Study Guide Biochemistry Department First Year MBBS

List of Practical:S. No1.2.3.4.5.Practical TopicsIntroduction to use of Laboratory EquipmentGlasswareSpectronic 20MicrolabIntroduction to use of Laboratory EquipmentIncubatorWater BathHot OvenIntroduction to use of Laboratory EquipmentCentrifuge MachineElectronic Balance pHMeterTypes of Solutions, their preparation and clinical significanceExperiments on Proteins Qualitative Analysis - IBiuret TestMillon’s Test6.Experiments on Proteins Qualitative Analysis - IINinhydrin TestAldehyde Test7.Experiments on Proteins Qualitative Analysis - IIISulphur TestXanthoproteic TestList of Case Based Learning (CBL):Topic: Cell (Leber Hereditary Optic Neuropathy LHON):A 27-year-old boy presented to ophthalmic OPD with rapid deterioration of vision inboth eyes. He felt blurring of central in right eye eight weeks back which graduallyincreased and now developed similar symptoms in other eye. His visual acuity is6/36 in right and 6/12 in left eye. On fundus examination optic disc showededematous retinal nerve fiber layer and telangectatic vessels. A CT scan brain didnot reveal any inflammatory or space occupying lesion before or after optic chiasma.These findings led the ophthalmologist to suspect LHON.The buccal mucosa sample was sent to human molecular biology laboratory foridentification of genetic mutation (if any) leading to the condition and confirmation ofprovisional diagnosis. The scientists in the lab separated mitochondria from the cellsby disrupting the cells and centrifugation at 700g once and at 12000 g twice for 15and 5 minutes. Sequencing of MT-ND1, MT-ND4, MT-ND4L and MT-ND6 genes wascarried out and MT-ND1 was found to have point mutation. The diagnosis of LHONwas confirmed. MT-ND1 is the gene spanning 3,307 to 4,262 of mtDNA and encodesfor NADH dehydrogenase of ETC.13

RELATED INVESTIGATIONS:Test NameVisual field testingCT Scan BrainResultCentral vision deteriorationNormal studyMitochondria are one of the most important cell organelles and work mainly aspowerhouse of the cell. Many of the enzymes of mitochondrial function are encodedby its own DNA called mtDNA which is inherited purely from mothers. Mutations andtheir transfer to next generation is found not only in nuclear DNA but also in mtDNA.Several diseases have been found to be caused by mitochondrial dysfunction whichis due to mutations in mtDNA and examples include lactic acidosis, mitochondrialencephalopathy, stroke-like-episodes, LHON and Leigh syndrome.LEARNING OBJECTIVES:1.Structure and function of different organelles of the cell.2.Structure, function and inheritance of mitochondria3.Techniques for isolation and study of cell components and their importance inclinical medicineREFERENCE BOOKS:1.Lippincott’s textbook of Biochemistry2.Harper’s text book of Biochemistry3.Davidson’s Practice of MedicineTopic: Cell (I- Cell Disease- lysosomal targeting problems)A female infant with a normal delivery after 38 weeks and normal intrauterine lifeshowed the physical findings characteristic of I-cell disease. She manifestedgargoyle face, progressive psychomotor retardation, and increased serum levels oflysosomal enzymes with decreased activities in peripheral blood lymphocytes. Thediagnosis was made by the analyses of lysosomal enzymes. The child died at theage of 2 years and 3 months due to respiratory insufficiency. By electronmicroscopy, various-shaped membrane-bound vacuoles were observed in thecytoplasm of various cells such as hepatocytes, myocardial muscle cells, epithelialcells of the renal glomeruli, proximal renal tubular cells, fibroblasts, andchondrocytes. By histochemical analyses we found that these intracytoplasmicstorage vacuoles contained glycosaminoglycan and proteoglycan.In general, peripheral blood smears are performed to obtain information with regardto various morphological features as an aid in the diagnosis of infection ormalignancy. This report presents a patient with I cell disease (inclusion cell disease),a fatal lysosomal storage disorder caused by a defect in an enzyme responsible forthe transfer of mannose-6-phosphate ligands to precursor lysosomal enzymes. As aconsequence, most lysosomal enzymes are transported outside the cell instead of14

being correctly targeted into the lysosomes, resulting in the storage ofmacromolecules in lysosomes. I cell disease, with its heterogeneous clinicalpresentation, can be diagnosed by the presence of intracellular vacuole-likeinclusions in lymphocytes and fibroblasts, high serum lysosomal enzyme activities,and a defect of N-acetylglucosamine-1-phosphotransferase. This report describesthe morphological aspects of peripheral lymphocytes in a blood smear of a patient,the first clue to the final diagnosis of I cell disease. The observed vacuole-likeinclusions in lymphocytes of this patient were negative for periodic acid Schiff (PAS)and Sudan black B staining, in contrast to earlier reports.LEARNING OBJECTIVES:1.Structure and function of different organelles of the cell.2.Structure, function and pathology of lysosomes3.Enzyme processing and targeting to organellesREFERENCE BOOKS:1.Lippincott’s textbook of Biochemistry2.Harper’s text book of Biochemistry3.Davidson’s Practice of MedicineTopic: Nucleic acids (Acute Gout):15

A moderately obese 54-year-old male appeared at the emergency departmentcomplaining of severe pain of 10 hours’ duration in his left big toe. He stated that hewas a regular consumer of meat and soda (alcohol and sea food consumption arealso risk factors). He had no other significant medical history. On examination, hisleft big toe was found to be red and markedly swollen around themetacarpophalangeal joint, and exquisitely sensitive. There was no evidence ofarthritis elsewhere. Because of the history and location of the affected joint, theattending physician suspected that the patient was having an attack of acute gout.She ordered a number of lab tests, including a white cell count, determination ofserum uric acid, and x-ray examination of the affected joint. The x-ray findings werenon-specific; no indication of chronic arthritis was evident. Findings of other tests aretabulated below. Under local anesthesia, arthrocentesis was performed on theaffected joint and a small amount of synovial fluid withdrawn and sent to thelaboratory for detection of cells and crystals. Typical needle-shaped crystals of MSUshowing negative birefringence were detected in the synovial fluid.LAB INVESTIGATIONS:Test NameSerum Uric acidESRWBC CountRA FactorResult680 µmol/L60 mm11.0 x 10 9 /LNegativeNormal ValuesChildren120-330µmol/LAdult Male210-430µmol/LAdult Female 150-360µmol/L1 – 10 mm in 1st hour4.0 x 11.0 x 10 9 / LNegativeGout is a disease caused by hyperuricemia mostly due to genetic factors while dietand lifestyle play a minor role in its causation. Uric acid is an end product of purinemetabolism and as it is already near its saturation limit in plasma, minor increase dueto mostly under-excretion from kidney or overproduction leads to its deposition incrystal form mostly where the solvent is stagnant like synovial fluid of relativelyimmobile joints. This crystallization appears first at the most immobile and coldestfluid body, typically big toe joint space and typically at night because temperature isfurther lower at night time and due to sleep and mobility is also further decreased.Crystals in a smooth lubricated environment play havoc and cause acuteinflammatory response leading to severe pain, redness, warmth and loss of functionlocally. Moreover, uric acid deposition in other soft tissues leads to formation oftophi.16

LEARNING OBJECTIVES:1.Structure and chemistry of nucleosides and nucleotides.2.Functions of nucleotides.3.The biochemical basis of various clinical featuresREFERENCE BOOKS:1.Harper’s text book of Biochemistry.2.Davidson’s Practice of Medicine.3.Lippincott’s textbook of BiochemistryTopic: Nucleic Acids (ADA Deficiency)A little girl aged 11 months was brought by her parents to a children's hospital. Shehad had a number of attacks of pneumonia and thrush (oral infection usually due to afungus Candida albicans) since birth. The major findings of a thorough workup werevery low levels of circulating lymphocytes (i.e. severe lymphopenia) and low levels ofcirculating immunoglobulins. The attending pediatrician suspected SCID. Analysis ofa sample of red blood Cells revealed a low activity of ADA and very high level (about50 times normal) of dATP. This confirmed the diagnosis of SCID due to deficiency ofADA, the enzyme that converts adenosine to inosine.The deficiency of ADA is inherited as autosomal recessive and accounts for almost15% cases of SCID. T lymphocytes express high activity of enzyme normally. Lackof ADA activity leads to accumulation of adenosine and dATP which is toxic to Tcells. Secondarily B lymphocytes are also affected and lead to impaired humoralimmunity.Defective immune system allows different opportunistic infection to occur and recur.An example of acquired immunodeficiency is AIDS. Such conditions can be treatedby, antibiotics, fortifying immune system by immunoglobulins and treating the rootcause.LEARNING OBJECTIVES:Synthesis, ingestion and fate of nucleotides in human bodyRole of Nucleotides in DNA synthesis and outcome of ADA deficiency Thebiochemical basis of various clinical featuresREFERENCE BOOKS:Harper’s text book of Biochemistry. (Page 616) Davidson’sPractice of Medicine.Lippincott’s textbook of BiochemistryTopic: Protein Chemistry (Creutzfeldt Jakob Disease)A 70 years old man reported for the third time in last 3 weeks in medical OPD withprogressive difficulty in walking. He had muscle stiffness, twitching and involuntaryjerks in both legs. This patient was being treated by psychiatrists for depression,agitation, mood swings, memory loss and thought problems for 2 weeks immediatelypreceding the onset of current symptoms. Taking into account the rapid progressionand pattern of symptoms he was provisionally diagnosed as a case of Creutzfeldt17

Jakob Disease. The findings of MRI, EEG and spinal tap were consistent with thediagnosis. Patient was put on supportive symptomatic treatment and relatives werecounseled.The protein misfolding which is contagious from abnormal to normal protein leads toprion diseases. Prion diseases, such as Creutzfeldt-Jakob disease, occur when prionprotein, which is found throughout the body but whose normal function isn't yetknown, begins folding into an abnormal three-dimensional shape. This shape changegradually triggers prion protein in the brain to fold into the same abnormal shape.Through a process scientists don't yet understand, misfolded prion protein destroysbrain cells. Resulting damage leads to rapid decline in thinking and reasoning as wellas involuntary muscle movements, confusion, difficulty walking and mood changes.LEARNING OBJECTIVES:Chemistry of amino acidsLevels of protein folding and how it is carried outAbnormalities in protein structure/foldingREFERENCE BOOKS:Lippincott’s illustrated reviews of BiochemistryHarper’s text book of Biochemistry.Davidson’s Practice of Medicine.Topic: Protein Chemistry (Emphysema- α 1 antitrypsin deficiency)A 68-year-old Caucasian man with a 25 pack-year smoking history presented withnew-onset dyspnea on exertion in the setting of workplace dust exposure. During hisevaluation, he was found to have α1-antitrypsin deficiency with evidence ofdevelopment of pulmonary emphysema. Workplace spirometric monitoring over 10years of surveillance for an on-the-job respirator fit program demonstrated a sharpdownward slope in forced expiratory volume in one second, or FEV 1, during hisperiods of most significant dust exposure, which was attenuated after discontinuationof his workplace exposure.Blood and other body fluids contain a protein, α1-antitrypsin (α1-AT, A1AT, currentlyalso called α1-antiproteinase), that inhibits a number of proteolytic enzymes (alsocalled proteases or proteinases) that hydrolyze and destroy proteins. α1-ATcomprises more than 90% of the α1-globulin fraction of normal plasma. α1-AT hasthe important physiologic role of inhibiting neutrophil elastase ––a powerful proteasethat is released into the extracellular space, and degrades elastin of alveolar walls,as well as other structural proteins in a variety of tissues. Most of the α1-AT found inplasma is synthesized and secreted by the liver. In the normal lung, the alveoli arechronically exposed to low levels of neutrophil elastase released from activated anddegenerating neutrophils. This proteolytic activity can destroy the elastin in alveolarwalls if unopposed by the action of α1-AT, the most important inhibitor of neutrophilelastase. Because lung tissue cannot regenerate, emphysema results from the18

destruction of the connective tissue of alveolar walls. Smoking causes the oxidationand subsequent inactivation of that methionine residue, thereby rendering theinhibitor powerless to neutralize elastase. Smokers with α1-AT deficiency, therefore,have a considerably elevated rate of lung destruction and a poorer survival rate thannonsmokers with the deficiency.LEARNING OBJECTIVES:Fibrous proteinsNormal structure and synthesis of collagen and elastinAbnormalities of fibrous proteinsREFERENCE BOOKS:Lippincott’s textbook of Biochemistry Harper’stext book of Biochemistry. (Page 616)Davidson’s Practice of Medicine.Topic: Porphyrins and Hemoglobin (Hepatitis A)A 31 years old man presented with jaundice, nausea, anorexia, restlessness,lethargy, fatigue and dark color urine for three days. Color of his stools was normaland there was no itching on the skin. He was not having pyrexia and intensity ofjaundice was not of fluctuating type. There was no history of significant weight loss.There was mild pain in the right hypochondrium. He did not have any knownhemoglobinopathy. He was non-alcoholic and there was no history of use of anydrug recently.Ultrasonography showed no fatty infiltration of liver.Lab Investigations:S/N123456TestSerum Total bilirubinConjugated Bil (direct)Unconjugated Bil (indirect)Urine bilirubinUrinary urobilinogenSerum ALTResult42 µmol/L10 µmol/L32 µmol/LPresentIncreased2800 U/L7ALP54 U/L89101112ASTGGTPlasma haptoglobinSerum albuminHep B surface antigen (HBsAg) inserum40 U/L32 U/Lnormal33 g/dLNegativeReference valuesAdult 2-17µmol/L0-4 µmol/L0-13 µmol/LAbsent0-4 mg/ 24 hrsMale Upto 42 U/LFemale upto 32132-365 U/L adultsLevels higher in childrenUpto 37 U/LUpto 30 U/L35-50g/LNegative19

13Anti HCV antibody (anti HCV Ab) inNegativeNegativeserum14 Anti Hep A antibody (IgM)PositiveNegativeHepatitis A is a viral infection and resultant inflammation of the liver caused by HepA virus. Unlike Hep B and C this virus does not cause chronic disease and causesacute severe and self-limiting hepatitis making the patient immune against this virusfor rest of his life. Unlike Hep B and C which are transmitted through blood or sex,hep A virus is transmitted through orofecal route. Senescent RBCs are broken inspleen and heme and globin separated and globin degraded into amino acids infixed leukocytes of spleen. Heme is oxidized to biliverdin and bilirubin which leavesreticuloendothelial system and travel in plasma in protein bound form. Hepatocytesuptake and conjugate bilirubin for excretion from body in biliary route. Viral infectionof liver affects not only conjugation but also other functions of the liver like albuminsynthesis. This results in jaundice hypoalbuminemia and edema (later in chroniccases only), though liver has got the capability to handle 300 times more bilirubin innormal state and a capacity of hepatocyte regeneration. Chronic cellular damage,fibrosis and regeneration leads to liver failure and a condition called cirrhosis of liverwhich is leading cause of death due to hep B and C infections.LEARNING OBJECTIVES:Synthesis and degradation of hemeMetabolism of bilirubin in bodyRole of hepatocyte in bilirubin handling and its diseases (inherited and acquired)REFERENCE BOOKS:Lippincott’s textbook of BiochemistryHarper’s text book of BiochemistryDavidson’s Practice of Medicine20

MODULE-IIBiochemistry21

Summary:CodeNameDurationBroad Themes of Module(Theme: a subject that is beingintegrated a majority of time ofmodule)Subject ThemesPrerequisite ModuleY1M2Biochemistry10 weeks1.Thorax2.Cardiovascular systemChemistry of carbohydratesChemistry of LipidsEnzymesBody FluidsMinerals & Trace ElementsY1M1Mode of Information Transfer:MITLecturesTutorials (PTT)CBLPracticalsClass testsBiochemistry learning outcomes:CarbohydrateChemistryLipid ChemistryUpon successful completion of this course, students willbe able ing of biochemical nature, significance ofimportant member of each group.Explain structure of carbohydrates, isomerism andproperties of monosaccharide.Enist different dietary sources and understand commondisorders related tochemistry of CHO.Describe important homo and hetero Polysaccharides,their important examples and biochemical role,Understand the biomedical importance of carbohydratesand their derivatives in health and disease conditionsBy the time the students finish the course, they will beable to:22

EnzymesDefine and classify lipids on different basis along withappropriate examples.Difference between oil, fat, waxes and vegetable gheeas well as the process of hydrogenation and iodination,saponification, acid number polansky,s number andother physical attributes.Describe saturated, unsaturated, poly unsaturated,essential, non essential, Trans and cis type of fatty acidsand their significance in health and disease.Distinguish structure of Glycero and sphingophospholidsas well as other different complex lipids and appreciatetheir biochemical significance.Describe Eicosanoids, their functions in health anddisease and the inhibitory action of NSAIDS and steroidson them.Recognize the sterol structure and different importantsteroids especially the cholesterol, its functions andsignificance with regards to IHD.Summarize classification of lipoproteins, chemicalcomposition, functions and disordersUnderstand the rancidity, its types and lipid per oxidationand its clinical implications.At the end of the course, students are expected to beable to:Define different terms e.g, Coenzymes, co-factors,holozymes, prosthetic group, ribozymes, zymogensisozymes etc.Classify enzymes and describe mechanism of enzymeactions.Explain different properties of enzymes and factorsaffecting enzymes activity.Illustrate enzyme kinetics in relation to Michaelis-MentenEquation and Lineweaver- Burke plot.Describe enzyme regulations, activation, inhibition andbiomedical importance of synthetic inhibitors.Understand role of enzymes in clinical diagnosis andtherape

Department of Biochemistry (2018-19) 1. Departmental introduction Biochemistry department since the inception of the college has made a study and note-worthy progress. The department is headed by Prof Dr Naheed Z Razwi ably supported by a team of seasoned and experienced teachers. This department is well