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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 cell
connected 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 H202
Anaerobic Dehydrogenases: Dehydrogenases use coenzymes
nicotinamides & riboflavin - as hydrogen carriers
Cytochomes :- All cytochromes (except CYTOCHROME OXIDASE ) are anaerobic
dehydrogenases
Monooxygenases
Fo complex:
O STANDS FOR OLIGOMYCIN
Made of 12 subunits . H+ passes through each subunit from membrane
space to inner space rotating the Fo complex
F1 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 IONS
ADP and Pi bind the alpha subunit
Binding 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
translocase
only 32 ATPs may be generated from glucose .
Inhibitor of ATP Synthesis:
Site : COMPLEX 1 to Co Q
Alkylguanide(guanethide), hypotensive drug
Rotenone ( insecticide and rat poison)
Chlorpromazine (tranquiliser)
Barbiturates (sedative)
Pericidin (antibiotic)
Site :COMPLEX III to Co Q (ubiquine)
BAL BRITISH ANTI LEWISITE WAR GAS
Napthoquinone
Site : Complex IV inhibitors
Carbon monoxide
Cyanide
Azide
Hydrogen Sulphide
Site : between succinate dehydrogenase and CoQ
Carboxin
Malonate : 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 cresol
CCCP (Chloro carbonyl cyanide phenyl hydrazone)
THERMOGENIN in brown adipose tissue
Thyroxine
MELAS: complex1 or complex 1 and 4 disease
Mitochondrial encephalopathy
Lactic acidosis
Stroke like episodes.
Lebers Hereditary Optic Neuropathy LHON complex -3 defect
Degeneration of Retinal ganglion layer.
Kearns-Sayre syndrome- Oculocraniosomatic neuromuscular disease with
ragged red fibers
Leighs 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?
Barbiturates
Piericidin A
Dimercaprol
Dinitrophenol
Cyanide
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 ETC
Cytochrome oxidase
The ATP-ADP antiporter
The F0 component of the F0-F1 ATPase
The F1 component of the F0-F1 ATPase
TCA Cycle
The 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 ATP
PDH is inhibited by its end product Acetyl Coa
PDH kinase inactivation of enzyme
PDH 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 ATP
Lactic acidosis, severe psychomotor retardation, damage to brain stem, cortex etc..,
Fluoroacetate- blocks aconitase
Arsenite- alpha keto glutarate dehydrogenase complex
Malonate- block succinate dehydrogenase
ATP Substrate level phosphorylation- enzyme used in succinate
thiokinase/succinate Co A synthetase
OAA 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 carboxylase
Pyruvate to malate=malate enzyme
allosteric 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 dehydrogenase
B. PFK1
C. GLUCOKINASE
D. PDH
E. LDH
Q. Which of the following is required for cholesterol synthesis in hepatocytes?
A. Citrate shuttle
B. Glycerphosphate shuttle
C. Malate-Aspartate shuttle
D. Carnitine shuttle
E. 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 dehydrogenase
Glucokinase
GLUT 1 transporter
PFK-1
Glucose 6 PO4 dehydrogenase
Carbohydrates
Clinical 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 epithelium
Lactulose: 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 & AMYLOPECTIN
Liver glycogen - first line of defense against declining blood glucose levels especially
between meals.
Lactate
Glycerol
Propionate
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 glucagon
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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 dehydrogenase
Alpha-ketoglutarate dehydrogenase
Lactate dehydrogenase
Malate dehydrogenase
PDH
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-phosphate
The high maximum reaction rate (high Vmax) of Glucokinase
The inhibition of Glucokinase by high glucose-6-phosphate
The lack of Glucokinase level regulation by insulin
The 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 shuttle
B. Glycerphosphate shuttle
C. Malate-Aspartate shuttle
D. Carnitine shuttle
E. Adenine nucleotide shuttle
HMP/Pentose Pathway
NADPH required for biosynthesis of fatty acids and steroids.
Generation of Ribose-5-phosphate for nucleotide synthesis
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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 gluconeogenesis
Epinephrine promotes glucagon
Insulin structure is kept together by disulphide bond
Insulin receptor-tyrosine receptor
Q. Which of the following substances will BE elevated in a starving cell?
A. 5AMP
B. c-AMP
C. ATP
D. GTP
E. glucose
Q. Which of the following statements correctly describe human glucose
metabolism?
A. Liver is impermeable to glucose in the absence of insulin
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B. Pancreatic -cells, liver and brain are freely permeable to glucose due to specific
glucose transporters
C. Liver glucokinase phosphorylates glucose at high rates under all conditions
D. Extrahepatic tissues are permeable to glucose when glucagon is present
E. 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 - GLYCINE
need B6 for ALA Synthase- rate limiting step
2/3 rd of TOTAL HEME SYNTHESIZED GOES FOR SYNTHESIS OF cytP450
apo-repressor= negative feed back for heme
Most common is PORPHYRIA is AIP
ALA Synthase- Sideroblastic anemia
ALA Dehydrogetase- inhibited by lead (ferrotchelase)
Uroporphyrinogen synthase/ deaminase 1: AIP
Uroporphyrinogen synthase 3: Congenital erythropoietic (Gunthers)- first time
you see photo sensitivity
Uroporphyrinogen decarboxylase: cutanea tarda
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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 moiety
B. Impairs proper folding of the alpha-helix in the beta-globin chain
C. Allows hydrophobic interaction among hemoglobin molecules
D. Impairs beta-globin interaction with 2,3-bisphosphoglycerate
E. 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 globin
B. Beta globin
C. Gamma globin
D. Delta globin
E. 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 AMP
B. 5 AMP
C. ADP
D.GDP
E. glucagon
LIPIDS:
Biosynthesis of FA
Substrates of fatty acid synthesis:
Acetyl Co-A
NADPH
ATP
Biotin
HCO3 source of CO2.
Steps of fatty acid synthesis
1.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
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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 red
Cerebrosides: - 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
enzymological
studies document a deficiency of arylsulfatase A (cerebroside
sulfatase)
in leukocytes. Which of the following is the most likely diagnosis?
A. Gaucher's disease
B. Krabbe's disease
C. Metachromatic leukodystrophy
D. Niemann-Pick disease
E. Tay-Sachs disease MC
Oxidation of fatty acids and ketogenesis
Hormone sensitive lipase: break down of triglycerides to FA and glycerol
Glycerol to Glycerol Po4 to glucose (gluconeogenesis) through glucokinase
FA to Acetyl CoA to liver
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RNA II = hnRNA
RNA III = 5S RNA, tRNA, snRNA
The promoter is the DNA sequence that RNA-pol can bind
The 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 polymerase
Prokaryotes have Shine Delgarno
Modification includes
Capping 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?
ATGC
GCTA
CGTA
AUCG
GCUA 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 strands
B. They are normally double-stranded
C. Their content of uridine equals their content of adenine
D. They have an overall negative charge at neutral pH
E. Their ratio of ribose to purine bases equals 1
Translation: (cytoplasm)
Prokaryotes= odd, 30,50,70
Eukaryotes = even 40,60,80
stop codons (UAA, UAG, UGA).
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Phenylalanine essential
Tyrosine non essential
Tryptophan essential
Phenylalanine to tyrosine require phenylalanine hydroxylase
Tyrosine to DOPA require Dihydrobiopterin reductase
DOPA to dopamine require B6
Dopamine 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 overproduction
Parkinsons disease : Damage to Nigro-striatal tract - dec. Dopamine
Treatment: Levo-DOPA + Carbidopa
Pheochromocytoma (epinephrine excess ) or Neuroblastoma-Excess of VMA in urine
Melanin is made from tyrosine
Catabolism of phenylalanine and tyrosine
~phenyl alanine hydroxylase= PKU
tyrosine aminotransferase= tyrosinemia II (Keratosis of palmar surface)
homogentiste= alkaptonuria
Fumaryl 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 synthesis
From tryptophan to Serotonin to Melatonin= require folate and B6 and SAM
MAO-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 decarboxylase
Monoamine oxidase
Tyrosine hydroxylase
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DOPA decarboxylase
COMT (catechol O-methyl transferase)
Branched Chained AA
Leucine uses Isovaleryl Co-A dehydrogenase def gives a cheesey
odor
Isoleucine 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, smallest
Leucine-ketogenic
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D.Lysyl oxidase]
E. FACTOR VIII
Q, Amino acid analysis of this patients plasma would most likely reveal an
abnormally elevated level of
A. Lysine
B.Leucine
C. methionine
D. Ornithine
E. Cysteine
Urea Cycle and its defects:
Nitrogen balance: positive= more ingested than lost
negative= more lost than ingested
Ammonia toxicity= Flapping Tremor (Asterixis)
( Correlate flapping tremor later on with Liver failure in Clinical
medicine )
Slurred Speech
Blurred Vision
COMA 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 aciduria
Hyperammonemia type-2: X-linked recessive, Defect in OTC,
orotic aciduria is present, spills into pyrimidine synthesis
3. Citrullinemia :
Defect in arginosuccinate synthase
Citrullinuria
Autosomal recessive
4. Arginosuccinic aciduria:
Defect in arginosuccinate lyase
Arginosuccinic acid blood, CSF, Urine
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5. Hyperargininemia :
Diet without arginine
Defect in arginase enzyme
Q. The first reaction in the degradation of the majority of common
amino acids involves participation of :
NAD +
Pyridoxal Phosphate
Thiamine Pyrophosphate(TPP)
FAD
NAD 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 levels
B. vitamin b12 assay
C. FIGLU excretion assay
D. Peripheral smear
E. serum bilirubin
Nucleotide Metabolism
Hydroxyurea- ribonucleotide reductase
5-flurouracil- Thymidylate synthesis
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Xanthine Oxidase
PRPP synthetase
Adenyl succinate synthase
Hypoxhantine guanine phosphoribosyl transferase
Nucleotides
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