Course Schedule
Syllabus
Old Exams  (under construction and at Old exams)
Exam Schedule (see schedule)
What to Do if You Miss an Exam
Conference Lists
Grading Policy (see syllabus)

Course Schedule:  The Medical Curriculum is integrated, and is divided into Blocks.  The first year, where most biochemical content appears, has three blocks:  Molecules and Cells, Structure and Function, and Medicine and Society.  The Molecules and Cells schedule will be posted as soon as it is available for 2003.

The Syllabus is currently (2003) being put in its entirety on the Web courtesy of the College of Medicine.  When it becomes available the address will be posted here.

Meanwhile here is a short section from a previous syllabus. Please ignore page references, as they have been changed.

1. Describe the difference between oxidases and oxygenases.

2. Show why the enzymes known as "cytochrome P-450s" are considered monooxygenases or mixed-function oxidases.

3. Explain why the family of cytochrome P-450 enzymes is considered important enough to have an entire lecture devoted to it.

4. Describe the hydrophobicity/hydrophilicity of the substrates and products of cytochrome P-450.

5. Name an example of an hydroxylation and a dealkylation reaction catalyzed by cytochrome P-450.

6. List the two subcellular organelles that are the site of mammalian cytochrome P-450.

7. Tell why different members of the cytochrome P-450 family are not considered true isozymes.

8. List binding sites for substrate, oxygen, and carbon monoxide on the cytochrome P-450 molecule.

9. Tell which two oxidation states of heme iron are found in the cytochrome P-450 reaction cycle.

10. Identify the source of electrons for the cytochrome P-450 reaction.

11. Name the prosthetic group of the enzyme that is the immediate electron donor to microsomal cytochrome P-450.

12. Name the type of protein that is the immediate electron donor to mitochondrial cytochrome P-450.

13. Name the prosthetic group of cytochrome P-450, and also name two other types of proteins that have similar prosthetic groups.

14. Give an example of drug-drug interaction via substrate competition for cytochrome P-450, and an example of a compound that induces cytochrome P-450.

15. Explain how cytochrome P-450 can "activate" a precarcinogen.

1. Oxygen and Oxygenase Reactions (Section 4.2)

A. Oxidase

 CCCXH + 0₂ -----> C = X + H₂0₂

B. Monoxygenase

X + 1/2 0₂ -----> X0

C. Dioxygenase

 X + 0₂ -----> X0₂

2. What is cytochrome P-450? Reactions catalyzed include hydroxylation, dealkylation, oxidation of thioethers, oxidative dehalogenation of halogenated hydrocarbons, epoxidation. Role in endogenous processes, xenobiotic metabolism, carcinogenesis and toxicity. (Section 23.6 - Fig. 23.7)

3. Cytochrome P-450 Reaction (Section 23.2)

RH + NADPH + O₂ -----> ROH + NADP⁺ + H₂O

4. Cytochrome P-450 Cycle (Figure 23.3)

Cytochrome P-450 has a binding site for substrate on the apoenzyme. The resting enzyme is in the Fe⁺³ state. In turn the Fe⁺³ is reduced by an electron from NADPH, and then bound to O₂ (or CO). The electron is then donated to the O₂, together with another electron from NADPH. H₂O and product are then released from the enzyme, which is now back in its resting state.

5. Microsomal Electron Transport Chain (Section 23.5 - Fig. 23.5)

NADPH --> FAD/FMN - cytochrome P-450 reductase --> cytochrome P-450

6. Microsomal, Mitochondrial and Bacterial Cytochromes P-450. Their functions and mechanisms. (Section 23.5- fig. 23.6)

7. Inducers of cytochrome P-450. Role of induction in drug-drug interaction. (Section 23.3)

8. Inhibitors of cytochrome P-450. Role of inhibitors in drug-drug interaction. (Section 23.4)

9. "Isozymes" of cytochrome P-450. Microheterogeneity. Species and tissue specificity. Role of isozymes in drug metabolism and carcinogenesis. (Section 23.3, Table 23.1)

1. List the three toxic form of oxygen, and name the form that is most damaging to living tissue.

2. List the 1,2,3, and 4-electron reduced forms of oxygen.

3. Name the form of oxygen used in bacterial killing by leukocytes.

4. Write a reaction that destroys superoxide, and name the enzyme.

5. Write a reaction that uses two molecules of hydrogen peroxide, and name the enzyme.

6. Name two other enzymes that can use hydrogen peroxide as substrate.

1. Toxic Oxygen Species.

O₂ + le^- ----> O₂ ^-

            2H⁺
O₂ + 2e^- ----> H₂O₂

             2H⁺
O₂ + 3e^- ----> COH + OH^-

             4H⁺
O₂ + 4e^- ----> 2H₂O

2. Superoxide Dismutase

2O₂ + 2H⁺ -----> H₂O₂ + O₂

Catalase

2H₂O₂ ----->2H₂O + O₂

                    Peroxidase

ROOH + HXOH -----> XO + ROH + H₂O

Glutathione Peroxidase

2GSH + H₂O₂ -----> GSSG + 2H₂O

3. Superoxide Dismutase - Cu⁺⁺ and Zn⁺⁺ (Mn⁺⁺)

Catalase and Peroxidase - Heme

                    Glutathione Peroxidase - Selenocysteine

1. List reasons that proteins and amino acids "turn over."

2. Name reactions that introduce or remove amino groups from amino acids.

3. Diagram transport of nitrogen from extrahepatic tissues to liver, and from liver to kidney.

4. Identify sources of carbon skeletons of non-essential amino acids.

5. List intermediary metabolites and other compounds resulting from metabolism of (a) non-essential amino acids and (b) essential amino acids noting metabolic diseases associated with amino acid metabolism.

OBJECTIVE 1: List the reasons proteins and amino acids "turn over."

1. Metabolic wear and tear (e.g., oxidation of protein).

2. Induction/repression of a given protein.

3. Need for amino acids; in starvation need carbons for glucose synthesis; in protein inadequacy need nitrogen; in essential amino acid deficiency need to obtain the amino acid.

4. Excess nitrogen results from excess dietary intake, or from use of only part of the amino acid (carbon skeleton), or selected amino acids (essential), as described above, leaving the remainder (nitrogen or other amino acids) to be disposed of.

OBJECTIVE 2: Name reactions that introduce amino groups into or remove amino groups from proteins.

1. Glutamate dehydrogenase; ammonia, α-ketoglutarate, NAD(P)H; liver; reversible. (p. 450-451)

2. Amino acid oxidases; D and L; L has low activity;flavoproteins using O₂ and making H₂O₂. (p. 452)

3. Transamination; pyridoxal phosphate; Schiff base; reversible; glutamate common intermediate, alanine, aspartate from pyruvate, oxaloacetate; other Schiff base eliminations. (p. 448 - 449 page M10)

4. Glutamine synthetase; glutamate, ammonia, ATP; glutaminase. (p. 451 - page M11)

5. Asparagine synthetase; aspartate, glutamine, ATP; asparaginase. (p. 452 - page M11)

OBJECTIVE 3: Diagram transport of nitrogen from extrahepatic tissue to liver and from liver to kidney.

1. 80% of excreted nitrogen is in the form of urea-synthesized in urea cycle. (p. 452-453)

2. Most amino acid degradation occurs in muscle; from branch chain amino acids; "N" from α-amino group to glutamate to ammonia to glutamine; carried in blood predominantly as glutamine; some as alanine; to liver. (p. 453)

3. In liver glutaminase produces ammonia. (p. 453)

4. Carbamoylphosphate synthetase I; CO₂, NH₃, 2ATP; N-acetylglutamate obligatory activator; mitochondrial matrix. (Note: first nitrogen for urea) (p. 454 - page M12)

5. Ornithine transcarbamoylase; ornithine plus carbamoyl phosphate to citrulline; citrulline is transported into cytosol. (p. 454 - page M12)

6. Citrulline plus aspartate (plus ATP to AMP) to argininosuccinate. (Note: second nitrogen for urea) (p. 454)

7. Argininosuccinate to arginine and fumarate; this is biosynthesis of arginine; fumarate may be linked with citric acid cycle. (p. 454)

8. Arginase; arginine to urea and ornithine; ornithine skeleton contains original carbons and is transported into mitochondria; note 4ATP equivalents are consumed per molecule of urea formed. (p. 454)

9. Regulation of cycle; enzyme induction; effect of starvation or high protein diet.(p. 455- p. M1)

10. Deficiencies in urea cycle enzymes cause build up of metabolite before the deficient step; restrict nitrogen intake; remove excess nitrogen; supplement diet with arginine. (p. 455-456)

11. Alternative routes of ammonia excretion; used therapeutically; sodium benzoate plus glycine to hippuric acid; phenyl acetate plus glutamine; both require CoA and ATP. (p. 456 - page M12)

1. Review glutamate, aspartate, glutamine, asparagine, alanine.

2. Glutamate can be decarboxylated to GABA (γ-amino butyric acid), a neurotransmitter; GABA is metabolized by transamination and the carbons re-enter metabolism as succinate. (p. 457 and 931- p. M13)

3. Arginine is the source of nitric oxide (NO), a vasodilator. (p. 457)

4. Serine is synthesized from 3-phosphoglycerate (a glycolytic intermediate); the amino group comes from glutamate, and the last step is a phosphatase.(p. 459 - p. M14)

5. Serine is metabolized by 3 pathways; (a) when the cell is in a gluconeogenic mode 3-phosphoglycerate is resynthesized, but by a pathway different from the serine synthetic pathway; (b) by serine dehydratase to give ammonia and pyruvate. This is irreversible and is the dominant pathway for energy production from serine; (c) by serine hydroxymethyltransferase when there is a need for one-carbon moieties for metabolism. (p. 459 - p. M14)

6. More on serine hydroxymethyltransferase; requires pyridoxal phosphate and tetrahydrofolate; produces glycine and N⁵, N¹⁰-methylene tetrahydrofolate; it is reversible. (p. 459, 461)

7. Tetrahydrofolate (THF) carries one carbon moieties at three different oxidation levels; the most reduced, methyl, is carried on nitrogen 5; the intermediate methylene group is bound to both nitrogen 5 and 10; oxidation leads to methenyl (N⁵, N¹⁰) and then hydrolysis to formyl (N¹⁰); at the same oxidation level as formyl is formimino (N¹⁰); the folate ring structure can also be oxidized and reduced (dihydrofolate and tetrahydrofolate) and there can be intramolecular transfer of electrons; vitamin deficiency and spina bifida. (p. 462-463 - p. M 14 & 15)

8. Glycine cleavage enzyme produces CO₂, NH₃, NADH, and 5,10 methylene tetrahydrofolate. (P. 461 - p. M14)

9. Glycine (which is not chiral) can be metabolized to glyoxalate by D-amino acid oxidase; the glyoxylate is further oxidized to oxalate, a component of renal calculi (calcium oxalate). (p. 461 - p. M14)

10. Selenocysteine is synthesized at the level of the aminoacyl tRNA. Seryl tRNA is modified with selenium to form selenocysteinyl tRNA; this particular tRNA has an anti-codon that recognizes the codon UGA, which acts as a stop codon except in the specific selenocysteinyl containing proteins. (p. 460 - p. M13)

11. Threonine (an essential amino acid) is included in this section because it can be metabolized by the same dehydratase as serine; ammonia is removed, leaving α-ketobutyrate; this is further metabolized to propionyl CoA (see later for disposition of this molecule); threonine can also be oxidized to an unstable intermediate that is further metabolized to either acetyl CoA (ketogenic) and glycine, or to lactate (glycogenic). (p. 464 - p. M16)

12. Proline and ornithine are synthesized from glutamate; the first step reduces the γ carboxyl group to an aldehyde; if an intramolecular Schiff base then forms the eventual product is proline; if the aldehyde is transaminated the product is ornithine. (p. 458 - p. M13)

13. Ornithine and proline can both be metabolized back to glutamate by a pathway that is not the exact reverse of the synthetic pathway; the result is, however, that the carbons of glutamate, proline, and ornithine are interchangeable. (p. 458 - p. M13)

14. Ornithine decarboxylase removes the carboxyl group to leave a symmetrical 4-carbon compound called putrescine; it is the lowest molecular weight member of a series of compounds called polyamines. (p. 459 - p. M13)

15. The hydroxylation of proline to 3- and 4- hydroxyproline occurs post- translationally. (p. 458)

OBJECTIVE 5(b): List intermediary metabolites and other compounds resulting from degradation of essential amino acids.

1. Review threonine.

2. Branched-chain amino acids (valine, leucine, isoleucine) share the same first two metabolic steps, a transamination and an oxidative decarboxylation, similar to pyruvate dehydrogenase, resulting in loss of the carboxyl group, oxidation of the resulting aldehyde, and addition of CoA; all three amino acids are metabolized by the same two enzymes. (p. 477 - p. M22)

3. The lack of the second enzyme mentioned above, the α-ketoacid dehydrogenase, causes excretion of the α-ketoacid forms of the amino acids; these α-ketoacids give rise to a compound in the urine that smells like maple syrup; this condition is called maple syrup urine disease and is often accompanied by mental retardation and a short life span, as well as ketoacidosis. (p. 477)

4. In the decarboxylation step one carbon is lost from the 5-carbon valine; after further metabolism the products are methylmalonyl semialdehyde (4 carbons) which is further metabolized to propionyl CoA. (p. 477)

5. Similarly the 6 carbon isoleucine is decarboxylated to a 5 carbon compound and the final products are acetyl CoA (2 carbons) and propionyl CoA (3 carbons). (p. 477)

6. Leucine (6 carbons) loses one carbon,but is recarboxylated later by an enzyme called methylcrotonylcarboxylase, a biotin-enzyme; the 6-carbons product eventually gives rise to acetyl CoA (2 carbons) and acetoacetate (4 carbons).(p. 478)

7. The propionyl CoA resulting from the metabolism of valine and isoleucine (and odd-chain fatty acids, threonine, methionine and the side-chain of cholesterol) is further metabolized; it is carboxylated by a biotin-containing carboxylase to D-methylmalonyl CoA; this is racemized to the L-isomer; L-methylmalonyl CoA mutase rearranges the carbons to succinyl CoA by a mechanism requiring vitamin B12 (cobalamin). (p. 478 - p. M23)

8. A deficiency in any of the three enzymes of propionyl CoA metabolism can lead to ketoacidosis. (p. 479)

9. The first step in the metabolism of methionine is the formation of S-adenosylmethionine (SAM); any one of the three substituents of the resulting sulfonium ion can be eliminated; frequently it is the methyl group that is donated, and SAM is the major source of methyl groups;  the resulting S-adenosyl-homocysteine is hydrolyzed to homocysteine and adenosine (p.469-472 - p.M19)

10. The resulting homocysteine is metabolized by one of 3 pathways; the pathway chosen is determined by the need of the organism; if cysteine is required the homocysteine condenses with serine; this reaction is catalyzed by cystathionine synthetase, a pyridoxal phosphate containing enzyme; the pyridoxal phosphate containing enzyme cystathionase cleaves cystathionine to cysteine and α-ketobutyrate; the α-ketobutyrate is metabolized to propionyl CoA. (p. 470 - page M19)

11. If methionine is needed, homocysteine can be remethylated, in a B₁₂ requiring reaction with N⁵-methyl THF; if neither methionine nor cysteine is needed cystathionase can metabolize cystathionine to ammonia, H₂S, and α-ketobutyrate. (p. 472)

12. Low activity of the methionine adenosyltransferase activity appears to result from a Km mutation in the enzyme; it gives rise to hypermethioninemia, but does not eliminate methylation reactions, and is consequently benign; the lack of cystathionine synthetase results in many severe symptoms; the lack of cystathionase is benign. (p. 471)

13. SAM can be decarboxylated and the resulting propylamino groups transferred to putrescine to form spermidine and spermine; the methylthioadenosine that remains is used to regenerate methionine. (p. 473 - p. M20)

14. Cystathionase can also produce thiocysteine from cystathionine. (P. 474)

15 Thiocysteine is used as sulfur donor for iron-sulfur proteins and in detoxification reactions of compounds such as cyanide. (p. 474 - p. M21)

16. Cysteine can also be the substrate for transamination, and the sulfur can then be incorporated into other compounds. (p. 474 - p. M21)

17. Oxidation of the sulfhydryl group of cysteine to cysteine sulfinate leads to two products; one is the product of decarboxylation and further oxidation (taurine) and the other is sulfate; most of the sulfate is excreted, but some is used to produce AMPS and PAPS; PAPS is the sulfate donor for sulfated macromolecules. (p. 474 - p. M20)

18. Defects in cysteine metabolism are related to two diseases; defective membrane transport leads to increased extra-cellular cysteine; this is insoluble and forms calculi; the other disorder is accumulation of cysteine in lysosomes; crystals form and can lead to renal failure. (p. 471)

19. The first step in phenylalanine metabolism is hydroxylation to form tyrosine; when this enzyme (phenylalanine hydroxylase) is missing, or when there is a deficiency in the cofactor, tetrahydrobiopterin, a disease called phenylketonuria results; in this condition phenylalanine is transaminated to phenylpyruvate and excreted; the accumulation of unmetabolized phenylalanine leads to mental retardation.(p. 464-465 - p. M26)

20. Metabolism of tyrosine in the liver starts with the inducible enzyme tyrosine amino-transferase; further metabolism leads to homogentisate and eventually to fumarate and acetoacetate. (p. 466)

21. A deficiency in homogentisate oxidase leads to excretion of homogentisic acid in the urine; this autooxidizes to a black color, giving the disease its name, alkaptonuria; the disease is generally benign. (p. 467)

22. Tyrosine is the precursor of catecholamines; tyrosine is first hydroxylated by a tetrahydrobiopterin-dependent enzyme to DOPA; decarboxylation to dopamine follows; it is the inability to produce DOPA in the brain that causes Parkinson's disease; in the adrenal medulla dopamine is further metabolized to norepinephrine and epinephrine; these neurotransmitters are deactivated by metabolism by monoamine oxidase and catecholamine-O-methyl transferase. (p. 466-468; 930, p. M18)

23. Tyrosinase is a Cu⁺⁺ containing enzyme that initiates the formation of melanin; a lack of this enzyme results in albinism. (p. 467-468, p. M17)

24. Tryptophan contains a double ring system; the first step in its metabolism is the opening of the 5-member ring to form formylkynurenine; this is catalyzed by tryptophan dioxygenase; loss of the formyl group gives kynurenine. (p. 475- p. M21)

25. Kynurenine can follow three pathways; in one a bicyclic compound (2 6-member rings) is formed; this is called kynurenate and appears to be a neuromodulator; cleavage of alanine from kynurenine gives anthranilate; both kynurenate and anthranilate are urinary excretion products; the third pathway is hydroxylation of kynurenine to 3-hydroxykynurenine; this is the second branch point in the pathway. (p. 475)

26. 3-hydroxykynurenate can either form xanthurenate, a double ring system, or lose alanine and remain as a single-ring compound. (p. 475)

27. This single ring compound can either be metabolized to various metabolites that include acetoacetyl CoA or the ring can undergo rearrangement and addition of PRPP to form nicotinic mononucleotide. (p. 475)

28. Hydroxylation and decarboxylation of tryptophan give the neurotransmitter serotonin; serotonin can also be deactivated by monoamine oxidase. (p. 476 -p.M22)

29. Histidine loses ammonia via the histidase reaction; the resulting urocanate is metabolized to formimino glutamate (FIGLU); the formino group is transferred to tetrahydrofolate, leaving glutamate as the final product; excretion of large amounts of FIGLU in the urine is an indicator of THF deficiency (p. 481- 482 - p. M24)

30. Histidine deficiency can be measured in skin, a tissue which lacks urocanase. (p. 482)

31. Histidine can be decarboxylated by a pyruvoyl enzyme to histamine; it also serves as precursor for carnosine and anserine in muscle. (p. 483)

32. Lysine presents a unique problem for disposition of its nitrogen, since it has two amino groups; the first step is via a Schiff base formation of the 0-amino group with α ketoglutarate; this Schiff base is reduced to saccharopine which is hydrolyzed to give glutamate and a compound that is eventually metabolized to acetoacetyl CoA after a second transamination with α-ketoglutarate. (p. 480 - p. M23)

33. There is also a minor lysine metabolic pathway. (p. 481)

34. Lysine, as part of a protein, can be methylated; when it is trimethylated and liberated by proteolysis it can undergo a series of reactions resulting in the formation of carnitine. (p. 482 - p. M23)

35. Creatine is formed from glycine, the guanidinium group of arginine, and a methyl group from SAM; creatine phosphate is formed from ATP, and is the major storage form of short-term energy in muscle; a given amount of phosphocreatine in each individual is spontaneously cyclized to creatinine each 24 hours; measurement of urine creatinine is an indicator of whether a 24 hour urine sample genuinely is a 24 hour sample. (p. 483-484 - p. M24)

36. Ethanolamine and choline are formed from serine; choline forms part of the neurotransmitter acetylcholine; this neurotransmitter is inactivated by acetylcholinesterase. (p.460 - p. M13)

37. Glutathione is a tripeptide; glutamate forms a peptide bond through its γ carboxyl group with cysteinyl glycine; the active part of the molecule is the sulfhydryl group; it can add covalently to xenobiotics for elimination, and fatty acid derivatives in the formation of prostaglandin PGE₂ and leukotrienes; the sulfhydryl group can be oxidized by glutathione peroxidase; this is glutathione in its antioxidant role.(p. 484-485 - p. M25)

38. The γ-glutamyl cycle functions in amino acid transport; it is energy-demanding but rapid; the γ-glutamate residue acts in a group transfer mechanism to transfer an amino acid into the cell; the tripeptide glutathione is then resynthesized for a new cycle. (p. 485)

 

 

Conference Lists

 These will be available within two days of the start of class.

Missed Examinations

Missed examinations must be made up in a timely manner according to the policies of the College of Medicine.  Only students presenting an official letter from Dean Cannon permitting them to make up an examination will be allowed to take a make-up examination.