and methionine all participate in its biosynthesis. Arginine source.

is

the

carbon

skeleton

Glycine acts as some kind of carbon acceptor. Methionine participates as SAM.

52. B, Putrescine.  See figure 30-1 of Harper, p. 263 and p. 265, figure 30-8.  Putrescine can be found in the biosynthesis of spermidine and spermine, polyamines that function in cell growth and proliferation.  The reaction is basically like this: Ornithine  PUTRESCINE  Spermidine  Spermine  Cadaverine is similar to putrescine but is a product of decarboxylation of LYSINE  Carnitine is biosynthesized from LYSINE or METHIONINE. (Recall that Vit C is needed for its synthesis!)

II. Matching Type (Last part na, yay!!) 53. Vanillylmandelic acid  D, Epinephrine  End-stage metabolite of epinephrine and norepinephrine.

54. Picolinic acid  E, Tryptophan  An isomer of nicotinic acid, and a catabolite of tryptophan.

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55. Tiglyl CoA  Uy binanggit ko na ‘to kanina!! C, Isoleucine. (See number 46 and Harper’s p.259) 56. Pipecolic Acid  B, Lysine  Intermediate in LYSINE metab; associated with epilepsy. III. 57. Albinism: A, Tyrosinase  A condition that occurs when melanocytes fail to produce melanin.  This can be due to the absence of tyrosinase, which is the enzyme needed in the conversion of tyrosine to melanin. 58. Alkaptonuria: B, homogentisic acid  A condition due to lack of homongentisate oxidase, thus causing accumulation of homogentisate or homogentisic acid. The urine darkens upon exposure to air due to oxidation of excreted homogentisic acid There is also arthritis and connective tissue pigementation (called ochronosis) due, again, to the oxidation of homogentisic acid (leading to formation of benzoquinone acetate which polymerizes and binds to connective tissue). Check p. 254 of Harper’s 28th edition if you don’t believe me :p (See pathway on p. 253) 59. Phenylketonuria: D, phenylalanine hydroxylase  The deficiency in this enzyme causes an inability accumulation of phenylalanine, leading to phenylketonuria.

to

process

phenylalanine.

This

leads

to

60. Maple Syrup Urine Disease: C, keto acid dehydrogenase  Also known as branched-chain ketonuria  Maple Syrup Urine disease is also known as branched-chain ketonuria, wherein there is a defect lies in the alpha-keto acid decarboxylase complex. Because of this, the plasma and urinary levels of leucine, valine, isoleucine, α-keto acids and α-hydroxy acids are ELEVATED.

------------------------------------------------------------------------------------------------------------------------------END OF REVIEW. Hello!! Sorry kung mahaba. Minsan kasi diba mas ok yung sobra kesa kulang? Hehehe. Tsaka meron din kasing concepts (tulad nung mga vitamins) na kakailanganin din sa next topics. Sorry din kung biglang nawala yung questions at naging answers na lang… If you have any questions or clarifications, just text STD! Psh Ateneo. We can do better! Hahaha!! Let’s go Batch 2014! :p

Our God is an AWESOME God. :)

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