Biochemquestionsslides.docx

Biological Oxidation: When a substance exists both in the reduced state and the oxidised state , the pair is called a REDOX COUPLE.

The redox potential of this couple is estimated by measuring the EMF of a sample half cellconnected to a standard half-cell.

LOWER AFFINITY FOR ELECTRONS = NEG. REDOX POTENTIAL = STRONG REDUCING AGENT AND VICE VERSA.cytochrome c and a have high redox potential (.22 and .29)Oxidases:Catalyze the removal of hydrogen from a substrate with the involvement of oxygen as a H acceptor.Aerobic Dehydrogenases: These enzymes catalyze the removal of hydrogen from a substrate but oxygen as well as other substances can act as acceptor . These enzymes are flavoproteins and the end product is usually hydrogen peroxide H202Anaerobic Dehydrogenases: Dehydrogenases use coenzymes nicotinamides & riboflavin - as hydrogen carriersCytochomes :- All cytochromes (except CYTOCHROME OXIDASE ) are anaerobic dehydrogenases

Monooxygenases : incorporates one atom of oxygen into the substrate & the other is reduced to water. Phenlyalanine hydroxylase , Tyrosine hydroxylase , Tryptophan hydroxylase-Microsomal cyt.P450 monooxygenases are involved with drug metabolism- Mitochondrial cyt P450 monooxygenaseSubstrate level phosphorylation: Bisphosphoglycerate kinase ( Glycolysis)(1,3 bisphosphoglycerate 3-phosphoglycerate) Pyruvate kinase (Glycolysis)(Phosphoenol pyruvate Pyruvate)Phosphagens :act as storage forms of high-energy phosphate and include creatine phosphate

Mitochondria: Outer-acyl Coa sythetase, Glycerol phosphate , acyl transferase Intermembrane: Adenylyl kinase, creatine kinase Inner Mitochondria membrane: impermeable to ions and most compounds ATP Synthase, ETC (complexes 1-4) Matrix: B-oxidation, TCA cycle enzymes, Citric acid cycle enzymes, Pyruvate dehydrogenaseMitochondria membrane is impermeable to NADH- need malate aspartate shuttle-used in the liver, kidney and heart (malate to OAA to aspartate)Also need Glycerol 3-phospate shuttle for muscle and brain (require FAD)

NADH-CoQ Dehydrogenase (Complex I)- Contains a flavoprotein (Fp)- FMN (Favin mono nucleoide): prosthetic group and an iron-sulphur protein (Fe-S). -at this moment 1 ATP is producedSuccinate-CoQ Dehydrogenase (Complex II) -The 3 major enzyme systems that transfer their electrons directly to ubiquinone are: Succinate dehydrogenaseFatty acyl CoA dehydrogenaseMitochondrial glycerol phosphate dehydrogenase.

CoQ-cytochrome c Reductase (Complex III)

Cytochrome c Oxidase (cyta-a3) (Complex IV)

Mobile complexes:Co-enzyme Q or ubiquinoneCyt C-Contains one heme prosthetic group .

It collects electrons from Complex III and delivers to Complex IV.

It is also the mediator of apoptosis (programmed cell death)

Flow of electrons:for NADH Complex 1 -> complex 3 -> complex 4for FADH Complex 2 -> complex 3 -> complex 4

Chemiosmotic theory- The transport of electrons from inside to outside of inner mitochondrial membrane is accompanied by the generation of a proton gradient across the membrane.

Protons accumulate outside the membrane creating an electrochemical potential.

This drives the synthesis of ATP by ATP synthase.

Oligomycin- blocks ATP synthase, blocks H+ from coming into to membrane

Fo complex: O STANDS FOR OLIGOMYCINMade of 12 subunits . H+ passes through each subunit from membrane space to inner space rotating the Fo complexF1 complex: Has 9 polypeptide chains ,(3 alpha , 3 beta , 1 gamma , 1 sigma , 1 epsilon)the chains have binding sites for ATP and ADP and beta chains have catalytic activity.ATP SYNTHESIS NEEDS Mg +2 IONSADP and Pi bind the alpha subunitBinding change mechanism - conformational change of beta subunits causes release of ATPs from the complex.

ATPs formed in the mitochondrial matrix are translocated to cytosol by ATP/ADP translocaseonly 32 ATPs may be generated from glucose .

Inhibitor of ATP Synthesis:Site : COMPLEX 1 to Co QAlkylguanide(guanethide), hypotensive drugRotenone ( insecticide and rat poison)Chlorpromazine (tranquiliser)Barbiturates (sedative)Pericidin (antibiotic)Site :COMPLEX III to Co Q (ubiquine)BAL BRITISH ANTI LEWISITE WAR GASNapthoquinone

Site : Complex IV inhibitorsCarbon monoxideCyanideAzideHydrogen Sulphide

Site : between succinate dehydrogenase and CoQCarboxinMalonate : competetive inhibitor of Succinate DH

Actractlyoside inhibits translocase whereas oligomycin acts through one of the proteins present in Fo-Fi stalk.Uncouplers:2,4 dinitro phenol,2,4 dinitro cresolCCCP (Chloro carbonyl cyanide phenyl hydrazone)THERMOGENIN in brown adipose tissueThyroxineMELAS: complex1 or complex 1 and 4 diseaseMitochondrial encephalopathyLactic acidosisStroke like episodes.Lebers Hereditary Optic Neuropathy LHON complex -3 defect Degeneration of Retinal ganglion layer.

Kearns-Sayre syndrome- Oculocraniosomatic neuromuscular disease with ragged red fibersLeighs disease- complex 4 defect, fatal by the age of 2

Q. A comatose laboratory technician is rushed into the emergency room. She dies while you are examining her. Her most dramatic symptom is that her body is literally hot to your touch, indicating an extremely high fever. You learn that her lab has been working on metabolic inhibitors and that there is a high likelihood that she accidentally ingested one. Which one of the following is the most likely culprit?

BarbituratesPiericidin ADimercaprolDinitrophenolCyanide

Q. A 53-year-old, previously successful man recently lost his job and is under investigation for racketeering. His wife returns home to find him slumped over the steering wheel of his idling car in the closed garage. He is unresponsive and has a cherry color to his lips and cheeks. Which of the following is inhibited?Complex I of the ETCCytochrome oxidaseThe ATP-ADP antiporterThe F0 component of the F0-F1 ATPaseThe F1 component of the F0-F1 ATPase

TCA CycleThe citric acid cycle is the final common pathway for the oxidation of carbohydrate, lipid, and protein because glucose, fatty acids, and most amino acids are metabolized to acetyl-CoA or intermediates of the cycle.-If hepatic cells are damaged as in acute hepatitis or replaced by connective tissue (as in cirrhosis) there will be damage

PDH : E1 - Thiamine pyro phosphate (TPP) (B1)E2 Lipoic acid Co-enzyme-A (Pantothenic acid)E3 NAD Niacin (B3) FAD Riboflavin (B2)

TLCFN: tender, loving, care for nancy: 3 Enzymes:-1)PDH,2)-KGDH(TCA cycle)3)Branched keto acid dehydrogenase

PDH is IRREVERSIBLE ( Fats cannot be converted to glucose.)-1 NADH is generated =2.5 ATPPDH is inhibited by its end product Acetyl CoaPDH kinase inactivation of enzymePDH Phosphatase - activation (insulin in adipose can activate it)

Congenital Lactic acidosis:-Deficiency of Pyruvate Dehydrogenase enzyme.Inability to convert Pyruvate to Acetyl co-A.Shunted to Lactate Dehydrogenase to form Lactic Acid.Deficient NADH leading to deficient ATPLactic acidosis, severe psychomotor retardation, damage to brain stem, cortex etc..,Fluoroacetate- blocks aconitaseArsenite- alpha keto glutarate dehydrogenase complexMalonate- block succinate dehydrogenase

ATP Substrate level phosphorylation- enzyme used in succinate thiokinase/succinate Co A synthetaseOAA is viewed as a catalyst , which enters into the cycle , causes complete oxidation of acetyl CoA , and is regenerated in the end without any loss. Oxidation of fats need the help of Oxaloacetate which enters into the cycle and is regenerated in the end . The major source of OAA is Pyruvate. (Carbohydrate)Excess carbohydrates are converted to neutral fats via citrate and ATP-citrate lyase but not vice versa because Pyruvate dehydrogenase step is irreversible.

TCA cycle plays an important role in Gluconeogenesis , Transmination and Deamination.OAA to phospoenol pyruvate to glucose -pathway of gluconeogenesis a-ketoglutarate to glutamate and vice versa (transmination and deamination)Precursor of heme through succinyl Co-A Pyruvate to OAA= pyruvate carboxylasePyruvate to malate=malate enzymeallosteric inhibition of citrate synthase by ATP and long-chain fatty acyl-CoA.Increased ATP and NADH will inhibit isocitrate dehydrogenase, so no alpha ketoglutarate , and theres a build of citrate and citrate inhibits pfk-1 so no glucolysis

Beriberi , Wernickes encephalopathy and Korsakoffs psychosis (WK syndrome)in Thiamine deficiency is due to failure of TCA cycle ( Pyruvate dehydrogenase and - a-ketoglutarate dehydrogenase)

Congenital deficiency of Pyruvate dehydrogenase Lactic acidosis and neurodeficit.

Congenital deficiency of Pyruvate carboxylase OAA is deficient failure of sparking of TCA severe mental retardation , lactic acidosis.

Q. During a myocardial infarction , the oxygen supply to an area of the heart is dramatically reduced , forcing the cardiac myocytes to switch to anaerobic metabolism.Under these conditions , which of the following enzymes would be activated by increasing intracellular AMP?

a. Succinate dehydrogenaseB. PFK1C. GLUCOKINASED. PDHE. LDH

Q. Which of the following is required for cholesterol synthesis in hepatocytes?

A. Citrate shuttleB. Glycerphosphate shuttleC. Malate-Aspartate shuttleD. Carnitine shuttleE. Adenine nucleotide shuttle

A 55 year old alcoholic was brought to the emergency department by his friends. During their usual nightly gathering at the local bar, he had passed out and they had been unable to revive him.Q. The physician ordered an injection of thiamine followed by overnight parental glucose. The next morning the patient was alert and serum thiamine was normal and blood glucose was 73mg/dl. The IV line was removed and he was taken home. At the time of discharge from hospital which of the following proteins would have no significant physiological activity in this patient?

Malate dehydrogenaseGlucokinaseGLUT 1 transporterPFK-1Glucose 6 PO4 dehydrogenase

CarbohydratesClinical application :- Benedicts test is a bed side test for detection of reducing sugar in urine(Clinitest, Urine)Sucrose- Bypasses metabolic check points- OBESITY Lactose intolerance: Deficiency of enzyme lactase in brush border epitheliumLactulose: Used in the treatment of hepatic encephalopathy

Metabolized by the colonic bacteria to acidic products CAUSES PURGATION

Promotes the excretion of ammonia in feces as protonated ammonium ions

Homoglycan: STARCH,GLYCOGEN, CELLULOSE, INULIN, DEXTRANS, CHITIN

Starch: Composed of AMYLOSE & AMYLOPECTINLiver glycogen - first line of defense against declining blood glucose levels especially between meals.Dextrans: In hypovolemic shock, given intravenously increases blood volumeHomoglycanChondroitin sulfate- most abundant, found in cartilage, tendon and ligamentDermatan sulfate-Helps in wound repair and fibrosis.Keratan sulfate-Absence of glucuronic acid, KSI CORNEAKS II Loose connective tissueHeparin-Found in mast cells, Acts as an anticoagulant binds antithrombin III and activates it Heparan sulfate-Found in basement membrane and cell surface, Skin fibroblasts and aortic wallsHyaluronic acid- Not sulfated, Not linked to any protein Found in synovial fluid of joints, vitreous humor of eye.Proteoglycans-Proteoglycans are proteins that contain covalently linked glycosaminoglycans. ( GAGS 95 % PROTEINS 5% approx.)Degradation of GAG: Degraded by lysosomes.Enzymes acid hydrolases. Extracelluar GAGs are brought inside by phagocytosis.Muccopolysacharides:Hurler Syndrome: Key features: corneal clouding, mental retardation, micrognathia, coarsening of facial features with macroglossia, inguinal and abdominal hernias, retinal degeneration.Hunter- no corneal cloudingSanfilippo-Severe neurological involvementMorqoiu- Severe skeletal dysplasia.

Q. A 30-month-old child presents with coarse facial features, corneal clouding, hepatosplenomegaly, and exhibiting disproportionate short-trunk dwarfism. Radiographic analysis indicates enlargement of the diaphyses of the long bones and irregular metaphyses, along with poorly developed epiphyseal centers. Other skeletal abnormalities typify the features comprising dystosis multiplex. The childs physical stature and the analysis of bone development indicate the child is suffering from which of the following disorders?(A) Hunter syndrome(B) Hurler syndrome(C) Maroteaux-Lamy syndrome(D) Morquio syndrome type B(E) Sanfilippo disease type A

Gluconeogensis: Liver and Kidney are the major gluconeogenic tissuesGlucogenic amino acidsLactateGlycerolPropionate

Proprionate- go to succinyl CoA to intermediates of TCA (remember methymalonyl CoA isomerase is here and needs B-12 coenzyme Three nonequilibrium reactions in glycolysis catalyzed by hexokinase, phosphofructokinase and pyruvate kinase, prevent simple reversal of glycolysis for glucose synthesis.Glucagon and epinephrine inhibit glycolysis and stimulate gluconeogenesis in the liver by increasing the concentration of cAMP.

-They also affect the concentration of fructose 2,6-bisphosphate which is the most potent positive allosteric effector of of Phosphofructokinase -1 and inhibitor of Fructose 1,6 bisphosphatase .Fructose 2, 6 bis- activated by insulin, inactivated by glucagonAcetyl -CoA as an is an allosteric activator of Pyruvate carboxylase-Acetyl -CoA as an is an allosteric activator of Pyruvate carboxylase. Malfunctioning of citric acid cycle def of oxaloacetateALCOHOL DEHYDROGENASE- convert alcohol to Acetaldehyde to Acetate creating NADHEXCESS LACTATE from PYRUVATE Excess Malate FROM OAAExcess Glycerol 3 P from DHAPNo or less Gluconeogenesis!!Hypoglycemia

Q. Immediately after completing a 25-mile marathon race, a healthy 24-yr old man was extremely dehydrated and thirsty. He quickly consumed a 6-pack of ice-cold beer and shortly thereafter became very weak and light-headed and nearly fainted. He complained of muscle cramping and pain. What is the most probable cause ?

Excess lactate in bloodExcess Alcohol in bloodExcess NADHDehydrationElectrolyte imbalance

Q. Which of the following enzymes can be induced genetically by hormones in a person with prolonged history of fasting?GlucokinasePyruvate CarboxylasePFK-1Acetyl co-A CarboxylasePhosphofructokinaseQ. In the citric acid cycle, succinate thiokinase catalyzes the cleavage of the succinyl Co-A to succinate with formation of a high energy compound. This compound can then be used by the body in which of the following biochemical pathways?

Oxidative phosphorylation GluconeogenesisFormation of creatine phosphateCholesterol synthesisFatty acid synthesisGlycolysisAerobic Glycolysis : formation of Pyruvate as end product with production of ATP and NADH when oxygen is availableAnaerobic Glycolysis : formation of lactate as end product with production of only ATP in the absence of oxygen .Allows continuous production of ATPs in cells without mitochondria or cells deprived of oxygenpfk-1 =rate limiting step-7ATP formedNADH produced during anaerobic Glycolysis is utilized during lactate dehydrogenase step Iodate acetate- inhibits G3 P dehydrogenousFlouride blocks enolaseHormonal regulation (mainly liver): Insulin favors Glycolysis and Glucagon inhibits GlycolysisHexokinase- found everywhere, low affinity, work at normal levels Glucokinase- found in liver and beta cells of pancreas, high affinity work at high levelsGlucagon inhibit pyruvate kinase by cAMP and protein kinase AInsulin activate pyruvate kinase through protein phosphataseSecond most common cause for enzyme deficiency related hemolytic anemia.Def causes decreased ATP production in RBCs

Decreased energy to fuel the pumps required to maintain the biconcave, flexible shape of RBCs.Red cell damage and phagocytosis premature death and lysis hemolytic anemia (chronic hemolysis) Absense of Heinz bodies ( to differentiate G6PD def)

Q. Under conditions of anaerobic glycolysis, the NAD+ required by glyceraldehyde-3-phosphate dehydrogenase is supplied by a reaction catalyzed by which of the following enzymes?

Glycerol-3-phosphate dehydrogenaseAlpha-ketoglutarate dehydrogenaseLactate dehydrogenaseMalate dehydrogenasePDH

Q, After consumption of a carbohydrate-rich meal, the liver continues to convert glucose to glucose-6-phosphate. The livers ability to continue this processing of high levels of glucose is important in minimizing increases in blood glucose after eating. What is the best explanation for the livers ability to continue this conversion after eating a carbohydrate-rich meal?

The Hepatocyte cell membranes permeability for glucose-6-phosphateThe high maximum reaction rate (high Vmax) of GlucokinaseThe inhibition of Glucokinase by high glucose-6-phosphateThe lack of Glucokinase level regulation by insulinThe low Michaelis-Menten (Km) constant of Glucokinase

Various fates of pyruvate : 1. to lactate 2. to Acetyl Coa 3. to OAA 4. to alanine (using pyridoxal phosphate- a transamination b6)

Q. Which of the following is required for cholesterol synthesis in hepatocytes?

A. Citrate shuttleB. Glycerphosphate shuttleC. Malate-Aspartate shuttleD. Carnitine shuttleE. Adenine nucleotide shuttle

HMP/Pentose PathwayNADPH required for biosynthesis of fatty acids and steroids.Generation of Ribose-5-phosphate for nucleotide synthesisInterconversion of carbohydrates into glycolytic and gluconeogenic intermediates.

Oxidative pathway irreversible- mainly occurs in tissues which require NADPH (irreversible)Non oxidative pathway reversible- Occurs in the tissues which require ribose for nucleotide synthesis.

Transketolase-Transfers a 2-C unit (C1 AND C2 ) of a ketose to aldehyde C of aldoseTransaldolase-Transfers a 3-C unit (dihydroxyacetone) from Seduheptulose 7P to glyceraldehyde 3P

Source of NAD: tryptophan and niacin, for NADPH Cytosolic Isocitrate dehydrogenase: and Malic enzyme:

Wernicke-Korsakoffs syndrome :- Genetic disease where a mutation in gene for transketolase which decreases the affinity of enzyme transketolase for Thiamine pyrophosphate (TPP)Treatment :- Give thiamineBeri Beri Thiamine deficiency

ALCOHOL -INHIBITS THIAMINE ALCOHOL, VERY LITTLE THIAMINE IN ALCOHOLIC BEVERAGES, POOR NUTRITION IN ALCOHOLICS

CHRONIC ALCOHOLICS WILL HAVE WERNICKES KORSAKOFFS SYNDROME + SYMPTOMS OF THIAMINE DEFICIENCYUses of NADPH: REDUCTIVE BIOSYNTHESIS e.g.Biosynthesis of steroidsFatty acid synthesisDrug metabolism cytochrome p 450 systemGlutathione reductaseNADPH Oxidase respiratory burst phagocytosis. by neutrophils and macrophagesReduction of hydrogen peroxide: NADPH aids in synthesis of superoxide radical during respiratory burst. Superoxide dismutase gives you hydrogen peroxide, then myloperoxidase gives you hypochlourus acid to kill the bacteriFunction of reduced glutathione: acts along with Glutathione Peroxidse reduce hydrogen peroxide to water in RBCs. (Neutralization of free radicals)Deficiency of enzyme NADPH oxidase Chronic Granulomatous Disease.Catalase Negative organisms produce hydrogen peroxide used by myeloperoxidase of the host to kill itInfection with Catalase positive bacteria

Synthesis of NO. (NADPH is a coenzyme Arginine from Citrulline

Mitochondrial system:Conversion of cholesterol to steroidBile acid synthesisHydroxylation of vitamin D.

Microsomal system: liverDetoxification of drugs, carcinogens, petroleum products, pesticides etc.

Q. A 19-year-old, African American male military recruit is about to be sent to Iraq on his assignment. In preparation for his tour of duty, he is given a prophylactic dose of primaquine to prevent malaria. Several days after he begins taking the drug, he develops fatigue and hemolytic anemia. Which of the following proteins is likely deficient?

Glucose -6- phosphataseGlucose 6-phosphate dehydrogenaseAldolase BMuscle phosphorylasePyruvate kinase

Q.Chronic granulomatous Disease is a condition where the macrophages cannot kill the bacteria with the help of oxygen mediated respiratory burst due to deficiency of which of the following enzymes?

Glucose-6-PO4 dehydrogenaseNADPH OxidaseGlutathione peroxidasePeroxidaseCatalase

Fructose and Galactose metabolism, Uronic acid pathwayURONIC ACID IS REQUIRED FOR :-A. Synthesis of GAGs Synthesis of Glycoproteins and ProteoglycansB. Conjugation of Bilirubin and DrugsL-xylulose reductase- blocked in pentosuriaPhosphorylation to fructose -1- phosphate by enzyme fructokinase in liver. (not dependent on insulin)extra hepatic tissues: glucose competes with fructose for hexokinase.Muscle which contains only hexokinase phosphorylates fructose to F6P which is a direct glycolytic intermediate. Fructokinase bypass PFk-1Fructokinase is blocked in essential fructosuria (excretion in urine, no other diagnosis) avoid fructoseAldolase B blocked in Hereditary Fructose Intolerance (build up of phosphate-F1-P) lead to liver failure, hypoglycemia, hyperuricemia,the liver failure lead to hypoglycemia because no glycogen phosphorylase and decreased ATP also Depletion of ATP.AMP rises and in absence of inorganic Pi , AMP is destroyed HyperuricemiaProlonged fructose ingestion in infants leads to poor feeding, vomiting, hepatomegaly, jaundice, hemorrhage, proximalrenaltubule syndrome (fanconi like syndrome)Aldolase B is present in liver, kidney and small intestine converts fructose 1-P into DHAP and glyceraldehyde 3P.

-increased rate of lipogenesis( fatty acid and triglyceride synthesis) in liver as a result of Acetyl CoA and glycerol-3-PO4 accumulation formed by the more rapid fructose metabolism then glycolysis due to the bypass of pfk-1

Can get fructose from glucose through aldose reductase and sorbitolIf you have diabetes, chill on the glucose because Hyperglycemia (as in diabetes) results in elevated levels of intracellular glucose in lens, nerve, kidney. This leads to water retention in these tissues due to osmotic effects of sorbitol swelling, cataract, peripheral neuropathy and vascular problems nephropathy and retinopathy as complications of diabetesAGEs-advanced glycated end product= glycated protein in plasma, they also attach to receptors=capillaries increase in thickness=attachment to AGE receptor=activation of NFKB

Galactose Metabolism: fxn=energy converts to glucose, (synthesis of lactose, synthesis of GAG, glycoprotein and proteoglycan these all require UDP Galactose)Galactokinase deficiency = Non classical galactosemia (just cataracts)Galactose 1-phosphate uridyl transferase deficiency= Classical galactosemia (worse)Galactosemia, Galactosuria, vomiting, Diarrhoea, jaundice, cataract formation (elevated galactitolLiver damage- cirrhosis and brain damage - mental retardationAccumulation would inhibit the production of the second messenger inositol in the signalling system and hence causing a mental retardation.

Q. A newborn vomits after each feeding of milk based formula and does not gain weight. Biochemical testing reveals a severe def of Galactose-1-phosphate uridyl transferase. If this condition goes untreated, which of the following is the likely outcome for this patient?

Benign disease except for cataract formationChronic emphysema appearing in early adulthoodChronic renal failure appearing in adolescenceMental retardation and later death in infancyGastrointestinal symptoms that remit with puberty

Q.A 4-month-old infant is brought to emergency clinic by the parents in an unconscious state. The mother complains that the child has had repeated attacks of unconsciousness, especially in the night, in the past few months. On examination, the child had massive Hepatomegaly. Biochemical tests revealed that the blood glucose level was 40mg/dL. The lactate and triglyceride and uric acid levels in circulation were increased. Urine did not contain any reducing sugar. The developmental milestones of the child were normal; however, the weight gain of the infant was poor. Administration of glucagon failed to increase the blood glucose level. What is the most probable biochemical defect?

Von Gierke diseaseClassical GalactosemiaHereditary fructose intoleranceEssential FructosuriaMedium chain acyl Co-A dehydrogenase deficiency

Glycogen metabolismIn health, liver glycogen maintain blood glucose level particularly between meals whereas muscle glycogen is a readily available source of glucose in the exercising muscles.

Glucose 6-phosphatase is absent in muscle-so NO contribution to plasma glucose level by muscle glycogen-only locally available glucose 6-P for glycolysis and HMP shunt

Glycogen synthase (regulated by insulin) in liver and muscle (Glut4)- can only elongate existing chains (alpha 1-4 linkage)branching enzyme- also known as glucosyl 4:6 transferase OR amylo [14] [1-6]transglucosidase an alpha (1-6 linkage) Glucagon turns off glycogen synthase Pyrophosphate - is hydrolyzed to inorganic phosphate by Pyrophosphatase and thus ensures the IRREVERSIBILITY of glycogen synthase.Glycogen acts a primer as well, but if theres no glycogen you can use GLYCOGENIN(16) glucosidase activity free glucose released.

Glycogen storage diseasesType 1: Von Gierkes Dx= def. in glucose 6 phosphatase hyperuricemia due to increase glucose 6 phosphate Type 2: Pompes= Lysosomal 14 and 16 glucosidase (acid maltase) (heart failure by 2)(cardiomegaly- normal blood glucose)Type 3: Limit dextrinosis, Forbe's or Cori's disease- Liver and muscle debranching enzyme is deficient, accumulation of characteristic branched polysaccharide (limit dextrin)Type 4: Amylopectinosis, Andersen's disease- branching enzyme-accumulation of amylopectin like polysaccharide with few branch pointsType 5: Myophosphorlylase deficiency, McArdle's syndrome, muscle phosphorylase deficiency - poor exercise toleranceType 6: Hers dx- liver phosphorylase Type 7: Tarui's disease- def in Muscle and erythrocyte PFK 1

Q. 6-month-old who is failing to thrive is brought to your clinic. Tests reveal hepatosplenomegaly, muscle weakness and atrophy, hypotonia, and decreased deep tendon reflexes. Blood tests reveal that the infant has normal glucose levels. Biopsy of the liver reveals initial stages of cirrhosis due to the accumulation of an abnormal glycogen with few branch points, whose structure resembles amylopectin. The clinical and laboratory results presented are indicative of which glycogen storage disease?

Von Gierke diseaseTarui diseaseAndersen diseaseCori or Forbes diseaseMcArdle disease

Q. An infant with growth retardation, hepatomegaly and hypoglycemia demonstrate hepatic fibrosis without fat accumulation on liver biopsy. There is also accumulation of small chain dextrin- like material within the cytosol of the hepatocytes. Which of the following enzymes is most likely deficient in this patient?

Glucose -6-phosphateGlycogen phosphorylaseDebranching enzymeAmylo- (1,6) glucosidasePyruvate kinase.

Q.After a meal, blood glucose enters cells and is stored as glycogen, particularly in the liver. Which of the following is the donor of new glucose molecules in glycogen?

UDP-glucose-1-phosphate UDP-glucose UDP-glucose-6-phosphate Glucose-6-phosphate Glucose-1-phosphate

Regulation of blood glucose level Glucose is the only fuel that will supply energy to skeletal muscle under anaerobic conditions.

Glucagon Binds To Specific Receptors In Hepatic Cell Plasma Membrane , And This Activates Adenylyl Cyclase Through a G Protein Linked Mechanism.

The c-AMP generated activates PHOSPHORYLASE and enhances rate of glycogen degradation while inhibiting glycogen synthase .

Glucagon has no effect on glycogenolysis in muscle.

Its a potent lipolytic agent also. It increases adipose tissue c-AMP levels and this activates the hormone sensitive lipase which breaks down TAG to FA +Glycerol.

It also enhances gluconeogenesisEpinephrine promotes glucagonInsulin structure is kept together by disulphide bondInsulin receptor-tyrosine receptor

Q. Which of the following substances will BE elevated in a starving cell?A. 5AMPB. c-AMPC. ATPD. GTPE. glucose

Q. Which of the following statements correctly describe human glucose metabolism?

A. Liver is impermeable to glucose in the absence of insulinB. Pancreatic -cells, liver and brain are freely permeable to glucose due to specific glucose transportersC. Liver glucokinase phosphorylates glucose at high rates under all conditionsD. Extrahepatic tissues are permeable to glucose when glucagon is presentE. Liver takes up glucose when serum glucose is normal but releases it when serum glucose is high

Hemoglobin Biosynthesis of heme: Succinyl CoA( FROM TCA CYCLE) 2)AA - GLYCINEneed B6 for ALA Synthase- rate limiting step2/3 rd of TOTAL HEME SYNTHESIZED GOES FOR SYNTHESIS OF cytP450apo-repressor= negative feed back for heme

Most common is PORPHYRIA is AIPALA Synthase- Sideroblastic anemiaALA Dehydrogetase- inhibited by lead (ferrotchelase)Uroporphyrinogen synthase/ deaminase 1: AIPUroporphyrinogen synthase 3: Congenital erythropoietic (Gunthers)- first time you see photo sensitivity Uroporphyrinogen decarboxylase: cutanea tarda

DRUGS that gives you porphryin :- Certain medicines, such as BARBITURATES(SEDATIVE ) , GRISEOFULVIN (ANTI-FUNGAL)birth control pills, antibiotics, and medicines for treating seizures.Why ? THEY ARE METABOLISED BY CYT P450 , hence UTILIZATION of HEME in CYTOCHROME P450 IS INCREASED .This DECREASES THE INTRACELLULAR CONCENTRATION.

Q. AIP is the major autosomal-dominant acute hepatic porphyria. This disease is caused by a deficiency in porphobilinogen (PBG) deaminase, an enzyme of heme biosynthesis. Patients afflicted with this disease would be expected to excrete excess amounts of which of the following?

(A) Delta-aminolevulinic acid (ALA)(B) Coproporphyrinogen III(C) Hydroxymethylbilane(D) Protoporphyrin IX(E) Type III uroporphyrinogen

skin blistering, prefer to work at night: Uroporphyrinogen decarboxylase-cutanea tardalives in an 80 years old house- ALA dehydratase

Q. A 25-year-old man has experienced chronic blistering and scarring of his skin when exposed to sunlight. This man is a smoker and drinks heavily, both of which exacerbate his responses to sunlight. Analysis of his urine and plasma indicates a high accumulation of complex porphyrins, predominantly uroporphyrin.The symptoms and clinical signs displayed by this patient indicate he is suffering from which of the following disorders?

(A) Acute intermittent porphyria (AIP)(B) Hereditary coproporphyria (HCP)(C) Porphyria cutanea tarda (PCT) decarboxylase(D) Variegate porphyria(E) X-linked sideroblastic anemia

Catabolism of HEME: ENZYME :- Glucuronosyltransferase

Q. An infant with severe jaundice that is not corrected by phototherapy is in danger of developing kernicterus. This can occur in infants with CriglerNajjar syndrome, a genetic disorder in which there is a near-complete deficiency of glucuronyl transferase. Which of the following laboratory findings would be expected in blood tests in an infant with CriglerNajjar syndrome?Decreased hematocritDecreased indirect bilirubinIncreased direct bilirubinIncreased indirect bilirubinIncreased reticulocyte count

Chemistry of hemoglobinLike water (polar and charged): lysine (+), arginine (+), aspartate (-) and glutamate (-) polar: serine, threonine, asparagine, glutamine, histidine and tyrosine hydrophobic: alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, cysteine, and methionineQ, What type of amino acids will be present in the core? Valine, arginine or glutamic acid ?

Porphyrins are pyrrole rings joined together by methenyl bridges (=HC-)bridges.4 nitrogens, 2 02, and a histidine Proximal histidine binds iron to heme, distal histidine stabilize O2 after iron bindsBinding sites: Oxygen and carbon monoxide Fe2+Carbon-di-oxide amino terminal end of globins.H+ ions histidine 146 of beta subunit.

hemoglobin abnormality that decrease P50 for hemoglobin for 26 to 20 mmHg= polycythemia, decreased p50, increased affinity carbon monoxide poisoning=cherry red blood, higher affinity Methemoglobin (Fe3+)= chocolate brown blood-use NADH and cytochrome B5 reductase together to reduce it or NADPH and methylene blue. since you need NAPH then you need G6PD or pyrivate kinase for NADHGlobin chain goes through splicing to make the hemoglobin

Sickle Cell: Mutation : is replaced by valine at 6th position of Beta chain. Hb S is less soluble in acidosis and dehydration However at acidic pH (citrate buffer)HbS moves faster than Hb AAlpha thalassemia-gene deletionsBeta thalassemia- decrease (frontal bossing), hair on end

Q. An Asian child has severe anemia with prominence of the forehead (frontal bossing) and cheeks. The red cell hemoglobin concentration is dramatically decreased, and it contains only beta-globin chains with virtual deficiency of alpha-globin chains. Which of the following mechanisms is the most likely explanation?

A. A transcription factor regulating the alpha-globin gene is mutatedB. A regulatory sequence element has been mutated adjacent to an alpha-globin geneC. A transcription factor regulating the beta-globin gene is mutatedD. A transcription factor regulating the alpha and beta -globin genes is deficientE. A deletion has occurred surrounding an alpha-globin gene

Q, HbC disease is caused by a single amino acid substitution (lysine instead of Glutamic acid) at position 6 in the bete-globin chain of the hemoglobin molecule. Patients homozygous for HbC have a mild chronic hemolytic anemia. HbS disease generally causes a more severe condition compared to HbC disease because HbS disease:

A. Impairs oxygen binding to the heme moietyB. Impairs proper folding of the alpha-helix in the beta-globin chainC. Allows hydrophobic interaction among hemoglobin moleculesD. Impairs beta-globin interaction with 2,3-bisphosphoglycerateE. Stabilizes iron moiety at ferric state (fe3+).

Q. An infant to a greek immigrant appears healthy at birth but develops transfusion dependent hemolytic anemia by the age of 6 months. his erythrocytes contain insoluble aggregates of hemoglobin subunits. The child developed normally in utero because at that time he produced high quantities of:

Alpha globinB. Beta globinC. Gamma globinD. Delta globinE. Epsilon globin

Biosynthesis of fatty acids

Q. Which of the following substances will be elevated in a cell following a high fatty meal ?

A. c AMPB. 5 AMPC. ADPD.GDPE. glucagonLIPIDS:Biosynthesis of FA

Substrates of fatty acid synthesis: Acetyl Co-ANADPHATPBiotinHCO3 source of CO2.

Steps of fatty acid synthesis1.Transport of acetyl Co-A to cytosol

2. Synthesis of Palmitate from acetyl CO-A

3. Elongation of Palmitate to increase the length of fatty acid

4. Desaturase system to produce unsaturated fatty acids.

Sources of NADPH: HMP pathway, MALIC enzyme (Malate to Pyruvate), Cytosolic Isocitrate dehydrogenase (cytosolic reducing equivalents (NADH) produced during glycolysis contribute to the reduction of NADP+ to NADPH needed for palmitoyl CoA synthesis.From cytosol to inner mitochondrial membrane require ATP-citrate lyase ~once there acetyl CoA is converted to Malonyl CoA through Acetyl Coa carboxylase (require biotin) rate limiting step and is activated by citrate

Q. Acetyl CoA is produced in mitochondria .Fatty acid synthesis occurs in cytosol .Which of the following enzyme is responsible for regeneration of acetyl CoA in cytosol for this process ?A. Acetyl CoA carboxylaseB. PDHC.Isocitrate dehydrogenaseD. Citrate synthaseE. ATP citrate lyase

Since glycerol kinase is activity is low in adipose tissue, the source of glycerol 3 p is by DHAP from glycolysis using glycerol 3P dehydrogenase

Lipolysis requires the presence of epinephrine , norepinephrine, glucagon, adrenocorticotropic hormone (ACTH), -and -melanocyte stimulating hormones , Thyroid stimulating hormone (TSH), Growth Hormone (GH ) , and vasopressin.

Many of these activate Hormone sensitive Lipase.This is done by increasing the concentration of c-AMP either by stimulating the enzyme adenylyl cyclase or by inhibiting the enzyme Phosphodiesterase.

Glucocorticoids can stimulate HSL directly.

Leptin is a product of the Ob gene.Leptin acts on receptors in the hypothalamus of the brain where it inhibits appetite

Eicosanoids:

Dietary linoleic acid- from plants Phospholipase lipase A2- cortisol inhibits, epinephrine and thrombin activated Aspirin-inhibited COXCOX 1- constitutive formCOX 2- mediate inflammatory responsePGI2 (Prostacyclins)- vasodilation, inhibit platelet aggregationPGF2 -stimulates uterine contraction & has role in LH- induced ovulation bronchoconstrictor

PGE2- bronchodilator, inflammation, feverPGE2 especially in adipose tissue decreases c-AMP and inhibits Lipolysis. PGE2 also increases calcium mobilization from bone and glycogen synthesis.PGs increase gastric motilityThromboxane promote platelet aggregation Induce labor (abortion) = PGE2 and PGF2APGE2= erectile dysfunction

The physiological actions of PGI3 and TXA3 are shifted in favor of prevention of blood clotting

COX -2 inhibitors :Celecoxib, Rofecoxib

Q. A 58-year-old woman is undergoing a myocardial infarct and is given 162 mg of aspirin, owing to the cardioprotective effects of aspirin during such an incident. Aspirin is a nonsteroidal anti-inflammatory drug that inhibits cyclooxygenase. Cyclooxygenase is required for which one of the following conversions?

(A) Thromboxanes from arachidonic acid(B) Leukotrienes from arachidonic acid(C) Phospholipids from arachidonic acid(D) Arachidonic acid from linoleic acid(E) HPETEs and subsequently hydroxyeicosatetraenoic acids (HETEs) from arachidonic acid

Q. The cardioprotective effects of aspirin occur due to the inhibition of the synthesis of which one of the following?

(A) PGF2(B) PGE2(C) TXA2(D) PGA2(E) PGI2

Q. A 40-year-old woman has rheumatoid arthritis, a crippling disease causing severe pain and deformation in the joints of the fingers. She is prescribed prednisone, a steroid that exerts its beneficial effects through anti-inflammatory pathways. What is the mechanism of steroidal anti-inflammatory agents?

(A) Prevent conversion of arachidonic acid to epoxides(B) Inhibit phospholipase A2(C) Promote activation of prostacyclins(D) Degrade thromboxanes(E) Promote leukotriene formation from HPETEs

Lipid Transport:

Apolipoproteins: C2 for lipoprotein lipase A1 for Lecithin cholesterol acyl transferaseligands (receptor): Apo B100 and APO E LDL receptor

APO A1 HDLAPO B48 ChylomicronsAPO -B100 VLDL, IDL, LDLAPO C and E present in all particles(with exceptions ) predominantly donated by HDL

LDL- highest cholesterolLipoprotein lipase- activated by insulin and co-factor apo C-II

Hypercholesterolemia or Familial Hypercholesterolemia- No cholesterol can come inside, no LDL receptors (atherosclerosis)

Abetalipoproteinemia :- No chylomicrons , VLDL, LDL, mutation in gene (MTP)Familial alpha lipoprotein deficiency

Drugs used in Hyperlipoproteinemia: Statins - HMG-CoA reductase inhibitors

Q. A lipoprotein synthesized in liver , containing high concentration of TG and mainly cleared from circulation by adipose tissue and muscle ?CHYLOMICRONSHDLIDLLDLVLDL

Q. Which of the following lipoproteins increase in Familial hypercholesterolemia Type 1 .

A. ChylomicronsB. LDLC. VLDLD. Total cholesterolE. IDL

Type I = increase chylomicronsType II =increased LDL

Lipid Chemistry

Fatty acid are never free, always bound to albuminSaturated= no double bonds

Even number- e.g.-Palmitic acid / hexadecanoic acid , stearic acid.Odd number e.g.-Propionic acid, Valeric acid

Trans-fat is harmful. Trans fat not broken by LIPASE- Body cant metabolize it -desaturase

Dipalmitoyl phosphatidyl choline acts as a surfactant in lungs. Reduces surface tension of alveoli

If its absence respiratory distress syndrome.Gangliosides Cerebrosides + Sialic acid (9 carbon sugar NANA).

Lysosomal enzymes:Gangliosides: hexoaminidase: Tay Sachs (no hepatosplenomegaly) cherry redCerebrosides: - Galactosidase ( FABRYS) - Galactosidase (krabbes ) - Glucosidase (Gauchers)(Glucocerebrosidase ) Sphingomyelin: Sphingomyelinase: Niemann Picks disease

Q. A two year old boy is brought to the OPD with hepatosplenomegal and mental retardation. He is also having erosion of long bones. A liver biopsy showed accumulation of glucosylseramide in liver cells. The abnormality lies in which of the following enzymes ? Hexosaminidase A Arylsulfatase A Sphingomyelinase Beta-glucosidase Alpha galactosidase

Q. 5A one-year-old baby presents with increasing flaccid paralysis, lack of coordination, and hyporeflexia. Over the next several years, the child's condition deteriorates to a bedridden vegetative state. Funduscopic examination reveals optic atrophy. Extensive enzymologicalstudies document a deficiency of arylsulfatase A (cerebrosidesulfatase) in leukocytes. Which of the following is the most likely diagnosis? A. Gaucher's disease B. Krabbe's disease C. Metachromatic leukodystrophyD. Niemann-Pick disease E. Tay-Sachs disease MC

Oxidation of fatty acids and ketogenesisHormone sensitive lipase: break down of triglycerides to FA and glycerolGlycerol to Glycerol Po4 to glucose (gluconeogenesis) through glucokinaseFA to Acetyl CoA to liver

Increased fatty acid oxidation is a characteristic of starvation and of diabetes mellitus, leading to ketone body production by the liver (ketosis). Ketone bodies are acidic and when produced in excess over long periods, as in diabetes, cause ketoacidosis, which is ultimately fatal.

Gluconeogenesis is dependent upon fatty acid oxidation, any impairment in fatty acid oxidation leads to hypoglycemia.

Alpha oxidation- occurs in peroxisomes (branched chained FA)Beta oxidation- in mitochondria (long and medium FA) and in peroxisomes (VLCFA)Omega oxidation- occurs only when mitochondria doesnt oxidize MCFA (accumulation of dicarboxylic acids adipic (C6), suberic (C8), sebacic (C10). Profound Hypoglycemia no ATPs for running gluconeogenesis. Absent ketone bodies in the blood why ? no acetyl Co-A Hyperammonemia - octanoic acid mitochondrial poison coma. Common cause of sudden infant death syndrome (SIDS)

Dicarboxylic aciduria and presence of medium chain acyl carnitines in urine

Step 1 : Activation of fatty acids (Acyl CoA synthetase) only step that require ATP2: CPT-1 moves acyl-Coa inside= rate limiting step3. Carnitine-acylcarnitine translocase- acylcarnitine is transported into the matrix in exchange for free carnitine4. CPT-II transfer of acyl group from carnitine to CoA in the mitochondrial matrix regenerating free carnitine Insulin upregulate Acyl Coa carboxy

Oxidation of fatty acid with odd no. of carbon atom yields acetyl CoA + Propionyl CoA( Enters TCA as Succinyl Co-A).Thus this portion of odd chain fatty is glucogenic.

Methylmalonic aciduriaDeficiency of vitamin B12 accumulation of methyl malonyl Co-A.Mutation in methyl malonyl Co-A mutase

Oxidation of fats need the help of Oxaloacetate which enters into the cycle and is regenerated in the end .Impaired oxidation of fatty acids gives rise to diseases associated with nonketotic hypoglycemia .

MCAD:Most common inborn error of fatty acid metabolismDefect in first step of beta oxidationPresent in milk seen in infants dependent on mothers milk.Accumulation of medium chain fatty acids.

Jamaica Vomiting dxUnripe Ackee fruit HypoglycinInactivates medium and short chain acyl Co-A dehydrogenase.Dicarboxylic aciduria due to omega oxidation.

Zellweger Syndrome: peroxisomal disorder

Q. A 4-month-old infant presents with a seizure. His mother reports that her infant has been irritable and lethargic over the past several days. The infant is found to be profoundly hypoglycemic and have low ketones . Short-chain dicarboxylic acids are found to be elevated in the serum. The most likely enzyme deficiency is which of the following?

(A) Medium-chain acyl CoA dehydrogenase (MCAD)(B) Carnitine acyltransferase I(C) Hormone-sensitive lipase(D) Pyruvate carboxylase(E) Fatty acyl CoA synthetase

Refsums disease is a rare neurologic disorder caused by accumulation of phytanic acid formed from Phytol , a constituent of chlorophyll .Susceptible people have a deficiency of phytanoyl-CoA hydroxylase that prevents -oxidation .

Q. What is the primary role of carnitine in fatty acid oxidation ?

(A) Activates long-chain fatty acids in the cytosol(B) Transport of acyl groups across the inner mitochondrial membrane(C) Is converted to enoyl CoA(D) Is converted to -hydroxyacyl CoA(E) Is involved in breakdown of even-chain, but not odd-chain, fatty acids

Q. An infant is born with a high forehead, abnormal eye folds, and deformed ear lobes and shows little muscle tone and movement. After multiple tests, he is diagnosed with Zellweger syndrome, a disorder caused by peroxisome malformation. What type of fatty acid would you expect to accumulate in patients with Zellweger syndrome?

(A) Short-chain fatty acids(B) Acetyl CoA(C) Dicarboxylic acids(D) Long-chain fatty acids(E) Very-long-chain fatty acids

Ketogenesis/ Ketolysis: Ketogenesis Occurs When There Is a High Rate of Fatty Acid Oxidation in the LiverLiver can only synthesize ketone bodies but it cannot utilize them.Only extrahepatic tissues can utilize acetoacetate because of the enzyme Succinyl-CoA-acetoacetate transferase (THIOPHORASE).HMG CoA Synthase= rate limiting step of ketogenesis

DKA: Kussumals breathing: metabolic acidosis., Fruity odour acetone

Q. A 12-year-old boy presents with fatigue, polydipsia, polyuria, and polyphagia. A fingerstick glucose measurement shows a glucose level of 350mg/dL in his serum. He is diagnosed with type 1 diabetes mellitus, a disease characterized by a deficiency of insulin. Which one of the following is most likely occurring in this patient?

A) Increased fatty acid synthesis from glucose in liverB) Decreased conversion of fatty acids to ketone bodiesC) Increased stores of Triacylglycerol in adipose tissueD) Increased production of acetoneE) Chronic pancreatitis

Biosynthesis of cholesterolCholesterol is only excreted through BILERate limiting step= HMG CoA reductaseWhats required? Acetyl CoA from Glycolysis, ATP and NADPH (from the 3 pathways)Need to know Farnesyl diphosphate gives you Co Q and dolichol (important for synthesis of glycoproteins)

Person complains after statin drug, they have Rhabdomyolysis, give Co Q pillsStatin drugs inhibit HMG Reductase so no mevalonate

Bile acid regulation require 7 alpha hydroxylase (need vit C)- rate limiting step Requires O2, NADPH, cytochrome P450

Q. Why are dietary fibers mainly helpful in decreasing cholesterol?A. They promote the GI motility and decrease cholesterol absorption.B. They are not digested and they dont produce Acetyl CoA upon metabolismC. They cause a fullness of stomach and decrease appetiteD. They bind to bile salts and decreases their reabsorptionE. They decrease cholesterol absorption from gut

Q.The anticholesterolemic action of simvastatin is based on its effectiveness as a competitive inhibitor of rate-limiting enzyme in cholesterol biosynthesis. The reaction product normally produced by this enzyme isA. SqualeneB.MethylmalonateC.LanosterolD.MevalonateE.acetoacetate

Q. Which of the following substances is decreased if HMG CoA reductase inhibitors are used for treatment of hypercholesterolemia?A. Acetyl Co AB. Malonyl CoAC. CoQD. Succinyl CoAE. ATP

Molecular Biology B-DNA is physically stable Topoisomerase and Gyrases removes super coilsHistones: Arginine and lysine90% of chromosomes dont code: Constitutive heterochromatin(densely packed )mRNA: Contains the genetic code for protein synthesis. It is the copy of DNA derived after transcription5 end has 7-methyl Guanosine triphosphate CAPPolyadenylate tail 20 to 30 residuesHn RNA is converted to m-RNA by by snRNAtRNA: Acceptor arm ends with CCA nucleotides aminoacid specificAnticodon arm - three base region that can base pair to the corresponding three base codon region on mRNA.D-arm recognition site for the enzyme aminoacyl t-rna synthase.T arm recognition site for ribosome to attachFxn of mRNA to ribosomes: 16s identifies Shine Dalgarno sequence in Prokaryotes18s identifies Kozak consenses sequence in EukaryotesNucleolus- rRNA

A sample of human DNA is subjected to increasing temperature until the major fraction exhibits optical density changes due to disruption of its helix (melting or denaturation). A smaller fraction is atypical in that it requires a much higher temperature for melting. This smaller, atypical fraction of DNA must contain a higher content of

a. Adenine plus cytosineb. Cytosine plus guaninec. Adenine plus thymined. Cytosine plus thyminee. Adenine plus guanineQ.In a given sample the amount of adenine nucleotide is 20%. Calculate the amount of cytosine content in DNA?

20%30%40%50%60%Q. During a laboratory experiment a scientist finds that one DNA strand contains 10 As, 12Gs, 14 Cs and 14 Ts. How many of each base is found in the complete double stranded molecule. A. A = 26, G = 22, C=22, T=26B. A=20, G =22, C=22, T=20C. A=24, G = 26, C=26, T=24D. A=10, G =12, C=14, T=14E. A=26, G=24, C=24, T=26

Q, Histones can bind DNA tightly as they have a positive charge. This is due to the amino acidA. aspartateB. glycineC. lysineD. prolineE. tyrosineDNA Replication:DNA synthesizing enzymes are called DNA polymerasesSince eukaryotes take so long to synthesis DNA replication initiates at many different sites simultaneously. origin of replicationsProkaryotes- have DNA polymerase I,II,III Eukaryotes have DNA polymerase alpha and deltaTelomerase have reverse transcriptaseQuinolones and Fluoroquinolones inhibit DNA gyrase

Q. The activity of which DNA polymerase is critical for determining accuracy of nuclear DNA replication?a. 5 to 3 polymerase activity of DNA polymerase b. 5 to 3 exonuclease activity of DNA polymerase c. polymerase activity of DNA polymerase IId. 3 to 5 exonuclease activity of DNA polymerase e. Primase activity of DNA polymerase IIIQ, The anti- Peudomonas action of Norfloxacin is due to inhibition of which enzyme of DNA replicaton?

A) DNA polymerase IB) topoisomerase IIC) DNA ligaseD) DNA Polymerase IIE) RNAaseHQ. It is well known that DNA polymerases synthesize DNA only in the 5 to 3 direction. Yet, at the replication fork, both strands of parental DNA are being replicated with the synthesis of new DNA. How is it possible that while one strand is being synthesized in the 5 to 3 direction, the other strand appears to be synthesized in the 3 to 5 direction? This apparent paradox is explained by

a. 3 to 5 DNA repair enzymesb. 3 to 5 DNA polymerasec. Okazaki fragmentsd. Replication and immediate crossover of the leading strande. Lack of RNA primer on one of the strands

Q, Given that the chromosomes of mammalian cells may be 20 times as large as those of Escherichia coli, how can replication of mammalian chromosomes be carried out in just a few minutes?

a, Eukaryotic DNA polymerases are extraordinarily fast compared with prokaryotic polymerasesb. The higher temperature of mammalian cells allows for an exponentially higher replication ratec. Hundreds of replication forks work simultaneously on each piece of chromosomal DNAd. A great many different RNA polymerases carry out replication simultaneously on chromosomal DNAe. The presence of histones speeds up the rate of chromosomal DNA replication

DNA Repair Mechanism: Mismatch repair: An enzyme called as the DAM methylase methylates DNA at N6 position for all adenines within 5 GATC sequences. Newly synthesized strands are not methylated immediately. This allows to distinguish b/w the two. HNPCC hereditary non polyposis colon cancer (LYNCH syndrome).Autosomal Dominant: hMSH-2 gene or hMLH1Base excision repair: Identified by DNA glycosylase and removed. The attached sugar and phosphate are removed by Apurinic or Apyrimidinic endonucleases.Nucleotide excision repair: Excision endonuclease (exinuclease), Defect in nucleotide excision repair (XPA and XPC) geneDouble stranded break repair: Ku protein and DNA dependent protein kinase are involved in repair.Bloom Syndrome: BLM gene Ataxia telengiectasia: Defect in the ATM gene

Q. Patients with hereditary nonpolyposis colon cancer [HNPCC(114500)] have genes with microsatellite instability, that is, many regions containing abnormal, small loops of unpaired DNA. This is a result of a mutation affectinga. Mismatch repairb. Chain break repairc. Base excision repaird. Depurination repaire. Nucleotide excision repair

Q. Following ultraviolet damage of DNA in skina. A specific excinuclease detects damaged areasb. Purine dimers are formedc. Both strands are cleavedd. Endonuclease removes the strande. DNA hydrolysis does not occur

Q. Following ultraviolet damage of DNA in skina. A specific excinuclease detects damaged areasb. Purine dimers are formedc. Both strands are cleavedd. Endonuclease removes the strande. DNA hydrolysis does not occur

Q. Dyskeratosis congenital is a genetic condition with impaired proliferation of stem cells. The defect has been traced to an inadequate production of an enzyme required for chromosome duplication in nuclei of dividing cells. This enzyme contains a single stranded RNA.What is the deficient enzyme?

A) DNA POLYMEASE B)DNA LIGASEC)PRIMASED)TELOMERASEE)DNA POLYMERASE

G1/S check point= Cyclin E/CDK-2= dissociate phospate from Rb/p53MDM-2 regulates p53 by feedback.

Recombinant DNA:PCR: Produces virtually unlimited copies of a very small DNA sampleRequirements:Taq polymerase (DNA polymerase)d-NTPsSpecific primersBufferMagnesium chlorideDNA template the problem with PCR: Both introns and exons will be present. Collect m-RNA of a particular gene and then synthesize C-DNA by using reverse transcriptase.Restriction endonucleases: Restriction endonucleases hydrolyze phosphodiester linkages in both the strands of DNA at highly specific sites. They recognize palindromes in 5 3 direction on both the strands. Sticky blunt ends that ligase will work on.The sticky ends= can go back together so homopolymer will be added HIV- Western blotGene therapy: Human DNA is synthesized and it integrates into HOST CELL DNAGene Regulation:Chaperones are heat shock proteins preventing aggregationUbiquitin- a tag for proteasomes, I=cellOperon- promoter regionOperator- binding site for proteins Histone acetylation and deacetylation: addition of acetyl groups to histones disruption of nucleosome and DNA separation

Q, The bacterial lac operon is controlled by both glucose and lactose levels. Which of the following conditions would result in the greatest level of transcription from the lac operon?

Both glucose and lactose presentGlucose present but no lactoseLactose present but no glucoseNo glucose or lactose present

Q. The lac operon is negatively controlled by the lactose repressor and positively controlled by which of the following?

Increased concentrations of glucose and cyclic AMP (cAMP)Decreased concentrations of glucose and cAMPIncreased concentrations of glucose, decreased concentration of cAMPDecreased concentrations of glucose, increased concentration of cAMPIncreased concentrations of glucose and adenosine triphosphate (ATP)

Q. A culture of E. coli is grown in a medium containing glucose and lactose. The expression of the lactose operon over time in the cells is shown in the graph below. Which statement best describes the change that occurred at point A?Lactose was added to the culturecAMP concentration increased in the cellsGlucose was added to the cultureRepressor protein dissociated from the operatorRepressor protein became bound to the

Transcription:The enzyme responsible for the RNA synthesis is DNA-dependent RNA polymerase.Rifampicin=inhibit the RNA synthesis.The mushroom Amanita phalloides (The Death Cap Mushroom) produces a toxin called alpha-amanitin which is a potent inhibitor of RNA polymerase II.RNA pol I = 45S RNARNA II = hnRNARNA III = 5S RNA, tRNA, snRNA

The promoter is the DNA sequence that RNA-pol can bindThe prokaryotic RNA-pol can bind to the DNA template directly in the transcription process.

The eukaryotic RNA-pol requires co-factors to bind to the DNA template together in the transcription process. The first nucleotide on RNA transcript is always purine triphosphate. transcription initiation complex. =pppGpN-OH, DNA, RNA polymeraseProkaryotes have Shine Delgarno Modification includesCapping at the 5- end ( CO-TRANSCRIPTIONAL)Tailing at the 3- end(POST TRANSCRIPTIONAL)mRNA splicing(POST TRANSCRIPTIONAL) (use a lariat)RNA editing (POST TRANSCRIPTIONAL)

Q, During Rna synthesis, the DNA template sequence TAGC would be transcribed to produce which of the following sequences?ATGCGCTACGTAAUCGGCUA The answer is E. RNA is antiparallel and complementary to the template strand

Q, Which of the following most correctly describes mammalian messenger RNAs?

A. They are usually transcribed from both DNA strandsB. They are normally double-strandedC. Their content of uridine equals their content of adenineD. They have an overall negative charge at neutral pHE. Their ratio of ribose to purine bases equals 1

Translation: (cytoplasm) Prokaryotes= odd, 30,50,70Eukaryotes = even 40,60,80stop codons (UAA, UAG, UGA).

mRNA = initiation requirements: the small and large ribosomal subunitsmRNAGTPcharged initiator tRNAinitiation factorsm-RNA is read from 5 3 end.m-RNA is identified by 18 s RNA through 7 methyl guanosine CAP

Phosphorylated eIF-2 binds tightly to and inhibits eIF-2 which is required for regeneration of GTP from GDP on factor 2Insulin increases protein synthesis by removing the phosphate and inactivating eIF-2a

cap independent translatinal initiation=elF-4GNontranslating mRNAs Can Form Ribonucleoprotein Particles that Accumulate in Cytoplasmic Organelles Termed P BodiesDrugs inhibiting 30s subunit: Streptomycin (aminoglycosides) interfering withbinding of formyl met-tRNA to P site and initiation of protein synthesis.Tetracyclins: binds to 16s rRNA. Prevent binding of aminoacyl t-RNA to A site.50S= Linezolid : prevents the formation of the initiation complex, composed of the 30S and 50S subunits of the ribosome, tRNA, and mRNA. Chloramphenicol binds to 50 s subunit. Inhibits peptidyl transferase activity of 23s rRNA.Macrolides (Erythromycin) binds to P site and prevents ribosomal translocation.

The anticodon of yeast serinyl-tRNA is 5-AGC-3. Which of the following is most likely to be a serine codon?5-ACG-35-CCG-35-GCU-35-UAG-35-UCG-3

Aromatic aminoacid metabolism:~BIosynthesis of non essential amino acids-need transamination and some need B6*Cysteine synthesis starts from MethioninePhenylalanine essentialTyrosine non essentialTryptophan essential

Phenylalanine to tyrosine require phenylalanine hydroxylaseTyrosine to DOPA require Dihydrobiopterin reductaseDOPA to dopamine require B6Dopamine to NE require Cu+ NE to E require S- Adenosyl Methionine (SAM) From E to Metanephrine require MAO/COMT then VMA is made

Schizophrenia Dopamine overproductionParkinsons disease : Damage to Nigro-striatal tract - dec. DopamineTreatment: Levo-DOPA + Carbidopa

Pheochromocytoma (epinephrine excess ) or Neuroblastoma-Excess of VMA in urineMelanin is made from tyrosine

Catabolism of phenylalanine and tyrosine~phenyl alanine hydroxylase= PKUtyrosine aminotransferase= tyrosinemia II (Keratosis of palmar surface)homogentiste= alkaptonuriaFumaryl acetoacetate hydrolase= tyrosinemia I (cabbage like odor)If the route from phenylalanine to tryosine is blocked, it will be converted to Phenyl acetyl Glutamine

Melatonin synthesisFrom tryptophan to Serotonin to Melatonin= require folate and B6 and SAMMAO-A inhibitors (Anti-Depressants)= keeps serotonin to make person feel good

Q. A patient presents with headaches, palpitations, nausea and vomiting and elevated blood pressure. These symptoms appear after the person has eaten a large meal containing aged cheeses and wine. The patients history indicates that he is on some medicaton for a different condition. Assuming that the medication is in some way involved in these symptoms, which enzyme might be the target of this drug?

Glutamate decarboxylaseMonoamine oxidaseTyrosine hydroxylaseDOPA decarboxylaseCOMT (catechol O-methyl transferase)

Tryptophan Metabolism: gives you niacin and acetoacetyl Co-ACarcinoid syndrome :- (Argentaffinomas )Diagnosis : HIAA in urine

Pellagra like synptoms : Def of B6 or Diarrhoea, Dementia and DermatitisRemember Hartnups diseaseMelatonin: promotes sleep sleep wake cycle

Q. The non essential amino acid that becomes essential in PKU is :-A. PhenylanalineB.TyrosineC.TryptophanD. ALANINEE. Cysteine

Q. The cause of light skin color in PKU is A. decreased synthesis of melanin from PheB. decreased synthesis of melanin from TyrC. excess melanin synthesis from PheD. excess of phenylketonesE.mental retardation causes decreased melatonin

Branched Chained AALeucine uses Isovaleryl Co-A dehydrogenase def gives a cheesey odorIsoleucine uses Propionyl Co-A carboxylase Valine uses Methylmalonyl Co-A mutase

Maple Syrup DX: Def of enzyme Alpha ketoacid decarboxylase /dehydrogenase

Amino Acid and Protein Chemistry:Glycine - inhibitory, smallestLeucine-ketogenic Sulphur containing- methionine and cysteineBasic(polar)= arginine. lysine and histidineOH groups: Serine, threonine, tyrosineArginine and histidine= semiessentialFirst class proteins: - They contain all essential a.a. in required proportion for ideal body growth and development. E.g egg albumin , milk casein

Q, Several complexes in the mitochondrial ETC contain non-heme iron tightly bound to a thiol group of which amino acid?A. GlutamineB.MethionineC.TyrosineD.CysteineE.Serine

Collagen Structural defects: Osreogenesis imperfecta COL1A1: type 1 collagen dxEhlers Danlos Syndrome= type 3 collagen defect (distensible +hypermoble joints)Alport=Ty[re 4 basement membraneFuch corneal= type 8 defectMenkes dx= ATP7A gene, decreased Cu because no lysl oxidase

Goodpasture: Produces IgG antibodies against Alpha-3 chain of type 4 Type IV collagenMarfan= fibrillinAlpha 1- Antitrypsin= SERPINAPseudoxantoma elastic=ABCC6 geneQ. A 4 month old infant who failed to grow and appeared to be mentally retarded was brought to the clinic for testing .The physician noted that the infant had abnormally kinky and hypopigmented hair. Arteriograms showed tortuosity of the major arteries.

Blood test showed that the infant had low serum ceruloplasmin and only 10% of normal copper levels.What is the clinical disorder?1)Osteogenesis imperfecta2)Scurvy3) Menkes disease4)Blue baby syndrome5)Phenylketonuria

abundant terminal disulfide bonds= due to impaired extracellular cleavage.

defect of elastin-associated glycoprotein = Marfans Syndrome Collagen and elastin:~in collagen formation, Hydroxylation of proline and lysineRequires a dioxygenase with Fe . (Vit C keeps the iron reduced )Cross links formed by lysyl/prolyl oxidase

~In elastin, cross links involve Lys and alLys lysyl oxidase 4 Lys can be cross-linked into desmosine Desmosines account for elastic propertiesMatrix metalloproteinases= degrade elastin

Keratin =properties depend strongly on the degree of disulfide cross-linking.Q. A culture of fibroblast cells is provided with equal all the 20 amino acids. After 10 days , the concentration of the amino acids is assessed .Which amino acid will have the lowest concentration?A. LysineB.methionineC.GlycineD.prolineE.CysteineQ. Elastin fibres in the alveolar walls of the lungs can be stretched easily during inspiration and recoil to their original shape once the force is released. This process facilitates expiration. The property described can be best explained by:

Heavy posttranslational hydroxylationHigh content of polar amino acidsChain assembly to form a triple helixInterchain crosslinks involving lysineAbundant interchain disulfide bridges

Q. A 14-year old male presents to your office complaining of easy bruising. Physical examination reveals soft and loose skin as well as multiple ecchymoses in the forearm and pretibial regions. Histologic evaluation with electron microscopy shows collagen fibrils that are abnormally thin and irregular. Which of the following stages of collagen synthesis is most likely impaired in this patient?

RNA signal sequence recognitionAmino acid incorporation into polypeptide chainTriple helix formationLysine residue hydroxylationcleavage of propeptides

Sulfur containing basic AAOxidation of fatty acid with odd no. of carbon atom yields acetyl CoA + Propionyl CoA( Enters TCA as Succinyl Co-A).Thus this portion of odd chain fatty is glucogenic.

Cystinuria: defect in renal and intestinal absorption of COLA , will have cystine stonesCystinosis- lysosomal disorder= Defective carrier mediated transport of cysteineMarfan= Lens dislocation is upwards and outwards Aortic incompetance / valvular heart disease Mental retardation absentCongenital homocysteinuria= Lens dislocation is downwards and inwards Ischemic heart disease due to thromboembolic phenomenon Mental retardation commonAcquired homocysteinuria = Vitamin deficiencies B6= increased homocycteine, increased methionineB12 +FOLATE def. is dec methionine but in homocysteine No Marfanoid habitusDiff btw folate and vit b12 but vit b12 deficiency you get methmalonic aciduria

Metabolism of histidine~ FIGLU= measure in folate acid deficiency histidemia: Diagnosis: sweat urocanate levels decreased FIGLU excretion decreased.

Arginine=urea, creatine phosphate, creatinine, NOGlycine=Formation of Heme: first step, Formation of Glutathione, Formation of Bile salts Glycocholic acid , Conjugation Hippuric acid (Hippuric acid), C4, C5, N7 of Purine Ring formationFrom glycine to glyoxalate = need B6 and Alanine glyoxylate Aminotransferasedef in Alanine glyoxylate Aminotransferase= Primary hyperoxaluria -1def in glyoxylate reductase= Primary hyperoxaluria-2CCauses for increased oxalate stones: Green leafy vegetables oxalatesAscorbic acid Vit CEthylene glycol poisoning antifreezePrimary oxaluria Type 1 and 2~~~~all leading to oxalate stone formation renal obstruction

Formation of Creatine and Creatinine: require SAM and Creatine Phospho KInase

Q. A 56 year old man is being evaluated for macrocytic anaemia. He was severely malnourished.Both homocysteine and methyl malonate were elevated in his blood and urine , and the transketolase level in his RBC was low.What is the best evidence cited that the anaemia is due to B12 deficiency?A. Macrocytic anaemiaB. Elevated methyl malonateC. elevated homocysteineD. decreased homocysteineE. severe malnutrition

Q. If there is B12 deficiency , which other conditions could develop in such a patient ?A.peripheral neuropathyB. GoutC. Wernickes Korsakoffs syndromeD. Destructon of parietal cellsE. Bleeding from gums

Q. A 49 year old man has ectopia lentis and comes to ER with deep vein thrombosis .He has a normal hematocrit and RBCs are normocytic normochromic.A mutation of genes coding for which of the following is the cause ?A. Cystathionine synthaseB. Homocysteine methyl transferase (thrombolytic :remember!)C.FibrillinD.Lysyl oxidase]E. FACTOR VIIIQ, Amino acid analysis of this patients plasma would most likely reveal an abnormally elevated level ofA. LysineB.LeucineC. methionineD. OrnithineE. Cysteine

Urea Cycle and its defects:Nitrogen balance: positive= more ingested than lostnegative= more lost than ingested Ammonia toxicity= Flapping Tremor (Asterixis)( Correlate flapping tremor later on with Liver failure in Clinical medicine )Slurred SpeechBlurred VisionCOMA Death

Fate of ammonia: Glutamate and Glutamine are involved in recycling of amino acids.Nitrogen part is toxic. Urea Neutral molecule Non toxic ( 80-85%)

High protein diet lead to activation of NAG which activated CPS-1 in the motochondria

Hyperammonemia type -1: Autosomal recessive, Defect in CPS- 1, No orotic aciduriaHyperammonemia type-2: X-linked recessive, Defect in OTC, orotic aciduria is present, spills into pyrimidine synthesis3. Citrullinemia :Defect in arginosuccinate synthaseCitrullinuriaAutosomal recessive

4. Arginosuccinic aciduria:Defect in arginosuccinate lyaseArginosuccinic acid blood, CSF, Urine

5. Hyperargininemia :Diet without arginineDefect in arginase enzyme

Q. The first reaction in the degradation of the majority of common amino acids involves participation of :NAD +Pyridoxal PhosphateThiamine Pyrophosphate(TPP)FADNAD and TPP

Q. After thorough investigations a man is diagnosed with orotic aciduria . To find out the cause of orotic aciduria which of the following investigations will you prefer?A. ALP levelsB. vitamin b12 assayC. FIGLU excretion assayD. Peripheral smearE. serum bilirubin

Nucleotide MetabolismHydroxyurea- ribonucleotide reductase5-flurouracil- Thymidylate synthesisDihydrofolate reductase- methrotrexate for eukaryotes, trimethoprimr2x04mghlCPS-!= in mitochondria, uses free ammonia as a source of nitrogen, activated NAG, in urea synthesis

CPS-II= in cytosol, uses glutamine as a source of nitrogen, activated by PRPP, involved in pyrimidine synthesis

Orotic aciduria= have megaloblastic anemia due to folate defeciency that unresponsive to vit B12 and folate, give uridine UTP is feedback inhibitor of CPS IIQ. A one year old female child is weak and anemic. The child was found to have megaloblastic anemia. The height and weight of the child are less than normal. Urine demonstrates an elevated level of orotic acid excretion and normal blood ammonia levels.Which of the following enzyme will be deficient ?A. Ornithine transcarbamoylaseB. Orotate Phosphoribosyl transferase

Purine Synthesis: PRPP Amidotransferase: inhibited by Allopurinol, 6- Mercaptopurine, AzathioprinePurine Catabolism: SCID= def. in ADENOSINE DEAMINASE, def in both T and B cellsAllopurinol also inhibit Xanthine oxidase, so no uric acidHGPRT deficiency- Lesch Nyan (no salvage pathway so excess uric acid and gout)Treatment of Gout: Colchicine inhibits migration of inflammatory cells NSAIDS Antiiflammatory and analgesics Xanthine oxidase inhibitors Allopurinol.Q. Gout is characterized by elevated uric acid concentrations in blood and urine due to a variety of metabolic abnormalities that lead to the overproduction of purine nucleotides. Allopurinol is used in the treatment of gout because this drug, and its metabolic product, alloxanthine, act as inhibitors of: a) Xanthine Oxidaseb) PRPP synthetasec) Adenyl succinate synthased) Hypoxhantine guanine phosphoribosyl transferase e) Nucleotides

Hereditary Orotic aciduria is characterized by severe anemia, growth retardation, and high levels of orotic acid excretion. It is produced by deficit of enzymes related with: a) synthesis of pyrimidine nucleotidesb) catabolism of pyrimidine nucleotidesc) synthesis of purine nucleotidesd) catabolism of purine nucleotidese) synthesis of Hemef) catabolism of Heme