Contents

Enzymes : Part 1  1

Enzymes : Part 2  5

Carbohydrates : Introduction  12

Metabolism of Carbohydrates : Part 1  19

Metabolism of Carbohydrates : Part 2  25

Chemistry of Lipids and Phospholipids  34

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Metabolism of Lipids  38

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Amino Acids : Part 1  49

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Amino Acids : Part 2  95 61
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Molecular Biology : Part 1  72

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Molecular Biology : Part 2  83

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Micronutrients: Vitamins and Minerals  89

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Miscellaneous Topics in Biochemistry  100

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 Enzymes : Part 1 1

ENZYMES : PART 1 ----- Active space -----

Basics of Enzymes 00:01:00

Definition : Specialized proteins that act as biological catalyst.

• Exception : Ribozymes (RNA).

Ribozyme Location Function

Peptidyl transferase 28 Sr RNA Translation
Sn RNA Spliceosome
RNA splicing

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Group II introns -

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Post-translational

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Ribonuclease P -

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modification of tRNA

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Properties of Enzymes : 95
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1. Made of protein. 4. Precipitated by protein precipitating

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2. 16% by weight : Nitrogen. agents.

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3. Heat labile.
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Types of Enzymes :
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Simple enzyme Complex enzyme

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(Only protein : Apoenzyme) (Holoenzyme)

components

Protein part Non-protein part

(Apoenzyme)

Cofactor Coenzymes :
(Inorganic molecule) • Heat stable.
• Organic molecule.
• Low molecular wt.
Metalloenzyme : Metal-activated enzyme :
• Cosubstrate.
Metal : Integral part. • Metal : Facilitator.
• Eg : Ca2+ in lipase.
Prosthetic group : Co-enzyme/Co-factor tightly integrated into apoenzyme.

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 2 Biochemistry

----- Active space ----- Coenzymes :

Vitamin Active form Reaction involved

Thiamine di/ • Oxidative decarboxylation
Thiamine
pyrophosphate (TDP/TPP) • Transketolase
Riboflavin FAD ; FMN Dehydrogenase (Succinyl, acyl CoA)
Niacin NAD+ NADP+ Most dehydrogenases
All reactions with acetyl CoA; Succinyl CoA;
Panthothenic acid CoA ; Acyl carrier protein
Fatty acid synthase complex
• Transamination
• Transulfuration Amino acid
Pyridoxine Pyridoxal phosphate • Decarboxylation metabolism

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• ALA synthase

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• Glycogen phosphorylase

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Folic acid THFA All 1 Carbon reactions

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Cobalamin
Methyl B12 95 Methionine synthase
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Adenosyl B12 Methyl malonyl CoA mutase
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Lipoate Lipoamide Oxidative decarboxylation

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Ascorbic acid - Hydroxylation (Prolyl & lysyl)

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Cofactors :
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Metal Reaction catalysed Zn deficiency features

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• Carbonic anhydrase • Acrodermatitis enteropathica

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• Carboxypeptidase A & B • Visual disturbances

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Zinc • Alcohol dehydrogenase (↓Retinol dehydrogenase)

• ALA dehydratase • Alopecia
• Cytosolic SOD (Scavenging enzyme) • Diarrhoea
ATP/PO4 group involved : • Perioral, acral rash
Magnesium • Kinase • Mutase
• Phosphatase • Enolase
Heme iron : Purine catabolism
• Complex III & IV of ETC (Cytochrome) Mb deficiency
Iron • No synthase, Peroxidase, Catalase
Non-heme iron : Hypouricemia
• Complex I & II of ETC (Fe-S cluster)
• Kinase • Mitochondrial SDD
Manganese
• Phosphatase
Molybdenum Xanthine oxidase
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 Enzymes : Part 1 3

Metal Reaction catalysed Cu deficiency ----- Active space -----

• Na - K ATPase
+ +
• Depigmentation
Potassium
• Pyruvate kinase • Neutropenia
• Tyrosinase (Melanin production) • X-ray : Similar to scurvy
• Complex IV of ETC (Cytochrome C
Copper oxidase)
• Lysyl oxidase (Covalent cross linking of
Collagen)

Note : Vitamin C leads to defective collagen D/t ↓lysyl hydroxylase.

Classification of Enzymes 00:17:14

Class Class name Details & examples.

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Oxidoreductases :

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NAD+ FAD required as election acceptor (Oxidative

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a. Dehydrogenase
decarboxylation)

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• Monooxygenase : Phenylalanine/Tyrosine/Tryptophan
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I b. Oxygenase hydroxylase, Cytochromes
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• Dioxygenase : Homogentisate oxidase

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c. Oxidase Complex IV ETC

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d. Peroxidase Glutathione peroxidase (H2O2 H2O)

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e. Catalase H2O2 H2O; Enzyme marker of peroxisome

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Transfers functional group

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II Transferase Eg Kinases (Hexo/glucokinase)

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Phosphorylases (Glycogen phosphorylase)

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• Breaks covalent bonds by adding H2O

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III Hydrolase
• Eg : All digestive enzymes, arginase, phosphatase
• Breaks covalent bond without H2O addition
• Form double bonds by atom elimination or adding groups
IV Lyase
• Eg : Aldolase, fumarase, aconitase, enolase, simple
decarboxylase
Eg Isomerase (Produces isomers)
V Isomerase Racemase (D&L isomers)
Mutase (intramolecular PO4 transfer)
• Coupling of molecules with breakdown of ATP
VI Ligase • Eg Synthetase
Carboxylase (Requires biotin)
• Transfer of ions/molecules across membrane
VII Translocase
• Eg: H+ pump/Ca2+ channel

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 4 Biochemistry

----- Active space ----- Applied biochemistry

Defective synthesis of tetrahydrobiopterin (BH4) from GTP :
• ↓ phenylalanine hydroxylase : Non-classical phenylketonuria
• ↓ tyrosine & tryptophan hydroxylase : Neurological symptoms (D/t ↓
catecholamines & serotonin)
• Resistant seizures in neonate : Supplement Vit. B6 (PLP) :
- Dopamine, serotonin, epinephrine & norepinephrine require PLP as co-factor
(simple decarboxylation)
• Fatigue in chronic alcoholics : D/t Vit. B1 deficiency (↓NADPH ↓ATP)
• Polished rice consumption Beri-Beri (D/t vit B1 deficiency)
• Raw egg consumption Fatigue, hypoglycemia, organic aciduria.
- Avidin (Raw egg) inhibits biotin (Vit. B7) & hence, all carboxylase reactions.

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Enzyme Mechanism of Action

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00:41:42

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• Substrate binding : Active site. 95
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• Site for regulator/modifier Allosteric site.
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Free energy change (DG) :

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• Free energy change =

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ΔG = Energy of reactants - Energy of products.

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• Enzyme ↓ activation energy.

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No change in ΔG.
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Enzyme-substrate complex :
Emil-Fischer's template theory : Koshland's induced fit theory :
Lock and key mechanism. Conformational change in active site
induced by substrate.

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 Enzymes : Part 2 5

ENZYMES : PART 2 ----- Active space -----

Enzyme Kinetics  00:00:12

Equilibrium Constant (Keq) :

Independent of enzyme action.
Keq = [Products]
[Substrates]

Factors Affecting Rate of Reaction :

1. Substrate concentration :

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• Hyperbolic curve.

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Velocity Active sites saturated

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• Michaelis Menten equation :

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Vmax
V x [S]
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Zero order
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kinetics km + [S]
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Vmax/2 ↑ [S] ≠ ↑rate • Km (Michaelis constant) :

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1st order
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- [S] at Vmax /2.

kinetics
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∝ [S] -∝
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Enzyme affinity
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km [S] to substrate
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• Ideal substrate : ↓Km.

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2. Enzyme concentration : 3. Temperature & pH :

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Vo or v1 Vo

Vmax

Denaturation
of enzymes
V0 or
V0 vor1 ∝v1 [E]
∝ [E]

[E] Optimum
• Temperature (35 to 40 0c).
• pH (5 to 9).
• Q10 : 100c ↑ = 2 x rate of reaction.

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 6 Biochemistry

----- Active space ----- Catalytic Constant :

AKA turnover number.
Kcat = [Vmax] ; Et = Total enzyme concentration.
[Et] K
Catalytic efficiency = cat
Km
Enzyme Inhibition  00:12:00

Competitive inhibition Non-competitive inhibition Uncompetitive inhibition

• Inhibitor : Structural • Inhibitor : Not a structural
Inhibitor binds to
analogue of substrate analogue
Features enzyme-substrate
• Compete for same site • Distinct binding site
complex.
as substrate • Usually irreversible

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V0 Vmax

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Vmax
Vmax1

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Vmax1
Effect on Vmax1 95
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Vmax/2
Vmax/2
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Vmax & km Vmax1/2

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Vmax1/2
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Km Km1 [S] Km= Km1 [S] Km1 Km

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1/V0
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Line
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1/Vmax1 1/Vmax
Burk plot
1/Vmax 1/Vmax1
1/V max
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-1/Km - 1/Km1 1/[S] -1/Km1 = - 1/Km -1/Km - 1/Km1

InhibitorEnzyme Inhibitor Enzyme
Dihydrofolate Cyanide Cytochrome c
Methotrexate
reductase CO oxidase
HMG CoA
Statins Fluoride Enolase Phenylalanine inhibits
reductase
Examples placental alkaline
Glyceraldehyde
Dicumarol Vit K epoxide Iodoacetate phosphatase
3-P-DH
Ethanol Alcohol DH
Malonate Fluoroacetate Aconitase
Succinate DH
(Poison)
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 Enzymes : Part 2 7

----- Active space -----

Applied biochemistry

1. Folic acid supplemented when patient is on methotrexate.

2. Dicumarol : Anticoagulant.
• Inhibits Vit. K dependent g carboxylation of clotting factors II, VII, IX & X.
3. Hooch tragedy : Methanol poisoning Antidote Ethanol (Competitively inhibits formaldehyde).
4. Fluoride oxalate used in estimation of blood glucose (Gray tube).

Suicide Inhibition :
Unreactive inhibitor Binds to enzyme Reactive inhibitor (Irreversible).
Suicide inhibitor Enzyme

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Allopurinol Xanthine oxidase

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Difluoromethyl ornithine Ornithine decarboxylase

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Aspirin Cyclooxygenase
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Regulation of Enzyme Activity  00:22:53

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Enzyme Quantity :
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• Heme Represses ALA synthase gene.

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• Dietary cholesterol Represses HMG CoA reductase gene.

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Porphyria : Take detailed drug history

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Drugs metabolized by cytochrome

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↓Heme levels

↑ALA synthase (Gene induction)

Accumulation of intermediates
Aggravates porphyria.

Covalent Modification :
1. Zymogen activation (Irreversible) :
• Gastrointestinal enzyme (Eg : Trypsinogen Trypsin).
• Clotting factors.

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 8 Biochemistry

----- Active space -----

2. Phosphorylation - dephosphorylation (Reversible) :

Phosphorylated state Dephosphorylated state

Insulin : Glucagon ratio Low High
Fed/fasting Fasting Fed
Inhibited by insulin Inhibited by glucagon
• Fructose - 1 , 6 - • Phosphofructokinase
bisphosphate • Glycogen synthase
Enzymes activated
• Glycogen phosphorylase • Pyruvate DH
• Hormone sensitive lipase • Acetyl CoA carboxylase
• HMG CoA reductase

Allosteric Regulation :

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• Substrate : Binds to catalytic site.

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• Modifier :

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- Not structural analogue of substrate.

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- Binds to allosteric site. 95
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Velocity Myoglobin
Allosteric enzymes :
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• Multi-subunit. Hb :
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Effect of
• Quaternary structure.
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allosteric enzyme
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• Cooperative binding Sigmoid curve.

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• Usually rate limiting step.

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Allosteric activator & inhibitor :

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Velocity Allosteric + Allosteric + Allosteric

activator enzyme inhibitor
Vmax
k0.5 ∝ 1
Affinity of enzyme
to substrate

K0.51 K0.5 K0.511

(Binding constant)

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 Enzymes : Part 2 9

Examples : ----- Active space -----

Enzyme Allosteric Inhibitor (Products) Allosteric Activator (Substrates)

ALA synthase Heme -
Aspartate transcarbamoylase CTP ATP
HMG CoA reductase Cholesterol -
Phosphofructokinase Citrate, ATP AMP, F2, 6P
Acetyl CoA carboxylase Acyl CoA Citrate
Citrate synthase ATP -
CPS-I - NAG
CPS-II ATP -

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Serine Proteases & Markers of Cell Organelles 00:40:30

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Serine Proteases : Marker Enzymes of Cell Organelles :

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Serine present in active site.
95 Cell organelle Marker
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Enzymes • 5’-nucleotidase
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1. Chymotrypsin : Bulky amino acids.

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Plasma membrane • Adenylyl cyclase

Breaks protein
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2. Trypsin : Basic amino acids. • Na+-K+ ATPase

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at this site.
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3. Elastase : Small amino acids. Smooth endoplasmic

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Glucose-6-phosphate
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4. Thrombin. reticulum
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5. Plasmin.
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Galactosyl
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6. Factor X. Golgi apparatus

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7. Factor XI.
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Mitochondria ATP synthase

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Lysosome Cathepsin
Peroxisome Catalase

Clinical Enzymology  00:42:45

Isoenzymes :
Lactate DH :
Isoenzyme Subunits Electrophoretogram Tissue localization % in serum Myocardial infarction
LDH-1 H4 Fastest Heart 30 • Normal : LDH2 > LDH1
LDH-2 H3M1 Faster RBC 35 • MI : LDH 1> LDH2
(Flipped pattern).
LDH-3 H2M2 Intermediate Brain 20
LDH-4 HM3 Slower Liver & 10
LDH-5 M4 Slowest skeletal muscles 5
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 10 Biochemistry

----- Active space ----- Creatine kinase (CK) :

Isoenzyme Subunits Electrophoretogram Tissue localization % in serum Clinical significance

CK-1 BB Fastest Brain 1 CVA
CK-2 MB Intermediate Heart 5 MI
Muscle injury,
CK-3 MM Slowest Skeletal muscle 80
Myopathies

Alkaline phosphatase :
Isoenzymes Location Clinical significance
Membrane of epithelium Marker of cholestasis
α-1-ALP
of biliary canaliculi Marker of hepatic injury

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α-2-ALP (Heat labile) Hepatic sinusoidal cells Most stable

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α-2-ALP (Heat stable) Placenta

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Marker of bone formation :

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Pre-β-ALP Osteoblast ↑ in Paget's & Vit D deficiency

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Gamma ALP Intestinal cells 95 Ulcerative colitis
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Leukocyte ALP Leukocytes Leukemia

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Cardiac Biomarkers in MI :
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Name Starts to rise Peak Return to baseline

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CK-MB
4-8h 24 h 48 - 72 h
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(Earliest enzyme marker)

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Troponin T 4-6h 24 h 7 - 10 d
Troponin I
4-6h 24 h 7 - 10 d
(↑Sensitivity)

Note :
NT Pro-BNP (Precursor of brain natriuretic peptide) : Marker of cardiac failure.

Enzyme Markers  00:53:02

Liver :
Markers of hepatic injury : Markers of cholestasis :
• S. ALT. • S. ALP.
• S. AST. • 5’ nucleotidase.
• S. GGT.

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 Enzymes : Part 2 11

Prostate : Pancreas : ----- Active space -----

• Acid phosphatase : Tartarate labile. • Serum amylase.
• Prostate specific antigen : Specific. • Serum lipase : Specific.
- Cut-off < 4 ng/mL.

Bone Disease :
Bone formation (From osteoblast) : Bone resorption (From osteoclast) :
• Pre-b ALP. • N-telopeptide of type I collagen.
• Osteocalcin. • C-telopeptide of type I collagen.
• Propeptide of type I collagen. • Urine free deoxypyridinoline.

Acute Kidney Injury :

• Kidney Injury Molecule 1 (KIM 1). • GGT.

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• Neutrophil Gelatin • Microalbumin.

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Associated Lipocalin (NGAL). • Osteopontin.

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• IL-8. • Liver fatty acid binding protein.

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• ALT. • 95
Sodium hydrogen exchange isoform.
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• Glutathione S-transferase. • Exosomal fetuin.
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 12

----- Active space ----- CARBOHYDRATES : INTRODUCTION

Chemistry of Carbohydrates 00:01:25

Carbohydrates : Aldose or keto derivatives of polyhydroxy alcohol.

Monosaccharides :

No. of carbon atoms Aldoses Ketoses

Triose (Simplest carbohydrates) Glyceraldehyde Dihydroxy acetone
Tetrose Erythrose Erythrulose

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Pentose Ribose Epimer Xylose Ribulose Epimer Xylulose

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Hexose Glucose, galactose, Mannose Fructose

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Disaccharides : 95
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Reducing disaccharides :
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Name Monomer units Linkage

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Maltose Glucose + glucose α 1, 4

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Isomaltose Glucose + glucose α 1, 6

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Lactose Galactose + glucose b 1, 4

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Lactulose Galactose + fructose a 1, b4

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Non-reducing disaccharides :
Name Monomer units Linkage
Trehalose Glucose + glucose a 1, 1
Sucrose Glucose + fructose a 1, b2

Polysaccharides :

Homopolysaccharides : Heteropolysaccharides :
• Made up of one type of • > 1 Monomer units.
monomer units. • Eg : Glycosaminoglycans (GAG).
• Eg : Starch, glycogen.

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 Carbohydrates : Introduction 13

Dietary Fibres & Glycosaminoglycans 00:12:28 ----- Active space -----

DIETARY FIBRES
Properties :
• Resistant to digestion & absorption by small intestine.
• Undergoes complete/partial fermentation in large intestine.

Classification :
soluble :
• Gums (Fenugreek)
↓Post prandial blood sugar level.
• Pectin
• Mucilage.
Insoluble (Crude fibres) :

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• Cellulose, AKA non-starch polysaccharide :

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- Made of beta-D-glucose.

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- Resistant to digestion d/t b-linkage and lack of cellulase in human
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intestine.
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• Hemicellulose.
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• Lignin : Neither digested nor fermented.

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Note :
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Lactose Not a dietary fibre as b-linkage in it is digested by lactase (Only

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digests lactose).
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RDA :
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40 g/2000 cal.
Energy released per gram : 2 kcal/g.
Uses :
• Adds bulk to the stool.
• Regulates bowel movements.
• Improves satiety.
• Prebiotic (Fibre) : Promote colonisation of probiotic bacteria.
• Sequesters bile salts ↓Cholesterol.
• Improves glucose tolerance.

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 14 Biochemistry

----- Active space ----- GLYCOSAMINOGLYCANS (GAG)/MUCOPOLYSACCHARIDES

Unbranched heteropolysaccharides made of repeating disaccharide units

Aminosugar Acidic sugar

Glucosamine Galactosamine Glucuronic acid Iduronic acid

Synthesis Site :
Rough endoplasmic reticulum & golgi apparatus.

Properties :
1. Negatively charged : Confers consistency of mucus & enables mobility at joints.

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2. Absorbs water : Provides cushioning effect at weight bearing joints.

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Composition :

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GAG 95
Repeating disaccharide unit
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Hyaluronic acid N-acetyl glucosamine + glucuronic acid
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Keratan sulphate N-acetyl glucosamine + galactose (No uronic acid)

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Heparin Glucosamine + iduronic acid

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Significance :
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1. Chondroitin sulphate :
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- Most abundant.
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- Found in bones & cartilage : Enables compressibility of cartilage.

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2. Keratan sulphate (KS) :

- KS-1 : Cornea Maintain corneal transparency.
- KS-2 : Loose connective tissue.

3. Dermatan sulphate :
- Widely distributed GAG found in the dermis.
- Maintains structure of sclera.
- Atherogenic GAG : Attract LDL.

4. Heparan sulphate :
- Responsible for charge selectiveness of GBM.
- Present on synaptic vesicle.
- Anchors lipoprotein lipase to vascular endothelium.
- Acts as plasma membrane receptors.

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 Carbohydrates : Introduction 15

5. Heparin : ----- Active space -----

- Only intracellular GAG.
- Anticoagulant.
- Used for estimation of lipoprotein lipase (LPL) in type 1 hyperlipoproteinemia.

6. Hyaluronic acid :
- Important role in cell migration : Wound healing, tumor metastases,
embryogenesis.
- Not attached to protein.
- Sulphate group : Absent.

Mucopolysaccharidoses 00:37:15

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Group of disorders a/w defect in degradation (In lysosomes) of GAG

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(Mucopolysaccharides)

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Belongs to lysosomal storage disorder. 95
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General Features :
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Gargoylic facies : Coarse facial features.

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• Frontal bossing.
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• Depressed nasal bridge.

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Short stature Protruding tongue

Clawing of hands
Umbilical hernia

Corneal clouding

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 16 Biochemistry

----- Active space ----- Xray - features :

Bullet shaped
middle phalanx Beaking of
vertebra

Dysostosis multiplex

MPS I & II :

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All are AR except Hunter's.

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Enzyme defect Features

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• Visual disturbances +
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Hurler's disease (MPS-I H) L-iduronidase 95 • Mental retardation
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• Hirsutism
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Sheie's disease (MPS-I S) L-iduronidase (Partial defect)

• Normal intelligence
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X-linked recessive
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Hunter's disease (MPS II) Iduronate sulfatase • Intellectual disability

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• Clear vision
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Other Mucopolysaccharidoses :
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Enzyme defect Specific feature

Enzyme that degrades heparan • M/c MPS
Sanfilippo disease (MPS III)
sulfate • Corneal clouding : Absent
• Normal Intelligence
Galactosamine-6-sulphatase, • Visceromegaly : Absent
Morquio disease (MPS IV)
b-galactosidase • Reilly body (Leucocyte)
inclusion : Absent
Maroteaux Lamy disease N-acetyl galactosamine-4-
Normal intelligence
(MPS VI) sulphatase
Natowicz syndrome (MPS IX) Hyaluronidase -

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 Carbohydrates : Introduction 17

Treatment Modalities : ----- Active space -----

Treatment modality MPS

1. Stem cell therapy MPS-I H
2. Enzyme replacement therapy
Aldurazyme MPS-I
Elaprase MPS-II
Nagalazyme MPS-VI
3. Substrate reduction therapy : Flavinoids MPS-I H

I (INCLUSION) CELL DISEASE

• Defect in protein targeting.
• Resembles MPS : Accumulation of GAG in lysosomes.

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• Enzyme defect : N-acetyl glucosamine phosphotransferase

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↓Mannose-6-phosphate : Signal for proteins tagged with it to get degraded in
the lysosome. 95
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Glucose Transporters 00:53:00

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SGLT
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• Sodium dependent.
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• Sodium-glucose symport ORS contains Na+ & glucose to facilitate Na+

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absorption.
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• Unidirectional.
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• Against concentration gradient.

• Secondary active transport.

Types of SGLT :

Type Location Function

Luminal side of intestine Absorption of glucose
SGLT-1
PCT
Reabsorption of glucose
SGLT-2 PCT

Applied Biochemistry :
1. Renal glycosuria :
- Mutation in SLC5A2 SGLT-2 defect ↓Renal threshold.

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 18 Biochemistry

----- Active space ----- - Findings :

i. OGTT (Blood glucose) : Normal.
ii. Urine Benedict's test : Positive.
iii. Urine Glucose oxidase test : Positive.
2. Gliflozines (OHA) : SGLT2 inhibitor Glycosuria UTI.

GLUTs Simple diffusion

• Sodium independent.

Rate of transport
• Bidirectional.
Facilitated diffusion
• Along concentration gradient.
• Ping pong mechanism. Hyperbolic/substrate
• Facilitated carrier mediated saturation curve
process (Passive).

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Solute concentration

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Location :
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GLUT Location Important points
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GLUT-1 Brain, placenta, kidney, RBC, retina, colon Low km (High affinity for glucose)
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• b cells of pancreas
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• Sinusoidal cells of liver • High km (Low affinity)

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GLUT-2
• Serosal side of intestine • Active in the fed state
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• Proximal renal tubules

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GLUT-3 Neurons, placenta, kidney Lowest Km

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• Heart
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GLUT-4 • Skeletal muscle Insulin dependent

• Adipose tissue
• Luminal side of intestine
GLUT-5 Fructose transporter
• Testes & sperm
GLUT-6 Spleen, leukocyte Pseudogene
GLUT-7 Liver SER Transports glucose-6-PO4 to SER
GLUT-8 Blastocyst -
• Uric acid transporter
GLUT-9 Intestine & kidney
• Defect Primary gout

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 1 19

METABOLISM OF CARBOHYDRATES : PART 1 ----- Active space -----

Fed & Fasting State Metabolism  00:00:10

Well Fed State :

1-4 hours within food intake.
↑ Dietary glucose via Glut 2
Pancreas
↑ Insulin

om
High insulin/glucagon ratio

l.c
ai
Via Glut-2 glucose enters

gm
@
Liver 95
19
Glucose
10

ss
02

Glycolysis
Ex c e

oy

Pyruvate PDH Acetyl CoA Exce

tr

ss
ee
nj

Glycogen
ira

TCA cycle
ch

Fatty acid synthesis

|
row

VLDL
ar
M
©

Peripheral tissues
Stored as Triacyl glycerol
(TAG)
- Insulin hSL
Fatty acid
Fasting State :
Stage Duration post food intake Source of energy

Early fasting 4-16 hours Hepatic glycogenolysis (D/t ↓ Insulin/glucagon ratio)

Fasting 16-48 hours Gluconeogenesis (ATP from fatty acid oxidation)

Prolonged fasting/starvation 48 hours-5 days TAG hsL Fatty acid Acetyl CoA Ketone body
synthesis
Muscle proteolysis : Breakdown structural proteins for
Prolonged starvation >5 days
energy

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 20 Biochemistry

----- Active space ----- Glycolysis 00:08:30

Features :
• Site : All organs (In cytoplasm).
• Only pathway that operates both aerobically & anaerobically.

Applied Biochemistry :
Condition Reason
Mature RBCS Lack mitochondria
Defect in glycolytic enzymes Hemolysis
Rely exclusively on anaerobic
glycolysis in fed/fasting state
Tolerance Heart muscles : Low D/t low glycolytic capacity

om
to hypoxia Skeletal muscles : High D/t enormous glycolytic capacity

l.c
ai
Aerobic Glycolysis :

gm
@
95
Preparatory phase : Stage of ATP utilization (2 ATPs used).
19
10

Glucose
02
oy

ATP
tr

Irreversible Hexokinase
ee

ADP
nj
ira
ch

Glucose-6-phosphate
|
owr

Phosphohexose isomerase
ar
M
©

Fructose-6-phosphate
ATP Phosphofructokinase (PFK - 1) :
Irreversible
ADP RLE/Bottle neck/Committed step
Fructose-1,6 - bisphosphate

Aldolase

Phosphotriose isomerase
DHAP Glyceraldehyde-3-phosphate

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 1 21

Pay off phase : Aerobic glycolysis. ----- Active space -----

2 x Glyceraldehyde-3-phosphate (Gly-3-PO4)
NAD+ Energetics
Inorganic Pi
Gly-3-PDH
NADH Electron transport chain 2 x 2.5 ATP 5 ATP
1,3-BPG
1 ADP
1,3 BPG kinase : Substrate level
1 ATP 2 x 1 ATP 2 ATP
Only reversible kinase
phosphorylation
3-PG (SLP)
Enolase

om
PEP

l.c
1 ADP

ai
gm
Pyruvate kinase (PK) Substrate level 2 x 1 ATP 2 ATP
1 ATP

@
phosphorylation Total : 9 ATP
Pyruvate. 95
19
10

Net ATP : 9 ATP - 2 ATP (Utilised in preparatory phase) = 7 ATP.

02
oy
tr

Applied biochemistry :
ee
nj

S. no Compound Enzyme inhibited Reason/Application

ira
ch

Blood glucose estimation : Gray

|
ow

1. Fluoride Enolase vacutainer containing fluoride

r
ar

oxalate used
M
©

2. Arsenate Arsenate & Iodoacetate resembles

Gly-3-PDH
3. Iodoacetate inorganic phosphate

Anaerobic Glycolysis :
Glucose
Energetics :
LDH • No net generation of NADH : Utilized by LDH
Pyruvate Lactate.
• 1,3-BPG : 2 x 1 ATP
4 ATP
NADH NAD+ • Pyruvate kinase : 2 x | ATP
• Utilization : 2 ATP
Total : 4 ATP-2 ATP = 2 ATP

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 22 Biochemistry

----- Active space ----- Rapaport Leubering Cycle :

Site : Takes place in 10% of RBCs.
Glucose 1, 3-BPG Mutas
e

atas
e 2, 3-BPG Energetics :
ph
Phos • Pyruvate kinase : +2 ATP
3-PG
• Hexokinase : -1 ATP
• PFK : -1 ATP
PEP
Net ATP : 0
PK
2 x 1 ATP
Pyruvate.

Significance of 2,3-BPG :

om
• Maintains taut state of hemoglobin.

l.c
ai
• Responsible for unloading of O2 at tissue site S hifts oxygen dissociation

gm
@
curve to the right.
95
19
Regulation of Glycolysis :
10
02
oy

1. Fed state : 2. Fasting state :

tr
ee

High insulin glucagon ratio Low insulin glucagon ratio

nj
ira
ch

Dephosphorylation of enzymes Phosphorylation of enzymes

|
ow
r
ar

Activation of PFK-2 Activation of F-2,6-BPase

M
©

PFK-2 F-6-P04 F-6-P04

F-2,6-BPase
F-2,6-BP04 F-2,6-BP04
Allosteric activator
↓F-2,6-BP04
PFK-1 -
+ +
Glycolysis
Glycolysis

Concept of Allosteric Regulation :

Substrates : Activators.
Products : Inhibitors.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 1 23

Enzyme Allosteric activator Allosteric inhibitor ----- Active space -----

Hexokinase - ATP
• F-6-P • ATP
PFK-1 • F-2,6-BP • Citrate
• 5’ AMP • Low pH
Pyruvate kinase - ATP

Metabolism in Cancer Cells :

Cancer cells have ↑ levels of glucose uptake.

Warburg hypothesis :
• Cancer cells undergo aerobic fermentation/aerobic glycolysis :
Even in the presence of ample 02, Glucose Lactate (Used in biosynthetic

om
pathways).

l.c
ai
gm
Metabolic reprogramming :

@
Normal cell : 95
Cancer cell : Uses glucose via aerobic glycolysis.
19
10
02

Glucose Glucose
oy
tr
ee
nj

PEP PEP
ira

PKM 1 (Pyruvate kinase) : PKM2 :

ch

• Tetramer • Dimer
|
ow

• High catalytic activity • Low catalytic activity

r

Pyruvate Pyruvate
ar
M

02
©

Lactate
Normal cell : Cancer cell : ↑ Affinity for glucose.
Glucose Glucose
7ATP
Pyruvate Pyruvate
2 NADH = 5 ATP
Acetyl CoA Lactate
2 x 10 ATP = 20 ATP Aerobic glycolysis : 2 ATP.
TCA cycle Application :
Usage of Fluorodeoxy glucose in PET scan
Functional
Aerobic oxidation : 1 Glucose 32 ATP.
screening
↑ Uptake by cancer cells

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 24 Biochemistry

----- Active space ----- Pyruvate Dehydrogenase (PDH) 00:41:00

Link Reaction :
• Link glycolysis to TCA cycle.
• Site : Mitochondria.

Enzymes Coenzymes :
1. E 1 : PDH. 1. Thiamine pyrophosphate (B1).
2. E2 : Dihydrolipoyl transacetylase. 2. Coenzyme A (B5).
3. E3 : Dihydrolipoyl dehydrogenase. 3. Lipoamide.
4. FAD (B2).
5. NAD+ (B3).

Significance of PDH :

om
l.c
• Irreversible & cannot be circumvented by another enzyme.

ai
gm
• Fat : Never converted to glucose :

@
Exceptions :
95
19
a. Glycerol.
10

b. Odd chain fatty acid (Propionyl CoA).

02
oy
tr
ee

NAD+ NADH (2-5 ATP)

nj

Pyruvate Acetyl CoA

ira
ch

b oxidation
|
ow

Fatty acid
r
ar

Hydrolysis
M

TAG
©

Applied Biochemistry :
1. Deficiency of PDH 2. B 1 deficiency :
Pyruvate Acetyl CoA
a) Chronic alcoholics PDH affected
Lactate b) Consumption polished rice
(↓aleurone layer) Energy depletion
Lactic acidosis

Note :
• PDH
• α ketoglutarate dehydrogenase Same coenzymes.
• Branched chain keto acid dehydrogenase

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 2 25

METABOLISM OF CARBOHYDRATES : PART 2 ----- Active space -----

Glycogen Metabolism 00:00:10

GLYCOGENESIS
Occurs in the well-fed state, high insulin-glucagon ratio.

Site :
Cytoplasm of liver & skeletal muscles.

Stages :

om
1. Formation of UDP glucose :

l.c
ai
Hexokinase Phosphoglucomutase

gm
Glucose Glucose-6-PO4 Glucose-1-PO4

@
UDP glucose UTP
95
19
pyrophosphorylase PPi
10

UDP glucose
02
oy

2. Formation of linear polymer :

tr
ee

UDP glucose Glucose

nj
ira

Glycogenin 4 glucose residues added

ch
|

• Polypeptide primer Glycogen synthase :

ow

• Tyrosine residues + • RLE

r
ar

• Active in dephosphorylated state

M
©

11-12 residues with

α 1-4 linkage added
Branching enzyme
(α 1-4, 1-6 glucan transferase)

Adds branches at α 1-6 linkage.

GLYCOGENOLYSIS
Occurs in the fasting state (4-16 hours).

Site :
• Cytoplasm of liver & skeletal muscles.
• Lysosomes Type II GSD (Pompe’s disease) is a lysosomal storage disorder.

Hepatic glycogenolysis : Source of glucose in early fasting states.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 26 Biochemistry

----- Active space ----- Stages :

Glycogen
phosphorylase α(1-4) (1-4)
B6 Glucan transferase
Glycogen (Pi)6 6 Glu-1-PO4 α (1-6)
glucosidase
+
Free glucose (O)
nPi Glycogen
Enters liver + muscle phosphorylase
Liver
(n) Glu-1-PO4
Glu-1-PO4 Skeletal muscle :
Phosphoglucomutase Glucose-6-phosphatase absent

om
Glu-6-PO4 Glu-1-PO4

l.c
ai
H2O Glucose-6-phosphatase

gm
Phosphoglucomutase
Pi (In SER)

@
Glucose Glu-6-PO4 95
Pyruvate Lactate
19
10

- α (1-4) glycosidic linkage.

02
oy

- α (1-6) glycosidic linkage.

tr
ee

Debranching enzyme : α (1-4) (1-4) Glucan transferase + α (1-6) glucosidase.

nj
ira

Note :
ch

• Phosphoglucomutase : Common to glycogen synthesis & glycogenolysis.

|
row

• Glucose-6-phosphate : Present in SER Hence Glucose not released immediately.

ar
M
©

Energetics in muscle : 1 Glu-6-PO4 3 ATP.

HORMONAL REGULATION/COVALENT MODIFICATION

Fasting State :
Glucagon/Epinephrine + Adenylyl cyclase

ATP cAMP
+
cAMP dependent protein kinase

Phosphorylation

Activation of : Inactivation of :
Glycogen phosphorylase Glycogen synthase

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 2 27

Fed State : ----- Active space -----

Insulin : cAMP 5’ AMP ↓↓cAMP

Dephosphorylation

Activation of : Inactivation of :
Glycogen synthase Glycogen phosphorylase

In the Muscle :
Regulation by :
1. cAMP dependent pathway.
2. cAMP independent calcium calmodulin dependent pathway.
3. 5’ AMP :

om
• Allosteric activator of glycogen phosphorylase.

l.c
ai
• Activated in extreme state of anoxia.

gm
@
ALLOSTERIC REGULATION 19
95
Inhibitors of Glycogenolysis : Activator of Glycogenesis :
10
02

• Glu-6-PO4. Glu-6-PO4.
oy

• Glucose (Only in liver).

tr
ee

• ATP.
nj
ira
ch

Glycogen Storage Disorder (GSD) 00:19:20

|
ow

Liver GSD :
r
ar
M

Prominent feature : Fasting hypoglycemia.

©

GSD type Enzyme defect

Type Ia GSD : Von Gierke’s disease Glucose-6-phosphatase
Type Ib GSD : Neutropenia + Glu-6-PO4 transporter in SER
Type III GSD : Cori’s disease/Forbes’ disease
Debranching enzyme
(Limit dextrinosis)
Type IV GSD : Anderson disease, Amylopectinoses Branching enzyme
Type VI GSD : Her’s disease Hepatic glycogen phosphorylase

Mnemonic : ABCD.
• Anderson disease : Branching enzyme.
• Cori’s disease : Debranching enzyme.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 28 Biochemistry

----- Active space ----- Muscle GSD :

Prominent feature : Exercise intolerance.
Muscle GSD Enzyme defect
With Hypertrophic cardiomyopathy (HCM) :
Type II GSD : Pompe’s disease Acid α 1-4 glucosidase/Acid maltase
Without HCM :
Type V GSD : McArdle’s disease (M/c) Muscle glycogen phosphorylase
Type VII GSD : Tarui’s disease Muscle & erythrocyte PFK

Disease Features Investigations

• Protruding abdomen
• Prominent buccal fat
• Thin extremities • S. glucose↓

om
• Convulsions, coma on fasting • Rothera’s test : Positive

l.c
• O/E : Massive hepatomegaly

ai
• S. Uric acid ↑↑

gm
• S. Lactate ↑↑ (Lactic acidosis)
Von Gierke’s

@
• AST & ALT : Normal
disease 95 • Liver biopsy : Accumulation of normal
19
10

glycogen.
02

• Ketosis
oy

• Hyperlipidemia
tr
ee
nj
ira
ch

• Floppy infant
|

• Generalized hypotonia
ow

• Fatal : Death within 2 years d/t

r
ar

cardiac failure.
M
©

Pompe’s
-
disease

Chest X-ray : Massive cardiomegaly

• Early morning hypoglycemia
• Not fatal
• S. Glucose↓
• Rothera’s test : Negative
• S. Uric acid
Cori’s Normal
• S. Lactate
disease
• AST & ALT : ↑
• Liver biopsy : Accumulation of limit
dextrin.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 2 29

Disease Features Investigations ----- Active space -----

• Fasting hypoglycemia
• Portal hypertension
• Cirrhosis
• S. Glucose↓
• Fatal : Death within 5 yrs of age d/t
• Rothera’s test : Negative
liver failure.
• S. Uric acid Normal
Anderson’s
• S. Lactate
disease
• AST & ALT : ↑↑
• Liver biopsy : Accumulation of
amylopectin

• Adolescent male
•

om
Pain in calf muscle on exercise
• No hemolysis • S. Glucose : ↓ during exercise

l.c
ai
McArdle’s • Second wind phenomena : Exercise • S. Lactate : ↓

gm
disease intolerance • AST & ALT : Normal

@
Pain in calf Rest Resume activity • Creatine kinase : ↑↑
95
19
during exercise with more ease
10

• Rhabdomyolysis Myoglobinuria
02

• Burgundy coloured urine

oy

• Exercise intolerance (No 2 wind

nd
tr

• S. Glucose : ↓ during exercise

ee

phenomena)
Tarui’s disease • S. Lactate : ↓
nj

• Myoglobinuria
ira

• Creatine kinase : ↑
• Hemolysis
ch
|

Fanconi Bickel
ow

GLUT 2 defect -
syndrome
r
ar

• No glycogen accumulation
M

Type 0 GSD Glycogen synthase defect

©

• No hepatomegaly

Gluconeogenesis 00:37:28

Synthesis of glucose from non-carbohydrate substrates.

Timeline :
16-48 hours of fasting.
Sites : Organelle :
1. Liver. Cytoplasm & mitochondria.
2. Kidney.
Substrate Forming Glucose :
• Glucogenic amino acids : Alanine (Cahill cycle). • Lactate (Cori’s cycle).
• Propionyl CoA (Odd chain fatty acid) Succinyl CoA. • Glycerol DHAP.
Note : Acetyl CoA Not a substrate for gluconeogenesis.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 30 Biochemistry

----- Active space ----- Enzymes :

Irreversible steps of glycolysis Key enzymes of gluconeogenesis
Glu-6-phosphatase
Glu-6-PO4 Glucose
1. Hexokinase
H2O Pi
Fructose-1,6-bisphosphatase
F-1,6-BP F-6-PO4
2. PFK
H2O Pi
Pyruvate carboxylase
a. Pyruvate OAA
• Acetyl CoA : Allosteric activator of pyruvate
carboxylase

om
• Only mitochondrial step

l.c
3. Pyruvate kinase (PK)

ai
• OAA : Transported to cytoplasm via Malate

gm
Aspartate shuttle
@
95
PEP carboxykinase
19
b. OAA PEP
10
02

CO2 GTP GDP

oy
tr
ee

Conversion of 2 lactate to 1 glucose : 6 ATP required.

nj

• Pyruvate carboxylase : 2 ATP.

ira
ch

• PEP carboxykinase : 2 ATP.

|
ow

• 1,3-BPG kinase : 2 ATP.

r
ar
M

Galactose & Fructose 00:45:20

©

Galactose Metabolism :
Types of disorders :

Classical galactosemia Non-classical galactosemia

Defect in Galactose-1-P04 uridyl transferase

Enzyme defect Disorders
Galactokinase Cataract
Benign condition
UDP hexose epimerase
with mixed features

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 2 31

Fructose Metabolism : ----- Active space -----

Site : Liver.
Types of disorders :
Enzyme defect Disorders Applied biochemistry of Fructose
Fructokinase Essential fructosuria Easily metabolized to Pyruvate Acetyl CoA
Hereditary fructose
Aldolase-B Causes dyslipidemia
intolerance TAG Fatty acid

Galactosemia vs Hereditary Fructose Intolerance (HFI) :

Classical Galactosemia HFI
Enzyme defect Galactose-1-PO4 uridyl transferase Aldolase-B
Age of onset 1st week of life 6 months

om
Trigger Breastfeeding Fruit juices

l.c
• Intellectual disability

ai
gm
• Convulsions, vomiting, jaundice, failure to thrive
C/f

@
• Hepatomegaly, liver failure
95
• Feeding difficulty, poor weight gain
19
10

+ Fructose Low renal

02

threshold
oy
tr

Cataract
ee

Fructosuria
nj
ira
ch

No cataract
|

Galactose-1-PO4 :
ow

• Hepatotoxic & neurotoxic

r
ar

• ↓Inorganic PO4
M

Fructose-1-PO4 :
Accumulated
©

• ↓Activity of glycogen phosphorylase • Hepatotoxic & neurotoxic

compound
• Eye : Converted to dulcitol • ↓Inorganic PO4

Cataract
Lab diagnosis :
Urine Benedict’s test Positive Positive
Glucose oxidase test Negative Negative
Enzyme studies & genetic mutation test
Rapid furfural test/
Specific test Mucic acid test : Positive
Seliwanoff’s test : Positive
• Stop breastfeeding
Rx • Lactose free diet up to 4-5 years Fructose free diet
of age

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 32 Biochemistry

----- Active space ----- HMP Shunt & Uronic Acid Pathway 00:54:40

HMP SHUNT PATHWAY

AKA Pentose phosphate pathway.

Site :
Cytoplasm of liver.

Phases :
Oxidative phase :
• Irreversible.
• Generate NADPH.
Steps :
Glu-6-PO4

om
NADP+

l.c
Glu-6-PO4 dehydrogenase : RLE

ai
(G6PD)

gm
NADPH

@
6 Phosphogluconate
95
19
NADP+
6-Phosphogluconate dehydrogenase
10
02

NADPH CO2
oy
tr

Ribulose-5-PO4
ee
nj
ira

Functions of NADPH :
ch

1. Free radical scavenging :

|

Glutathione
ow

reductase
r
ar

H2O2 Reduced glutathione NADP+

M
©

H2O Oxidized glutathione NADPH

Glutathione
peroxidase
Sites :
- RBC : Prevents RBC lysis.
- Lens : Maintains transparency of lens.
2. Maintains iron in Hb in the reduced state Prevent formation of
methemoglobin.
3. Reductive biosynthesis of fatty acids & steroids :
• Sites :
- Liver. - Gonads.
- Adipose tissue. - Adrenal cortex.
- Lactating mammary gland.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Carbohydrates : Part 2 33

Non-oxidative phase : ----- Active space -----

• Reversible.
• Generate pentoses required for DNA synthesis.
Enzymes :
Applied biochemistry
• Transketolase : Requires vit. B1
Erythrocyte transketolase : Indicator of
• Transaldolase.
Vit B1 status
Site (Rapidly proliferating cells) : Bone marrow, skin, mucosa.
G-6-PD Deficiency :
• M/c enzyme deficiency.
• X-linked recessive.

C/f : Defect in G6PD ↓NADPH.

om
l.c
• Hemolysis Anemia, jaundice.

ai
gm
• Methemoglobinemia Cyanosis.

@
Aggravating factor : Drugs, fava beans, infections. 95
19
10
02

Protective against : Plasmodium falciparum.

oy
tr

Peripheral smear : Bite cells, Heinz body.

ee
nj
ira
ch

URONIC ACID PATHWAY Bite cells

|
ow

Oxidative pathway for glucose.

r
ar
M

Site : Organelle :
©

Liver. Cytoplasm.
Functions :
• Produces uronic acid : Glucuronic acid GAG.
Conjugation of bilirubin.
• Minor synthesis of pentoses.
• Synthesis of ascorbic acid : Absent in humans d/t lack of L-gulonolactone
oxidase.

Essential Pentosuria :
• Benign condition.
• Benedict test : Positive.
• Bial’s test : Positive.
• Defect : Xylitol dehydrogenase/Xylulose reductase.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 34

----- Active space ----- CHEMISTRY OF LIPIDS AND PHOSPHOLIPIDS

Classification of Fatty Acids (FA) 00:00:30

Lipid : Soluble in non-polar solvents only.

Classification of lipids Applied biochemistry
• Short chain (C2 to C6) Essential FA deficiency :
Based on • Medium chain (C8 to C14) : Coconut oil • Acanthosis
no. of carbon atoms • Long chain (> C16) • Follicular hyperkeratosis (aka
• Very long chain (> C20) phrynoderma/Toad skin)

om
Based on • Saturated FA (Single bonds only) • Fatty liver

l.c
double bonds • Unsaturated FA (Double bonds) • Mitochondrial membrane damage

ai
gm
• Essential FA :
Docosahexaenoic acid (DHA)/

@
Based on - Linoleic acid : Safflower oil
Cervonic acid :
diet - α-linolenic acid 95
19
• Can cross placenta
• Non-essential FA
10

• Deficiency : Retinitis pigmentosa

02

Unsaturated FA
oy

↑Trans FA :
tr

Based on • Monounsaturated FA : Mustard/Rapeseed oil

ee

no. of double bonds • Polyunsaturated FA : Safflower oil • ↓Fluidity of membrane

nj

• Insulin resistance
ira

Polyunsaturated FA
ch

• Dyslipidemia, CV risk
• Omega - 3 FA :
|

• ↑Inflammation
ow

- α-linolenic acid : Flax - seed oil

r
ar

- Timnodonic acid Significance of omega - 3 FA :

M

Based on position - Cervonic acid : Breast milk, Fish & algal oil • Decreases :
©

of final double bond • Omega - 6 FA : - Cardiovascular risk (↓TG)

- Gamma linolenic acid - Platelet aggregation
- Linoleic acid - Mental illness, degenerative
- Arachidonic acid disease risk
• Cis FA - Inflammation
Based on • Trans FA : Vanaspati • Infant brain development
isomer (Partially hydrogenated vegetable oil) • Benefits in Type 2 DM, ADHD,
• RDA : 2 to 7 g/d Non-alcoholic fatty liver disease

: Richest source.
Note : Phrynoderma d/d Vitamin A deficiency.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Chemistry of Lipids and Phospholipids 35

Phospholipids (PL) & Glycolipids 00:10:00 ----- Active space -----

Glycerophospholipids :
Glycerophospholipid Constituents Present in
Phosphatidic acid Diacyl glycerol (DAG) + PO4 Cell membrane
Lecithin DAG + PO4 + choline Lung surfactant,
(Most abundant PL in cell membrane) (Phosphatidyl choline) Cell membrane
Cardiolipin 2 x Phosphatidic acid (PA) Inner mitochondrial
(Diphosphatidyl glycerol) + Glycerol membrane
Phosphatidyl serine PA + Serine Apoptosis
Phosphatidyl inositol

om
PA + Inositol Cell membrane

l.c
(2nd messenger in hormonal pathways)

ai
gm
@
Cardiolipin
95
19
• Alw Barth syndrome (Cardioskeletal myopathy) :
10
02

- Cardiomegaly + myopathy
oy

- Mitochondrial disease
tr
ee

• Only antigenic PL
nj
ira

• Cross reacts with Treponema pallidum :

ch

False positive syphilis test

|
ow
r
ar

Sphingophospholipids :
M
©

Present in :
• Myelin sheath. Lecithin : Sphingomyelin ratio
• White matter of brain. ↑Ratio Lung maturation
• Lung surfactant.

Glycolipids :
Glycosphingolipids Constituents Uses
Ceramide + monosaccharide -
Cerebroside Galactocerebroside Neural tissues
Glucocerebroside Extra-neural tissues
Globoside Ceramide + oligosaccharide -
Ceramide + oligosaccharide +
Ganglioside -
N-acetyl neuraminic acid (NANA)
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 36 Biochemistry

----- Active space ----- SPHINGOLIPIDOSES

Degraded in
Sphingolipids Lysosomes.
Sphingolipidoses : Type of lysosomal storage disease.

Disorders Enzyme defect Features

• Frontal bossing, depressed nasal bridge, long philtrum, low
GM1 gangliosidosis
set ears
(Autosomal recessive) β-galactosidase
• Cherry red spot (CRS) on macula
(AR)
• Angiokeratoma
GM2 gangliosidosis (AR)
• Developmental delay
Tay-Sach's disease β-hexosaminidase A • Muscular weakness
• Visual disturbances

om
• No hepatosplenomegaly

l.c
Sandhoff's disease β-hexosaminidase A & B

ai
• Hyperacusis

gm
• CRS on macula

@
Cherry red spot
95
19
Globoid cell
10
02

Galactocerebrosidase/ • Gross developmental delay

oy

• Opisthotonus posture
tr

β-galactosidase
Krabbe’s disease
ee

(Galactocerebroside accu- with clenched fists

nj

mulation in neural tissue) • No hepatosplenomegaly

ira
ch
|

White matter of brain

ow

• Protruding abdomen
r
ar

• Crumpled tissue paper appearance

M
©

β-glucocerebrosidase/ • Massive hepatosplenomegaly

Gaucher’s disease β-glucosidase (Glucocere- • Thrombocytopenia
(AR) broside accumulation in bone • Erlenmeyer flask deformity
marrow, liver) • Pain & pathological fractures of long bones
• No mental retardation (MR)/CR spot

• Developmental delay • CR spot

• Zebra body inclusions

Neimann-Pick disease
Sphingomyelinase
(AR)

Farber’s disease Ceramidase Resembles rheumatoid arthritis

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Chemistry of Lipids and Phospholipids 37

----- Active space -----

Disorders Enzyme defect Features

• Angiokeratoma • No CR spot or MR
• Lenticular opacities

Fabry’s disease (X-linked

a-galactosidase
recessive)

• Maltese cross : Urinary sediments

Metachromatic
Aryl sulfatase No visceromegaly
leukodystrophy
Note :
Wolman’s disease (Cholesteryl ester storage disease) : Acid lipase defect.

om
(Lysosomal storage disease)

l.c
ai
• Calcification of adrenal gland.

gm
• Watery green diarrhoea.
@
95
19
DIAGNOSTIC ALGORITHM
10

Check for organomegaly

02

+ -
oy
tr
ee

Check for cherry red (CR) spot on Check for CR spot & MR
nj

macula & mental retardation (MR)

ira
ch

+ - CRS - MR -
CRS + MR + CRS - MR +
|
ow

Neimann-Pick Gaucher’s disease :

r
ar

disease. Crumpled tissue paper

M
©

appearance Krabbe’s disease

GM2 gangliosidosis :
• Tay-Sach’s disease
• Sandhoff’s disease

Opisthonus posture
with clenched fists

Gaucher cell Check for Maltese cross

urinary sediment
+ -
Fabry’s disease. Metachromatic
leukodystrophy.

Maltese cross

Erlenmeyer flask deformity

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 38

----- Active space ----- METABOLISM OF LIPIDS

Metabolism in Fasting State  00:00:22

Lipolysis :
Hydrolytic cleavage of TAG.

Site : Adipose tissue.

Steps :
Hormone Sensitive Lipase (HSL) HSL
TAG 2,3-DAG 2-MAG

om
Fatty acid (Diacyl glycerol) Fatty acid (Monoacyl glycerol)

l.c
ai
gm
2 MAG esterase Fatty acid

@
95
19
Glycerol
10
02

Activators :
oy

Applied biochemistry :
• Glucagon
tr
ee

1. Insulin resistance ↑Hydrolysis of stored TAG

• Epinephrine
nj
ira

• ACTH ↑Free fatty acid level in blood

ch

• TSH
|
ow

• Thyroxine Fatty liver disease.

r
ar

• MSH (Melanocyte Stimulating

M

2. Niacin : Locks TAG in the adipose tissue

©

Hormone)
Hence, used to treat hypertriglyceridemia.
Inhibitors :
• Insulin
• PGE1
• Niacin
Metabolic fuel during starvation:
1. Early fasting : Hepatic glycogenolysis
ATP
2. 16-48 hrs of starvation : Gluconeogenesis (ATP is given by TAG FA Acetyl CoA)
3. Prolonged fasting (>2 days of starvation) : ketone bodies (TAG FA Acetyl CoA KB)

Starvation ketosis

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Lipids 39

Beta Oxidation 00:06:49 ----- Active space -----

Sequential removal of 2 carbon acetyl CoA + oxidation of β carbon atoms.

Site : Organelle :
• Liver Mitochondria.
• Skeletal muscle
• Adipose tissue

Steps :
1. Activation of fatty acid : Occurs in the cytoplasm.
Acyl CoA synthetase/Thiokinase
Fatty acid Acyl CoA

om
1 ATP 1 AMP

l.c
(2 ATP equivalents)

ai
gm
2. Carnitine transport : Transports Acyl CoA into mitochondria.
@
95
19
FA Acyl CoA
10
02

Outer Mitochondrial Thiokinase

oy

Membrane (OMM)
tr
ee

AcylCoA + Carnitine
nj
ira

CAT 1/CPT 1 :
ch

• RLE
|
ow

• Gateway of β oxidation
r
ar

Acyl Carnitine Transported

M

Inner Mitochondrial back to IMM

©

Translocase
Membrane (IMM)

Index : Acyl Carnitine

CAT : Carnitine Acyl Transferase CAT 2/CPT 2 :
CPT : Carnitine Palmitoyl Transferase
AcylCoA + Carnitine

Note :
• FA with <14 carbon atoms Do not require carnitine.
(Medium chain & short chain FA)
• Carnitine deficiency Muscle weakness.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 40 Biochemistry

----- Active space ----- 3. Fatty acid oxidation :

Acyl CoA
dehydrogenase Hydratase Energetics :
Acyl CoA α,β unsaturated β hydroxyacyl CoA 1 FADH2 : 1.5 ATP
+ H2O
Acyl CoA NAD β-OH acyl CoA 1 NADH : 2.5 ATP
FAD FADH2
dehydrogenase Total : 4 ATP
NADH
Thiolase
Acyl CoA β Ketoacyl CoA

Energetics of palmitic acid (C16) : M/c FA to undergo β oxidation.

No. of acetyl CoA = 16 = 8 acetyl CoA 8 x 10 = 80 ATP.
2
C16 β oxidation = C16 - 1 = 7 β oxidation 7 x 4 = 28 ATP.

om
2

l.c
ai
Activation : Utilizes 2 ATP equivalents - 2 ATP.

gm
Total : 108 - 2 = 106 ATP
@
95
19
Regulation :
10
02

CPT-1 gateway : Inhibited by Malonyl CoA.

oy
tr

Low I/G ratio - Acetyl CoA carboxylase ↓Malonyl CoA + CPT - 1

ee

• Fasting
nj

(RLE for FA synthesis)

ira
ch

• Fed state High I/G ratio + AcetylCoA carboxylase ↑Malonyl CoA - CPT - 1
|
ow

(RLE for FA synthesis)

r
ar
M
©

Other Oxidation Pathways & Disorders of Fatty Acid Oxidation 00:19:24

OTHER OXIDATION PATHWAYS

Oxidation pathway Site Important feature

Acyl CoA dehydrogenase step is bypassed

β oxidation of unsaturated fatty acid Mitochondria
1.5 ATP less for every double bond

β oxidation of odd chain fatty acid Mitochondria Biproducts : Propionyl CoA (Gluconeogenic) + Acetyl CoA
Alpha oxidation : • Peroxisome : Major • No acetyl CoA
Branched chain FA (Phytanic acid) • SER : Minor • No ATP produced
• Product : Dicarboxylic acid
Omega oxidation SER (Microsome) • No acetyl CoA
• No ATP produced

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Lipids 41

DISORDERS OF FATTY ACID OXIDATION ----- Active space -----

1. MCAD (Medium Chain Acyl CoA Dehydrogenase) Deficiency :
Causes SIDS (Sudden Infant Death Syndrome)/Cradle death.
Medium chain FA
MCAD absent

↓β oxidation

↓Acetyl CoA ↓ATP Enters omega oxidation

No ketone bodies synthesis : Fasting hypoglycemia Dicarboxylic acid

Rothera’s test -

om
l.c
2. Jamaican Vomiting Sickness :

ai
gm
D/t consumption of unripe Ackee fruit Containe hypoglycin.

@
Acyl Co A
95
- Hypoglycin
19
Acyl CoA
10

dehydrogenase
02
oy

↓β oxidation
tr
ee
nj
ira

↓Acetyl CoA ↓ATP

ch
|
ow

↓Gluconeogenesis Ketone bodies absent :

r
ar
M

Rothera’s test -
©

Fasting hypoglycemia
3. Refsum’s Disease :
Defect : Phytanoyl CoA oxidase (Hydroxylase) Alpha oxidation
Features :
• Asymptomatic > Symptomatic.
(Aggravates on consuming
curd/milk)
• Retinitis pigmentosa.
• Ichthyosis
• Peripheral neuropathy.
• Cardiac arrhythmias.
Rx : Restrict dairy products & green
Ichthyosis (Scaly skin) Retinitis pigmentosa
leafy vegetables.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 42 Biochemistry

----- Active space ----- 3. Zellweger Syndrome/Cerebrohepatorenal disease :

Defect : Peroxisome Targeting Sequence (PTS)

Defective phytanic acid & very long chain FA oxidation.

C/f : Resembles Down’s syndrome

• Mongoloid facies.
• Hypertelorism
• Unslanting palpebral fissure.
• Frontal bossing.
• High forehead.
• Brushfield spots.
• Intellectual disability.

om
l.c
Zellweger Syndrome : Resembles Down’s syndrome

ai
Diagnosis :

gm
• Peroxisomal (Vacant) ghost.
@
• Accumulation of VLCFA & phytanic acid. 95
19
10
02

Ketone Body Synthesis

oy

00:33:38
tr
ee

Site :
nj
ira

Exclusively liver mitochondria.

ch
|

Steps :
ow

Acyl CoA
r
ar

β oxidation
M
©

Acetoacetyl CoA (4C)

Acetyl CoA (2C) HMG CoA Synthase : RLE

HMG CoA (6C)

HMG CoA Lyase
Acetoacetate (Primary ketone body)

β OH butyrate NADH
dehydrogenase NAD+ CO2

β OH butyrate : Acetone :
Predominant • Volatile 2˚ ketone body.
ketone body (2˚) • Responsible for fruity breath smell
in starvation/Diabetic ketoacidosis.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Metabolism of Lipids 43

Ketone Body Utilization : ----- Active space -----

Thiophorase/
• Acetoacetate Acetoacetyl CoA Acetyl CoA TCA.
CoA transferase

• Never utilized by :
a. Liver : D/t lack of thiophorase.
b. RBC : D/t absence of mitochondria.

Diabetic Ketoacidosis :
Diabetes : ↓Insulin/Insulin resistance Low I/G ratio (Simulates fasting state).

+
↓Glucose uptake by heart, HSL Liver:

om
skeletal muscle, adipocytes • ↑Glycogenolysis

l.c
• ↑Gluconeogenesis

ai
(GLUT 4 : Insulin dependent) ↑Hydrolysis of TAG

gm
@
↑↑Blood glucose Acetyl CoA 95
19
+
10

Depletion of OAA ↑↑Blood glucose

02

KB synthesis
oy
tr

Lab Diagnosis :
ee
nj

1. Rothera’s test : Purple ring indicative of acetoacetate.

ira

2. Ketostix : Detects urine ketone bodies.

ch
|
ow
r
ar
M
©

Rothera’s test : Purple ring

Metabolism in Fed State 00:43:20

Fatty Acid Synthesis : Mnemonic : Car burns fuel, sit & synthesize
Site : Cytosol (Extramitochondrial). • Carnitine : β oxidation.
Substrate : Acetyl CoA. • Citrate : FA synthesis.
Transporter of acetyl CoA : Citrate (Tricarboxylic acid transporter).
Release of acetyl CoA : ATP citrate lyase.
Steps :
Acetyl CoA carboxylase : RLE
1. Acetyl CoA Malonyl CoA
(Active in dephosphorylation)
• ATP
• Biotin
• CO2

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 44 Biochemistry

----- Active space ----- 2. Fatty acid synthase complex :

• Homodimer.
• Each monomer : 3 subunits
i. Condensing unit.
ii. Reduction unit : Requires NADPH.
iii. Releasing unit : Thioesterase.
• Acyl Carrier Protein (ACP) : Contains pantothenic acid.

Cholesterol Synthesis :
Exclusive animal steroid, not a metabolic fuel. Applied biochemistry :
Site : Liver, adipose tissue, gonads, adrenal cortex. Statins
Organelle : Cytoplasm + SER -
Steps :

om
HMG CoA reductase
2 x Acetyl CoA

l.c
ai
gm
↓Coenzyme Q
Acetoacetyl CoA + Acetyl CoA

@
(Derived from Farnesyl)
HMG CoA synthase 95
19
10

Myopathy
HMG CoA
02
oy

HMG CoA reductase : RLE

tr
ee

Mevalonate Cholesterol (27C)

nj
ira
ch
|

2 x Isopentenylor (5C) Geranyl (10C) 2 x Farnesyl (15C) Squalene (30C)

ow

Compounds Derived from Cholesterol :

r
ar
M

1. Bile acids (Excretory product). 3. Vitamin D.

©

2. Steroid hormones.
Bile Acid Synthesis :
Site :
• Liver (Primary bile acid). • Intestine (Secondary bile acid).
Steps : Cholesterol
Vit C 7 α hydroxylase : RLE
7 OH cholesterol
Conjugation by
1˚ bile acids Cholic acid Taurine + Glycine Chenodeoxycholic acid
Undergoes least
2˚ bile acids Deoxycholic acid Lithocholic acid Enterohepatic
circulation
Enterohepatic circulation
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Metabolism of Lipids 45

Lipoproteins 00:52:45 ----- Active space -----

Characteristics :
• Maximum cholesterol : LDL
• Maximum TAG.
• Minimum density. Chylomicron Chylomicron
• Remains at the point of application. VLDL
• Maximum size. Density Size
LDL
• Maximum density.
HDL HDL
• Minimum size.
• Fastest electrophoretic mobility.
Functions :

om
• Carry exogenous TAG to peripheral organs : Chylomicron.

l.c
• Carry endogenous TAG to peripheral organs : VLDL.

ai
gm
• Carry cholesterol from peripheral tissue to adrenals : HDL.

@
95
19
Electrophoretic Pattern :
10
02
oy

Origin Chylomicron
tr
ee
nj
ira

LDL (β-Lipoprotein)
ch
|

Mobility VLDL (Pre β-Lipoprotein)

owr
ar

IDL (Broad β)
M
©

HDL (α-Lipoprotein)

Anode (+)
METABOLISM OF LIPOPROTEINS
1. Chylomicron :

Site : Intestine Adipose tissue Liver : Receptor mediated

Chylomicron : Nascent Mature chylomicron endocytosis
chylomicron • TAG Remnant chylomicron
• TAG • B48 • Apo E : Ligand
• B48 • Apo A • B48
• Apo A • Apo E • Apo C2
• Apo CII • Apo A
TAG
+ • ↓↓TAG
Lipoprotein lipase
FA + glycerol

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 46 Biochemistry

----- Active space ----- 2. VLDL/LDL :

Site : Liver : Circulation Liver :

VLDL : Nascent VLDL Mature VLDL Remnant VLDL : AKA IDL
• B100 • B100 Loses Apo E, TAG
• TAG • TAG
• Cholesterol Receptor Only has Apo B100 + Cholesterol
• Cholesterol
• Apo E mediated
• Apo CII endocytosis LDL
via Apo E Enters
TAG
+ as ligand
Lipoprotein lipase Liver (70%) Extrahepatic tissue (30%)
FA + Glycerol (Apo B100 :
(FA enters adipose Ligand) Enters circulation
tissue, stored as TAG)

om
Excreted via bile Risk of thrombosis

l.c
ai
gm
@
3. HDL : Facilitates reverse cholesterol transport.
95
19
Liver & intestine Spherical HDL3 :
10

Receives cholesterol from Spherical HDL2

02

Discoidal HDL
peripheral tissues via
oy

• Phospholipid
• ABCA 1
tr

• Cholesterol
ee

• SRB 1 Cholesterol dislodged to

nj

• Apo A 1 Cholesterol
ira

• ABCG 1 liver
+
ch

LCAT
|
ow

Cholesterol
Spherical HDL3
r

ester
ar
M
©

Disorders of Lipoprotein 01:03:43

Mode of inheritance Defect Lipoprotein accumulated Lipid levels

• TAG ↑↑↑
AR LPL or Apo CII Chylomicron > VLDL
• Cholesterol : Normal
C/f
Familial chylomicronemia Pancreatitis (Abdominal pain) can also be seen.
(Type 1 HL)
Latest Rx modalities :
• Lipogene Tiparvovec.
• GOF LpL variant.

Eruptive xanthoma Milky white Lipemia retinalis

plasma

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Metabolism of Lipids 47

----- Active space -----

Mode of Lipoprotein
Defect Lipid levels
inheritance accumulated
• Cholesterol : ↑↑↑
LDL receptor or
AD LDL (Risk of CAD)
Apo B100 mutation
• TAG : Normal
C/f
Familial hypercholesterolemia Family h/o CAD (Coronary Artery Disease).
(Type II HL)
Latest Rx modalities :
• Lomitapide (MTTP - )
• Mipomersen
• VERVE 101 : Genome editing

om
on CRISPR cas9.

l.c
ai
gm
Corneal arcus

@
Tendon xanthoma :
95 M/c achilles tendon
19
10

Remnant
• TAG : ↑↑
02

AR Apo E chylomicron &

oy

• Cholesterol : ↑↑
VLDL
tr
ee

C/f
nj
ira
ch
|

Familial dysbetalipoproteinemia
ow

(Type III HL)

r
ar
M
©

Bunch of grapes/ Palmar xanthoma

Tubero-eruptive xanthoma

Tangier’s Disease :
Defect : ABC A1
Findings : Cholesterol ↑↑
Features :

Hepatosplenomegaly Orange tonsils

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 48 Biochemistry

----- Active space ----- Abetalipoproteinemia :

Defect : MTTP/MTP (Microsomal Triglyceride Transfer Protein).

Findings :
• ↓Chylomicron Bleeding manifestations.
(Transports fat soluble vitamins such as Vitamin K)
• ↓VLDL
• ↓IDL
• ↓LDL

Features :

om
l.c
ai
gm
@
95
19
10
02

Pigmentary retinopathy Petechial rash

oy
tr
ee
nj
ira
ch
|
ow
r
ar
M
©

Acanthocytes

Sitosterolemia (Type II HL) : Fish Eye Disease :

Defect : Defect : Partial LCAT deficiency.
• ABC G5
• ABC G8
Finding : ↑Cholesterol.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Amino Acids : Part 1 49

AMINO ACIDS : PART 1 ----- Active space -----

Classification & Properties of Amino Acids 00:00:20

CLASSIFICATION
Based on Side Chain :
Group Amino acids
Glycine
Simple
Alanine
Aliphatic Leucine

om
l.c
Branched chain Isoleucine

ai
gm
Valine

@
• Serine
OH group containing • Threonine 95
19
•
10

Tyrosine
02

• Cysteine
oy

Sulphur containing
• Methionine
tr
ee

• Aspartic acid (Aspartate)

nj

Acidic
ira

• Glutamic acid (Glutamate)

ch

• Asparagine
|

Amides
•
ow

Glutamine
r

•
ar

Histidine
M

Basic • Arginine
©

• Lysine
• Phenylalanine : Benzene ring
Aromatic • Tyrosine : Phenol ring
• Tryptophan : Indole ring
Imino acid Proline : Pyrrolidine ring

Based on Side Chain Characteristics :

Polar Non - polar :

• Branched chain.
• Aromatic.
Charged : ABC Uncharged : • Simple : Alanine.
• Acidic : Aspartate, Glutamate. • Amides : Asparagine, Glutamine. • Methionine.
• Basic : Histidine, Arginine, Lysine. • OH group : Serine, Threonine. • Proline.
• Simple : Glycine.
• Sulphur containing : Cysteine.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 50 Biochemistry

----- Active space ----- Based on Metabolic Fate :

Ketogenic : Ketogenic + glucogenic : Glucogenic :

5. Leucine. 1. Phenylalanine. Remaining amino acids.
6. Lysine. 2. Isoleucine.
3. Tyrosine.
4. Tryptophan.
Based on Nutritional Requirement :

Semi-essential : Essential : Non-essential :

Arginine. • Methionine. • Lysine. Remaining amino acids.
• Leucine. • Valine.

om
• Tryptophan. • Histidine.

l.c
• Phenylalanine. • Isoleucine.

ai
gm
• Threonine.

@
DERIVED AMINO ACIDS 95
19
Properties :
10
02

• No codons.
oy

• Formation :
tr
ee

- Post translational modification.

nj
ira

- Intermediate of metabolic pathways.

ch
|

Classification :
row
ar
M

Seen in proteins : Not seen in proteins :

©

• Hydroxylysine • Ornithine, argininosuccinate, citrulline.

Collagen.
• Hydroxyproline • Homoserine & homocysteine.
• Gamma carboxy glutamate : Factors 2, 7, 9, 10.
• Desmosine : Lysine.
• Methyl lysine : Myosin.
STANDARD AMINO ACIDS
Selenocysteine Pyrolysine
Reading process + +
Coded by Stop codon UGA UAG
Precursor amino acid Serine Lysine
Protein formation 21st protein forming amino acid 22nd protein forming amino acid
Cotranslational process + +

Mnemonic : Serina’s sister Selena from UGAnda.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Amino Acids : Part 1 51

Enzymes Containing Selenocysteine/Selenium : ----- Active space -----

• Glutathione peroxidase.
• Thioredoxin reductase.
• Deiodinase.
• Selenoprotein P.

PROPERTIES OF AMINO ACIDS

1. Isomerism :
• D & L isomerism.
• Exception : Glycine (Optically inactive).

2. Absorption of Light :
• Colourless : Do not absorb visible light.

om
• UV light absorption : Phenylalanine, tyrosine, tryptophan

l.c
Tryptophan : 280 nm (Maximum UV absorption).

ai
gm
@
3. Buffering :
95
19
Maximum with imidazole group of histidine (pH = pKa).
10
02

4. Exist in Charged States :

oy
tr

Ampholytes/zwitter ions : Compounds with Isoelectric pH (Net charges = 0).

ee
nj

• Maximum precipitability, minimum solubility.

ira

• Minimum buffering (pH = pI).

ch
|
ow

TITRATION CURVE
r
ar

Compound with Single Ionizable Group :

M
©

Completely ionized

Partially ionized
pH
pH = pKa : Point of maximum buffering capacity

Un-ionized

Alkali added

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 52 Biochemistry

----- Active space ----- Compound with Multiple Ionizable Groups :

pk2

pH pk1 + pk2
pI =
pk1 2

pH = pI : Point of minimum buffering capacity

Alkali added

om
Proteins 00:25:00

l.c
ai
gm
Peptide bond :

@
• B/w 2 amino acids Forms proteins.
95
19
• Uncharged.
10

• Partial double bond.

02
oy

• Trans in nature.
tr
ee
nj

STRUCTURE OF PROTEINS
ira
ch

Primary : Peptide (Covalent) bond.

|
ow
r

Secondary : Coiling of linear structure. Primary structure Secondary structure

ar
M
©

Alpha helix : Beta sheets :

• M/c 2° structure. • 2 m/c.
nd

• Most stable : Intrachain hydrogen bonds. • Zig zag/extended.

• Disrupted by proline. • Interchain hydrogen bonds.
• Glycine : Induces bend in α-helix.

Tertiary :
• 3D structure that can perform function.
• Non-covalent forces + .
• Eg : Domain.

Quaternary :
• > 1 polypeptide interact via subunit.
• Non-covalent forces/subunit interaction. Tertiary structure Quaternary structure
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Amino Acids : Part 1 53

Protein Folding : ----- Active space -----

Molecular chaperones : Auxiliary proteins.
• BiP (Immunoglobulin heavy chain binding protein).
• GRP-94 (Glucose regulated protein).
• Calreticulin
Bind Ca2+.
• Calnexin
• Heat shock proteins.
Enzymes :
• Protein disulfide isomerase.
• Peptide prolyl isomerase.

Protein misfolding diseases :

om
• Prion diseases.

l.c
• Amyloidosis.

ai
gm
• Prion related protein diseases :

@
7. Alzheimer’s disease. 95
11. Huntington’s disease.
19
8. Parkinson’s disease. 12. Pick’s Disease (FTD).
10
02

9. b Thalassemia. 13. Amyotrophic Lateral Sclerosis (ALS).

oy

10. Cystic fibrosis. 14. Lewy body dementia.

tr
ee
nj
ira

Pathology :
ch

PrP : a helix Mutation PrP Sc : b sheet.

|
ow

• Hydrophobic amino acids exposed.

r
ar

• Resistant to degradation.
M
©

Protein Degradation :
Proteasomal degradation : Ubiquitin mediated (kiss of death), ATP dependent.
• Proline
• Glutamate PeST sequence is required
• Serine for binding with ubiquitin.
• Threonine
Lysosomal degradation : ATP independent.

Collagen 00:37:20

Features :
• Most abundant protein.
• Fibrous protein in ECM.
• Glycine : Most abundant amino acid.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 54 Biochemistry

----- Active space ----- Structure :

1. Poly proline a chain :
• Glycine X-Y repeat.
• Left handed turn.
• Composed of 1000 amino acids.

2. Triple helix 3a chain :

• Vit C Hydroxylation of proline & lysine.
• 3 together in R direction.

3. Quarter staggered arrangement :

• Lateral arrangement of triple helix.
• Cu & lysyl oxidase Covalent cross-links + .

om
l.c
Synthesis :

ai
gm
Intracellular Extracellular

@
Site RER of fibroblast 95 ECM
19
10

Product Procollagen Tropocollagen

02

1. Hydroxylation : Prolyl & Lysyl hydroxylase 1. Cleavage

oy
tr

Events 2. Glycosylation : Hydroxy lysine residue 2. Quarter staggered

ee
nj

3. Triple helix 3. Covalent cross-links : Lysyl oxidase

ira
ch
|

Types :
row
ar

Type Diseases associated

M
©

Type 1 :
• Osteogenesis imperfecta
• Most abundant type
• Osteoporosis
• Present in bone
• Ehler-Danlos type VII
• Ubiquitous in hard & soft tissue
• Severe chondrodysplasias
Type 2 : Present in cartilage
• Osteoarthritis
Type 3 Ehler-Danlos type IV
Type 4 : Present in GBM Alport syndrome
Type 6 : Ubiquitous in microfibrils Bethlem myopathy
Epidermolysis bullosa
Type 7 : Seen in anchoring fibrils
(Dystrophic)
Type 10 Schmid metaphyseal dysplasia

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 Amino Acids : Part 1 55

Elastin v/s Collagen : ----- Active space -----

Collagen Elastin
Types Many types Only 1 type
Triple helix + -
Gly - X - Y + -
Hydroxylysine + -
Glycosylation + -
Cross-links Covalent cross-links Desmosine cross-link

Disorders a/w Elastin :

1. William Beuren syndrome.
2. Cutis laxa.

om
l.c
Keratin :

ai
gm
• Component of outer layer of skin, nails & hair.

@
• Rich in cysteine : Confers hardness to nails. 95
19
• Associated disorder : Epidermolysis bullosa (Classical type).
10
02
oy

Fibrillin :
tr
ee

• Glycoprotein in scaffolding of elastin.

nj
ira

• Fibrillin 1 mutation : Marfan’s syndrome.

ch
|
ow

Amino Acid Metabolism 00:47:40

r
ar
M

Reactions : NH3
©

1. Deamination Ketoacid.
CO2
2. Decarboxylation Amines.

Toxic nature of ammonia :

↑GABA (Inhibitory neurotransmitter)
CO2

Glutamate + NH3 Glutamine : Causes cerebral edema.

α KG from TCA cycle

↑NH3 ↑Formation of Glutamine ↓α KG ↓ATP.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 56 Biochemistry

----- Active space ----- 1. Transamination :

Site : Cytoplasm of all organs.

Examples :
Alanine α Ketoglutarate Aspartate α Ketoglutarate

B6 ALT B6 AST

Pyruvate Glutamate Oxaloacetate Glutamate

Properties :
• Toxic amino group Non-toxic glutamate.
• Reversible reaction.

om
• Significance : Biosynthesis of non-essential amino acids.

l.c
• Ping pong mechanism/Bibi reaction : 2 substrate 2 product reaction.

ai
gm
@
Transamination of non-alpha amino acid :
95 Applied biochemistry
19
Enzyme : δ ornithine aminotransferase.
10

Gyrate atrophy of retina & choroid :

02

• Defect in δ ornithine aminotransferase

oy

• Treatment :
tr
ee

- Restrict ornithine & arginine

nj
ira

- Supplement PLP (B6)

Exceptions to transamination :
ch
|

1. Proline. 3. Lysine.
ow

2. Hydroxyproline. 4. Threonine.
r
ar
M
©

2. Transport of NH3
Sources of ammonia :
• Amino acids Glutamate.
• Amino sugars
• Pyrimidine Glutamine synthetase 1st line defense of
NH3 (In mitochondria)
• Purine hyperammonemia.
• Porphyrins
Glutamine : Transport form of NH3

Transport form from skeletal muscles : Alanine.

3. Oxidative Deamination :
Site : Liver & kidney.
Organelle : Mitochondria.

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 Amino Acids : Part 1 57

Glutamine ----- Active space -----

Glutamate
Alanine
NADP • Activator : NAD+/ADP.
Glutamate dehydrogenase (GDH)
• Inhibitor : ATP.
NADPH
NH3 Urea cycle
αKG
Urea Cycle 01:02:35

AKA Kreb’s Henseleit/Ornithine cycle.

Note : Reactions occurring in
Site : Exclusively in liver.
both cytoplasm & mitochondria
Organelle : Cytoplasm + mitochondria.
Mnemonic : PUBG
Contributions to Structure : • Pyrimidine synthesis

om
• 1st Nitrogen : Ammonia. • Urea cycle

l.c
• 2nd Nitrogen : Aspartate. • Blood : Heme synthesis

ai
gm
• Carbon atom : Respiratory CO2. • Gluconeogenesis

@
95
19
Urea Bicycle : Aspartate
10
02
oy

TCA cycle Urea cycle

tr
ee
nj
ira
ch

Fumarate
|
ow
r

Reactions of Urea Cycle :

ar

CO2 + NH3
M
©

2 ATP I. Carbamoyl phosphate synthetase I (CPS-I) : Rate limiting enzyme

Mitochondria NAG : Obligate allosteric activator
2 ADP
Carbamoyl phosphate TCA cycle
II. Ornithine
transcarbamylase (OTC) Aspartate
Ornithine Citrulline
Ornithine (VII) Citrin transporter (VI)
transporter
Citrulline + Aspartate
Ornithine
Urea Arginase (V) 1 ATP
1 AMP AS synthetase (III) Energetics :
H2O Argininosuccinate (AS)
Arginine CPS 1 : 2 x PO4
Cytoplasm AS lyase (1v)
AS lyase : 2 x PO4
Fumarate (C4) Total required : 4 PO4
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 58 Biochemistry

----- Active space ----- Urea Cycle Disorders :

Defect Disorder
CPS I Hyperammonemia Type I
OTC Hyperammonemia Type II
AS synthetase Citrullinemia Type 1
AS Lyase Argininosuccinic aciduria
Arginase Argininemia
Citrin transporter Citrullinemia Type 2
Ornithine transporter HHH syndrome

Hyperammonemia Type II :
• M/c Urea cycle disorder.

om
• X-linked recessive.

l.c
ai
• Defect : OTC.

gm
@
95
Carbamoyl phosphate accumulates Shunted for Pyrimidine synthesis
19
10
02
oy

Excretion of Accumulation
tr
ee

pyrimidines of orotic acid

nj
ira

in urine
ch

Orotic aciduria.
|
ow

HHH syndrome :
r
ar
M

• Defect : Ornithine transporter Hyperornithinemia.

©

• Carbamoyl phosphate + lysine Homocitrulline Homocitrullinemia.

• Accumulation of NH3 Hyperammonemia.

Arginemia :
• Least hyperammonemia.
• Spastic diplegia + scissoring of
lower limbs.

Spastic Diplegia Scissoring gait

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Amino Acids : Part 1 59

Argininosuccinic aciduria : ----- Active space -----

Trichorrhexis nodosa : Brittle hair.

Argininosuccinic aciduria
General clinical features of urea cycle disorders :
• Encephalopathy.
• Respiratory alkalosis.
• Tachypnoea.
• Hyperammonemia A/w ↑ Plasma glutamine levels
↑↑NH3
Glutamate Glutamine

om
Neonates : Feeding difficulties, failure to thrive, lethargy, convulsions, coma.

l.c
ai
gm
Management of Urea Cycle Disorders :

@
Investigations :
95
19
↑/Normal : Urea cycle disorders.
1. pH of blood
10
02

↓Organic aciduria.
oy
tr

2. Tandem mass spectrometry : Gold standard screening technique for all

ee
nj

metabolic disorders.
ira
ch

Interpretation :
|
ow
r
ar
M

Specific amino acids↑ : Non-specific amino acids↑

©

• ↑Citrulline : Citrullinemia.
• ↑Ornithine : HHH syndrome. Plasma orotic acid
• ↑Arginine : Arginemia.
• ↑Argininosuccinate : Argininosuccinic aciduria. ↑ Normal

Hyperammonemia Hyperammonemia
Type II. Type I.
Treatment :
1. Supplement with arginine :
• Source of ornithine. • Essential amino acid.
• Activator of NAG. • C/I in arginase defect.

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 60 Biochemistry

----- Active space ----- 2. Acylation therapy :

Phenyl butyrate & sodium benzoate : NH3 scavengers.
• Phenyl butyrate Phenyl acetate Phenyl acetyl glutamine
(prodrug) +
Glutamine
Excreted through kidneys.
Glycine synthase
• Sodium benzoate + glycine Benzoyl glycine

NH3 + CO2 + 1 Carbon group. Excreted through kidneys.

om
l.c
ai
gm
@
95
19
10
02
oy
tr
ee
nj
ira
ch
|
row
ar
M
©

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 Amino Acids : Part 2 61

AMINO ACIDS : PART 2 ----- Active space -----

Metabolism & Disorders of Phenylalanine & Tyrosine 00:00:10

Phenylalanine Tyrosine

Catabolic pathway Anabolic pathway

Ketogenic + glucogenic. • Melanin.

• Catecholamine.

om
• Thyroid hormones.

l.c
ai
gm
Phenylalanine hydroxylase
Phenylalanine Tyrosine.

@
95
19
BH4 BH2
10
02

Dihydrobiopterin reductase
oy
tr
ee

NADP+ NADPH
nj
ira
ch

Catabolic Fate :
|

Tyrosine transaminase
ow

Phenylalanine Tyrosine Para/4 hydroxy phenyl pyruvate

r
ar
M

PHPP hydroxylase/
©

4HPP dioxygenase

Homogentisic acid/dihydroxyphenyl acetate

Homogentisate oxidase/dioxygenase
OR
Dihydroxyphenylacetate dioxygenase

Maleyl acetoacetate (MAA)

MAA isomerase
Glucogenic Fumarate FAA hydrolase
Fumaryl acetoacetate (FAA)
1˚ ketone body Acetoacetate

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 62 Biochemistry

----- Active space ----- DISORDERS

Enzyme Defect Disorder
Phenylalanine hydroxylase Classic phenylketonuria (PKU)
• DHB Reductase
• GTP synthesis BH4
- GTP cyclo hydrolase Non-classic PKU
- Pyruvoyl THB synthase
- Sepiapterin reductase
Homogentisate oxidase Alkaptonuria
FAA hydrolase Tyrosinemia type 1
Tyrosine transaminase Tyrosinemia type 2
PHPP Tyrosinemia type 3

om
l.c
ai
Classic Phenylketonuria :

gm
@
Clinical features : X Melanin : Hypopigmentation.
95
19
Phenylalanine X Tyrosine X Catecholamine : Agitation, hyperactivity,
10
02

mental retardation, intractable vomiting.

oy
tr

X T3, T4.
ee

Phenyl pyruvate
nj
ira
ch

Phenyl acetate Mousy/musty/barny odour.

|
ow

Note :
r
ar

Persistence of neurological symptoms after

M
©

phenylalanine restriction Non-classic PKU.

Lab diagnosis :
1. Guthrie’s test (Bacterial inhibition test) : Growth of
Bacillus subtilis.
PKU : Hypopigmentation
2. Ferric chloride test : Positive.
3. Blood phenyl alanine levels.
4. Enzyme studies.

Treatment :
• Phenylalanine restricted diet.
• Synthetic THB (Non-Classic) : Sapropterin
dihydrochloride/Kuvan.
• Large neutral amino acid
(Tryptophan & tyrosine). Ferric chloride test

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Amino Acids : Part 2 63

Alkaptonuria : ----- Active space -----

Part of Garrod’s tetrad :
1. Cystinuria.
2. Alkaptonuria.
3. Pentosuria.
4. Albinism.
Alkaptonuria : Black pigmentation
Defect :
Phenylalanine Tyrosine PHPP Homogentisic acid Homogentisate
X oxidase MAA.

Alkaptone bodies Excreted in urine

Urine turns black

om
IV disc Skin. Cartilage. on air exposure/

l.c
ai
alkalinization.

gm
Ochronotic arthritis.

@
95
19
Clinical features :
10
02

• Age of onset : Middle age. • Black pigmentation of skin, IV

oy

• Present with back pain. disc, cartilage.

tr
ee

• No intellectual disability. • Blackening of urine on standing.

nj
ira
ch

Lab diagnosis :
|
ow

• FeCl3 test. • X-ray :

r
ar

• AgNO3 test. - Bamboo spine.

M

• Alkalinize urine. - Vacuum phenomenon (Air

©

• Benedict’s test : Positive. space in vertebra).

Rx : Nitisinone Inhibits PHPP hydroxylase.

Type 2 Tyrosinemia :
AKA Oculo-cutaneous tyrosinemia/Richner Hanhart syndrome.

Defect : Tyrosine transaminase.

Features :
• Skin : Non-pruritic • Corneal ulcers :
hyperkeratotic plaque Poorly stained
on soles & palms. with fluorescein.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 64 Biochemistry

----- Active space ----- Derivatives of Tyrosine 00:18:55

Catecholamines :
Tyrosine hydroxylase Dopa decarboxylase
Tyrosine DOPA Dopamine
PLP
BH4 Dopamine beta hydroxylase

Norepinephrine
SAM
N-methyl transferase
SAH
Epinephrine.
Degradation of catecholamines :
• Dopamine Homovanilic acid (HVA).
• Norepinephrine
Vanilyl Mandellic Acid (VMA).

om
• Epinephrine

l.c
ai
gm
Pheochromocytoma :

@
Palpitations
19
95
10
02

Triad
oy

Profuse sweating Headache

tr
ee

Lab diagnosis :
nj
ira

1. 24 hr urinary tests for : 2. Plasma tests for :

ch

• VMA : Highest specificity.

|

• Catecholamines.
ow

• Catecholamines. • Free metanephrines : Highest

r
ar
M

• Fractionated metanephrines : sensitivity.

©

Highest sensitivity.
• Total metanephrines.

Melanin :
Site of synthesis : Melanosomes (Stratum basale).
Tyrosinase : Cu containing Tyrosine : Cu containing
Tyrosine DOPA Dopaquinone

Melanin.
Albinism : Defect in tyrosinase.
• Milky white skin & hair.
• Photophobia.
• Lacrimation.

Albinism
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Amino Acids : Part 2 65

Tryptophan 00:23:00 ----- Active space -----

Properties :
• Aromatic AA. • Essential.
• Non-polar. • Ketogenic + glucogenic.
Catabolic Fate :
Tryptophan pyrrolase 1 THFA Formyl THFA
dioxygenase :
Heme containing
Tryptophan N-formyl kynurenine Kynurenine

3-OH kynurenine
PLP
Alanine Glucogenic

om
Kynurinase

l.c
ai
3-OH anthranilic acid Ketogenic

gm
Quinolinate phosphoribosyl

@
transferase (QPRTase) : RLE
95
19
Vitamin B6 deficiency :
10

• 3-OH kynurenine Xanthurenic acid. Niacin.

02
oy

• ↓Synthesis of niacin Pellagra.

tr
ee
nj

Niacin :
ira

• Endogenously synthesized vitamin.

ch
|

• 60 mg tryptophan 1 mg niacin.
owr
ar

Derivatives :
M

Tryptophan Amino acid

©

hydroxylase decarboxylase
Tryptophan 5-Hydroxy tryptophan Serotonin
BH4 PLP
(5-Hydroxy tryptamine)

Degradation
5HIAA
SAM
Melatonin : Acetyl serotonin
(Methyl acetyl serotonin)
• Neurotransmitter
• Antioxidant
• Regulates circadian rhythm.
Site : Argentaffin cells of
1. Intestine.
2. Brain.
3. Platelets.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 66 Biochemistry

----- Active space ----- DISORDERS

Carcinoid Syndrome :
Tumor of argentaffin cells ↑↑Serotonin ↓Niacin.

C/f :
• Intermittent diarrhea. • Sweating. • 24-hr 5 HIAA↑.
• Flushing. • Features of pellagra.
Hartnup’s Disease :
Mutation : SLC 6A 19 Mutation Defect of tryptophan transporter

↓Tryptophan

↓Serotonin & ↓niacin.

C/f :

om
l.c
• Asymptomatic.

ai
gm
• Accumulation of Bacterial
Indoxyl compounds Excreted in urine
tryptophan in intestine decomposition
@
95
19
• Ataxia. Bluish discoloration of diaper.
10

• Wide based gait.

02
oy

• Cutaneous photosensitivity : M/c symptom.

tr
ee
nj

Test : Obermeyer test.

ira

Rx : Lipid soluble esters of tryptophan.

ch
|
ow

Derivatives of Tyrosine
r
ar

00:33:10
M
©

Cysteine : Methionine :
• Glucogenic • Glucogenic
• Polar • Non-polar
• Non-essential. • Essential.
Metabolism : Methionine
THFA adenosyltransferase (MAT) S-adenosyl methionine :
Methionine
Methyl B12 Principle methyl donor
Methyline THF
reductase B12
CH3
N5 methyl Homocysteine S-adenosyl homocysteinase
S-adenosyl homocysteine
THFA + Serine
B6 Cystathionine β synthase

Cystathionine Cystathionase Homoserine + Cysteine.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Amino Acids : Part 2 67

DISORDERS ----- Active space -----

Enzyme defect Disorders

MAT Primary hypermethioninemia
Cystathionine β synthase Classic homocystinuria
Cystathionase Cystathioninuria
• Methyline THF reductase
Non-classic homocystinuria
• Defect in methyl B12 formation
Note :
B6, B12, B9 deficiency ↑Homocysteine in blood Risk factor for thrombosis.

Folate trap/THFA starvation :

B12 deficiency : N5 methyl THFA X THFA.

om
l.c
ai
Functional deficiency

gm
↓DNA synthesis Nucleocytoplasmic asynchrony

@
of THFA
95
19
Megaloblastic anemia.
10
02

Homocysteinuria :
oy
tr

Clinical features : Resembles Marfan’s syndrome.

ee
nj

• Developmental delay.
ira

• Mental retardation.
ch
|

• Tall & thin extremities.

ow

• Skeletal deformities.
r
ar
M

• Visual disturbances : Ectopia

©

lentis (M/c : Inferomedial).

• Muscular hypotonia.
• H/o CAD.
Ectopia lentis Thromboembolism
• Thromboembolism.

Arachnodactyly Tall stature High arched palate

Skeletal deformities in homocysteinuria

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 68 Biochemistry

----- Active space -----

Pectus excavatum Pectus carinatum Pes cavus Genu valgum/varus

Skeletal deformities in homocysteinuria

Test : Cyanide nitroprusside test + .

om
Classic homocysteinuria Non-classic homocysteinuria

l.c
ai
Methyl B12 formation ;

gm
Enzyme Cystathione β synthase

@
Methylene THF reductase
95
19
Defect in Formation of cysteine Remethylation of homocysteine to methionine
10

Homocysteine ↑ ↑
02
oy

Cysteine ↓ Normal
tr
ee

Methionine Normal ↓
nj
ira

• Cysteine supplementation
ch

• High dose Vit B6 • Methionine supplementation

|

Rx
ow

• Betaine (trimethyl glycine) • Vit B12, B6, folic acid

r
ar

• Vit B12 & folic acid

M
©

Cystinuria
• Defect : Dibasic amino acid transporter in kidney.
• Excretion of : COLA.
- Cystine.
- Ornithine.
- Lysine.
- Arginine.

Cystinosis :
• Defect : Cystine transporter in lysosome. Cystine crystals : Colourless,
flat, hexagonal ; acidic urine
• Manifestations :
- Renal failure. - Corneal opacity.
- Bone marrow suppression. - Liver failure.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Amino Acids : Part 2 69

DERIVATIVES OF CYSTEINE ----- Active space -----

Glutathione Taurine
Glutathione (GSH) :
• Tripeptide : Glutamic acid + cysteine + glycine.
• Active group : SH of cysteine.
• Atypical peptide.

Functions :
1. Transport of ammonia : Meister’s cycle/Gamma glutamyl cycle. 3. Conjugation.
2. Free radical scavengers : Glutathione peroxidase. 4. Coenzyme.

om
Other Amino Acids 00:49:55

l.c
ai
gm
Glycine :

@
Derivatives :
95
19
1. Purine (C4, C5, N7). 3. Heme.
10

2. Creatinine : Glycine + arginine + 4. Glutathione.

02
oy

methionine. 5. Collagen.
tr
ee
nj

Hyperoxaluria :
ira

Primary : Defect in glyoxylate amino transferase.

ch
|

Secondary : D/t
ow

• Vit C excess.
r

• Ethylene glycol poisoning.

ar
M

• Vit B6 deficiency. • Methoxyflurane. Oxalate stones : Envelope shaped

©

Serine :
Functions :
1. Synthesis of :
a. Cysteine. c. Choline.
b. Phosphatidyl serine. d. Betaine.
2. Produces ethanolamine on decarboxylation.
3. Precursor of selenocysteine.

BASIC AMINO ACIDS Histidine

Histidine :
Derivatives : FIGLU (Formimino glutamic acid)
• FIGLU. THFA
• Histamine. Formimino THFA
Glutamic acid.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 70 Biochemistry

----- Active space ----- Histidine load test : B9 deficiency FIGLU excreted in urine.

Arginine : Derivative compounds are

1. Nitric oxide.
• Synthesized by NO synthase.
• Reactive free radical.
• Acts via GMP.
• Endothelium derived relaxing factor.
2. Ornithine & Urea.
3. Creatine

BRANCHED CHAIN AMINO ACIDS (BCAA)

BCAA

om
PLP Transamination.

l.c
ai
gm
BC ketoacid

@
BC ketoacid NAD+
dehydrogenase CO2 NADH 95 Oxidative decarboxylation.
19
10

Acyl group
02

FAD
oy

FADH2 FAD dependent dehydrogenation.

tr
ee

Product.
nj
ira

Maple Syrup Urine Disease

ch
|

Defect : Branched chain ketoacid dehydrogenase.

ow

Features :
r
ar
M

• Age of onset : Neonate.

©

• Feeding difficulty, convulsion, lethargy, coma.

• Boxing/kicking movement (Alternating hypo & hypertonia).
• Burnt sugar odour of urine.
Lab diagnosis :
• ↑BCAA & ↑BCKA in blood & urine.
• Dinitrophenyl hydrazine (DNPH) test.
• Rothera’s test : Positive.
Rx
• Restrict BCAA.
• Supplement thiamine.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Amino Acids : Part 2 71

Revision Tables 00:57:35 ----- Active space -----

Test Aminoaciduria
Ferric chloride test PKU/Alkaptonuria
Dinitro phenyl hydrazine test MSUD
Guthrie test PKU
LABORATORY TESTS Obermeyer test Hartnup disease
Cyanide nitroprusside test Homocystinuria
La Brosse VMA spot test Pheochromocytoma
5 HIAA Carcinoid syndrome

Disorder Defective enzyme

Albinism Tyrosinase

om
l.c
MSUD Branched chain keto acid dehydrogenase

ai
gm
Isovaleryl CoA dehydrogenase
Isovaleric acidemia

@
(A/w leucine catabolism)
95
19
ENZYME DEFECTS Homocystinuria Cystathionine β synthase
10

Phenylalanine hydroxylase/DHB
02

Phenylketonuria
reductase/Defect in THB synthesis
oy
tr

Homogentisate oxidase/Dihydro phenyl

ee

Alkaptonuria
nj

acetate dioxygenase
ira

Tyrosinemia type I Fumaryl acetoacetate hydrolase

ch
|

Tyrosinemia type II Tyrosine transaminase

ow
r

Tyrosinemia type III PHPP hydroxylase

ar
M
©

Disorder Odour
Glutaric acidemia (Type 2) Sweaty feet
Hawkinsinuria : Defect in PHPP hydroxylase
Swimming pool
(Partially active)
Isovaleric aciduria Sweaty feet
MSUD Maple syrup/Burnt sugar

PECULIAR ODOURS Hypermethioninemia Boiled cabbage

Multiple carboxylase deficiency Tomcat urine
Oasthouse urine disease Hops-like
PKU Mousy/Musty
Trimethylaminuria :
• Defect in trimethylamine oxidase Fish odour
• Rx : Choline restriction
Tyrosinemia Boiled cabbage/Rancid butter

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 72

----- Active space ----- MOLECULAR BIOLOGY : PART 1

Nucleotides & Nucleic Acids 00:00:10

Steps to Identify Nucleotide :

1. Identify the ribose sugar.
2. Identify the nitrogenous base.
3. Identify if PO43- group present.
4. Identify nucleotide Monomer made up of :
a. Nitrogenous base
Nucleoside

om
b. Pentose sugar

l.c
c. PO43- group

ai
gm
@
Types of Nitrogenous Bases :
95
19
10

Double ring : Purine Single ring : Pyrimidine

02
oy

Adenine (6-amino purine)

tr
ee
nj
ira
ch
|
ow
r
ar
M

Guanine (2-amino, 6-oxopurine)

Cytosine Deamination Uracil Methylation
©

Thymine
(2-oxo, 4-amino (2,4-dioxo (2,4-dioxo,
pyrimidine) pyrimidine) 5-methyl pyrimidine)

Important Linkages :
β-N glycosidic bond : B/w N9 of purine/N1 of pyrimidine to C1’ of pentose sugar.
Ester bond : B/w nucleoside & 1st phosphate group.
Acid anhydride bond : B/w adjacent PO43- groups (Energy rich bonds).

Nucleic Acids :
• Formed by 31-51 phosphodiester bond b/w nucleotides.
• Exhibit polarity.
• Sequenced from 51 31.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Molecular Biology : Part 1 73

DNA vs. RNA : ----- Active space -----

DNA RNA
Hydroxyl group Only at 31 position At 21 and 31 positions
Pentose sugar Deoxyribose sugar Ribose
Free functional group - Reactive 21 OH group +
Stability Stable Unstable
Nucleotides in RNA vs. DNA :
Nitrogenous base Nucleoside Ribose monophosphate Deoxyribose monophosphate
Adenine Adenosine Adenosine monophosphate (AMP) d AMP
Guanine Guanosine Guanosine monophosphate (GMP) d GMP
Uridine monophosphate (UMP)
Uracil Uridine -
(Only in RNA)

om
Hypoxanthine Inosine Inosine monophosphate (IMP) -

l.c
ai
Xanthine Xanthosine Xanthine monophosphate (XMP) -

gm
Cytosine Cytidine Cytidine monophosphate (CMP) d CMP

@
Thymine Thymidine - 95
d Thymidine monophosphate (Only in DNA)
19
10
02

Metabolism of Nucleotides 00:13:20

oy
tr
ee

PURINE SYNTHESIS
nj

De-novo Purine Synthesis :

ira
ch

Site : Occurs in all organs except brain, RBC & WBC.

|
ow

Contributors of purine ring :

r
ar
M
©

PRPP glutamyl
PRPP synthetase amidotransferase : RLE
Ribose-5 Phosphoribosyl Phosphoribosyl amine
phosphate pyrophosphate
ATP AMP (PRPP) Glutamine Glutamate IMP
Aspartate : NH3 IMP dehydrogenase

AMP XMP GMP

Glutamine : NH3
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 74 Biochemistry

----- Active space ----- Salvage Pathway :

Significance :
• Recycles purine nucleosides & bases to purine nucleotides.
• Conserves energy in organs without de novo synthesis.

Phosphorylation reactions :
Substrate Donor Enzyme End product
Adenine Adenine phosphoribosyl transferase (APRTase) AMP
Hypoxanthine PRPP Hypoxanthine guanine IMP
Guanine phosphoribosyltransferase (HGPRTase) GMP
Adenosine AMP
ATP Kinase
Guanosine GMP

om
Disorders of Purine Synthesis :

l.c
ai
Lesch Nyhan Syndrome :

gm
@
Defect : HGPRTase.
95
19
• Hypoxanthine IMP
10

↑Purine catabolism ↑Uric acid.

• Guanine GMP
02
oy

C/f :
tr

Rx :
ee

• Compulsive self-mutilation. • Allopurinol

nj
ira

• Hyperuricemia • High fluid intake.

ch

• Neurological defects.
|

• Alkalization of urine.
row
ar

Kelley Seegmiller syndrome :

M

Lesch Nyhan Syndrome :

©

Partial defect of HGPRTase.

Gout :
C/f :
• Acute inflammatory arthritis (M/c : 1st MTP) :
Characteristic of acute gout.
• Hyperuricemia.
• Uric acid nephrolithiasis
• Tophi (MSU crystals in s/c tissue) :
Characteristic of chronic gout.
Definitive diagnosis : MSU (Monosodium Urate) crystals
Needle shaped negatively birefringent MSU
Tophi crystals on polarized light microscopy.

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 Molecular Biology : Part 1 75

Disorders of Purine Catabolism : ----- Active space -----

End product of purine catabolism : Uric acid.
Enzyme deficiency Features
Adenosine deaminase SCID : Both T cells & B cells affected
Purine nucleoside ribosyl transferase Immunodeficiency affecting only T cells
• Xanthinuria
Xanthine oxidase
• ↓Uric acid

PYRIMIDINE BIOSYNTHESIS
Site : Liver
Organelle : Cytoplasm & mitochondria.
Sources of Pyrimidine Ring :

om
l.c
ai
Aspartic acid

gm
Glutamine

@
95
19
10

Respiratory CO2
02
oy
tr
ee

Pathway :
nj

Aspartate
CO2 + Glutamine CPS II Carbamoyl transcarbamoylase Carbamoyl aspartic acid
ira
ch

phosphate Dihydroorotase
|
ow

Dihydro orotic acid

r
ar
M

Dihydroorotate NAD+
Only step that occurs
©

dehydrogenase
in mitochondria NADH
Orotic acid
CMP
TMP UMP OMP
End Products of Pyrimidine Catabolism :
• β-alanine (From cytosine & uracil)
Water soluble
• β-amino isobutyrate (From thymine)

Disorder : Hereditary Orotic Aciduria :

Defect : De novo synthesis of pyrimidines.

Type 1 orotic aciduria :

Orotate phosphoribosyl transferase.
Defect in : UMP synthase
Orotidine monophosphate decarboxylase.

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 76 Biochemistry

----- Active space ----- C/f :

• Macrocytic, megaloblastic anemia : Does not respond to Vit B12/Folic acid/
Fe supplementation.
• Intellectual defect + .

DNA 00:30:40

Watson & Crick Model :

• Right handed antiparallel double helical structure.
A T
• Base pairing rule
G C
• Chargaff’s rule : A + G = C + T (Purines = Pyrimidines)
• Base stacking :

om
- Vertical force of interaction b/w base pairs.

l.c
ai
- D/t hydrophobic interactions & Van der Waals forces.

gm
@
Organization of DNA : 95
19
Nucleosome : Histone octamer + ds DNA.
10
02
oy

• Basic proteins.
tr
ee

• Rich in arginine & lysine.

nj
ira

• Positively charged.
ch

• Made up of core histones (H2A, H2B, H3, H4).

|
row
ar

DNA Replication :
M
©

Salient features :
• Both strands act as templates. • Semidiscontinuous
• Bidirectional : Always 5’ 3’. • Semi conservative.
• Occurs in S phase • Requires primer.

Steps of replication :
1. Identification of site of origin :
Ori : Fixed point on DNA where replication begins.
- E. coli : Ori C.
- Bacteriophage : Ori λ
- Yeast : Autonomous Replicating Sequence (ARS).
- Human : Multiple ori + , similar to ARS.

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 Molecular Biology : Part 1 77

2. Binding of ori-binding protein to ori Unwinding of AT rich regions ----- Active space -----

Binding of SSB (Single Strand Binding) protein :

Prevents local reannealing of DNA.

3. Helicase : Further unwinding of DNA.

Topoisomerase : Nicking, resealing enzyme that relieves topological constraints.
4. Leading strand synthesis :
a. Leading strand template (31 51).
b. RNA primase added at 31 end.
c. DNA polymerase III :
Adds nucleotides continuously from 51 31 of daughter strand.

om
d. DNA polymerase I : Removes the RNA primer.

l.c
ai
5. Lagging strand synthesis :

gm
a. Lagging strand template : 51 31.
@
95
b. Multiple RNA primers added & DNA polymerase III adds short segments of
19
10

nucleotides (Okazaki fragments).

02

c. DNA polymerase I : Removes the RNA primer.

oy
tr

d. Ligase fills the gap on RNA primer removal.

ee
nj
ira

DNA Polymerase (DNAP) :

ch
|
ow

Enzyme Function Enzyme Function

r
ar

Prokaryotic DNAP Eukaryotic DNAP

M

DNAP I • Removal of primers & gap filling. ε Leading strand synthesis

©

(AKA Kornberg’s • DNA repair (Major). δ Lagging strand synthesis + DNA proofreading
enzyme) • DNA proof reading.
γ Mitochondrial DNA synthesis
• DNA repair.
DNAP II β DNA repair activity
• DNA proof reading.
α Primase activity
• Leading strand synthesis.
DNAP III • Synthesis of Okazaki fragments.
• DNA proofreading.

Klenow fragment :
• DNAP I is without 51 31 exonuclease activity.
• Used in Sanger’s sequencing.

Telomere :
• Ends of the chromosomes.
• At 31 end : TTAGGG tandem repeats + .

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 78 Biochemistry

Hayflick limit:
----- Active space -----
On removal of primer from 31 end :
The primer nucleotide sequence is not replicated in the daughter strand
Hayflick limit :
End replication error
After 50 cell divisions
After multiple cell divisions
DNA replication stops.
Telomere attrition.
(Leads to aging)
(Shortening of ends of chromosomes)
Telomerase :
Terminal telomere transferase
Function : Adds DNA segments at 31 end

om
l.c
Prevents telomere shortening

ai
gm
(No Hayflick limit.)

@
Applied Biochemistry
Properties : 95
19
Cancer
1. Contains an intrinsic RNA template.
10

+
02

2. Reverse transcriptase activity + .

oy

Telomerase activity
tr

Absent in : Somatic cells. -

ee
nj

Premature aging.
ira

Present in : Skin cells, hematopoietic cells, germ line cells,

ch

cancer cells, lymphocytes.

|
ow
r
ar

DNA Repair Defects :

M
©

Defects in DNA Repair mechanisms Associated disorders

• Xeroderma pigmentosa
Bulky adducts/ - Cutaneous photosensitivity
Pyrimidine dimers Nucleotide Excision Repair (NER) - ↑Risk of skin cancer
(UV exposure) • Cockayne syndrome
• Trichothiodystrophy
Abasic sites Base Excision Repair (BER) MUTYH-associated polyposis
Base mismatch Mismatch Repair (MMR) Hereditary Non-Polyposis Colorectal Cancer (HNPCC)
• SCID
Non-Homologous End Joining (NHEJ)
• Radiosensitive SCID
• Double strand breaks • Ataxia telangiectasia like disorder
• Single strand breaks • Nijmegen Break Syndrome
• Intrastrand cross- • Bloom’s syndrome
links Homologous Recombination (HR)
• Werner syndrome
• Rothmund Thomson syndrome
• Breast cancer susceptibility

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 Molecular Biology : Part 1 79

Transcription 01:00:50 ----- Active space -----

DNA RNA.
Only one strand transcribed : Template/Minus/Antisense strand.
Other strand : Coding/Plus/Sense strand.
- Strand not involved in transcription.
- Same sequence as that of RNA with T replaced by U.

Enzyme :
RNA polymerase (RNAP).
• Prokaryotic : Multisubunit
- β subunit : Catalytic, binds to Mg2+.
- σ subunit : Binds to promoter.

om
• Eukaryotic RNAP

l.c
ai
gm
RNAP-I RNAP-II RNAP-III

@
Sensitivity to α-amantin Least Highest Intermediate
95
• mRNA
19
10

rRNA • miRNA • tRNA

Major products
02

(Most abundant) • snRNA • 5S rRNA

oy

• lncRNA
tr
ee
nj

Promoters of Transcription :
ira

• Coding region sequences that specify the start site of transcription.

ch
|

• Gene-specific
ow

-3 -2 -1 +1 +2 +3
r
ar
M
©

Start
Upstream Downstream
E.g : site
Prokaryotes Eukaryotes :
• Pribnow box : -10 bp. • TATA box : -25 bp
• TGG box : -35 bp. • CAAT box : -70 bp to -80 bp

Enhancers/Silencers/Repressors :
• ↑ or ↓ transcription of eukaryotic gene.
• Present upstream/downstream.
• Non-specific

ρ Dependent Termination :
ρ factor binds to RUT site (C-rich region of RNA)

Detaches RNA from DNA.

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 80 Biochemistry

----- Active space ----- POST TRANSCRIPTIONAL MODIFICATION

1. 51 capping :
Step Enzyme Site
1. Addition of 7 methyl guanosine cap at 51 end Guanyl transferase Nucleus
2. Methylation of N7 of guanine & 21 OH group of ribose Methyl transferase Cytoplasm
Functions :
• Stabilizes mRNA : Prevents the attack of 51 31 exonuclease.
• Facilitates initiation of translation.
• Binding of mRNA to initiation complex (43s preinitiation complex).

2. 3’ Poly A Tailing :
• Addition of 40-200 adenosine residues at 31 end.

om
• Enzyme : Polyadenylate polymerase.

l.c
ai
gm
Functions :

@
• Stabilizes mRNA : Prevents the attack of 31 51 exonuclease.
95
19
• Facilitates exit of mRNA from nucleus Cytoplasm for translation.
10

• Recruitment of 40s ribosome.

02
oy
tr

3 Splicing Of Exons & Removal Of Introns :

ee
nj
ira

Sn RNA (Ribozyme) : Rich in uracil +

SnRNP/
ch

Carried out by spliceosomes 60 proteins : RR, SR motif +

|

Snurps
ow

Primary transcript
r
ar
M

Steps :
©

1. Spliceosome cuts at splice sites (Exons-introns junctions) :

Ist exon (Coding) - intron junction : SnRNP binds SnRNA cuts the junction.
2. The cut end loops back & connects to middle of intron : Lariat formation.
3. Spliceosome makes 2nd cut at end of intron releasing the lariat.
4. Joining of exons via 31 51 phosphodiester bond.

Alternate RNA Processing/Differential RNA Processing :

Linking of exons in different sequences

Different proteins formed

Significance : 20,500 genes >1 lakh proteins synthesized.

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 Molecular Biology : Part 1 81

RNA Editing : ----- Active space -----

Exception to central dogma.

Eg :
Fully translated
• Liver : Apo B (CAA) Apo B100.
Cytosine deamination
• Intestine : Apo B (CAA) UAA (Stop codon)
NH3 Partial translation
Apo B48 (Truncated protein)

RNA 01:27:28

om
• Every RNA except mRNA (Coding) is non-coding.

l.c
• Histone mRNA : Poly A tail - .

ai
gm
• hnRNA for histone gene : No introns.

@
• SLE : D/t autoimmune response to snurps. 19
95
• Nucleus : M/c site of post-transcriptional processing.
10
02

• Nucleolus : Site of post-transcriptional processing of rRNA

oy
tr

tRNA :
ee
nj

Non-coding RNA made of 74-91 nucleotides.

ira
ch
|

Structure :
ow

• 2˚ structure : Clover leaf shape.

r
ar

• 3˚ structure : Inverted L shape.

M
©

• 4 arms :
a. Acceptor arm : Contains CCA at 31 end Binds to specific amino acids.
b. Anticodon arm : Binds to specific codons.
c. TψC (Only RNA that contains thymine) arm/Pseudouridine arm :
Binds to ribosome.
d. DHU arm/D-arm : Binds to aminoacyl tRNA synthetase.

Ribosomal RNA :
Present in the ribosomal assembly.
40s : 18S rRNA + 30 proteins
80s ribosome
60s : 28S rRNA + 5.8S rRNA + 5S rRNA + 50 proteins

Peptidyl transferase activity.

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 82 Biochemistry

----- Active space ----- miRNA :

Small non-coding ssRNA of 21-22 nucleotide length.

Function : Post-transcriptional regulation of gene expression.

Sources :
• miRNA : Endogenous (Pri micro RNA gene).
• siRNA : Exogenous.

Formation :
Pri miRNA gene

Precursor miRNA

om
Drosha DGCR8

l.c
ai
Transported out of

gm
nucleus via Exportin
@
95Dicer
19
10

ss miRNA
02
oy
tr

RNA Induced Silencing Complex (RISC) : miRNA + Ago protein

ee
nj
ira
ch

Bind with 31 UTR of mRNA

|
ow
r
ar

mRNA mRNA Translation

M
©

degradation destabilization arrest

Gene silencing/Gene knockdown/RNA interference

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 Molecular Biology : Part 2 83

MOLECULAR BIOLOGY : PART 2 ----- Active space -----

Mutations  00:00:05

Point mutation (Base substitution) : M/c.

Nonsense mutation Silent mutation
U A A U C A U C U
(Termination codon) (Codon for serine) (Codon for serine)

Missense mutation

om
C C A

l.c
ai
(Codon for proline)

gm
@
Frame shift mutation :
95
19
Insertion/deletion of nucleotide Distorted reading frame.
10
02

Nonsense suppressor tRNA (Suppressor tRNA mutation) :

oy
tr

mRNA : Coding codon Base substitution Stop codon

ee
nj

(UAC) (UAG)
ira

tRNA can bind with stop codon on mRNA

ch

tRNA : AUG Counter mutation AUC

|

(No translation arrest).

ow

(On anticodon arm)

r
ar
M

Epigenetics
©

00:05:32

Heritable, reversible chemical modification of DNA or chromatin.

No change in DNA sequence.

Functions :
• Regulation gene expression. • Genomic imprinting.
• X chromosome inactivation. • Aging process.

Common modifications :
• DNA methylation.
• DNA acetylation.
Eg :
- Histone acetylation Euchromatin formation Gene activation.
- Histone deacetylation Heterochromatin formation Gene silencing.

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 84 Biochemistry

----- Active space ----- Detection of epigenetic modification :

• Methylation specific PCR. • Bisulphite sequencing.
• DNA chromatin immunoprecipitation • Methylation sensitive restriction
(ChIP). endonuclease digestion.
Translation 00:09:31

Salient Features of Genetic Code :

• Triplet codon : 3 nucleotides. • Degenerate (Wobble hypothesis) : 1
• Universal : Each codon codes for amino acid can
same protein in all species. have > 1 codon (In 3rd base).
• Unambiguous : • Non-overlapping.
1 codon codes for only 1 protein. • Start codon : AUG.
• Stop codons : UAA, UGA, UAG.

om
l.c
STEPS OF TRANSLATION

ai
gm
Charging of tRNA :

@
95
Process of amino acid (AA) attaching on acceptor arm of tRNA.
19
10

tRNA
02
oy

+ Specific amino acid Aminoacyl tRNA synthetase Aminoacyl tRNA.

tr
ee

A A A (Phenylalanine)
nj

U U U
ira

mRNA ATP AMP

ch
|

Initiation :
ow

GTP + eIF-2 (initiation factor) + tRNAi

r
ar
M
©

Ternary complex
+ 40s
43s pre initiation complex + mRNA 48s initiation complex + 60s 80s initiation
Elongation : complex
Ribosome : 80s (60s + 40s) initiation complex.
1. 3 sites :
- E site.
- P site : Initiator tRNA (Codes for methionine).
- A site : Depending on codon, tRNA charged with AA binds.
2. Peptide bond synthesis (From P site to A site).
3. Translocation of ribosome on mRNA to free A site :
- E site : Free tRNA.
- P site : Polypeptide.
- A site : Free to bind tRNA charged with AA.
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Molecular Biology : Part 2 85

Termination : ----- Active space -----

Ribosome reaches Binding of Peptidyl transferase Polypeptide
stop codon releasing factor + GTP freed.

Hybridisation Techniques 00:17:00

BLOTTING TECHNIQUES
Southern blot Northern blot Western blot/Immuno blot
Target molecule DNA RNA Protein
Transfer medium Nitrocellulose/Nylon membrane Nitrocellulose membrane
Labelled DNA probe : Complimentary DNA :
Probe used Complimentary sequence to Complimentary to RNA Labelled antibody

om
target sequence. (By reverse transcriptase)

l.c
ai
• RNA detection

gm
Detect specific protein/
Application DNA detection
• Study of gene expression antigen

@
95
19
South-Western blot : For DNA - protein interaction.
10
02

MICROARRAY
oy
tr

DNA identification :
ee

Chip with known oligonucleotide + Fluorescent labelled

nj
ira

Unknown DNA
ch

RNA identification :
|
ow

Chip with known cDNA + Fluorescent labelled Fluorescence

r

Unknown RNA
ar

detected.
M

Protein identification :
©

Chip with known antigen/antibody + Fluorescent labelled

Unknown Ag/Ab
KARYOTYPING
Steps :
1. Collect cells from peripheral vein 3. Incubation at 37°C for 3 days.
using heparin syringe. 4. Harvest with colchicine.
2. Culture in phytohemagglutinin. 5. Routine staining with Giemsa.
Banding Techniques :
Banding technique Use
Giemsa (G) Light & dark banding
Quinacrine (Q) Similar to Giemsa, but examination with UV fluorescence microscope
Reverse (R) Denatured chromosome Light & dark bands in reverse pattern
Centromeric (C) Heterochromatin (Centromere) stained preferentially

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 86 Biochemistry

----- Active space ----- Note :

Human Genome Project : 2003 Sequencing of human genome complete.
FLUORESCENT IN-SITU HYBRIDISATION (FISH)
23 distinct fluorescent probes used for each chromosome.
Uses :
To detect :
• Microdeletions. • Translocations.
• Amplification. • Aneuploidy.
Types :
Metaphase FISH Interphase FISH

om
l.c
ai
gm
@
95
19
10
02
oy

• Non-dividing cells.
tr
ee

• Rapid results & more sensitivity.

nj
ira

Recombinant DNA Technology 00:34:59

ch
|
ow

Restriction endonuclease (RE) :

r

• Present in bacteria : Restrict phage entry.

ar
M

• Molecular scissors : Cut at specific palindromic sequence.

©

Vector : Carriers of foreign DNA

1. Plasmid : Extrachromosomal bacterial dsDNA Confer antibiotic resistance.
Insert size : 0.1 to 10 kbp.
2. Phage DNA : Linear DNA in phages.
Insert size : 10 to 20 kbp.
3. Artificial chromosome (AC).
- Bacterial (BAC)
300 kbp.
- Phage (PAC)
- Yeast (YAC) : 1000 to 3000 kbp.
Restriction map :
• Unique band pattern formed when DNA is treated with specific restriction
enzyme.
• Same restriction enzyme Unique pattern in each individual.
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 Molecular Biology : Part 2 87

Restriction fragment length polymorphism : ----- Active space -----

• Mutation of gene Abolish restriction site.
Create restriction site.
• Based on band pattern Mutation detected.

DNA Fingerprinting :
• Band pattern of unknown DNA Matched with Band pattern of known DNA.
• Used in medico-legal cases (Identifying suspect etc).

DNA Footprinting :
• Study of DNA-protein interaction.
• Method :
DNA is mixed with protein

om
DNAase

l.c
Breakdown of DNA areas not bound to protein.

ai
gm
On gel electrophoresis.

@
- Only broken fragments seen. 95
19
- Fragments bound to proteins not visualized (Footprint regions).
10
02
oy

POLYMERASE CHAIN REACTION

tr
ee

• Exponential amplification of target DNA.

nj
ira

• No. of DNA after n cycles = 2n.

ch
|
ow
r
ar
M

(90 to 94°C)
©

(50 to 60°C)

(72°C)
+ deoxynucleotide
+ Taq polymerase

Steps of PCR

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 88 Biochemistry

----- Active space ----- Real Time PCR : Reverse Transcriptase PCR (RT-PCR) :
• A fluorescent probe with dye Study of RNA (Gene expression).
on one end & quencher (nullifies
fluorescence when bound to probe)
on other end.
Fluophore Quench
Probe
• Eg :
- Taqman probe
- SYBR green
- Ethidium bromide
• During elongation probe cleaved &

om
dye displaced emitting fluorescence.

l.c
• ↑Fluorescence

ai
Amount of DNA

gm
quantified real time.

@
DNA SEQUENCING 95
19
10

Sanger’s Sequencing :
02
oy

First sequencing method : Frederick Sanger.

tr
ee
nj

Components :
ira

• Dideoxy NTs (ddNT).

ch
|

• Klenow polymerase.
ow

• dNTs.
r
ar
M
©

Principle :
No functional No 3’-5’ phospho- Controlled chain
Dideoxy NT
3’-OH group diester bond termination.
Technique :
DNA for sequencing added to 4 test tubes with different ddNT.

ddNT in test tube : ddT ddG ddC ddA

Chain termination at : A site C site G site T site

Electrophoresis

Bands of different length for each test tube

Sequence of nucleotides can be found out.

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 Micronutrients : Vitamins and Minerals 89

MICRONUTRIENTS : VITAMINS AND MINERALS ----- Active space -----

Endogenous vitamins :
• Synthesised by the body : • Produced in the body : By microbiome
- Niacin : From tryptophan. - Vitamin K.
- Vitamin D : From cholesterol. - Pantothenic acid.
- Biotin.

Fat soluble vitamins : A, D, E & K.

Water soluble vitamins : B complex & C.

om
Vitamin A vs Vitamin D

l.c
00:01:25

ai
gm
Vitamin A Vitamin D

@
• Retinal 95 • Ergocalciferol (D2) : Plant sources
19
Forms • Retinoic acid • Cholecalciferol (D3) : Animal sources/Self
10

• Retinol synthesised
02
oy

7-dehydrocholesterol
tr
ee

UVB rays (290-315 nm)

Intestine Skin
nj

b-carotene (Diet) Retinol

ira

Cholecalciferol
ch

+ D-binding protein 25-hydroxylase

|
ow

25-hydroxycholecalciferol
Metabolism C arried in Retinyl ester
r

Liver : Stored PTH

ar

Liver
chylomicron
M

in Ito cells (↑Ca2+, ↓PO4)

©

+
1-α-hydroxylase
Transported by Retinol Binding
Plasma Kidney 1,25-dihydroxycholecalciferol
Protein (RBP) & transthyretin
(Biologically active form)
1. Vision : Generation of impulse
2. Regulation of gene expression
3. Normal reproduction
1. Regulation of Ca2+ & P043-
4. Maintainence of normal epithelium of skin &
- Bone
mucosa
- kidney ↑Ca2+, ↑PO43-
5. Anti-oxidant : b-carotene
Functions - Intestine
6. Therapeutic use :
2. Immunomodulatory : Prevent TB
- b-carotene cutaneous photosensitivity
3. Anti-proliferative : prevent Ca
- All-trans retinoic acid : Promyelocytic
Colon, Breast, prostate.
leukemia (Differentiation therapy)
- 13-cis-retinoic acid (Isotretinoin) : Cystic
acne & childhood neuroblastoma

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 90 Biochemistry

----- Active space -----

Vitamin A Vitamin D
1. Eye manifestations :
- Nyctalopia (Night blindness) :
• ↑Unmineralised matrix :
↑Dark adaptation time
- Before closure of epiphysis : Rickets.
- Conjunctival Corneal xerosis
- After closure : Osteomalacia.
Deficiency - Bitot’s spots
• Genu valgum & genu varum
- Corneal ulcer Keratomalacia
• Windswept deformity
2. Skin manifestations :
• Rachitic rosary
- Follicular hyperkeratosis
- Squamous metaplasia
1. Acute toxicity :
- Pseudotumor cerebri (In arctic explorers)
- Exfoliative dermatitis

om
- Hepatomegaly

l.c
Toxicity 2. Chronic toxicity (> 50,000 IU/d) : • Calcinosis : Ca2+ deposited in blood Vessels

ai
- Bony exostoses

gm
- Hepatomegaly (Cirrhosis)

@
3. Pregnancy : Teratogenic 95
19
10
02

• Halibut liver oil (Richest)

oy

• Plant sources : Carrots (Richest), green leafy • Fish

Sources
tr

vegetables • Fortified food

ee
nj

• Animal sources : Egg, milk, fish, meat

ira

• ↑Dark adaptation time • Vit. D assay

ch

Assessment
• Carr & Price reaction : Direct assay • S. osteocalcin
|
ow

• Children (1 to 6 y) : 400
r

• Children : 400
ar

• Men & women : 600

M

RDA (IU/d) • Adults : 200

• Pregnancy : 800
©

• Pregnancy : 400
• Lactation : 950

Wald’s visual cycle :

Inactive phosphodiesterase.
Rhodopsin Transducin : cGMP
Active phosphodiesterase
• Opsin + Cis retinol. • Opsin + Trans retinal. 5’GMP
• Inactive GPCR. • Active GPCR
Hyperpolarisation of Na+ channels

Nerve impulse generated.

Note :
• Vit A deficiency : M/c preventable cause of blindness.
• Earliest symptom : Loss of vision to green light.

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 Micronutrients : Vitamins and Minerals 91

----- Active space -----

Conjunctival & corneal dryness Bitot’s spot Corneal ulcer

om
l.c
ai
gm
@
Genu valgum & Genu varum Windswept deformity 95 Rachitic rosary
19
10
02
oy

Vitamin E vs. Vitamin K 00:20:28

tr
ee
nj

Vitamin E Vitamin K
ira

• K1 : Phylloquinone (Dietary Source)

ch
|

• K2 : Menaquinone (Bacterial flora)

Forms Alpha tocopherol
ow

• K3 : M enadione (Synthetic; Water

r
ar

soluble)
M

1. Post-translational gamma carboxylation

©

(Biotin independent) :
1. Most potent anti-oxidant. - Prothrombin - Matrix gla protein
(Chain-breaking) (Factor II) - Factor X
2. Prevents LOL Oxidation. - Factor VII - Nephrocalcin
3. Protects PUFA in membranes from - Factor IX - Protein C
lipid peroxidation. - Product of - Protein S
4. Therapeutic uses : gene gas-6 - Osteocalcin
Functions 2. Pro-coagulant
- Retrolental fibroplasia
- Intermittent claudication Glutamic Gamma carboxy
- Bronchopulmonary dysplasia acid glutamic acid
- Intraventricular hemorrhage
- Slow aging Reduced Epoxide of
- Prevent fatty liver Vit. K Vit. K
Vit.k epoxidase
Oxidised Vit. K

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 92 Biochemistry

----- Active space ----- Vitamin E Vitamin K

• Axonal degeneration
• Peripheral neuropathy
• Spinocerebellar ataxia
• Bleeding manifestations : ↑CT, PT
• Hemolytic anemia
Deficiency • Common in premature babies
• Eye manifestations :
(Prevent : Inj Vit. K at birth)
- Pigmentary retinopathy
- Ophthalmoplegia
- Nystagmus
Hemolysis Hyperbilirubinemia
• Interferes with platelet aggregation
Toxicity
• Interferes with Vit. K function
Kernicterus (In babies)
• Males : 10 mg/d
• Females : 8 mg/d
RDA -
• Pregnancy : 10 mg/d

om
• Lactation : 12 mg/d

l.c
ai
gm
Note :

@
95
• Vit. K epoxidase inhibitors : Warfarin & dicumarol (Anticoagulants).
19
• Breast milk : Poor source of Vit. K.
10
02
oy

Hematopoetic Vitamins 00:27:02

tr
ee
nj

Folic Acid v/s Vitamin B12 :

ira
ch

Folic acid (Vit. B9) Vit B12

|
ow

Tetrahydrofolic acid : • Adenosyl B12 :

r
ar

Carrier of 1 carbon groups : Methyl malonyl CoA mutase

M

• Formyl Methyl malonyl CoA Succinyl CoA

©

Form & • Methyl B12

• Methyl
function Homocysteine methyl transferase/
• Methylene
• Methenyl methionine synthase
• Formimino Homocysteine B12, B9 Methionine
• Mainly animal sources
Green leafy vegetables
Sources • Only vegetarian source : curd
(Plant sources only)
(D/t lactobacillus)
1. Megaloblastic anemia
2. Neural tube defects
Spina bifida
1. Megaloblastic anemia
Anencephaly
2. Subacute combined degeneration :
Deficiency 3. Homocysteinemia : D/t defective
sulfur-containing amino acid - Numbness
manifestations
metabolism - Loss of reflex
- ↑ Risk for thrombosis - Peripheral neuropathy
- ↓ Methionine ↓SAM : Alters
epigenetic modifications.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Micronutrients : Vitamins and Minerals 93

Folic acid (Vit. B9) Vit B12 ----- Active space -----

• Serum folate/Red cell folate

• Serum cobalamine
• Histidine load test : FIGLU excretion
• Serum homocysteine
in urine.
• Urine homocysteine
Assessment • Serum homocysteine
• Serum methylmalonyl CoA specific
• Serum Amino Imidazole
• Schilling test
Carboxamide Ribose-5-phosphate
• Peripheral smear
(AICAR)

Bone marrow
& peripheral
smear

om
Megaloblast in bone marrow
Macrocytes in peripheral sinear

l.c
ai
gm
Causes of Vit. B12 deficiency :

@
1. Nutritional : Strict vegans. 3. Intestinal :
95
19
2. Gastric : ↓Intrinsic Factor (IF) from - Crohn’s disease.
10

parietal cells - Fish tapeworm (Diphyllobothrium

02
oy

- Autoimmune pernicious anemia. latum).

tr
ee

- Gastrectomy. - Stagnant loop syndrome.

nj
ira
ch

Energy Releasing Vitamins 00:40:36

|
ow

Vitamin B1 vs. Vitamin B2 :

r
ar
M
©

Vitamin B1 (Thiamine) Vitamin B2 (Riboflavin)

• Sources :
• AKA Warburg yellow enzyme
- Aleurone layer of grains
• Heat stable
- Animal food : Egg, meat
• Present in flavoproteins.
Features • Functions : Coenzyme role (TPP)
• Active form :
- Oxidative decarboxylation
- FAD : Acyl CoADH, Succinate DH
- PDH, BCKDH, AKGDH
- FMN : Complex I ETC
- Transketolase

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 94 Biochemistry

----- Active space ----- Vitamin B1 (Thiamine) Vitamin B2 (Riboflavin)

Causes : 1. Red beefy/magenta coloured
- Polishing of rice tongue
- Chronic alcoholism

Manifestations :
1. Dry beri-beri
- Symmetrical motor & sensory
neuropathy
- Loss of reflexes, Muscle cramps 2. Angular stomatitis & cheilosis
- Muscle atrophy (If severe) : PNS 3. Fissures in lips.
affected

2. Wet beri-beri

om
- Peripheral edema

l.c
Deficiency - Dyspnea

ai
- Cardiomegaly

gm
- Pulmonary edema

@
- High output cardiac failure 95
19
10

3. Wernicke’s Encephalopathy (WE) :

02

- Horizontal nystagmus
oy

4. Corneal vascularisation : Difficulty in

tr

- Ophthalmoplegia
ee

vision, lacrimation
- Ptosis
nj
ira

- Truncal ataxia
ch

- Global confusion
|
ow

4. Wernicke Korsakoff’s :
r
ar

Features of WE + dementia +
M
©

confabulatory psychosis

• Erythrocyte transketolase level • Erythrocyte glutathione reductase

Assessment
• Urinary thiamine excretion • Urinary riboflawin

Vitamin B3 (Niacin) :
Functions :
1. Coenzyme :
- NAD + All OH except Acyl CoA DH & SDH.
- NADPH generating :
• HMP oxidative.
• Cyt isocitrate DH.
• Malic enzyme.
- NADPH utilising : All reductases.
2. Therapeutic use : Lipid modifying drug (Hyper triglyceridemia).
Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Micronutrients : Vitamins and Minerals 95

Deficiency of Vit. B3 : Pellagra ----- Active space -----

1. Dermatitis (Photosensitivity) : 3. Dementia.
Casal’s necklace. 4. Death.
2. Diarrhoea

Niacin toxicity :
1. PG mediated flushing :
- Pre treatment : Aspirin.
- Laropiprant (PG antagonist).
2. Hyperuricemic.
3. Glucose intolerance.
4. Cystoid macular edema.
5. Gastric irritation.

om
6. Fulminant hepatitis.

l.c
ai
gm
Note :

@
Pellagra-like symptoms. 95
19
• Hartnup’s disease : ↓Absorption of tryptophan ↓Niacin.
10
02

• Carcinoid syndrome : ↑Tryptophan Shunted Serotonin (↓Niacin production).

oy

• Maize/Corn diet : Niacin in bound form + poor source of tryptophan.

tr
ee

• Jowar/Sorghum staple diet : ↑Leucine - QPRTase ↓Niacin production.

nj
ira
ch

Vitamin B5 (Pantothenic Acid) :

|
ow

Function : Present in CoA & Acyl carrier protein (FA synthase complex).
r
ar

Deficiency : Gopalan’s burning foot syndrome/nutritional melalgia.

M
©

Biotin (Vitamin H/B7) :

Function : Coenzyme role
• Carboxylation reaction
- Pyruvate carboxylase.
- Acetyl CoA carboxylase.
- Propionyl CoA carboxylase.

Deficiency :
• Cause :
- Raw egg consumption : Avidin Inhibits Biotin.
• Symptoms :
- Depression, hallucinations.
- Scaling, seborrheic dermatitis & erythematous rash.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 96 Biochemistry

----- Active space ----- Biochemical tests :

• Urinary biotin concentration.
• Serum & urine propionic acid level.
• ↓Activity of biotin dependent enzymes in lymphocyte.

Note :
• Biotin independent carboxylation.
- Gamma carboxylation.
- Carbamoyl phosphate synthetase.
- Malic enzyme.
- AIR carboxylase.
• Leiner’s disease : ↓Biotin linked to complement 5a deficiency.

om
Vitamin B6 :

l.c
Active form : Pyridoxal phosphate.

ai
gm
Function : Coenzyme role.

@
• Transamination 95 • Heme synthesis : ALA synthase
19
• Simple decarboxylation. • Glycogenolysis : Glycogen
10
02

• Transsulfuration phosphorylase.
oy

• Tryptophan metabolism :
tr
ee

Kynureninase.
nj
ira
ch

Deficiency manifestations :
|
ow

• Pyridoxine dependent seizures.

r
ar

• Sideroblastic anemia.
M

• Pellagra-like symptoms :
©

D/t ↓kynureninase ↓Niacin.

Urinary metabolites in B6 deficiency :
Ringed sideroblast
• Homocystine.
• Oxalate.
• Xanthurenic acid.

Assessment :
• Enzyme activity : Erythrocyte transaminase.
• Load test : Tryptophan load test Excretion of xanthurenic acid.
• Direct measurement : Estimation of B6.

Toxicity of B6 : Sensory neuropathy.

Note : RDA of B6 depends on protein intake.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 Micronutrients : Vitamins and Minerals 97

Vitamin C (Ascorbic Acid) : ----- Active space -----

Synthesis : Humans can't synthesise Vit. C Lack L-gulonolactone (Uronic acid pathway).
Functions :
1. Collagen synthesis : Prolyl & lysyl hydroxylase.
2. Iron absorption : Ferrireductase.
3. Tyrosine metabolism : PHPP hydroxylase.
4. Bile acid synthesis : 7-α-hydroxylase.
Sources : Citrus fruits. (Richest source).
Deficiency :
• Scurvy :
a. Bleeding manifestation

om
b. Iron deficiency anemia.

l.c
c. Scorbutic rosary.

ai
gm
@
95
19
Hemarthrosis Splinter hemorrhages Petechial rashes
10
02
oy
tr
ee

• Barlow’s disease (Infantile scurvy)

nj
ira

• Cause : D/t deficiency during weaning (6 to 12 months)

ch

• Treatment : Supplement Vit. C.

|
ow
r
ar

Minerals 01:02:40
M
©

Copper :
Copper deficiency :
Wilson’s disease Menke’s disease/Kinky or steely hair syndrome
Mutation in ATP7B gene : Mutation in ATP7A :
Etiology Defective Cu transport • X-linked recessive
(Cu accumulates in tissues) • Defect in Cu transporter in intestine
• Kayser Fleischer rings seen
• Assessment :
Enzymes affected :
- ↓s. ceruloplasmin
• Xanthine oxidase
Features - Liver copper assay (Gold standard)
• Lysyl oxidase (Collagen affected)
- ↓3-methyl histidine excretion in
• Tyrosinase (Depigmentation)
urine
- 24h urine copper

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 98 Biochemistry

----- Active space ----- Iron

Absorption :

om
l.c
ai
gm
@
95
19
10
02
oy

Selenium, Zinc & Chromium :

tr
ee

Selenium Zinc Chromium

nj
ira

• Anti-oxidant
ch

• Metalloenzymes Potentiates action of

• Selenocysteine containing
|

Functions • Stabilise human insulin insulin in impaired glucose

ow

enzymes : Glutathione
r

• Spermatogenesis tolerance.
ar

peroxidase.
M
©

• Keshan disease (Seen

in China) : Endemic • Hypogeusia : ↓Taste.
cardiomyopathy • Acrodermatitis
Deficiency (D/t dietary deficiency) enteropathica : diarrhoea -
• Kashinbeck disease : + perioral & perineal
Chronic joint disorder rashes.
(Also d/t ↓iodine levels)

Note :
• Highest concentration of Zn : Hippocampus & prostate.
• Chromium 6 (Hexavalent) Pulmonary carcinogen (Stainless steel welding).

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Micronutrients : Vitamins and Minerals 99

RDA of Minerals : ----- Active space -----

Mineral RDA
• Adult : 0.5 g
Calcium • Children : I g
• Pregnancy : 1.5 g
• Males : 15-20 mg
Iron • Females : 20-25mg
• Pregnancy : 40-50 mg
• Males : 150-200 µg
Iodine
• Females : 200-250 μg
Zinc 8-10 mg
Selenium 50-200 μg

om
Copper 1.5-3 mg

l.c
ai
Sodium 5-10 g

gm
Acrodermatitis enteropathica :

@
Potassium 3-4 g Perioral & perianal rashes
95
19
10

Miscellaneous Topics on Nutrition

02

01:15:09
oy
tr

Energy available from macronutrients (in kCal/g) :

ee
nj

• Carbohydrate : 4.
ira

• Protein : 4.
ch
|

• Fat : 9.
ow

• Alcohol : 7.
r
ar
M
©

Specific dynamic action (Thermic effect of food) :

Energy used for digestion of absorption of food :
• Carbohydrate : 5.
• Protein : 30 (Max).
• Lipids : 15.
• Mixed food : 10.

Respiratory quotient :
RQ = Co2 exhaled/02 consumed :
• Carb : 1
• Protein : 0.81
• Lipids : 0.71.
• Alcohol : 0.66.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 100

----- Active space ----- MISCELLANEOUS TOPICS IN BIOCHEMISTRY

TCA Cycle 00:00:10

Acetyl-CoA
Citr
S a
Malate Oxaloacetate y nth te
ase
dehydrogenase CoA-sh
H20
NADH + H+
Citrate
NAD+
L-Malate Aconitase
H20

om
Fumarase Cis-aconite

l.c
H20

ai
gm
Fumarate Fe2+
H20

@
Aconitase
dehydrogenase

FADH2 95
Succinate

19
Isocitrate
10

FAD NAD +
02

Isocitrate
oy

decarboxylation
tr

Succinate NADH + H + dehydrogenase

ee

Oxidative
nj

ATP/GTP
Oxalosuccinate
ira

CoA-sh
SLP
ch

Succinate ADP + Pi/GDP + Pi

Isocitrate
|

Co2
ow

thiokinase dehydrogenase
r

Succinyl-CoA
ar

a-Ketoglutarate
M

NADH + H+ NAD
©

a-Ketoglutarate CoA-Sh
Co2 Energetics :
dehydrogenase
• 3 NADH
Oxidative • 1 FADH2
decarboxylation • 1 ATP
Total : 10 ATP
Features :
• Amphibolic pathway.
• Final common oxidative pathway of lipids, carbohydrates & proteins.
• Acetyl CoA : Completely oxidised.
• Unidirectional steps :
- Citrate synthase.
- a ketoglutarate dehydrogenase.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Miscellaneous Topics in Biochemistry 101

• SLP : Succinate thiokinase. ----- Active space -----

• Anaplerotic reaction : Filling up of intermediates of TCA cycle.
- Pyruvate carboxylase Allosteric activator AcetyI CoA.

Vitamins Involved : Inhibitors :

• Pantothenic acid (CoA). Inhibitor Enzyme
• Thiamine (a-KGDH). Fluoroacetate Aconitase
• Riboflavin (FAD). Arsenate
a ketoglutarate
• Niacin (NAD+). dehydrogenase
Malonate Succinate dehydrogenase

Electron Transport Chain (ETC) 00:06:00

om
l.c
Series of redox couples seen in inner mitochondrial membrane.

ai
gm
Succinate
complex

@
II
NADH 4H NAD Fumarate
95 Intermembrane
+ +
2H+
19
e - 4H+ space(IMS)
10

e- complex (Final e- Fo
e -
02

complex I e -
complex III IV O2 acceptor) complex
e
oy

-
CoQ 1mm
Cyt c e- V
tr

H2O
ee

F1
nj

4H+ 4H+ 2H+ Confirmational change

ira

Matrix
in b subunit
ch
|
ow

ADp + Pi ATP
r
ar
M

Complexes :
©

Complex Name Protons pumped Inhibitors

1. Rotenone
Complex I NADH Q oxido-reductase 4H+ 2. Amobarbital
3. Piericidin A
Succinate Q 1. Malonate
Complex II None
oxido-reductase 2. Carboxin
Q cytochrome c 1. Antimycin A
Complex III 4H+
oxido-reductase 2. BAL (Dimercaprol)
1. CO
Complex IV Cytochrome c oxidase 2H+ 2. Cyanide
3. H2S
Inhibitors of oxidative phosphorylation :
1. Atractyloside : ADP/ATP transporter
Complex V ATP synthase None
2. Oligomycin : F0 complex
3. Venturicidin

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 102 Biochemistry

----- Active space ----- Uncouplers of Oxidative Phosphorylation :

Chemical : Physiological :
1. 2, 4 Dinitrophenol. 1. Thermogenin (Uncoupling protein 1).
2. Dinitrocresol. 2. Thyroxine.
3. FCCP. 3. Long chain fatty acid.
4. High dose aspirin. 4. Ionophores : Valinomycin, gramicidin.

Note : High energy compounds A TP, 1-3-Bisphosphoglycerate, Phosphoenol

pyruvate, Acetyl CoA, Succinyl CoA, Phospho
creatine, Phosphoarginine.

Heme Metabolism 00:16:16

om
Heme containing proteins :

l.c
1. Hemoglobin. 5. Catalase.

ai
gm
2. Myoglobin. 6. Tryptophan pyrrolase.

@
3. Cytochrome c. 95 7. Nitric oxide synthase.
19
4. Cytochrome P450.
10
02
oy

HEME SYNTHESIS
tr
ee

Site :
nj
ira

Liver, erythrocyte precursors.

ch
|

Organelle :
ow

Partly cytoplasmic & partly mitochondrial.

r
ar
M
©

Steps :
Succinyl CoA + glycine
ALA Synthase B6
Lead ALA
ALA dehydratase Lead
Heme
Porphobilinogen Ferrochelatase
HMB synthase/PBG Protoporphyrin III
deaminase/Uroporphyrinogen
Protoporphyrinogen
I synthase
oxidase
Hydroxymethylbilane Protoporphyrinogen III
Uroporphyrinogen III
Uroporphyrinogen Coproporphyrinogen
synthase
decarboxylase oxidase
Uroporphyrinogen III Coproporphyrinogen III.

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025

 Miscellaneous Topics in Biochemistry 103

Factors Affecting : ----- Active space -----

Drugs : Drugs utilizing cytochrome ↓Heme synthesis Aggravate porphyria.

Lead Poisoning :
• Inhibits : ALA dehydratare, Ferrochelatase.
• H/o : Occupational exposure (Paints), children playing with painted toys.
• C/f : Abdominal pain.
• Biomarkers :
- Urinary ALA. - Coproporphyrin.
- Protoporphyrin.
INH : ↓Vitamin B6 ↓Activity of ALA synthase ↓Heme.
Porphyrias :

om
Mode of inheritance : M/c is autosomal dominant except

l.c
• Congenital Erythropoietic Porphyria (CEP).

ai
gm
• ALAD enzyme deficiency (ADP).

@
• Erythropoeitic Protoporphyria (EPP). 95
19
• X-Linked Protoporphyria (XLP).
10
02
oy

Types :
tr
ee

Porphyria Defective enzyme C/F

nj
ira

ADP ALA dehydratase -

ch
|

Neuro visceral manifestations

ow

HMB synthase (M/C : Abdominal pain)

r
ar

Acute intermittent
M

porphyria Accumulation of :
©

(M/c acutely) • Porphobilinogen

• ALA

Cutaneous photosensitivity +

Congenital
Uroporphyrinogen III
Erythropoietic
synthase
porphyria (CEP)
Erythrodontia Non-immune Hydrops
fetalis

Porphyria cutanea Uroporphyrinogen

tarda (M/c) decarboxylase

Cutaneous photosensitivity : Blisters +

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025
 104 Biochemistry

----- Active space ----- Porphyria Defective enzyme C/F

Erythropoeitic
protoporphyria (M/c in Ferrochelatase Non- blistering photosensitivity
children)
Hereditary Coproporphyrinogen
-
coproporphyria oxidase
Protoporphyrinogen
Variegate porphyria -
oxidase

Diagnosis :
1. Ehrlich test : Non-specific Pink : Urobilinogen (UBG).
Red : Porphobilinogen (PBG).
2. Hoesch test.

om
3. Watson Schwartz test : Differentiates b/w UBG & PBG.

l.c
4. Soret band at 400 nm.

ai
gm
5. Wood's lamp : Red fluorescence.

@
Note : Ehrilch's test + in hemolytic jaundice also.
95
19
10

Differentiation of Jaundice :
02
oy

Test Prehepatic Hepatic Obstructive

tr
ee

Direct bilirubin (Conjugated) Normal Normal/↑ ↑

nj
ira

Indirect bilirubin (Unconjugated) ↑ Normal/↑ Normal

ch

Urine bile salt - +/- +

|
ow

Urine bile pigment - +/- +

r
ar
M

Urine UBG + +/- -

©

ALT Normal ↑↑ Normal

AST Normal ↑↑ Normal
ALP Normal ↑ ↑↑↑

Biochemistry Revision • v4.1 • Marrow 8.0 • 2025