Introduction to Biochemistry - Lecture

• Fuel metabolism and body fluid compartments
• Define the term Biochemistry and Medical Biochemistry
• Distinguish between anabolism and catabolism
• Describe the role of ATP in metabolism
• Define autosomal recessive, autosomal dominant and X-linked disorders
• Describe the fluid compartments (ICF, ECF, blood and interstitial fluid)
• Describe the distribution of major electrolytes in the ECF and ICF compartments
• Define osmolality and discuss the clinical significance of osmolality
• Define edema, and analyze importance of serum albumin in causation of edema

 

Normal pH Homeostasis - Lecture: 

• Distinguish between strong and weak acids and bases
• Define pH, pKa and buffers
• Describe the Henderson-Hasselbalch equation and its application in drug absorption
• Explain the mechanism of buffer action
• Identify the sources of H+ formation – CO2 and nonvolatile acids
• Analyze the role of HCO3¯  as a buffer (its formation and role in buffering)
• Summarize the role of lung in maintaining acid base balance
• Summarize and analyze the role of kidney in maintaining acid base balance
  • Reabsorption of HCO3¯
  • Secretion of H+
  • Role of phosphate and ammonia in renal tubule
• Analyze the biochemical effects of carbonic anhydrase inhibitors (acetazolamide)

 

Acid-base Disorders - Lecture:

• Describe the physiological regulation of acid base balance
• Differentiate between metabolic / respiratory acidosis and alkalosis
• Describe the causes, compensatory responses and biochemical basis of treatment of
  • metabolic acidosis and alkalosis
  • respiratory acidosis and alkalosi
• Identify acid base disorders when arterial blood gas analysis is provided
• Analyze the compensatory mechanisms that are active in the four acid base disorders
• Interpret ABG data (pH, PCO2 and HCO3¯ ) and solve problems related to disorders of acid base balance

 

Structure and Functions of Amino acids and Proteins I and II (2 lectures) - Lecture:

• Describe the general structure and stereochemistry of amino acids.
• Classify amino acids based on their R groups (with examples for each group).
• Name the amino acids with a charged side chain, the amino acids containing a hydroxyl group and the amino acids containing sulphur.
• Discuss the acid/base properties of amino acids with the aid of a graph (eg. histidine).
• Discuss the role of histidine residues as a  buffer in hemoglobin
• Describe the concept of the formation of biological active amines
• Discuss the biomedical importance of derivatives of amino acids (GABA, histamine, serotonin and catecholamines).
• Describe the main features of the peptide bond.
• Outline the general functions of proteins
• Discuss in general the synthesis of proteins and the concept of formation of peptide hormones from precursor proteins
• Differentiate between the hierarchical levels of protein structure.
• Discuss the significance of bond forces involved in maintenance of protein structure (covalent bonds and hydrogen bonds, ionic bonds, hydrophobic forces and Van der Waals forces)
• Describe the structure of insulin
• Define secondary structures including α – helix and β – pleated sheet.
• Discuss the change of secondary structure of protein in Prion disease 
• Describe the role of chaperone proteins in protein folding
• Discuss protein denaturation in vivo and in the laboratory.

 

Hemoglobin - Lecture:  

• Distinguish between hemoglobin (Hb) and myoglobin structures.
• Explain the mechanism of oxygen binding to the heme prosthetic group of a single Hb subunit.
• Describe the conformational change in the Hb molecule following oxygen binding.
• Discuss how carbon monoxide (CO) binds to Hb and how this interferes with normal oxygen binding.
• and how this is produced by cooperative binding of O2 to Hb.
• Describe the function of 2,3-BPG in regulating oxygen binding to Hb. Justify the role of 2,3 BPG in adaptation to high altitude, and its role in oxygen binding to  fetal hemoglobin, and in blood transfusion.
• Explain the Bohr effect and its significance in regulating oxygen release from oxyHb (H+, CO2).
• Compare and contrast the subunits of HbA, HbA2 and HbF.
• Propose the biochemical mechanisms for the occurrence of sickling in patients with HbS (reading assignment)

 

Enzymes I and II (Introduction, Kinetics, Inhibition and regulation of enzymes) (2 lectures) - Lecture:

•  Outline the properties of enzymes and the chemistry of the active site
• Describe the factors that influence enzyme reaction rates (pH and temperature)
• Describe the role of enzymes related to activation energy, and DG of a reaction with the aid of a graph (Lippincott p. 55, 56)
• Discuss the significance of coenzymes and apoenzymes
• Discuss conformation of enzymes and changes of conformation in relation to enzyme regulation. (allosteric regulation, reversible covalent modification  and proteolytic cleavage)
• Discuss enzyme regulation via the concentrations of substrates or products
• Describe enzyme regulation via the modulation of  enzyme concentrations
• Describe the concept of proteolytic activation of digestive enzymes (eg. Zymogens such as trypsinogen)
• Describe regulation of allosteric enzymes related to changes of K 0.5 or Vmax
• Differentiate between homotropic and heterotropic allosteric effectors
• Discuss in general the regulation of metabolic pathways related to feedback inhibition and feed-forward activation
• Describe Michaelis-Menten kinetics, define Km and Vmax and discuss their significance with the help of a graph (Lippincott p. 58)
• Discuss the kinetics of allosteric enzymes and explain the sigmoidal graph (Lippincott p. 57)
• Compare and contrast the mode of action and kinetics of reversible competitive and non-competitive inhibitors 
• Graphically differentiate competitive and noncompetitive  inhibition using the Michaelis-Menten graph and the Lineweaver-Burk plot (Lippincott p. 60, 61)
• Distinguish between reversible and irreversible inhibitors
• Discuss the inhibition caused by aspirin and diisopropylfluorophosphate (DFP) and statin drugs (enzymes inhibited, biochemical effects of the inhibition)

 

Enzymes and Proteins in Clinical Diagnosis - Lecture: 

• Discuss how inherited enzyme deficiencies and nutritional deficiencies may result in disease
• Discuss the effects of necrosis and inflammation on serum enzyme levels.
• Describe structure and function of isozymes in general
• Differentiate the isozymes of creatine kinase (CK) and lactate dehydrogenase (LDH) based on tissue location and subunit composition
• Discuss the utility of serum injury markers following myocardial infarction.
• Use of serum cardiac troponins I and T as markers
• Use of CK/CKMB ratio for evaluation of myocardial infarction
• Time frame of serum injury markers (myoglobin, cardiac troponin, CKMB) with the help of a graph (Fig. 5.22 Lippincott and Jaffe et al, JAMCollCardiol.2006, 48:1-11, http://content.onlinejacc.org/cgi/content/full/48/1/1/FIG3)
• Describe the application of sALT, sAST, sALP and sGGT as markers of hepatocellular disease, biliary disease and alcohol liver disease.
• Discuss the significance of serum amylase and lipase related to pancreatic disease
• Indicate specific serum injury markers for bone disease (sALP), prostate cancer (PSA) and liver cancer(α-fetoprotein)

 

Bioenergetics - Lecture: 

• Define and explain the equation for Gibb's free energy
• Distinguish between standard and actual free energy change, particularly with respect to the determination of spontaneity of a reaction
• Discuss the role of ATP in energy metabolism
• Identify the major high-energy compounds and compare to ATP in terms of their group transfer potential and standard free energy of hydrolysis
  • PEP, 1,3 bisphosphoglycerate, Creatine-phosphate, Thiolesters, pyrophosphate
• Describe the importance of metabolic reaction coupling
  • Explain how to calculate the ΔG of coupled reactions
• Explain the role of adenylate kinase in metabolism
• Compare the different metabolic roles of NADH & NADPH

 

Structure & Functions – Nucleic Acids - Lecture: 

• Distinguish between purines, pyrimidines; ribonucleosides, deoxyribonucleosides; ribonucleotides and deoxyribonucleotides.
• Describe the phosphodiester bond
• List and describe the important features of the Watson-Crick DNA double helix (complementary, antiparallel, and forces stabilizing the helix).
• Discuss some of the physicochemical properties of DNA
• Describe the basic structures and roles of the major classes of RNA (mRNA, tRNA, rRNA, snRNA, miRNA)
• Discuss the medical significance and mechanism of action of nucleoside and nucleotide analogs used as drugs listed below.

Clinical examples utilized in lecture:

• Anti-viral nucleosides:  Azidothymidine (AZT), Didanosine (ddI), acyclovir
• Anti-viral nucleotides:  Tenofovir
• Anti-cancer agents:  cytosine arabinoside (Cytarabine), adenosine arabinoside (Vidarabine)
• DNA hypomethylation agents:  5-azacytidine, 5-aza-2’-deoxycytidine (Decitabine)

DNA Packaging - Lecture:  

• Define the term supercoiling
• Differentiate between a supercoiled and a relaxed molecule.
• State the reasons why supercoiling of DNA molecules is important.
• Compare and contrast DNA packaging in prokaryotes and eukaryotes.
• List the antibiotic drugs that interfere with DNA gyrase.
• Describe the structure of chromatin and histone proteins.
• Explain how dsDNA and histones associate to form the nucleosome.
• Describe the different structural conformations of DNA packaging in eukaryotes (10 nm fiber, 30 nm fiber and metaphase chromosomes).
• Describe how histone modification can influence transcriptional activity.

Clinical examples utilized in lectures:

• Inhibitors of DNA gyrase – Quinolone drugs (Ciprofloxacin)

 

DNA Replication - Lecture: 

• Compare and contrast the similarities and differences between DNA Pol I and DNA Pol III of E. coli.
• Describe how DNA is synthesized from its 5’ to 3’ end.
• Explain the significance of the origin of replication.
• Explain the problems associated with unwinding of the DNA double helix.
• Describe the role of helicase enzymes in unwinding DNA prior to its replication.
• Describe the role of single-strand binding protein & topoisomerases in DNA replication.
• Outline the order of events from RNA priming to completed DNA during replication in E.coli.
• Describe the action of Type I and Type II topoisomerase enzymes
• Differentiate between DNA replication in eukaryotes and  prokaryotes.
• role of telomeres and telomerase in eukaryotic DNA replication.
• Outline the mechanisms of action of drugs that interfere with DNA replication.

 Clinical examples utilized in lectures:

• Inhibitors of DNA gyrase – Quinolone drugs (Ciprofloxacin)
• Inhibitors of DNA replication – actinomycin D
• Inhibitors of Type I and Type II topoisomerase (anti-cancer) – Camptothecin and etoposide, respectively.

Transcription - Lecture: 

• Describe the structural features of a gene and their functions.
• Describe the types and functions of the four different cellular RNAs (mRNA, tRNA, rRNA, snRNA).
• Describe the major steps of RNA synthesis in prokaryotes and eukaryotes.
• Explain the function and structure of DNA sequences that are involved in the initiation and termination of transcription.
• List the RNAs that are transcribed by the different types of RNA polymerases in eukaryotes.
• Explain how antibiotics and other compounds target and inhibit specific components of the transcription process.

Clinical examples utilized in lectures:

• Inhibitors of RNA polymerase II - -amanitin from Death Cap mushroom
• Drugs that inhibit transcription:  Ciprofloxacin, Rifamycin (Rifampin), Actinomycin D.

 

Transcription, Post-transcriptional Modification - Lecture: 

• Differentiate between the structures of prokaryotic and eukaryotic mRNAs
•  Describe the post-transcriptional modifications of eukaryote mRNA and the significance of these modifications (5’ capping, polyadenylation, and splicing).
• Predict the effects of splice site mutations on the mature mRNA and ultimately the translated protein.
• Describe how RNA editing affects our understanding of the transmission of genetic information from the genome to protein
• Describe human disease conditions that may be associated with mRNA modification and errors in this process

Clinical examples utilized in lectures:

• Systemic Lupus Erythematosus – autoantibodies to U1 Snrpn spliceosome component, and histone proteins
• Errors in splicing - -thalassemia, Limb girdle muscular dystrophy
• Human RNA editing – apo-B gene and the glutamate receptor gene
• Parasite RNA editing – Trypanosome and Leishmania

 

Structure and Functions of Lipids - Lecture: 

• Review the grouping of lipids (Fatty acids, acylglycerols, phosphoacylglycerols, sphingolipids, steroids)
• Discuss the biomedical importance of fatty acids and cholesterol
• Describe fatty acid structure and discuss the melting points related to chain length and desaturation and relate its significance in humans
• Discuss the biological importance of dietary essential fatty acids and describe in detail the structures of linoleic acid (6) and -linolenic acid (3)
• Discuss the grouping of fatty acids into the ω-6 and ω-3 families and describe in general the synthesis of arachidonic acid and of docosahexaenoic acid (DHA)
• Describe the structures and functions of triacylglycerols, and distinguish between phospholipids and glycolipids with examples for each
• Indicate the composition and functions of phosphatidylcholine, phosphatidylethanolamine, plasmalogens, phosphatidylserine, phosphatidylinositol, cardiolipin, sphingomyelin, cerebrosides, globosides and gangliosides
• Discuss role of lung surfactant in respiratory distress syndrome
• Describe the structure and biomedical importance of cholesterol

 

Signal Transduction 1 & 2 (2 Lectures) - Lecture:

• Describe the different types of cell signalling: endocrine, paracrine, neuronal & contact-dependent.
• Describe the different types of extracellular signal molecules.
• Discuss the events involved in signal transduction.
• Describe the different types of receptor families.
• Explain the role of the different families of G-proteins.
• Describe the different targets of G proteins.
• Explain how cholera toxin modifies Gs.
• Discuss the roles of cAMP, IP3 and DAG as mediators of signal transduction in different cell types
• Explain the relevance of signal amplification.
• Identify the signalling mechanisms associated with α and β adrenergic receptors, glucagon receptors and insulin receptors.
• Define KD and fractional occupancy.

 

Membrane Structure and Transport - Lecture:

• Describe the fluid mosaic model for membrane structure
• Discuss the general complex lipid composition of the plasma membrane
• Compare the composition of hepatic plasma membrane to the mitochondrial membrane
• Discuss the factors involved in regulating membrane fluidity
• Discuss the function of cholesterol in the plasma membrane
• Differentiate between active and passive transport systems based on energy requirement, and movement along the concentration gradient
• Discuss facilitated diffusion using the families of glucose transporters GLUT 1-5 as examples
• Distinguish between  primary active transport (Na+/K+-ATPase) and secondary active transport (SGLT)
• Explain the role of ABC transporters using CFTR as an example
• Describe how defects in membrane transport lead to diseased states like cystic fibrosis

 

Structure & Functions – Carbohydrates - Lecture: 

• Outline the classification of monosaccharides based on number of carbon atoms and functional group
• Differentiate between pyranoses and furanoses
• Differentiate between L- and D-, α-  and β-anomers of glucose
• Define the terms enantiomer & epimer with examples for each
• Differentiate between and indicate the bonds present in each of the examples listed below
• Monosaccharides (glucose, galactose, fructose, ribose)
• Disaccharides (maltose, sucrose, lactose)
• Oligosaccharides
• Polysaccharides (starch, glycogen and cellulose)
• Identify: sugar alcohols (sorbitol), sugar acids (glucuronic acid, ascorbic acid), and aminosugars (glucosamine and galactosamine)

• Identify important glycoconjugates and derivatives of monosaccharides (hyaluronic acid, chondroitin and chondroitin sulfate)

 

Digestion and Absorption I and II (2 lectures) - Lectures: 

• Discuss the medical importance of digestion and of absorption of the major food groups (carbohydrates, lipids, proteins)
• Describe the digestion in the mouth and in the stomach (role of salivary amylase and gastric lipase)
• Discuss the biochemical and clinical consequences of insufficient acid production in the stomach and effect of antacids
• Discuss the digestion of lipids found in breast milk
• Describe the role of gastrin and the activation of pepsinogen in the stomach
• Explain the mechanisms involved in the release and the functions of cholecystokinin and secretin
• Indicate the role of HCO3¯ in pancreatic secretion and bile
• Describe the proteolytic activation of zymogens using trypsinogen, pancreatic  proteases and prophospholipase A2 as examples
• Describe the specific cleavage sites in proteins of digestive proteases like trypsin, chymotrysin and elastase
• Discuss the intestinal digestion of proteins (endo- and exopeptidases), lipids (pancreatic lipase, cholesterol esterase and phospholipase A2), carbohydrates (amylase and disaccharidases), and nucleic acids (nucleases).
• Describe the function of bile salts in digestion. Predict the consequences of decreased bile salts on digestion of dietary lipids
• Discuss the uptake of primary and secondary bile acids into the liver via the enterohepatic circulation
• Predict the effect of bile duct obstruction on lipid digestion and absorption
• Predict the consequences of pancreatic disease (cystic fibrosis and pancreatitis) on digestion
• Describe the absorption of amino acids, monosaccharides and fats into intestinal mucosal cells
• Differentiate primary, secondary and congenital lactose intolerance based on age of onset and the primary biochemical defect
• Describe the absorption of  glucose into intestinal mucosal cells
• Describe the fate of purine bases after uptake into intestinal mucosal cells
• Describe the formation of chylomicrons in the intestinal mucosal cells
• Indicate the biochemical mechanisms in the various causes of steatorrhea (pancreatic disease, biliary tract obstruction, intestinal mucosal disease)

 

Glycolysis - Lecture: 

• Define glycolysis and explain its role in the generation of metabolic energy.
• List the reactions and enzymes that convert glucose into pyruvate (emphasize key enzymes and irreversible reactions)
• Define substrate level phosphorylation and identify those reactions in glycolytic pathway
• Explain significance of lactate production in anaerobic glycolysis. Indicate the further fate of lactate formed in muscle (Cori cycle)
• Outline the regulation of glycolysis indicating the regulatory enzymes. Appraise the role of AMP, ATP and fructose 2,6 bisphosphate on glycolysis
• Outline the function of glycolysis in specific tissues (RBC, liver, brain, muscle, eye, tumor cells)
• Analyze the effect of pentavalent arsenate and fluoride ions on glycolytic enzymes
• Identify the biochemical mechanisms involved in the occurrence of lactic acidosis in states of poor tissue perfusion/ oxygenation
• Explain biochemical mechanism for the occurrence of hemolysis in inherited pyruvate kinase deficiency
• Differentiate between pyruvate kinase deficiency and glucose 6-phosphate dehydrogenase deficiency

 

Tricarboxylic Acid Cycle - Lecture: 

• Indicate how pyruvate is transported from the cytosol into the mitochondrial matrix
• Summarise the overall reaction catalysed by the PDH complex.
• Outline the multienzyme nature of PDH  complex and the cofactors that it requires (TPP, lipoic acid, FAD)
• Explain in outline the regulation of the PDH complex (role of NADH, acetyl-CoA and phosphorylation)
• Indicate the inhibitory effects of trivalent arsenic compounds on PDH
• Discuss the consequences of thiamine deficiency (Wernicke-Korsakoff syndrome,Beri-Beri), and its effect on PDH and α-ketoglutarate dehydrogenase complexes.
• Summarize the congenital abnormalities affecting the action of the PDH complex and their clinical consequences.
• Explain the central role of the TCA cycle in metabolism, including both its catabolic and anabolic functions (amphibolic role).
• Outline the intermediates and the enzymes of the TCA cycle
• Explain the energetics of the cycle, including reactions where reducing equivalents (NADH and FADH2) are produced, and the production of GTP by substrate level phosphorylation.
• Explain why aerobic metabolism of glucose using the TCA cycle is much more efficient than anaerobic glycolysis.
• Explain the regulatory mechanisms for the TCA cycle. Indicate the effect of NADH, ATP, succinyl-CoA, Ca2+, and oxaloacetate
• Indicate the effect of fluorocitrate and malonate on TCA cycle.

 

Mitochondrial Shuttles, Electron Transport Chain (ETC) and Oxidative Phosphorylation (2 lectures) - Lectures:

• Outline the aspartate-malate (humans) and glycerophosphate (primarily white muscle tissue) shuttles and their significance in regenerating cytoplasmic NAD+
• Describe the role of the inner mitochondrial membrane in electron transport and oxidative phosphorylation.
• Outline the different types of electron carriers found in the ETC complexes
•  Describe the path electrons follow from NADH and FADH2 to oxygen, through the ETC complexes I through IV.
• Discuss the mode of action and the effects of specific inhibitors of the ETC (including antimycin A, azide, hydrogen sulphide, cyanide, rotenone, piericidin A, carbon monoxide).
• Differentiate between: direct inhibitors of  the ETC,                                   uncouplers of oxidative phosphorylation, ATP synthase inhibitors (oligomycin) and inhibitors of the ATP/ADP translocase
• Explain how the electrochemical gradient is generated during electron transport
• Describe ATP synthesis with reference to Mitchell’s Chemiosmotic theory.
• Describe the mode of action of the mitochondrial ATP synthase and its inhibition by oligomycin.
• Define uncoupling of oxidative phosphorylation with reference to the different types of uncouplers (including 2,4-DNP, valinomycin, gramicidin A).
• Discuss respiratory control of the ETC and the P/O ratio
• Outline the role of natural uncoupling in brown adipose tissue.
• Discuss transport of ADP into, and ATP out of the mitochondrion and inhibitors of this process (including atractyloside and bongkrekic acid).
• List diseases involving mutations in mitochondrial DNA: Leber Hereditary Optic Neuropathy, Myoclonic Epilepsy and Ragged-Red Fiber Disease, MELAS, Aminoglycoside Induced Deafness.

 

Gluconeogenesis - Lecture: 

• Discuss the importance of  gluconeogenesis including its role in the Cori cycle
• Indicate where in the cell and in which organs gluconeogenesis occurs
• List the main substrates for gluconeogenesis, and under what conditions each is important
• Describe the gluconeogenic pathway starting from pyruvate and highlight the irreversible reactions of gluconeogenesis
• Explain how carbons formed from other sources (eg. glucogenic amino acids, lactate and glycerol) integrate into gluconeogenesis
• Justify why there can be no net production of glucose from acetyl CoA or its progenitors eg. fatty acids and ketone bodies.
• Compare and contrast the action of glucokinase and hexokinase
• Distinguish the role of glucagon and insulin on gluconeogenesis. Explore the role of fructose 2,6 bisphosphate on gluconeogenesis.
• Compare the regulation of glycolysis and gluconeogenesis in liver in the fed and fasted state

 

Regulation of Glycolysis / Gluconeogenesis - Lecture:

• Discuss the regulation of glycolysis in skeletal muscle
• Explain the energetic advantages of using glycogen as a source of glucose
• Discuss the regulation of gluconeogenesis and glycolysis in liver and how they are reciprocally controlled
• Describe how precursors are channelled into gluconeogenesis during starvation
• Explain the role of glucokinase in regulating blood glucose levels.
• Discuss the links between lipolysis, gluconeogenesis and glycolysis, highlighting the role of acetyl-CoA in glucose sparing
• Explain the effects of high ethanol consumption on gluconeogenesis

 

Glycogen Metabolism & Storage Diseases - Lectures: 

• Describe the structure and function of glycogen
• Outline where in the body glycogen is synthesized, stored and degraded
• Differentiate the role of glycogen in skeletal muscle and liver
• Describe glycogenolysis indicating the regulatory enzyme
• Describe the glycogenic pathway indicating the regulatory enzyme
• Differentiate the regulation of glycogenesis and glycogenolysis in liver and in muscle. Evaluate the role of insulin and glucagon in the reciprocal regulation of glycogenesis and gluconeogenesis in the liver. Justify the role of calcium in the regulation of glycogenolysis
• List the glycogen storage diseases ( Types I through VII )
• Explain the biochemical basis for clinical manifestations of each type of glycogen storage disease – hypoglycemia, lactic acidosis in type I, decreased exercise tolerance in type V
• Outline the biochemical reasons for the seizure and hypoglycemia in Jim Bodie (Marks textbook case)

 

Metabolism of fructose & galactose - Lecture: 

• Describe the pathway by which dietary fructose enters glycolysis.
• Outline the hereditary diseases affecting fructose metabolism (Essential Fructosuria, Candice Sucher case in Marks textbook) and Hereditary Fructose Intolerance). Compare and contrast the biochemical findings in urine, the enzyme deficiency and the clinical manifestations of Essential Fructosuria and Hereditary Fructose Intolerance 
• Describe the polyol pathway, its function and its importance in diabetic patients.
• Describe the pathway by means of which dietary galactose enters general metabolism.
• Outline the hereditary diseases affecting galactose metabolism indicating the deficient enzymes (Galactokinase Deficiency; Classical Galactosemia, and the Erin Galway case in Marks textbook). Predict the biochemical basis for the occurrence of cataracts, liver disease in galactosemic children fed with galactose. Justify the biochemical basis for the dietary management of patients with galactosemia.
• Compare and contrast the biochemical basis and clinical features and management of children with galactosemia and lactose intolerance
• Discuss lactose synthesis in mammary tissue.

 

Pentose Phosphate Pathway (PPP) - Lecture: 

• List the tissues in which the PPP is active, and identify its subcellular location
• Summarize the function of the PPP (metabolic roles of pentoses and NADPH).
• Outline the overall reactions of the PPP
• State the reactions of the oxidative portion of the PPP (emphasize the significance of G6PD)
• State the enzymes and provide an overview of the intermediates of the non-oxidative part of the PPP
• Explain how the PPP is regulated and how different parts of the pathway are used, depending on the needs of the cell.
• Evaluate the use of NADPH in
  • Detoxification of hydrogen peroxide
  • Phagocytosis
  • Nitric oxide synthesis
  • Reductive biosynthesis
• Discuss the clinical relevance of a deficiency of glucose 6-phosphate dehydrogenase.
  • Identify the precipitating factors
  • Predict the symptoms and laboratory findings in the disorder
  • Analyze biochemical basis of symptoms and laboratory findings
  • Correlate role of PPP in hydrogen peroxide metabolism

 

Regulation of Blood Glucose Level (Mark’s textbook pg 383) - Lecture:

• Analyze the changes in blood glucose levels following a meal
  • Predict changes in hormonal levels following a meal (insulin and glucagon)
  • Appraise the fate of dietary glucose in liver
  • Appraise the fate of glucose in peripheral tissues
• Analyze the following in the fasted state
  • Predict changes in hormonal levels during fasting (insulin and glucagon)
  • Assess the significance of liver glycogenolysis in regulation of blood glucose level
  • Determine the significance of gluconeogenesis in regulation of blood glucose level
  • Identify the precursors of gluconeogenesis during fasting and determine the relative significance of each precursor (lactate, amino acids, glycerol)
• Analyze changes in blood glucose levels during prolonged fasting (starvation)
• Predict the sources for gluconeogenesis during prolonged fasting
• Justify the application of oral glucose tolerance test in the diagnosis of diabetes mellitus
• Determine the significance of FBS and PPBS in the diagnosis and management of diabetes mellitus
• Identify the effects of prolonged hyperglycemia:
  • osmotic effects,
  • protein glycation (using HbA1C as an example)
  • sorbitol formation
• Propose the biochemical basis for the occurrence of hypoglycemia in
  • Von Gierke’s disease
  • Acute alcohol intoxication 
  • Hereditary fructose intolerance

 

Reactive Oxygen Species - Lecture:

• Define the terms radical, free radical and reactive oxygen species (ROS).
• Describe formation of superoxide anion radical related to the ETC or cytochromes
• Distinguish between the reactions catalyzed by oxidases, peroxidases and oxygenases
• Discuss the formation of hydroxyl radicals related to ionizing radiation, Haber-Weiss reaction and Fenton reaction
• Discuss cellular damage and effects of ROS
• Indicate non-enzymatic radical scavengers like vitamin C and E
• Describe the reactions catalyzed by superoxide dismutase, catalase and glutathione peroxidise and indicate the ROS scavenged by these enzymes
• Discuss the compartmentation of free radical defence in the cell
• Discuss the beneficial role of ROS formation as an immunological response in phagocytosis, and describe the reactions catalyzed by NADPH oxidase and myeloperoxidase. Indicate the biochemical defect in chronic granulomalous disease.
• Discuss the direct and potential effects of excess nitric oxide formation

 

Proteoglycans and Glycoproteins - Lecture:

• Describe the general structure of proteoglycans 
• Discuss the general composition of GAGs and the possible bottle-brush structure of proteoglycans
• Describe the synthesis of proteoglycans inside fibroblasts
• Describe the synthesis of hyaluronic acid and the extracellular assembly of proteoglycan aggregates using link proteins leading to shock absorbing aggregates
• Discuss the function of hyaluronic acid related to facilitation of cell migration
• Discuss the structure and function of heparin
• Discuss some of the roles of glycoproteins (glycocalyx, blood proteins, mucins) 
• Outline the synthesis of O-linked glycoproteins and indicate the amino acid side chains involved
• Outline the synthesis of N-linked glycoproteins and indicate the significance of dolichol-pyrophosphate and mannose involvement (see Fig.14.16 Lippincott p. 168).
• Compare the concepts of the synthesis of O-linked and N-linked glycoproteins

 

Fibrous Proteins - Lecture: 

• Describe the essential features of the extracellular matrix (ECM).
• Describe the amino acid composition, structure and function of collagen.
• Discuss the synthesis of procollagen in fibroblasts and its release into the ECM
• Discuss the biochemical consequences on collagen structure in Vitamin C deficiency (scurvy)
• Describe the role of covalent cross-linking between tropocollagen molecules in maintenance of collagen stability
• Discuss biochemical defects in Ehlers-Danlos Syndromes (EDS)
• Discuss the biochemical defect in Osteogenesis Imperfecta (OI). Correlate the biochemical basis for occurrence of fractures and the presence of blue sclerae in OI.
• Describe the amino acid composition, structure and function of elastin and desmosine
• Discuss the function of lysyl oxidase related to collagen and elastin synthesis
• Describe the biochemical defect in Marfan’s syndrome
• Differentiate EDS, Marfan’s syndrome and OI based on biochemical defect and clinical features

 

Lysosomal Storage Disorders - Lecture:

• Describe the general lysosomal degradation of GAGs, glycoproteins, and sphingolipids
• Outline the causes of lysosomal storage disorders in general
• Describe the biochemical basis of symptoms of patients with lysosomal storage disorders (hepatosplenomegaly, mental retardation, macular cherry red spot)
• Describe the symptoms and biochemical basis of Hunter’s and Hurler’s syndrome; include the deficient enzyme and indicate the products that accumulate in the two disorders.
• Describe Tay-Sachs’disease and relate to the deficient enzyme, accumulating  compound, (onion-shell inclusions) and the biochemical basis for the cherry-red macula
• Describe Fabry’s disease and relate to the deficient enzyme, accumulating compound, and physical appearance of patients (dark reddish skin lesions with bathing trunk distribution, impaired sweating, muscle weakness)
• Describe Gaucher’s disease and relate to the deficient enzyme, accumulating compound, general cell appearance (crumpled tissue paper); discuss the infantile and adult forms of Gaucher’s disease
• Describe Niemann-Pick disease and relate to the deficient enzyme, accumulating compound, general cell appearance (Foamy appearing cells); discuss Type A and Type B
• Discuss the role of the mannose-6-P marker for transport of lysosomal enzymes into lysosomes. Indicate the biochemical defect in I-Cell disease
• Distinguish between the lysosomal storage diseases (Hurler, Hunter, Tay-Sachs’, Fabry’s, Gaucher’s, Niemann-Pick and I-Cell disease) based on deficient enzyme, accumulating product, and clinical features.

 

Genetic Code, Translation and Post-translational Modifications (2 lectures) - Lecture:

• Explain why the genetic code is collinear with DNA, triplet in nature, redundant (degenerate), and non-overlapping.
• Define the terms reading frame and frame-shift mutation.
• Demonstrate how to translate and interpret the standard genetic code table.
• Memorize the initiation codon and the 3 terminator codons.
  • Discuss the universal nature of the genetic code (with minor differences in mitochondria)
• Discuss how protein synthesis proceeds from the N-terminal to their C-terminal ends.
• Explain how this creates a naming convention for peptides
• List and describe the major function of the major types of RNA in cells.(Also dealt with in structure/function of nucleic acids)
• mRNA
• tRNA
• rRNA
• snRNA
• snoRNA
• miRNA

 

Translation and post-translational modifications - Lecture:

• Describe the subunit composition and the basic structure of prokaryotic 70S and eukaryotic 80S ribosomes including the basis for their names
• Describe the structure, function, and charging of tRNAs.
• Describe the codon/anticodon interaction and discuss the wobble hypothesis
• Describe the sequence of events that occurs during translation in prokaryotes
• Describe the A site, the P site, and the E site on the ribosome
• List the major differences between prokaryotic and eukaryotic translation
• Explain how diphtheria toxin interferes with eukaryotic translation.
• Describe proteolytic processing using insulin as an example.
• List and explain the mode of action of common antibiotics that interfere with translation
• Initiation inhibitors (streptomycin )
• Elongation inhibitors (Tetracycline, chloramphenicol, erythromycin, puromycin)
• List and review the major types of post-translational modifications
• Zymogen activation (trypsinogen à trypsin as example)
• Serine/threonine phosphorylation
• Tyrosine phosphorylation
• O-linked glycosylation
• N-linked glycosylation
• Lipid anchoring (farnesyl groups to RAS as an example)
• Describe proteolytic processing using insulin as an example

 

Use of Molecular Genetics in Medicine (2 lectures) - Lecture:

• Explain the concept of hybridization between two complementary single stranded DNA molecules.
• Explain the general principles and utilization of the following molecular biology techniques:
• Polymerase chain reaction (PCR)
• Gel electrophoresis
• DNA sequencing
• Southern blot and RFLP analysis
• Allele Specific Oligonucleotide (ASO) probes
• Allele Specific PCR
• Northern blot
• Western Blot
• Describe how a DNA fragment is cloned into a vector molecule. 
• List some of the different uses for vector molecules such as those used to replicate segment of DNA, sequencing vectors and protein expression vectors
• Predict the application of molecular biology techniques for detection of a
• single base mutation
• small insertion or deletion of DNA sequence, and
• changes in the expression of genes in the form of mRNA or protein.

 

Fatty Acid Synthesis - Lecture:

• Indicate the main sites in the body and the metabolic condition under which fatty acid de novo synthesis takes place
• Outline the actions of citrate lyase and the malic enzyme in the liver.
• Explain how acetyl-CoA carboxylase synthesizes malonyl-CoA and how the reaction is regulated (short-term and long-term)
• Outline the fatty acid synthetic pathway and indicate the role of the acyl carrier protein in the pathway
• Identify the sources of NADPH for fatty acid synthesis
• Discuss malonyl-CoA inhibition of carnitine-palmitoyl transferase I (CPT I)
• Outline the elongation and desaturation of fatty acids in humans. Explain the conversion of linoleic acid to arachidonic acid 
• List the major tissues of triacylglycerol synthesis and storage
• Distinguish between the glycerol-3-P pathway and the MAG pathway for triacylglycerol synthesis

 

Cholesterol Metabolism - Lecture:

• List the functions of cholesterol in the human body
• Outline cholesterol synthesis and discuss the branch-point at the level of farnesyl-PP
• Explain how the pathway is regulated at the level of HMG-CoA reductase
• Differentiate between short-term and long-term regulation of the regulated enzyme
• Describe how cholesterol affects transcription of HMG-CoA reductase
• Discuss how increased cellular cholesterol leads to the degradation of HMG-CoA reductase
• Outline bile acid synthesis and its regulation; indicate the rate limiting step in bile acid synthesis
• Describe the conjugation of primary and secondary bile acids in the liver and its significance
• Discuss bile composition and predict biochemical reasons for gallstone formation
• Describe the biochemical basis for use of chenodeoxycholic acid for management of cholelithiasis

 

Lipoproteins I & II (2 lectures) - Lectures:

• Discuss lipid transport in the blood by lipoproteins and albumin.
• Describe the location and function of lipoprotein lipase (heart, skeletal muscle and adipose tissue)
• Discuss chylomicron metabolism starting from formation to its uptake into the liver
• Discuss the transport of dietary triacylglycerols from the intestine to the peripheral tissues
• Describe the conversion of VLDLs into IDLs and their uptake into the liver
• Describe the conversion of IDLs to LDLs performed by hepatic TAG lipase
• Discuss the uptake of LDL into the liver and extra-hepatic tissues by receptor mediated endocytosis
• Describe the regulation of LDL-receptor synthesis
• Outline the receptor-mediated process involving LDL and LRP receptors
• Discuss the functions and effects of deficiency of the main apolipoproteins (apo B-48, apo B-100, apo C-II, apo E and apo A-1)
• Describe the reverse cholesterol transport performed by HDL
• Describe the synthesis, location and action of lecithin: cholesterol acyltransferase (LCAT)
• Describe biochemical basis of atherosclerosis in Tangier disease and name the defective transporter
• Describe the function of cholesterol ester transfer protein (CETP)
• Explain how cholesterol esters from HDL can reach the liver via IDL and LDL
• Describe the delivery of cholesterol esters to the liver by HDL2 via SRB-1 and using the phospholipase activity of hepatic lipase
• Explain how oxidized LDL particles are formed and how they are involved in foam cell development and atherosclerosis
• Discuss the significance of Lp(a)
• Describe Type I, IIa, IIb, III, IV and V hyperlipidemias (causes, lipid profile abnormalities, biochemical basis of clinical manifestations)
• Describe the biochemical basis for the use of statins and bile acid sequestering agents in hypercholesterolemia

 

Steroid Hormones - Lecture:

• Name the five classes of steroid hormones (glucocorticoids, mineralocorticoids, androgens, estrogens and progestins)
• Discuss steroid hormone synthesis related to STAR and desmolase (CYP11A)
• Describe the steroid hormones synthesized and released from the adrenal cortex (specified for zona fasciculata, z. glomerulosa and z. reticularis)
• Indicate the synthesis and the metabolic actions of cortisol
• Indicate the synthesis and the metabolic actions of aldosterone
• Indicate the synthesis of DHEA and testosterone in the adrenal cortex
• Describe the synthesis of testosterone in testes and of estradiol in ovaries
• Discuss congenital adrenal hyperplasias (CAH) and describe clinical features and biochemical basis of manifestations in patients with CYP 21 and CYP 11B and CYP 17 deficiencies
• Indicate the hormone abnormality in Cushings’ and Addison’s disease

 

Eicosanoids - Lecture:

• Describe in general the formation of eicosanoids including prostaglandins, thromboxanes and leukotrienes
• Discuss the role of cortisol in eicosanoid synthesis
• Outline the cyclic and linear pathways starting with arachidonic acid.
• Describe the general effects of PGI2 versus TXA2, and PGE2 versus PGFα2
• Describe the two enzyme activities of prostaglandin H synthase and cyclooxygenase (COX)
• Differentiate between COX-1 and COX-2 and discuss their inhibition by NSAIDs
• Indicate the eicosanoids formed from EPA and their biomedical activity compared to series-2 eicosanoids.
• Describe the synthesis of leukotriene LTA and the following change to LTB and to LTC
• Indicate the synthesis of  components and actions of the slow-reacting substance of anaphylaxis (SRS-A)
• Discuss the biochemical basis for using corticoids, LOX-inhibitors or inhibitors of CysLT receptors in the management of asthma. 

 

Oxidation of Fatty Acids & Ketogenesis (2 lectures) - Lectures: 

• Describe adipose tissue lipolysis and the regulation of hormone sensitive lipase. Indicate mechanism of fatty acid transport to the tissues
• Describe fatty acid activation
• Describe the carnitine shuttle mechanism.
• Explain the biochemical consequences of defects in transport of fatty acids (carnitine deficiency and CPT deficiency)
• List the reactions of the mitochondrial β-oxidation pathway (not substrate names)
• Outline the energetics of  β-oxidation
• Indicate the end products of oxidation of odd chain fatty acids
• Outline oxidation of branched chain fatty acids and indicate the biochemical defect in Refsum’s disease.
• Distinguish between medium-chain acyl-CoA dehydrogenase deficiency and Jamaican vomiting sickness based on the pathogenetic mechanism and biochemical alterations
• Outline peroxisomal α- and β-oxidation.
• Discuss Zellweger’s syndrome as a disorder of peroxisomes
• Describe the pathway of hepatic ketogenesis and list the ketone bodies
• Explain ketone body utilization in peripheral tissues
• Prepare a concept map indicating the steps involved in the generation of ketosis in starvation and uncontrolled type 1 diabetes mellitus.
• Correlate laboratory data in ketoacidosis (laboratory data in blood and urine) to the clinical signs in the patient; include hyperventilation

 

Hormonal Regulation of Fuel Metabolism: The feed fast cycle - Lecture:

• Explain metabolic homeostasis (including intrinsic & extrinsic regulation) and describe the mechanisms involved in the inter-tissue integration required for metabolic homeostasis.
• Explain the special role of glucose in metabolic homeostasis.
• Describe the roles of insulin and glucagon as the two major hormones that regulate fuel storage and mobilization.
• Describe the roles of other counter-regulatory hormones such as epinephrine, norepinephrine & cortisol.
• Describe the effect of changes in the insulin/glucagon ratio and plasma epinephrine  levels on carbohydrate, lipid and protein metabolism.
• Outline the metabolic changes that occur during the feed/fast cycle.
• Discuss which pathways are active/ inactive in each major organ/tissue during the feed/fast cycle and describe how these pathways are controlled and coordinated in different metabolic states.
• Describe the long-term effects triggered by enzyme induction as a consequence of the elevation of hormone levels.
• Outline the major metabolic changes that occur after prolonged starvation

 

Introduction to Nitrogen Metabolism - Lecture: 

• Explain in broad terms the concept of the ‘amino acid pool’
  • Write the sources of amino acids for the amino acid pool and the utilization of amino acids from the pool
  • Define and enumerate the essential and nonessential amino acids in humans
• Distinguish between the two major mechanisms of intracellular protein degradation:
  • Proteasome and ubiquitin
  • Lysosomal
• Describe the role of liver and kidney in nitrogen metabolism and excretion of non-protein nitrogenous substances
• Describe the mechanism of transport of amino acids in the renal tubule and in GIT
• Analyze and correlate clinical features and laboratory findings to the biochemical basis of cystinuria and Hartnup’s disease
• Represent the general scheme of amino acid catabolism
• Distinguish the fates of C- skeletons of amino acids:
• Glucogenic amino acids
• Ketogenic amino acids
• Glucogenic & Ketogenic amino acids
• Enumerate examples of amino acids in the three groups
• Revise the important TCA cycle intermediates formed from the glucogenic amino acids and integrate their further fate in metabolism
  • Link [glutamate and glutamine] to the TCA cycle and metabolism
  • Link [aspartate and asparagine] to the TCA cycle and metabolism
  • Link [alanine] to pyruvate and metabolism

 

Disorders of Amino Acid Catabolism - Lecture:

• Outline the catabolic pathway of the following amino acids:
• Phenylalanine and tyrosine
• Describe the disorders associated
• Phenylketonuria (Classic-PKU I  and tetrahydrobiopterin deficiency – PKU II, maternal PKU), Alkaptonuria, Tyrosinosis
• Branched chain amino acids
• Maple syrup urine disease
• Methylmalonic aciduria
• Methionine and cysteine
• Homocystinuria
• For each of the disorders listed above
• Specify the enzyme deficient and coenzyme required
• Correlate clinical and biochemical features with biochemical basis of the disorder
• Explain the biochemical basis of management (Amino acid dietary changes and coenzyme supplementation)

 

Urea Cycle - Lecture: 

• Identify the transport forms of ammonia from peripheral tissues (alanine & glutamine)
• Describe the transamination (aminotransferase) reaction and its role in the transfer of amino groups.  Indicate the importance of vitamin B6 (pyridoxal phosphate)
• Describe the role of glutamate dehydrogenase in donating NH3 for the urea cycle
• List the reactions that form ammonia in the liver:
• Explain the formation of ammonia in the intestine and its detoxification.
• Analyze the significance of intestinal ammonia formation in patients with compromised liver function
• Regarding the urea cycle,
• Identify the sources of nitrogen for the formation of urea
• Recall the subcellular location of the urea cycle enzymes and energy utilized for the formation of urea
• Explain the regulation of the urea cycle (regulatory enzyme and mechanisms of regulation) and analyze the significance of N-acetyl glutamate
• Compare and contrast the five inherited disorders associated with the urea cycle (Specify enzyme deficient, correlate clinical and biochemical features, and generalize the biochemical basis for management of hyperammonemia for each of the disorder)
• Regarding acquired hyperammonemia:
• Identify causes of hyperammonemia
• Analyze the mechanisms of neurotoxicity of hyperammonemia
• Explain the biochemical basis of management of hyperammonemia

 

Conversion of Amino Acids to Specialized Products - Lecture: 

• Discuss the products of the amino acids listed below. For each specialized product:
• specify the reactions and coenzymes involved
• analyze the biochemical significance of the specialized product
• Phenylalanine/ tyrosine:
• Catecholamines
• Biosynthetic pathways of catecholamines
• Explain the role of MAO and COMT during degradation
• Describe VMA and homovanillic acid as the degradation product of the catecholamines & its clinical significance
• Melanin
• Tryptophan:
• Serotonin
• Explain the formation of 5-HIAA formation and analyze its clinical significance
• melatonin
• Glutamic acid:
• GABA
• Histidine:
• Histamine
• Arginine:
• Nitric oxide
• Creatine:
• Amino acids required for formation
• Function of creatine-phosphate in the muscle
• Excretion product of creatine
• Explain creatinine formation
• Interpret the clinical significance of serum creatinine estimation
• Glutathione:
• Amino acids required for formation
• Revise the functions of glutathione
• Correlate each of the inherited/ acquired disorder listed below to the biochemical basis of the manifestations and the associated laboratory features
• Parkinson’s disease
• Pheochromocytoma
• Carcinoid syndrome
• Albinism

 

Metabolic roles of folic acid and vitamin B12 (One carbon metabolism) - Lecture:

• Specify the one- carbon donors in metabolism and the groups they donate (SAM, THF, Cobalamin)
• Explain the formation of SAM and the reactions requiring SAM
• Analyze the metabolism of homocysteine, vitamins/ coenzymes required for metabolism & interpret the clinical significance of homocysteine
• Explain the formation of THF from folate and specify the mechanism of action of their inhibitors
• Summarize the formation of one carbon groups from amino acid metabolism and the utilization of 1-C groups for nucleotide synthesis
• Indicate the different forms of THF (formyl, methylene and methyl) and reactions requiring the different forms of THF
• Identify the reactions requiring B12
• Compare and contrast the causes, clinical and biochemical features of folate and vitamin B12 deficiency
• Indicate the role of intrinsic factor in vitamin B12 absorption
• Justify the mechanism of the occurrence of folate trap in B12 deficiency

Purine Metabolism - Lecture:

• Identify the differences between N-base, nucleoside and nucleotide with examples
• Regarding purine biosynthesis
  • Enumerate the C & N donors of the purine ring (amino acids and 1-C groups)
  • Outline purine biosynthesis
  • Discuss the regulation of purine biosynthesis (Identify the regulatory enzyme and positive and negative modulators)
  • Correlate the mechanism of action of sulfa drugs, trimethoprim, methotrexate, mycophenolic acid to their clinical application
  • Explain the formation of deoxyribonucleotides from ribonucleotides (Specify the coenzyme and inhibitor)
• Regarding salvage pathway of purine bases
  • Identify the reactions catalyzed by HGPRT and APRT
  • Correlate the clinical and biochemical features of Lesch Nyhan syndrome (Specify enzyme deficient)
• Regarding purine nucleotide catabolism
  • Explain uric acid formation
  • Analyze causes of hyperuricemia, correlate the biochemical basis of the clinical features and explain the biochemical basis of use of allopurinol in the management of hyperuricemia
• Propose the biochemical basis of SCID (ADA deficiency)

 

Pyrimidine Metabolism - Lecture:

• Regarding pyrimidine biosynthesis
• Enumerate the donors of C & N atoms to pyrimidine ring
• Outline pyrimidine biosynthesis (UTP & CTP). Distinguish purine and pyrimidine biosynthetic pathways
• Summarize the regulation of pyrimidine biosynthesis (regulatory enzymes, regulators)
• Indicate the formation of deoxyribonucleotides from ribonucleotides
• Explain the synthesis of dTMP
• Indicate the mechanism of action of 5 fluoro uracil and methotrexate and their clinical application
• Regarding orotic aciduria
• Specify enzyme deficiency and correlate biochemical features to the clinical features
• Compare and contrast orotic aciduria due to defect in pyrimidine biosynthesis and defect in urea cycle

• Indicate the end products of catabolism of the pyrimidine nucleotides

 

Heme Synthesis: Porphyrias - Lecture: 

• Describe in detail ALA synthase and ALA dehydratase reactions.
• Outline heme synthesis starting from glycine and succinyl CoA to the formation of heme
• Distinguish between the different regulatory processes of heme synthesis in the liver and in the erythroid cells.
• Explain how pyridoxine deficiency affects heme synthesis.
• Discuss the effects of lead poisoning on heme synthesis.
• Categorise the different types of porphyrias based on clinical manifestations such as abdominal pain, photosensitivity and neuropsychiatric symptoms.
• Describe the biochemical basis for the clinical features (abdominal pain and photosensitivity, dark colored urine) occurring in acute intermittent porphyria, congenital erythropoitic porphyria and porphyria cutanea tarda. Indicate the deficient enzyme and products accumulating in the above mentioned disorders.

 

Heme Degradation and Jaundice - Lecture: 

• Outline the steps in the degradation of heme to bilirubin in the macrophages.
• Explore the relationship of serum albumin and the transport of bilirubin
• Explain the biochemical consequence of a block in each of the steps in the uptake and conjugation of bilirubin in liver. Distinguish the activity of UDP-glucuronyl transferase in adults versus premature babies.
• Analyze the steps in the processing of conjugated bilirubin in the intestine and its excretion in feces and urine
• Identify the sequential steps in heme catabolism beginning with heme till the formation of urobilinogen and stercobilin; identify the various tissues/organs involved in each step
• Compare and contrast conjugated and unconjugated bilirubin with reference to chemical composition, water solubility, tissue deposition, excretion in urine and common clinical conditions where they are elevated
• Distinguish conjugated and unconjugated hyperbilirubinemia theoretically using lab tests
• Explain the biochemical mechanisms involved in the development of physiological jaundice of the newborn
• Explain the rationale of phototherapy and phenobarbital in the therapy for premature babies with jaundice.
• Distinguish prehepatic, hepatic and post hepatic jaundice based on lab data.
• Interpret laboratory data in the different types of jaundice
• Prehepatic: sickle cell anemia, G6PD deficiency
• Hepatic: alcoholic cirrhosis, hepatitis
• Obstructive jaundice due to gall stones or cancer of head of pancreas
• Differentiate between inherited disorders: Gilbert’s syndrome and Crigler-Najjar syndromes I and II based on the pathogenetic mechanisms and biochemical alterations

 

Serum Proteins and Associated Disorders - Lecture:  

• Describe how plasma proteins can be separated by electrophoresis and classify plasma proteins based on electrophoretic mobility.
• Describe the functions of serum albumin and globulins.
• Predict three common causes of hypoalbuminemia (liver disease, nephrotic   syndrome, protein malnutrition) and explain the biochemical basis for the occurrence of edema in hypoalbuminemia
• Distinguish the functions of proteins that are found in the
  • α1-globulin fraction (α1- antitrypsin, α fetoprotein, retinol binding protein, transcortin)
  • α2-globulin fraction (α2 macroglobulin, haptoglobin, ceruloplasmin)
  • β-globulin fraction (transferrin, hemopexin, β lipoproteins)
  • γ-globulin fraction (Immunoglobulins Ig G, M, A, D, E)
• Explain the consequences of inherited α1-antitrypsin deficiency on the liver and the lungs
• Interpret the utility of C-reactive protein as an inflammatory marker
• Recognize the serum protein electrophoretic pattern in the following diseases (hypoalbuminemia, α1-antitrypsin deficiency, polyclonal gammopathy, monoclonal gammopathy)

 

Blood Coagulation and Fibrinolysis - Lecture:

• Outline the four phases of hemostasis.
• Discuss vascular spasm and the role of endothelin.
• Describe platelet activation.
• Explain the role of integrins GPIb and GPIa. 
• Describe the role of platelet-activating factors (ADP, serotonin, TXA2 and thrombin).
• Describe the role of integrin GPIIb/IIIa in platelet aggregation.
• Describe the coagulation cascade, including the extrinsic, intrinsic and common pathways.
• Indicate the role of calcium in hemostasis
• Discuss the role of vitamin K in the post-translational modification of clotting factors
• Predict the clinical manifestations in a patient with vitamin K deficiency
• Discuss the regulation of coagulation, and fibrinolysis; outline the role of PGI2, antithrombin III, protein C,TFPI, t-PA and plasmin.
• Discuss the biochemical basis of the following genetic disorders of hemostasis: hemophilia (A, B & C), Von Willebrand Disease, Bernard-Soulier Syndrome, Thrombasthenia of Glanzmann and Naegeli.

 

Liver Function Tests - Lecture: 

• List the important functions of the liver
  • Excretion of bilirubin
  • Synthesis of plasma proteins
  • Detoxification of ammonia
• Interpret the values of the following laboratory tests in the diagnosis, follow up and prognosis of a patient with liver disease (acute hepatitis, alcoholic liver disease, cholestatic disease)
  • Serum (total, conjugated and unconjugated) and urine bilirubin
  • Serum enzymes (ALT, AST, GGT, 5’NT, LDH)
  • Serum proteins (albumin and globulin)
  • Prothrombin time
  • Special tests in evaluating liver function: Serum ammonia, AFP, α1- antitrypsin, ceruloplasmin, serum iron, transferrin and ferritin
• Compare and contrast the changes in liver function tests in hepatocellular diseases and disorders associated with cholestasis
• Differentiate between acute and chronic liver disease based on liver function tests
• Explain the biochemical mechanisms for the following symptoms and signs in patients with liver disease – edema, icterus, ascites, encephalopathy, bleeding tendency

 

Alcohol and Xenobiotic Metabolism in Liver - Lecture:

• Explain the basic mechanisms of drug metabolism.
• Define phase I and phase II reactions.
• Describe the role of cytochrome P450 enzymes in drug metabolism.
• Outline the different human P450 families and their main functions.
• Describe the mechanisms of enzyme induction and enzyme inhibition and their clinical consequences.
• Outline the genetic polymorphisms of cytochrome P450 and their clinical implications.
• Describe examples of cytochrome P450 detoxification reactions (Aflatoxin B1 and acetaminophen metabolism).
• Describe the mechanism of acetaminophen toxicity and the biochemical basis for its management.
• Describe the routes for ethanol metabolism. Discuss the role of alcohol dehydrogenase, acetaldehyde dehydrogenases, and the microsomal ethanol oxidizing system in the metabolism of ethanol.
• Outline the fate of acetate formed from ethanol
• Discuss the physiological relevance of induction of CYP2E1 by ethanol.
• Describe the biochemical basis for the acute and chronic toxic effects of ethanol abuse.

 

Adipose tissue, muscle and Brain metabolism (2 lectures) - Lecture:

Adipose:

• Recognize the 4 major functions of adipose tissue and compare and contrast the two general  types of adipose tissue (white and brown)
• Energy storage (TAG)
• Endocrine gland (adipokines, leptin, adiponectin)
• Thermogeneration
• Insulation
• Review TAG hydrolysis and synthesis in adipose tissue – relate to the fed/fast state
• Discuss the role and the source of glycerol for TAG synthesis in adipose tissue and liver
• Discuss the association of abdominal fat with increased risk of coronary heart disease.
• Indicate the biochemical defect in congenital generalized lipodystrophy and relate the defect to its clinical features

Muscle:

• Differentiate between white and red fiber metabolism.
• Differentiate between aerobic and anaerobic exercise
• Compare energy metabolism in resting muscle and exercising muscle tissues
• Compare and contrast energy metabolism in cardiac muscle and skeletal muscle

Brain:

• Review the concept of the ‘blood brain barrier’ in relation to brain metabolism.
• Discuss the nutrient molecules that are used for energy production in the CNS
• Fed state
• Changes that occur after prolonged fast
• Identify the major excitatory (glutamate) and inhibitory (GABA) neurotransmitters
• Describe the metabolism of GABA in the brain, including the GABA shunt.
• Review the pathways of the biosynthesis of neurotransmitters
• Catecholamines – dopamine, nor-epinephrine, epinephrine
• Serotonin, melatonin
• Acetylcholine
• Describe the structure and function of myelin and indicate the changes in myelin in a patient with Multiple Sclerosis
• Review the effects of vitamins B1 and B12 deficiencies on brain metabolism.
• Compare and contrast the biochemical mechanisms underlying the neurodegenerative disorders of Alzheimer’s and Prion diseases.

 

Vitamins and Minerals I and II (2 lectures) - Lectures:

• List and group the major vitamins of the human diet (water soluble and lipid soluble)
• Discuss the significances of vitamin B and vitamin C deficiencies
• Indicate the coenzyme forms, the reaction requiring and the biochemical basis of clinical manifestations of deficiency of thiamine (B1), riboflavin (B2), niacin (B3), and pyridoxine (B6)
• Describe the absorption of fat-soluble vitamins. Predict the reason for occurrence of fat soluble vitamin deficiency in patients with fat malabsorption
• Describe the use of vitamin K as coenzyme for g-carboxylation of inactive blood clotting factors in the liver.
• Discuss hemorrhagic disease of the newborn. Predict the causes and effects of vitamin K deficiency.
• Discuss inhibition of g-carboxylation by warfarin and compare and contrast the anticoagulant action of heparin and warfarin.
• Describe the deficiencies of dietary vitamin A and retinoids and discuss use of retinoids as drugs in medicine
• Discuss the formation and action of retinoic acid
• Describe the function of cis-retinal in vision. Indicate why retinoic acid cannot be used to treat night blindness.
• Describe the formation of vitamin D in the skin and the formation of calcitriol (role of liver and kidney)
• Describe the functions of 1,25 dihydroxy-D related to calcium metabolism
• Describe the biochemical basis of clinical manifestation in rickets and osteomalacia.
• Indicate the functions of some trace minerals like chromium, manganese, molybdenum and selenium.
• Discuss the role of copper as cofactor for enzymes
• Discuss clinical manifestations and biochemical defects of defective copper metabolism in Wilson’s disease and Menke’s syndrome.
• Discuss the laboratory findings and biochemical basis for clinical manifestations in hereditary Hemochromatosis
• Indicate the nutritional causes of microcytic anemia.

 

Introduction to Nutrition - Lecture:

• Summarize the concept of energy equilibrium, positive and negative energy balance with relevant examples.
• Analyze the components of daily energy expenditure
• Resting energy requirement (REE/ RMR/ BMR) and enumerate factors affecting it
• Physical activity
• Diet induced thermogenesis (SDA)
• Differentiate the macronutrient ratios of a balanced diet, energy content of macronutrients and list important sources of - carbohydrates, proteins, fats, ethanol and dietary fiber
• Indicate the significance of dietary carbohydrate and predict the significance of glycemic index of carbohydrates
• Determine the significance of dietary fats in relation to coronary heart disease, and essential fatty acids
• Explore the significance of dietary fiber and correlate it to clinical applications of dietary fiber
• Analyze the significance of dietary protein and differentiate between the sources of high and low quality protein. Indicate states of positive and negative nitrogen balance
• Explore the roles of various hormones involved in appetite regulation (leptin, insulin, ghrelin)
• Solve problems involving calculation of energy expenditure in an individual (based on activity)
• Solve problems involving dietary macronutrient ratios for a balanced diet
• Distinguish the methods to assess nutritional status (anthropometry and biochemical)

 

Obesity - Lecture:

• Definition of obesity in terms of BMI
• Analyze methods for diagnosis of obesity
• Compare the various methods available for diagnosis of obesity: BMI, waist circumference, Waist to hip ratio, bioelectric impedence
• Discuss the significance of location of body fat (‘apple’ vs ‘pear’) in obesity
• Summarize the factors contributing (multifactorial) to obesity
• Genetic
• Environmental and behavioral factors
• Explore the role of leptin in obesity
• Analyze the metabolic changes in obesity
• Dyslipidemia – Correlate biochemical changes in lipid profile to metabolic changes in obesity
• Syndrome X (Metabolic syndrome) – Correlate clinical and biochemical features and explain the significance of insulin resistance
• Explain the biochemical basis for management of obesity
• Determine the role of drugs (sibutramine and orlistat) and surgery in obesity management

 

Starvation and Undernutrition - Lecture:

• Summarize hormonal, metabolic changes and changes in the various organs (liver, muscle, brain, adipose tissue) in the various phases listed below
• Postprandial phase
• Post – absorptive phase
• Early phase of starvation
• Prolonged starvation – adaptations to increase survival, role of kidney
• Predict the deleterious effects of prolonged starvation
• Correlate important clinical features with biochemical basis for anorexia nervosa
• Regarding protein energy malnutrition
• Distinguish and define types of PEM
• Compare and contrast features of marasmus and kwashiorkor 
• Correlate biochemical basis for the clinical features of both
• Identify associated vitamin and mineral deficiencies in PEM

 

Metabolic Response to Trauma - Lecture:

• Generalize the features of the hypermetabolic response and enumerate its causes
• Correlate hormonal and metabolic changes (carbohydrate, protein and lipid) following trauma in the three phases.
  • Ebb phase (Unresuscitated phase)
  • Flow phase (Adrenergic – corticoid phase)
  • Recovery phase (convalescent/ anabolic phase)
• Indicate the significance of acute phase proteins in response to trauma
• Explore the significance of nutritional support and role of glutamine supplementation
• Distinguish the pros and cons of enteral vs parenteral nutrition support
• Distinguish the metabolic response to stress and starvation

 

Diabetes Mellitus - Lecture:

• Define diabetes mellitus
• Distinguish between the types of diabetes: type I and type II (differences between the two types in terms of insulin)
• Correlate the presenting features of diabetes and biochemical basis for the clinical features
• Summarize the complications of diabetes and correlate to biochemical and metabolic changes
• Acute complications of diabetes mellitus:
  • Sequence of metabolic changes resulting in diabetic ketoacidosis (type I)
  • Compare and contrast biochemical and laboratory findings in hyperosmolar non-ketotic coma and diabetic ketoacidosis
  • Relate the occurrence of hypoglycemia in diabetic patients on insulin
• Chronic complications: Distinguish the microvascular and macrovascular complications
• Identify biochemical basis for mechanism of microvascular changes (sorbitol, AGE formation)
• Evaluate the significance of the laboratory tests for diabetes
  • Tests for diagnosis of diabetes: Fasting blood glucose, postprandial blood glucose, role of GTT
  • Tests for long term management:
    • Tests to assess glycemic control (Fasting blood glucose, postprandial blood glucose, glycated hemoglobin)
    • Tests for lipid profile
    • Tests to assess renal function

Hypoglycemia - Lecture:

• Summarize the hormonal regulation of blood glucose
• Analyze the effects of hypoglycaemia
  • Explain the release of counter-regulatory hormones
  • Discriminate the manifestations of hypoglycemia - Adrenergic, neuroglycopenic symptoms
• Distinguish and discuss the mechanisms of causation of hypoglycemia and the differences between them
  • Fasting hypoglycaemia
  • Reactive (postprandial) hypoglycemia
  • Alcohol induced hypoglycemia
  • Factitious hypoglycemia
  • Hypoglycemia of insulinoma
• Justify the significance of estimation of serum insulin, C-peptide, proinsulin in the various types of hypoglycaemia
• Integrate knowledge from previously studied metabolic pathways to identify some of the causes of hypoglycemia in infancy and childhood (von Gierke’s disease, MCAD and carnitine deficiency)

Molecular Mechanisms in Inherited Diseases - Lecture:

• Describe the molecular basis, biochemical basis for symptoms, biochemical basis of use of diagnostic tests and biochemical basis of treatment of
  • Cystic Fibrosis
  • Hereditary Spherocytosis
• Duchenne Muscular Dystrophy and Becker Muscular Dystrophy