Learning Objectives for Dr. Woodbury's Lectures
Learning Objectives for “Enzyme Mechanisms and Regulation”
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms: active site, enzyme specificity, cofactor, coenzyme, prosthetic group, serine protease, substrate, acyl-enzyme intermediate, metallo-enzyme, general acid-base catalysis, transition state, transition state analog, allosterism, allosteric effector.
2. List and describe the 6 general types of reactions catalyzed by enzymes; list at least one enzyme for each type of reaction.
3. Describe the salient characteristics of active sites in enzymes.
4. Explain the origin of the catalytic power of enzymes; list and apply the basic physico-chemical factors that contribute to catalysis.
5. State what a cofactor is, and distinguish between coenzymes and prosthetic groups. State why cofactors are needed for certain enzyme reactions.
6. Describe the substrate specificity of the enzymes: RNase A, chymotrypsin, trypsin, elastase, carboxypeptidase A, hexokinase, aspartate transcarbamoylase
7. Describe, with appropriate diagrams or sketches, the catalytic mechanisms for the enzymes RNase A, chymotrypsin, and carbonic anhydrase.
8. Describe the physiological roles of the enzymes lysozyme, chymotrypsin, trypsin, carbonic anhydrase, carboxypeptidase A, (more)
9. Describe the enzymatic conformational changes that occur during catalysis by the enzymes hexokinase and ATCase. Relate these to the concerted model and induced-fit model of enzyme action.
10. List different mechanisms by which enzyme activity may be regulated. Differentiate between noncovalent and covalent mechanisms. Note the importance of phosphorylation and of proteolysis, and the possibility of many other types of covalent modification.
Learning Objectives for “Enzyme Kinetics”
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms turnover number, KM, Michaelis constant, Vmax, maximal velocity, half-saturation point, diffusional control, “perfected” enzymes, competitive inhibitor, mixed inhibition, irreversible inhibition, suicide substrate.
2. Describe the general two-step reaction model for the Michaelis-Menten treatment of enzyme kinetics. State under what conditions the reaction is essentially bimolecular and overall second order, and when it is apparently unimolecular and first order.
3. Interpret various graphs (compute slopes, intercepts) of enzyme kinetic data, deducing from them numerical values for various enzyme parameters (k+2, kcat, KM, KI).
4. Draw a diagram, showing kinetic relations among enzyme, substrate, and inhibitor, to illustrate the concept of competitive inhibition.
5. Give examples of competitive inhibition, naming both enzyme and inhibitor, that are relevant to pharmacy.
6. Explain the basis for the toxicity of heavy metals, in terms of enzyme action.
7. Describe the basis for active-site directed irreversible inhibition. Give examples of this type of inhibition, naming both enzyme and inhibitor, that are relevant to pharmacy.
8. State the basic concept behind the interest in enzyme inhibitors as pharmaceutical agents.
9. Explain the rationale behind combination chemotherapy.
10. List the four basic strategies for the design of enzyme inhibitors. Give practical examples or applications of each strategy.
Learning Objectives for "Basic Concepts in Metabolism"
After studying lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms metabolism, catabolism, anabolism, feedback, committed step, crossover theorem, catalyst concentration, compartmentalization, enzyme activation/deactivation, covalent modification, cofactor, coenzyme, vitamin, prosthetic group, holoenzyme, apoenzyme, cosubstrate, nicotinamide, niacin, NADH, NADPH, flavin, FADH2, FMNH2, riboflavin, flavoprotein, semiquinone, coenzyme A, ATP, reaction coupling, phosphoanhydride, phosphoester, thioester, nucleotide kinase, energy charge.
2. List major food components, and compare their relative energy value.
3. Distinguish between vitamins and minerals; between fat-soluble vitamins and water-soluble vitamins. List the main biochemical functions for these vitamins and minerals.
4. List the three main stages in catabolism. Summarize in a diagram the main pathways for the digestion of foodstuffs.
5. Describe the concept of feedback, as applied to metabolic pathways. Distinguish between positive and negative feedback. Note important common features of metabolic regulation involving key steps and end-products. Apply the “plumbing analogy” appropriately to metabolic pathway regulation.
6. List and describe the four major mechanisms for control of metabolism.
7. Define and distinguish among cofactors, coenzymes, vitamins, and prosthetic groups. Give examples of each.
8. Draw the structure of ATP and identify phosphoester and phosphoanhydride bonds in the structure. Explain how ATP functions as a "carrier" of free energy in metabolism, and describe the cycling of ATP with ADP. Explain why ATP serves as a "good" donor of phosphoryl groups, giving the structural and electronic basis for this.
9. Recognize the structure of coenzyme A. Identify functionally important chemical groups on this molecule and relate them to coenzyme A's function as a carrier of activated acyl groups.
10. Recognize the structures of NAD+, NADH, NADP+, NADPH, FAD, and FADH2. For each, explain their role in metabolism. Identify functionally important chemical groups on these molecules.
11. Explain the role of kinetic stability in the metabolic functioning of ATP, NADH, and FADH2.
12. Recognize the structures of thiamine and lipoic acid. List the main biochemical roles of each.
Learning Objectives for "Major Pathways of Carbohydrate Metabolism"
After studying the lecture notes and attending the lectures you should be able to:
1. Define and use correctly the terms: Glycolysis, three-stage model, nicotinamide pool, anaerobic pathway, glucose 6-phosphate, fructose 6-phosphate, fructose 1,6-bisphosphate, dihydroxyacetone phosphate (DHAP), induced fit mechanism, thermodynamic inefficiency, hexokinase, phosphofructokinase (PFK), clockwork model, global regulation model, alcoholic fermentation, lactate fermentation, gluconeogenesis, glucose 6-phosphatase, pyruvate carboxylase, lactate dehydrogenase, Cori cycle, isoenzyme (isozyme), glycogen, glycogen synthase, cyclic AMP, phosphorylase isozymes, glycogen breakdown “cascade”, epinephrine, glucagon, von Gierke’s disease, McArdle’s disease
2. Explain how glycolysis produces metabolic energy as well as producing intermediates for further metabolic reactions.
3. Diagram the glycolytic pathway. Describe how glycolysis can be divided into three stages.
4. List and describe the reactions in glycolysis, in correct metabolic order. List the intermediates (the compounds) in the glycolytic pathway. Note where ATP is consumed and where it is produced. Note the role of nicotinamide cofactors
5. Describe how fructose can be converted into glyceraldehyde 3-phosphate.
6. Explain how glycolysis is regulated. Describe how allosterism is important for regulating phosphofructokinase. List and describe other enzymes important in regulating glycolysis.
7. Explain how pyruvate may be converted to acetyl CoA, to ethanol, or to lactate. Relate the latter two reactions to the regeneration of NAD+ for continued glycolytic functioning.
8. Describe the major physiological functions of gluconeogenesis, glycogen synthesis, and glycogenolysis. Note important precursors for each of these pathways. List important organs or tissues, and intracellular locations, for each of these pathways.
9. Describe the regulation of gluconeogenesis, glycogen synthesis, and glycogenolysis. Note key enzymes, activators, and inhibitors.
10. Describe the linkages among gluconeogenesis, glycogen synthesis, and glycogenolysis, as well as their connections to glycolysis and the TCA cycle.
11. Compare glycolysis to gluconeogenesis, noting points in common and points of disparity.
12. Compare glycogen synthesis to glycogen breakdown, noting points in common and points of disparity.
13. Compare and contrast the effects of insulin versus glucagon, on glycolysis and gluconeogenesis. Do the same for glucagon and epinephrine, for their effects on glycogen metabolism.
14. Describe the Cori cycle and relate it to the glycolytic pathway, tissue-specific pools of reduced and oxidized nicotinamides, gluconeogenesis, and the functioning of the H and M isozymes of lactate dehydrogenase.
15. Describe the structure of glycogen and relate this to the biological advantages of glycogen as an energy-storage polymer. Explain why this is efficient.
16. Describe the function of glucose 6-phosphatase in the liver. Compare this to what happens in brain and muscle.
17. Explain the role of UDP-glucose in glycogen synthesis.
18. List several examples of different glycogen storage diseases. Relate each to the underlying biochemical defect, and explain the connection to clinical symptoms.
Learning Objectives for “Mitochondrial Metabolic Reactions”
After studying the lecture notes and attending the lectures you should be able to:
1. Define and use correctly the terms Substrate transport systems, pyruvate, pyruvate dehydrogenase, TPP, lipoate, beri-beri, mitochondrial compartmentalization, TCA cycle, anaplerotic cycle, citrate, oxaloacetate, malate, fumarate, succinate, succinyl CoA, α-ketoglutarate, isocitrate, citrate synthase, isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, succinyl CoA synthetase, succinate dehydrogenase, fumarase, malate dehydrogenase,
2. Describe the organization of a typical mitochondrion, listing and locating membranes, enzymes, respiratory complexes, the F0-F1 complex, and important transporter proteins.
3. Describe the structure and composition of the pyruvate dehydrogenase complex. Write a scheme for the reactions it catalyzes. Relate the scheme to the structure and composition of the complex.
4. Describe how the pyruvate dehydrogenase complex is regulated. Describe the actions and effects of kinases and phosphatases involved in the regulation. Note other activators and inhibitors involved.
5. Describe the ATP-ADP translocase, and explain how it functions.
6. State the cellular location of the enzymes of the TCA cycle and list several of the most important of these enzymes.
7. Describe the overall function of the TCA cycle in metabolism, and explain its strict requirement for aerobic function.
8. Diagram the TCA cycle. Name the metabolic intermediates, in correct order, of the TCA cycle.
9. List the TCA cycle intermediates that participate in anaplerotic reactions, as biosynthetic precursors or as derived from compounds other than glucose.
10. Describe generally the regulation of the TCA cycle, noting important activators and inhibitors, and their points of action.
11. Explain the consequences of a dietary deficiency in thiamine, and relate this to beri-beri.
12. Explain how reducing equivalents are transported across the mitochondrial membrane. Diagram the glycerol phosphate shuttle.
Learning Objectives for “Respiratory Complexes and ATP Synthesis”
After studying the lecture notes and attending the lectures you should be able to:
1. Define and use correctly the terms: electron transport chain, respiratory chain, membrane shuttles, respiratory complexes, Coenzyme Q/ubiquinone, non-heme iron,, iron-sulfur complexes, cytochromes, F0F1-ATPase, stalk domain, headpiece, binding change model, respiration, phosphorylation, proton pump, quinone, chemiosmotic model, electrochemical potential, proton gradient, respiratory poisons, uncoupling agents.
2. Describe the organization of a typical mitochondrion, listing and locating membranes, enzymes, respiratory complexes, the F0-F1 complex, and important transporter proteins.
3. List the respiratory complexes of mitochondria in appropriate order, along with intermediate electron carriers. Note which complexes are proton pumps.
4. Compare the entry of electrons to the respiratory chain via complex I versus complex II. Explain the consequences for generation of cellular energy.
5. List compounds that block electron transport, noting their sites of action. Explain the consequences for the cell.
6. Explain the chemiosmotic model of oxidative phosphorylation. List examples of energy conversions involving proton gradients.
7. State the biochemical function of the F0-F1 complex, relating it to the chemiosmotic model and the flow of protons. Describe the structure of the F0-F1 complex, and relate this structure to the binding-change model and catalytic cooperativity.
8. Explain how uncoupling agents can interfere with ATP generation, and how they can be used for thermogenesis.
Learning Objectives for "Other Pathways of Carbohydrate Metabolism"
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms: Glucose 6-phosphate dehydrogenase, transketolase, stages 1 & 2 of pentose phosphate path, glutathione, sulfhydryl buffer, glutathione reductase, malarial protection, hemolytic anemia, glucuronic acid, glucuronides, glycoprotein, glycolipid, UDP-glucose, Wernicke-Korsakoff syndrome, galactosemia
2. Describe the role of the pentose phosphate pathway, noting important products, intermediates, and precursors in this pathway (e.g., fructose 6-phosphate, ribose 5-phosphate, NADPH). Describe how there are two stages to this pathway.
3. Recognize the compound glutathione. Describe its multiple biochemical roles in the cell. Explain how levels of reduced and oxidized glutathione are related to NADPH levels in the cell. Relate this to protection against malaria.
4. Outline how galactose may be converted to glucose. Note the role of UDP-activated intermediates. Explain why nucleotide sugars often appear as intermediates in the interconversion of sugars and in the biosynthesis of complex carbohydrates.
5. Describe the symptoms and common biochemical cause of galactosemia. Describe treatment for this disease.
6. Describe how glucuronic acid is made. Explain how and where glucuronic acid plays a role in the cell.
7. Describe the symptoms and common biochemical cause of Wernicke-Korsakoff syndrome. Describe treatment for this disease.
Learning Objectives for “Survey of Biological Lipids”
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms triglycerides, palmitic acid, phosphatidic acid, lysophosphatidic acid, phosphoglycerides, inositide, cardiolipin, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, lecithin, bile acid, steroid hormones, cholesterol, HMGCoA reductase, sphingolipids, ceramide, sphingosine, sphingomyelin, cerebroside, eicosanoids, arachidonic acid, cyclo-oxygenase, NSAID
2. List the five lipid classes. List the four major roles of lipids.
3. Use proper chemical nomenclature to describe various fatty acids.
4. Recognize the structures of palmitate, stearate, oleate, linoleate, linolenate, arachidonate, and aspirin.
5. Relate features of chemical structure of lipids to their physical behavior (aqueous solubility, melting temperature, effect on membrane fluidity, etc.).
6. Describe what is meant by “essential” fatty acid. Name the essential fatty acid (for humans), and be able to recognize its structure.
7. Recognize the structure of cholesterol. List biochemical roles for cholesterol. Outline its biosynthesis, noting the role of HMGCoA reductase and the importance of this enzyme as a drug target.
8. Recognize the structure of sphingosine. List several common sphingolipids. List biochemical roles for these sphingolipids. Relate these to the diseases called lipidoses.
9. Recognize the structure of arachidonic acid. Relate it to the formation of prostaglandins, leukotrienes, and thromboxanes. List the general biological roles played by these compounds.
10. Relate the action of aspirin and other nonsteroidal anti-inflammatory agents to the functioning and inhibition of cyclo-oxygenases.
Learning Objectives for “Lipid Biosynthesis”
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms ACP, phosphopantetheine, malonyl CoA, ACC/acetyl CoA carboxylase, citrate shuttle, FAS/fatty acid synthase, biotin.
2. Describe the biochemistry of the synthesis of fatty acids. Note starting materials and necessary cofactors.
3. Describe the committing step for fatty acid biosynthesis, naming the enzyme and discussing the regulation of its activity. Compare the short-term and long-term regulation of fatty acid biosynthesis.
4. Explain why the synthesis of fatty acids costs energy.
5. Explain how palmitate serves as a precursor for other fatty acids. Describe briefly how FA chains may be elongated beyond palmitate, how they may have carbon-carbon double bonds or chain branches incorporated, and how they may be converted to fatty alcohols.
6. Sketch the biosynthesis of triglycerides.
7. Describe the citrate shuttle and explain its role in the biosynthesis of lipids from carbohydrates, noting especially the role of membrane compartmentalization.
Learning Objectives for “Energy Production from Lipids”
After studying the lecture notes and attending lecture you should be able to:
1. Recognize the structures of carnitine, ketone bodies and cobalamin.
2. Explain how fatty acids are stored as a fuel reserve by the body. Relate the structure of triacylglycerols (triglycerides) to their ability to store metabolic energy.
3. Describe the process of lipolysis, noting important reactions, enzymes, cellular locations, and mechanisms of regulation.
4. Describe the beta-oxidation pathway for fatty acids, noting important cofactors. Relate the production of acetyl CoA here to the need for oxaloacetate for complete oxidation of fatty acids via the TCA cycle, and to the production of ketone bodies.
5. Describe the role of carnitine in the transport of fatty acyl moieties into the mitochondrial matrix by the acylcarnitine:carnitine antitransporter. Note the roles of CPT1 and CPT2; describe how CPT1 is sensitive to malonyl CoA and how this relates to cellular demand for energy.
6. Describe how the cell breaks down fatty acids with an odd number of carbon atoms. Relate this to the use of succinyl CoA from the TCA cycle and metabolism when carbohydrates are missing or depleted in the diet.
7. Explain the molecular basis for the disease, pernicious anemia.
8. Explain how ketone bodies arise, and relate them to the pathology of diabetes.
Learning Objectives for "Amino Acids and Nitrogen Excretion"
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms transamination, oxidative deamination, Schiff base linkage, aldimine, ketimine, methylmalonic aciduria, urea, pyridoxal phosphate/PLP, hyperammonemia, carbamoyl phosphate, N-acetyl glutamate, urea cycle, carbamoyl phosphate, carbamoyl phosphate synthetase, N-acetylglutamate, hyperammonemia, latent pathways.
2. Summarize the fate of dietary protein. Explain what happens in general terms to amino acids that are not immediately used in protein biosynthesis. State where in the body the bulk of amino acid metabolism occurs.
3. Describe the process of transamination, noting the role played by Schiff bases involving pyridoxal phosphate. Note which enzymes are involved, and distinguish their role from that of glutamate dehydrogenase. Explain how serine and threonine lose their amino groups.
4. Recognize the structures of pyridoxal phosphate (PLP), and pyridoxamine phosphate (PMP). Recognize the structures of all 20 of the common amino acids. Recognize the structure of urea.
5. Describe the reaction catalyzed by glutamate dehydrogenase, and explain its importance. Explain how this enzyme is regulated.
6. Explain the metabolic toxicity of ammonia and describe the possible causes of hyperammonemia, especially in relation to deficiencies in urea cycle enzymes. Describe possible therapies for hyperammonemia, including the use of alternative (“latent”) routes for nitrogen excretion.
7. Describe the urea cycle. Diagram the urea cycle, naming enzymes and intermediates, and noting intracellular locations. Explain the energy requirement for urea cycle functioning.
8. Explain regulation of the urea cycle. Note the role of N-acetyl glutamate in short-term regulation, and relate it to the enzyme carbamoyl phosphate synthetase.
9. Describe connections between the TCA cycle and the urea cycle.
10. Note especially the several roles of the amino acid glutamate in nitrogen excretion.
Learning Objectives for "Pathways of Amino Acid Catabolism"
After studying the lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms ketogenic, glycogenic/glucogenic, ketosis, PKU, phenylketonuria, methylmalonic aciduria, essential/nonessential amino acids, tetrahydrofolate/THF, pteridine, PABA, folate antagonist.
2. Explain how and why various amino acids are classified as ketogenic, glycogenic, or both. List the 20 amino acids according to these classifications.
3. Explain why catabolism of amino acids is increased during periods of fasting.
4. Relate the catabolism of glycogenic amino acids to TCA cycle intermediates. Draw a diagram to illustrate the connections.
5. Explain why ketosis may arise during periods of fasting.
6. Describe the most common biochemical defect leading to phenylketonuria. Explain the consequences of this defect, and give possible therapies.
7. List the essential amino acids, distinguishing those that may be required for infants but not for adults. Explain briefly why the other amino acids are non-essential, in terms of intermediates in the TCA cycle and elsewhere.
8. List important biochemicals for which serine is a precursor. Do the same for glycine.
9. Sketch the biosynthesis of serine, noting important cofactor requirements.
10. Recognize the structure of serine, glycine, cysteine, methionine, homocysteine, S-adenosylmethionine, and THF, and indicate the constituent pteridine, glutamate, and p-aminobenzoate moieties in THF.
11. Explain what a folate antagonist is and how it works, and give examples of such drugs.
12. Explain the “methyl trap hypothesis”, relating it to metabolic reactions involving folate, S-adenosylmethionine, and cobalamin.
Learning Objectives for Biosynthesis of Nucleotides:
After studying lecture notes and attending lecture you should be able to:
1. Define and use correctly the terms: salvage pathway, de novo synthesis, ribonucleoside, ribonucleotide, deoxyribonucleoside, deoxyribonucleotide, 5-phosphoribosyl-1-pyrophosphate (PRPP), thymidylate synthase, dihydrofolate reductase (DHFR), 5-fluorouracil (F-dUMP), gout, Lesch-Nyhan syndrome.
2. List the five major roles of nucleotides in the cell.
3. Describe the steps in the pathway leading to the synthesis de novo of pyrimidines; of purines.
4. Explain why folate analogs may be powerful inhibitors of cell growth.
5. Explain and describe the mechanism of action of 5-fluorouracil in the inhibition of thymidylate synthase.
6. Relate the breakdown of purines to the diseases gout and Lesch-Nyhan syndrome.
7. Recognize the structures of PRPP, F-dUMP, 5-fluoro-uracil, carbamoyl phosphate, N-carbamoyl-L-aspartate, folic acid/folate, ribose, deoxyribose, uracil, adenine, thymine, guanine, cytosine.