MD (Biochemistry)

Approximate distribution of Topics for Theory Papers
See VNSGU documents for latest information
PaperTopics
1 Relevant topics of chemistry, physics, physiology,anatomy, microbiology, pathology,pharmacology,medical education technology, Medical ethics, Research methodology
2Biochemistry of Carbohydrate,Lipids,Proteins,hemoglobin and other important proteins,enzymes,Water,pH,minerals,vitamins.
3Nucleic acid metabolism and genetics, immunology and endocrinology
4Laboratory medicine,Clinical chemistry,Molecular diagnostics and recent advances
The Postgraduate study is integrative in nature. Overlap of topics is expected in all papers

(Incomplate) Example List of questions for PG (MD Biochemistry Students)

Core biochemistry

  1. How NADPH is formed in pantose phosphate pathway? How H2O2 is formed in human body? Describe biochemical reactions causing H2O2 mediated damage to cell membrane lipid? How NADPH is used to metabolize H2O2? How G6PD mutations are inherited? What are biochemical events causing hemolysis in G6PD deficiency? Explain principle of Methelene Blue based screening test for diagnosis of G6PD deficiency.
  2. Explain role of Fe2+, heme and globins in hemoglobin mediated O2 and CO2 transport. Emphasize role of distal and proximal histidine of globin. Enlist series of molecular events responsible for increased O2 affinity of Hb when one of its globin bind O2. Explain molecular basis of relationship between O2 and carbon monoxide in context of hemoglobin structure and function. What is carbon monoxide concentration in various environment? Explain relationship of 2,3 BPG with globin structure in HbA and HbF.
  3. Describe biochemical structure of bacterial cell wall and give overview of its synthesis. How does it differ in Gram positive and negative organisms? Describe biochemical mechanism of action of antibiotics affecting bacterial cell wall. Explain biochemical strategies used by bacteria to develop resistance to these antibiotics. Explain mechanism of autoimmune disease following bacterial infection and immune-mediated hypersensitivity to antibiotics.
  4. Protein life cycle
  5. Protein sequencing using Edman reaction
  6. Protein folding and its perturbation causing diseases
  7. Post-translational modifications in collagen
  8. Enzymatic pathways of methemoglobin reduction and biochemical basis for use of methelene blue in treatment of methemoglobinemia.
  9. Enzymatic pathways of methemoglobin reduction and biochemical basis for use of methelene blue in reagents for diagnosis of G6PD deficiency.
  10. Amino acid substitutions in hemoglobin variants and correlation with electrophoretic mobility and sickling test
  11. Single molecule enzymology
  12. Molar absorptivity of NADH and calculation of enzyme factors
  13. Recombinant fusion proteins in affinity chromatography purification of proteins
  14. Ribozymes: artifacts from RNA world
  15. Enzymes do not affect equilibrium of chemical reaction.
  16. Km and Vmax in competitive and noncompetitive enzyme inhibition
  17. Catalytic constant and catalytic efficiency
  18. Difference between feedback regulation and feedback inhibition
  19. Compare and contrast five Basic Local Alignment Search Tools (BLAST)
  20. Cytochrome P-450
  21. Cyanide poisoning – biochemical consequences and biochemical basis of its treatment
  22. States of respiratory control
  23. Uncouplers of respiratory chain
  24. Thermogenesis in brown adipose tissue
  25. Overview of carbohydrate metabolism
  26. Overview of fatty acid metabolism
  27. Overview of cholesterol metabolism
  28. Overview of amino acid metabolism
  29. Overview of transport of lipids in blood
  30. HDL/VLDL/LDL/Chylomicron
  31. Metabolic interrelationship among adipose tissue, liver and extrahepatic tissue
  32. Interconversion among glucose, TG and amino acids
  33. Reactions unique to gluconeogenesis
  34. Metabolism of propipnate
  35. Control of glycolysis and gluconeogenesis by Fructose 2-6 biphosphate
  36. Major Glucose transporters
  37. Screening and diagnosis of gestational diabetes mellitus
  38. Regulation of ketogenesis
  39. Biochemical events leading to of ketoacidosis in diabetes mellitus
  40. Regulation of acetyl Co-A carboxylase.
  41. Regulation of Carnitine palmitoyl transferase 1 (CPT 1) by insulin
  42. Mechanism of action of aspirin as anti-platelet-aggregation agent.
  43. Mechanism of action of corticosteroid as anti-inflammatory agent
  44. Aspirin vs. corticosteroid as drugs acting on eicosanoid synthetic pathway
  45. Three groups of eicosanoids and their biosynthetic origin
  46. EPA and DHA – biochemical basis of their role in health
  47. HDL/VLDL/Chylomicron metabolism
  48. Triacylglycerol metabolism and its regulation in adipose tissue
  49. Perilipin and adipose tissue lipid droplets
  50. Hormones and adipose tissue
  51. Biochemical events in adipose tissue after a meal
  52. Biochemical events in adipose tissue in fasting
  53. Molecular basis for regulation of cholesterol biosynthesis in a cell
  54. Molecular basis for regulation of HMG Co-A reductase in a cell
  55. Functions of non-cholesterol product of cholesterol synthetic patway
  56. Factors affecting cholesterol balance at cellular level
  57. Transport of cholesterol among tissues in humans
  58. Structure, genetics and biomedical importance of Lp(a)
  59. Inherited disorders of plasma lipoproteins
  60. Biochemical basis of etiology, clinical features, diagnosis and treatment of various hyperphenylalaninemia
  61. Non-protein nitrogen products of tyrosine and tryptophan and various drugs affecting their metabolism
  62. Maple syrup urine diseases
  63. Biosynthesis and metabolism of serotonin and metatonin
  64. Biochemical basis of etiology, clinical features, diagnosis and treatment of various hyperhomocystinemia
  65. Biochemical basis of etiology, clinical features, diagnosis and treatment of various disorders of lipid malabsorption
  66. Biochemical cause of major signs and symptoms of porphyrias
  67. Biochemical basis of etiology, clinical features, diagnosis and treatment of unconjugated neonatal hyperbilirubinemia.
  68. DNA packaging in metaphase chromosomes
  69. Possible roles of modified histones
  70. Major features of human mitochondrial DNA
  71. Viral integration and transposons in human genome
  72. Structure, function and inhibitors of DNA topoisomerases
  73. DNA damage – causes, types, repair pathways and repair fedality
  74. Double stranded break repair mechanisms
  75. Transcription cycle
  76. Transcription control regions for eukaryotic genes
  77. Post-trancriptional modification of primary transcript
  78. Mechanism of intron removal and alternative splicing
  79. Alternative promotor utilization
  80. Biogenesis and function of miRNA
  81. Degeneracy of genetic code, concept and mechanism of wobbling phenomenon
  82. Properties of genetic code
  83. Point mutations and frame shift mutations
  84. Circularization of mRNA during translation
  85. Role of methyl-GTP cap and poly-A tail in translation
  86. Antibiotics inhibiting protein synthesis
  87. cis and trans epigenetic signals
  88. Propagation of epigenetic signal after DNA replication
  89. Properties of enhancers
  90. DNA motifs
  91. Various ways of gene regulation
  92. Regulation of mRNA stability
  93. Restriction endonucleases
  94. Enzymes used in recombinant DNA research
  95. structure pf plasmid pBR322 and its use in recombinant DNA technology
  96. genomic and cDNA library
  97. DNA sequencing by Sanger's method
  98. Transgenic animals and knockout animals
  99. Membrane asymmetry
  100. specialized plasma membranes
  101. Structure of K+ channel and selectivity filter
  102. Structure and function of clathrin coated vesicles
  103. Group 1 and group 2 hormones
  104. Biosynthesis, molecular mechanism and disorders of calcitriol.
  105. Iodide metabolism in thyroid follicles
  106. Regulation of gene expression by class 1 hormones
  107. G protein coupled receptors
  108. Phospholipase C mediated second messenger system
  109. Insulin signaling pathways
  110. Nuclear receptor superfamily
  111. Absorption of iron
  112. Biochemical functions of various types of vitamin A and provitamin A
  113. Vitamin K cycle and drugs acting on it
  114. Mechanism of methotrexate and 5-flurouracil
  115. Mechanism of carboxylation by biotin
  116. Sources of free radicals and tissue damages caused by them
  117. Antioxidents can be pro-oxidents
  118. Cotranslational targeting of secretory proteins to endoplasmic reticulum
  119. Peroxismal protein sorting and Zellweger syndrome
  120. Entry of protein from cytoplasm to nucleoplasm
  121. Entry of protein from cytoplasm to mitochondia
  122. Cotranslational insertion of membrane proteins
  123. Chaperones
  124. Ubiquitin mediated protein degradation
  125. COP 1, COP2 and clathrin coated vesicles
  126. Lectins
  127. Role of dolichol in synthesis of N-linked glycoprotein
  128. GPI anchored proteind
  129. Formation and consequences of advanced glycation endproducts
  130. Biochemical basis of difference in clinical presentation of seasonal flu and bird flu/swine flu
  131. Order and location of various post-translational processing of collagen
  132. Biochemical mechanism of bone resorption in ostoclast
  133. Molecular organization in cartilages
  134. Biochemical events occurring during skeletal muscle contraction
  135. Biochemical peculiarities and functions of sarcoplasmic reticulum
  136. Dystrophin and musle cytoskeleton
  137. Regulation of smooth muscle contraction
  138. Difference in biochemical mechanism between skeletal and smooth muscle contraction
  139. Metabolism and function of nitrogen oxide
  140. Biochemical difference between muscle fibers and fuel used by sprinter and marathon runner
  141. Non-heme transport of iron in enterocytes
  142. Transferrin cycle
  143. Regulation of synthesis of Ferritin and Transferrin-receptor
  144. Role of hepcidin in iron metabolism
  145. Changes in various laboratory tests in iron deficiency anemia
  146. alpha-1 antitrypsin function and deficiency
  147. genetics of ABO blood groups
  148. Metabolism of RBC
  149. Important reactions related to oxidative stress in various cells
  150. RBC cytoskeleton and hereditary spherocytosis
  151. Respiratory burst in neutrophils and related disorders
  152. Role of NADPH oxidase and myeloperoxidase in neutrophils
  153. Properties of cytochrome P450
  154. Various types of type-2 reactions in metabolism of xenobiotics
  155. Xenobiotic mediated cell inury
  156. Mitochondrial theory of aging
  157. Role of protein glycation in protein-protein crosslinking
  158. Metabolic theory of aging
  159. Telomere – structure, function and its replication
  160. Ames test for detection of carcinogens
  161. Oncogenes
  162. Biochemical basis of apoptosis
  163. Biochemical aspects of metastasis
  164. Mechanism of action of various anticancer drugs
  165. Hypoxia induced molecular events leading to altered gene expression
  166. Explain leuminescence, chemileuminescence, bioleuminesence, enhanced chemileuminesence, and electrochemileuminesence
  167. Dietary reference intake
  168. Shotgun sequencing
  169. Ethics in medical laboratory
  170. Principle of electrochemileuminesence
  171. Cost minimization, cost-benifit, cost-effectiveness and cost-utility analysis for laboratory tests
  172. Various types of blood collection tubes for serum separation
  173. Lactic acidosis – causes and biochemical basis of expected results of various laboratory examination
  174. Causes and biochemical basis of expected results of various laboratory examination in diabetic ketoacidosis
  175. Biochemical basis of expected results of Blood gas analysis in severe emphysema
  176. Biochemical basis of expected results of various laboratory examination in renal tubular acidosis
  177. Capillary blood sampling – methods and uses
  178. Types questions clinicians try to answer by requesting laboratory examinations
  179. Voltametry in clinical chemistry
  180. Types of bilirubin in plasma and its detection by various methods
  181. Limitations of use of SI units in clinical chemistry
  182. Blunt end recombination of DNA

Laboratory Medicine

  1. ISO 15189:2012
  2. ISO 15189:2012 vs 2007
  3. NABL-112
  4. Process of NABL accreditation
  5. Explain any 10 special terms and definitions used in ISO 15189:2012
  6. Document control [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  7. Identification, control, correction and prevention of nonconformity [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  8. Internal audit [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  9. Risk management [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  10. Quality indicators [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  11. Personnel records [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  12. Equipment records [in NABL accredited clinical laboratory / requirements in ISO 15189:2012]
  13. Reagents and consumables [ requirements in ISO 15189:2012 / management in NABL accredited clinical laboratory ]
  14. Requirements in ISO 15189:2012 about Information for patients and users
  15. Requirements in ISO 15189:2012 about Request form information
  16. Requirements in ISO 15189:2012 about verification and validation of examination procedure
  17. Explain measurement uncertainty and its requirements in ISO 15189:2012
  18. Requirements in ISO 15189:2012 about documentation of examination procedures
  19. Report content requirements in ISO 15189:2012
  20. Requirements in ISO 15189:2012 about release of reports
  21. Information system management requirements in ISO 15189:2012
  22. Describe detailed process map of blood sample centrifugation. Identify risks involved in the process and possible steps to mitigate them.

Medical Education

  1. Microteaching
  2. OSPE and OSCE
  3. Teaching methods for large group
  4. Teaching methods for small group
  5. Problem based learning
  6. Teaching aids
  7. Characteristics of good poster presentation
  8. Characteristics of good slide presentation to 150 student class
  9. How to write good MCQ question paper?

Pharmacology (Biochemical Mechanism of Action of Drugs) and Microbiology

  1. statin
  2. fibrate
  3. Niacin
  4. cholestyramin
  5. ezetimibe
  6. penicilline
  7. quinolone
  8. folate antagonists
  9. sulphonamide
  10. neuraminidase inhibitors
  11. protease inhibitors
  12. M protein inhibitor- amantidine
  13. Reverse trascriptase inhibitors
  14. integrase inhibitors
  15. anti cancer drugs mechanism
  16. H1N1
  17. HIV

Immunology

  1. Immunoglobulin
  2. Complement
  3. B cell Receptor
  4. T Cell receptors
  5. MHC
  6. Immune diversity: Allelic exclusion, DNA rearrangement in B and T cell, Junctional diversity, Somatic hypermutation, Isotype switching
  7. Extracelluar and intracellular antigen presentation
  8. T Cell activation
  9. B Cell activation
  10. T cell and B cell effector functions
  11. ADA, Chronic granulomatous disease, Ataxia Telegactesia
  12. Autoimmunity:
    1. Self tolerance
    2. Central:
    3. Peripheral
    4. Loss of self tolerance
    5. structural molecular mimicry
    6. sequestration
    7. Neoantigen
    8. Epitope spreading

Clinical Chemistry

  1. Ethical issues in clinical chemistry
  2. Process of introducing new laboratory method in routine use
  3. Repeatability, reproducibility, intermediate precision and interlaboratory precision
  4. Measurement of within run precision using 20 sets of within-batch-duplicate measurement
  5. Precision profile of an examination at different analyte concentration
  6. Evaluation of the Linearity of Quantitative Measurement Procedures CLSI EP 06-A
  7. LoB,LoD,LoQ and LoL
  8. Procedures for setting analytical goals for clinical chemistry examinations
  9. Bland Altman plot for comparison between two methods
  10. Absolute and relative Bland Altman plot for comparison between two methods
  11. Regression analysis
  12. Concept of significant digits in clinical chemistry
  13. Traceability and measurement uncertainty
  14. Sensitivity and specificity of diagnostic test and ROC curve
  15. Types of clinical questions addressed in laboratory medicine with examples
  16. Hierarchy of evidences for decision making about appropriateness of a laboratory examination
  17. Standards for reporting diagnostic accuracy (STARD) used for evaluating evidence published for accuracy of laboratory test
  18. Critical appraisal and systemic review of diagnostic tests
  19. Economic evaluation of diagnostic tests
  20. Different meanings of “Normal Value” and difference from “Reference value” and “Clinical decision limits”
  21. Conditions to compare patient results with reference values
  22. Strategies for selecting reference individuals for determining reference values of a diagnostic test
  23. Parametric and nonparametric methods for determining reference values
  24. Univariate, multiple univariate and multivariate reference values
  25. Subject based reference values
  26. Circadian rhythm as preanalytical variable
  27. Diet and alcohol as preanalytical variable
  28. Noncontrollable preanalytical variable
  29. Biological variability of clinical chemistry examinations
  30. Recommended order of draw, stopper color, content and inversions
  31. Types of vacuum tubes for collection of blood for serum
  32. Newer advances in vacuum tubes technology for patient and phlebotomist safety
  33. Skin puncture for sample collection
  34. Arterial puncture for sample collection
  35. Various anticoagulents and preservatives in blood
  36. Collection of urine specimen
  37. Cost of Quality with reference to clinical laboratory
  38. Concept of six sigma and measurement of sigma in a clinical chemistry laboratory
  39. Calibrator traceability
  40. LJ Chart for quality control
  41. Westgard rules for interpretation of QC results
  42. Control of quality using patient data from single and multiple patients
  43. Desirable characteristics of EQA program for clinical chemistry
  44. Explain Trueness, accuracy and precision with examples
  45. Explain repeatability and reproducibility with examples
  46. mole, molarity, molality and normality
  47. Concentration quantities and units in clinical biochemistry
  48. SI units in clinical biochemistry
  49. Standardized reporting of test results
  50. Reagent grade water – CLSI specifications and preparation/instrumentation
  51. Reference materials, Reference methods and Reference laboratories
  52. Measurement of volume in clinical chemistry
  53. Micropipette/Pipette/ Volumetric flask calibration
  54. Types, operating principles, calibration, care and maintenance of centrifuges
  55. Buffers in clinical chemistry reagents – principles, preparation and uses
  56. Ethical issues in clinical chemistry
  57. Hazards in clinical laboratory
  58. Classification of fires and fire extinguisher requirements
  59. Color coding, order of draw, mixing recommendations of vacuum tubes for sample collection
  60. Causes and prevention of error and hazards in sample collection
  61. Beer's law, relationship between Transmittance and Absorbance and its application in clinical chemistry.
  62. Explain concept and application of Molar Absorptivity giving suitable examples.
  63. Draw diagram of a spectrophotometer. How double-beam-in-time spectrophotometer differ from double-beam-in-space spectrophotometer?
  64. Light sources in analytical equipments
  65. Spectral isolation in optical analytical equipments
  66. Wavelengh accuracy, spectral band width, stray light and photometric accuracy of optical analytical equipments
  67. Principle, instrumentation and use of atomic absorption spectrometry in clinical chemistry
  68. Zeeman correction in atomic absorption spectrometry
  69. Principle of flurometry and fluroscence polarization
  70. Components of flurometric equipment
  71. Principles of Luminecence, bioluminecence, chemiluminecence, enhanced chemileuminecence and electrochemileuminicence
  72. Principle and instrumentation of nephelometry and turbidimetry
  73. Potentiometry using Ion selective electrodes for H+, Na+, K+ and Cl-
  74. Potentiometry electrodes for pCO2
  75. Amperometric electrode for pO2
  76. Amperometric O2 based and H2O2 based glucose electrodes
  77. Potentiometric enzyme electrode for blood urea
  78. Biosensors – enzyme based and affinity based
  79. Affinity sensors for specific protein and DNA detection
  80. Electrophoresis support media
  81. Isoelectric focusing
  82. Principle of SDS PAGE
  83. Troubleshooting SDS PAGE
  84. Principle, instrumentation and uses of capillary electrophoresis
  85. Microchip electrophoresis
  86. Separation mechanisms used in chromatography
  87. Size exclusion chromatography
  88. Affinity chromatography
  89. Explain chromatographic resolution and efficiency
  90. Instrumentation of HPLC
  91. HPLC sample injector
  92. HPLC columns
  93. HPLC detectors
  94. Instrumentation of Gas Chromatography
  95. GC detectors
  96. Principle of electron and chemical ionization in mass spectrometer
  97. Electrospray Ionization for mass spectrometry
  98. MALDI mass spectrometry
  99. Principles of various mass analysers for mass spectrometry
  100. Quadruple mass analysers
  101. Magnetic sector mass analysers
  102. TOF mass analysers
  103. Quadrupole and linear ion trap mass analysers
  104. Tandom mass spectrometry
  105. Clinical applications of mass spectrometer
  106. Define isoenzymes. Explain genetic origin of isoenzymes. Enlist non-genetic modifications of enzymes resulting in isoforms.
  107. Measurement of enzymes by reaction rates
  108. Strategy for detection of above-linearity range ALT in automated chemistry analysers
  109. Traceability of enzyme measurement
  110. Enzymes as analytical reagents
  111. Monoclonal antibody productions
  112. Labeled immunochemical assays
  113. Competitive vs. noncompetitive immunoassay
  114. Labels used for nonisotopic immunoassay and their detection limits
  115. Heterogenous vs. homogenous immunoassay
  116. CEDIA and EMIT
  117. Homogenous polarization fluroimmunoassay
  118. Principle of PCR
  119. PCR optimization and primer design
  120. PCR contamination control
  121. Hot start PCR
  122. Asymmetric PCR
  123. Allele specific PCR
  124. Single molecule PCR
  125. Isothermic PCR amplification based on transcription
  126. PCR application detection techniques
  127. PCR amplicon discrimination techniques
  128. PCR-RFLP
  129. Single stranded conformation polymorphism for discrimination of PCR products
  130. Denaturing gradient and temperature gradient electrophoresis for discrimination of PCR products
  131. Dideoxy terminal sequencing of DNA principle and automated sequencing
  132. Emulsion PCR
  133. Bridge amplification
  134. Absorbance melting curve of double helical nucleic acid
  135. Dot-blot hybridization assay
  136. Two color DNA microarray
  137. DNA copy number variation assay
  138. Single copy visualization assay
  139. real time PCR with dsDNA binding dyes
  140. Real time monitoring of PCR and melting analysis
  141. Detection, quantification and identification of amplicon in real time PCR
  142. Common probes and dyes for realtime PCR
  143. Microchip electrophoresis device
  144. Automation in sample identification and data collection
  145. Automation in sample transporters
  146. Describe components of a automated discrete analyser.
  147. Use of barcoding in clinical laboratory
  148. Components of Integrated automation system in clinical laboratory
  149. Advantages and disadvantages of POCT
  150. Ideal requirements of POCT
  151. Classification of POCT devices
  152. Principle of electrochemical glucose strip used in glucometers
  153. Principle of lateral flow immunoassay
  154. Principles of HbA1C POCT instruments
  155. Assessing need for POCT service
  156. Principles, advantages,disadvantages, clinical interpretation of various methods for measurement of ALT, AST, Amylase, LDH, CKMB, Psudocholinesterase, ALP, Lipase, total protein, albumin, creatinine, urea, uric acid, Glucose,Cholesterol, TG, HDL, LDL, iron, TIBC HbA1C, Bilirubin, TSH, T4, Free T4, Other hormones and tumor markers
  157. Describe genetics, clinical significance,methods for determinations, reference intervals for serum alkaline phosphatase
  158. Current applications of tumor markers and their limitations
  159. Current recommendations on use of tumor markers
  160. Enzymes as tumor markers
  161. Screening for urine microalbuminuria in diabetes mellitus
  162. Describe formation of creatinine in body. Describe salient features of chemical and enzymatic methods for serum creatinine measurement. Give account of quality issues in creatinine measurement. List advantages and disadvantages of markers of GFR. Explain use of IDMS traceable MDRD equation for estimating GFR from serum creatinine.
  163. DM diagnostic guideline
  164. ATP IV Hypercholesterolemia diagnostic guidline
  165. Cholesterol reference material, method and laboratories
  166. beta thalassemia – genetics, pathogenesis, diagnosis
  167. Explain different types of isoenzymes and isoforms of Creatine Kinase in humans. Describe principle of measurement of CK-MB by catalytic method and mass method. Why the catalytic method generally contain N-acetyl cysteine, AMP and diadenosine-pentaphosphate? Explain reason why hemolysis may result in spurious elevation in CK-MB? Explain why very high CK-MM may also cause high CK-MB.