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

Metabolism of Lipids  38

Amino Acids : Part 1  49

Amino Acids : Part 2  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
Group II introns -
Post-transcriptional
Ribonuclease P -
modification of tRNA

Properties of Enzymes :
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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)

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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 (Succinate, 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
• ALA synthase
• Glycogen phosphorylase
Folic acid THFA All 1 Carbon reactions
Methyl B12 Methionine synthase
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Cobalamin
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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(↓Retinol dehydrogenase)
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Zinc • Alcohol 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.

Oxidoreductases :
NAD+ FAD required as election acceptor (Oxidative
a. Dehydrogenase
decarboxylation)
• 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

III Hydrolase
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• 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.

Enzyme Mechanism of Action 00:41:42

• Substrate binding : Active site.

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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 :
Velocity Active sites saturated • Hyperbolic curve.
Vmax • Michaelis Menten equation :
Zero order V x [S]
V1 = max
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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-∝ 1
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∝ [S] 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
V0 Vmax
Vmax
Vmax1 Vmax1
Vmax1
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Effect on 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]
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Km= Km1 [S] Km1 Km

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1/V0
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Line
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weaver
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1/Vmax1 1/Vmax1 1/Vmax

Burk plot
1/Vmax
1/Vmax1
-1/Km - 1/Km1 1/[S] -1/Km1 = - 1/Km -1/Km1 - 1/Km
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
Allopurinol Xanthine oxidase
Difluoromethyl ornithine Ornithine decarboxylase
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
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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 :
• Substrate : Binds to catalytic site.
• Modifier :
- Not structural analogue of substrate.
- Binds to allosteric site.
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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

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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 -

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

Serine Proteases : Marker Enzymes of Cell Organelles :

Serine present in active site.
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

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Breaks protein
2. Trypsin : Basic amino acids. • Na+-K+ ATPase
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at this site.
3. Elastase : Small amino acids.
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Smooth endoplasmic
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4. Thrombin. Glucose-6-phosphate
reticulum
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5. Plasmin. Galactosyl
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6. Factor X. Golgi apparatus

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transferase
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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
α-2-ALP (Heat labile) Hepatic sinusoidal cells Most stable
α-2-ALP (Heat stable) Placenta Marker of bone formation :
Pre-β-ALP Osteoblast ↑ in Paget's & Vit D deficiency
Gamma ALP Intestinal cells 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
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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
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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.
• Neutrophil Gelatin • Microalbumin.
Associated Lipocalin (NGAL). • Osteopontin.
• IL-8. • Liver fatty acid binding protein.
• ALT. • 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
Pentose Ribose Epimer Xylose Ribulose Epimer Xylulose
Hexose Glucose, galactose, Mannose Fructose

Disaccharides :
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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 :
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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) :

• Cellulose, AKA non-starch polysaccharide :
- Made of beta-D-glucose.
- 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.
2. Absorbs water : Provides cushioning effect at weight bearing joints.

Composition :
GAG 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

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

(Mucopolysaccharides)

Belongs to lysosomal storage disorder.

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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 :
All are AR except Hunter's.
Enzyme defect Features
• Visual disturbances +
Hurler's disease (MPS-I H) L-iduronidase
• Mental retardation
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• Hirsutism
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Sheie's disease (MPS-I S) L-iduronidase (Partial defect)

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• 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.
• Enzyme defect : N-acetyl glucosamine phosphotransferase

↓Mannose-6-phosphate : Signal for proteins tagged with it to get degraded in

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the lysosome.
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Glucose Transporters
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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.

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• 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).

Solute concentration
Location : om

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
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• 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

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 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

High insulin/glucagon ratio

Via Glut-2 glucose enters

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Glucose
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Glycolysis
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Ex c e

Pyruvate PDH Acetyl CoA Exce

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Glycogen
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TCA cycle Fatty acid synthesis

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VLDL
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©

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 • v4.2 • 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
to hypoxia Skeletal muscles : High D/t enormous glycolytic capacity

Aerobic Glycolysis :
Preparatory phase : Stage of ATP utilization (2 ATPs used).
om
l.c

Glucose
ai
gm

ATP
s@

Irreversible Hexokinase
jb

ADP
lra
ni

Glucose-6-phosphate
bi
|
w
ro

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 • v4.2 • 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

PEP
1 ADP
Pyruvate kinase (PK) Substrate level 2 x 1 ATP 2 ATP
1 ATP
Pyruvate. phosphorylation
om
Total : 9 ATP
l.c

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

ai
gm

Applied biochemistry :
s@
jb
lra

S. no Compound Enzyme inhibited Reason/Application

ni

Blood glucose estimation : Gray

bi
|

1. Fluoride Enolase vacutainer containing fluoride

w
ro

oxalate used
ar
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 • v4.2 • Marrow 8.0 • 2025

 22 Biochemistry

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

Site : Takes place in 10% of RBCs.
Glucose 1, 3-BPG Mutas
e
ase 2, 3-BPG Energetics :
hat
Phosp • 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 :
• Maintains taut state of hemoglobin.
• Responsible for unloading of O2 at tissue site S hifts oxygen dissociation
om curve to the right.

Regulation of Glycolysis :
l.c
ai
gm

1. Fed state : 2. Fasting state :

s@

High insulin glucagon ratio Low insulin glucagon ratio

jb
lra
ni
bi

Dephosphorylation of enzymes Phosphorylation of enzymes

|
w
ro
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 • v4.2 • 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
pathways).

Metabolic reprogramming : om
Normal cell : Cancer cell : Uses glucose via aerobic glycolysis.
l.c
ai

Glucose Glucose
gm
s@
jb

PEP PEP
lra

PKM 1 (Pyruvate kinase) : PKM2 :

ni
bi

• Tetramer • Dimer
|

• High catalytic activity • Low catalytic activity

w
ro

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 • v4.2 • 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 :
• Irreversible & cannot be circumvented by another enzyme.
• Fat : Never converted to glucose :
Exceptions : om
a. Glycerol.
l.c

b. Odd chain fatty acid (Propionyl CoA).

ai
gm
s@

NAD+ NADH (2-5 ATP)

jb
lra

Pyruvate Acetyl CoA

ni
bi

b oxidation
|

Fatty acid
w
ro
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 • v4.2 • 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 :
1. Formation of UDP glucose :
Hexokinase Phosphoglucomutase
Glucose Glucose-6-PO4 Glucose-1-PO4
om UDP glucose UTP
pyrophosphorylase PPi
l.c

UDP glucose
ai
gm

2. Formation of linear polymer :

s@
jb

UDP glucose Glucose

lra

Glycogenin 4 glucose residues added

ni
bi

• Polypeptide primer
|

Glycogen synthase :
w

• Tyrosine residues + • RLE

ro
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 • v4.2 • 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
Glu-6-PO4 Glu-1-PO4
H2O Glucose-6-phosphatase Phosphoglucomutase
Pi (In SER)
Glucose Glu-6-PO4 Pyruvate Lactate
om
l.c

- α (1-4) glycosidic linkage.

ai
gm

- α (1-6) glycosidic linkage.

s@

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

jb
lra

Note :
ni
bi

• Phosphoglucomutase : Common to glycogen synthesis & glycogenolysis.

|
w
ro

• 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 • v4.2 • 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 :
• Allosteric activator of glycogen phosphorylase.
• Activated in extreme state of anoxia.

ALLOSTERIC REGULATION
om
Inhibitors of Glycogenolysis : Activator of Glycogenesis :
l.c
ai

• Glu-6-PO4. Glu-6-PO4.
gm

• Glucose (Only in liver).

s@

• ATP.
jb
lra
ni

Glycogen Storage Disorder (GSD)

bi

00:19:20
|
w
ro

Liver GSD :
ar

Prominent feature : Fasting hypoglycemia.

M
©

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 • v4.2 • 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↓
• Convulsions, coma on fasting • Rothera’s test : Positive
• O/E : Massive hepatomegaly • S. Uric acid ↑↑
• S. Lactate ↑↑ (Lactic acidosis)
Von Gierke’s
• AST & ALT : Normal
disease
om
• Liver biopsy : Accumulation of normal
l.c

glycogen.
ai

• Ketosis
gm

• Hyperlipidemia
s@
jb
lra
ni

• Floppy infant
bi
|

• Generalized hypotonia
w

• Fatal : Death within 2 years d/t

ro
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 • v4.2 • 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
• Pain in calf muscle on exercise
• No hemolysis • S. Glucose : ↓ during exercise
McArdle’s • Second wind phenomena : Exercise • S. Lactate : ↓
disease intolerance • AST & ALT : Normal
Pain in calf Rest Resume activity om • Creatine kinase : ↑↑
during exercise with more ease
l.c

• Rhabdomyolysis Myoglobinuria • Burgundy coloured urine

ai
gm

• Exercise intolerance (No 2nd wind

s@

• S. Glucose : ↓ during exercise

phenomena)
jb

Tarui’s disease • S. Lactate : ↓

• Myoglobinuria
lra

• Creatine kinase : ↑
ni

• Hemolysis
bi

Fanconi Bickel
|

GLUT 2 defect -
w

syndrome
ro
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 • v4.2 • 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
• Only mitochondrial step
3. Pyruvate kinase (PK) • OAA : Transported to cytoplasm via Malate
Aspartate shuttle
PEP carboxykinase
om
b. OAA PEP
l.c
ai

CO2 GTP GDP

gm
s@

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

jb
lra

• Pyruvate carboxylase : 2 ATP.

ni

• PEP carboxykinase : 2 ATP.

bi
|

• 1,3-BPG kinase : 2 ATP.

w
ro
ar

Galactose & Fructose

M

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 • v4.2 • 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 1 week of life
st
6 months
Trigger Breastfeeding Fruit juices
• Intellectual disability
• Convulsions, vomiting, jaundice, failure to thrive
C/f
• Hepatomegaly, liver failure
• Feeding difficulty, poor weight gain
om
l.c

+ Fructose Low renal

ai
gm

threshold
s@

Cataract Fructosuria
jb
lra
ni

No cataract
bi
|

Galactose-1-PO4 :
w
ro

• Hepatotoxic & neurotoxic

ar

• ↓Inorganic PO4 Fructose-1-PO4 :

M

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 • v4.2 • 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
NADP+
Glu-6-PO4 dehydrogenase : RLE
NADPH (G6PD)
6 Phosphogluconate om
NADP+
6-Phosphogluconate dehydrogenase
l.c
ai

NADPH CO2
gm
s@

Ribulose-5-PO4
jb
lra

Functions of NADPH :
ni
bi

1. Free radical scavenging :

|

Glutathione
w
ro

reductase
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 • v4.2 • 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.

• Hemolysis Anemia, jaundice.

• Methemoglobinemia Cyanosis.
Aggravating factor : Drugs, fava beans, infections.
om
l.c

Protective against : Plasmodium falciparum.

ai
gm
s@

Peripheral smear : Bite cells, Heinz body.

jb
lra
ni
bi

URONIC ACID PATHWAY Bite cells

|
w

Oxidative pathway for glucose.

ro
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 • v4.2 • 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)
Based on • Saturated FA (Single bonds only) • Fatty liver
double bonds • Unsaturated FA (Double bonds) • Mitochondrial membrane damage
• Essential FA :
Docosahexaenoic acid (DHA)/
Based on - Linoleic acid : Safflower oil
Cervonic acid :
diet - α-linolenic acid
om
• Can cross placenta
• Non-essential FA
l.c

• Deficiency : Retinitis pigmentosa

ai

Unsaturated FA
gm

Based on • Monounsaturated FA : Mustard/Rapeseed oil ↑Trans FA :

s@

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

jb
lra

• Insulin resistance
Polyunsaturated FA
ni

• Dyslipidemia, CV risk
bi

• Omega - 3 FA : • ↑Inflammation
|
w

- α-linolenic acid : Flax - seed oil

ro

- Timnodonic acid
ar

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 • v4.2 • 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
PA + Inositol Cell membrane
(2nd messenger in hormonal pathways)

Cardiolipin om
• Alw Barth syndrome (Cardioskeletal myopathy) :
l.c
ai

- Cardiomegaly + myopathy
gm

- Mitochondrial disease
s@

• Only antigenic PL
jb
lra

• Cross reacts with Treponema pallidum :

ni
bi

False positive syphilis test

|
w
ro
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 • v4.2 • 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
• No hepatosplenomegaly
Sandhoff's disease β-hexosaminidase A & B • Hyperacusis
• CRS on macula
om Cherry red spot
Globoid cell
l.c
ai

Galactocerebrosidase/ • Gross developmental delay

gm

β-galactosidase • Opisthotonus posture

s@

Krabbe’s disease
(Galactocerebroside accu- with clenched fists
jb
lra

mulation in neural tissue) • No hepatosplenomegaly

ni
bi

White matter of brain

|
w
ro

• Protruding abdomen
ar

• Crumpled tissue paper appearance

M

• Massive hepatosplenomegaly
©

β-glucocerebrosidase/
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 • v4.2 • 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.
(Lysosomal storage disease)
• Calcification of adrenal gland.
• Watery green diarrhoea. om
DIAGNOSTIC ALGORITHM
l.c

Check for organomegaly

ai

+ -
gm
s@

Check for cherry red (CR) spot on Check for CR spot & MR
jb
lra

macula & mental retardation (MR)

ni
bi

+ - CRS + MR + CRS - MR - CRS + MR +

|
w
ro

Neimann-Pick Gaucher’s disease :

ar

disease. Crumpled tissue paper

M

appearance
©

GM2 gangliosidosis : Krabbe’s disease

• 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 • v4.2 • 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
Fatty acid (Diacyl glycerol) Fatty acid (Monoacyl glycerol)

2 MAG esterase Fatty acid

om
Glycerol
l.c
ai

Activators :
gm

Applied biochemistry :
• Glucagon
s@

1. Insulin resistance ↑Hydrolysis of stored TAG

jb

• Epinephrine
lra

• ACTH
ni

↑Free fatty acid level in blood

bi

• TSH
|
w

• Thyroxine Fatty liver disease.

ro
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 • v4.2 • 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
1 ATP 1 AMP
(2 ATP equivalents)

2. Carnitine transport : Transports Acyl CoA into mitochondria.

om
FA Acyl CoA
l.c
ai

Outer Mitochondrial Thiokinase

gm

Membrane (OMM)
s@
jb

AcylCoA + Carnitine
lra
ni

CAT 1/CPT 1 :
bi

• RLE
|

• Gateway of β oxidation
w
ro

Acyl Carnitine Transported

ar
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 • v4.2 • 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.
2
Activation : Utilizes 2 ATP equivalents - 2 ATP.
Total : 108 - 2 = 106 ATP
om

Regulation :
l.c
ai

CPT-1 gateway : Inhibited by Malonyl CoA.

gm
s@

• Fasting Low I/G ratio - Acetyl CoA carboxylase ↓Malonyl CoA + CPT - 1
jb
lra

(RLE for FA synthesis)

ni
bi

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

(RLE for FA synthesis)

ro
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 • v4.2 • 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 -
2. Jamaican Vomiting Sickness :
D/t consumption of unripe Ackee fruit Containe hypoglycin.
Acyl Co A
om
- Hypoglycin
Acyl CoA
l.c

dehydrogenase
ai
gm

↓β oxidation
s@
jb
lra
ni

↓Acetyl CoA ↓ATP

bi
|
w
ro

Ketone bodies absent : ↓Gluconeogenesis

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 • v4.2 • 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.
Zellweger Syndrome : Resembles Down’s syndrome
Diagnosis :
• Peroxisomal (Vacant) ghost.
• Accumulation of VLCFA & phytanic acid.
om
l.c
ai

Ketone Body Synthesis

gm

00:33:38
s@

Site :
jb
lra

Exclusively liver mitochondria.

ni
bi
|

Steps : Acyl CoA

w
ro
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 • v4.2 • 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:
skeletal muscle, adipocytes • ↑Glycogenolysis
(GLUT 4 : Insulin dependent) ↑Hydrolysis of TAG • ↑Gluconeogenesis

↑↑Blood glucose Acetyl CoA

om
+
l.c

Depletion of OAA ↑↑Blood glucose

ai

KB synthesis
gm

Lab Diagnosis :
s@
jb

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

lra
ni

2. Ketostix : Detects urine ketone bodies.

bi
|
w
ro
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 • v4.2 • 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 : HMG CoA reductase
2 x Acetyl CoA
↓Coenzyme Q
Acetoacetyl CoA + Acetyl CoA (Derived from Farnesyl)
HMG CoA synthase
om

Myopathy
l.c

HMG CoA
ai
gm

HMG CoA reductase : RLE

s@
jb

Mevalonate Cholesterol (27C)

lra
ni
bi

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

|
w
ro

Compounds Derived from Cholesterol :

ar

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

M
©

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 • v4.2 • 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 :
• Carry exogenous TAG to peripheral organs : Chylomicron.
• Carry endogenous TAG to peripheral organs : VLDL.
• Carry cholesterol from peripheral tissue to adrenals : HDL.
om
Electrophoretic Pattern :
l.c
ai
gm

Origin Chylomicron
s@
jb
lra

LDL (β-Lipoprotein)
ni
bi

Mobility
|

VLDL (Pre β-Lipoprotein)

w
ro

IDL (Broad β)
ar
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 • v4.2 • 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)
Excreted via bile Risk of thrombosis

3. HDL : Facilitates reverse cholesterol transport.

om
Liver & intestine Spherical HDL3 :
l.c

Receives cholesterol from Spherical HDL2

ai

Discoidal HDL
peripheral tissues via
gm

• Phospholipid
• ABCA 1
s@

• Cholesterol
• SRB 1 Cholesterol dislodged to
jb

• Apo A 1 Cholesterol
lra

• ABCG 1 liver
+
ni

LCAT
bi
|

Cholesterol
w
ro

ester Spherical HDL3

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 • v4.2 • 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
on CRISPR cas9.

Corneal arcus Tendon xanthoma :

M/c achilles tendon
om
l.c

Remnant
• TAG : ↑↑
ai

AR Apo E chylomicron &

gm

• Cholesterol : ↑↑
VLDL
s@
jb

C/f
lra
ni
bi

Familial dysbetalipoproteinemia
|
w

(Type III HL)

ro
ar
M
©

Bunch of grapes/ Palmar xanthoma

Tubero-eruptive xanthoma

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

Hepatosplenomegaly Orange tonsils

Biochemistry Revision • v4.2 • 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

Pigmentary retinopathy Petechial rash

gm
s@
jb
lra
ni
bi
|
w
ro
ar
M
©

Acanthocytes

Sitosterolemia (Type II HL) : Fish Eye Disease :

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

Biochemistry Revision • v4.2 • 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
Branched chain Isoleucine
Valine
• Serine
OH group containing • Threonine
om

• Tyrosine
l.c
ai

• Cysteine
gm

Sulphur containing
• Methionine
s@

•
jb

Aspartic acid (Aspartate)

Acidic
lra

• Glutamic acid (Glutamate)

ni
bi

• Asparagine
Amides
|

• Glutamine
w
ro

• Histidine
ar
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 • v4.2 • 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.
• Tryptophan. • Histidine.
• Phenylalanine. • Isoleucine.
• Threonine.
DERIVED AMINO ACIDS
om

Properties :
l.c
ai

• No codons.
gm

• Formation :
s@
jb

- Post translational modification.

lra
ni

- Intermediate of metabolic pathways.

bi

Classification :
|
w
ro
ar

Seen in proteins : Not seen in proteins :

M
©

• 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 • v4.2 • 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.
• UV light absorption : Phenylalanine, tyrosine, tryptophan
Tryptophan : 280 nm (Maximum UV absorption).

3. Buffering : om
Maximum with imidazole group of histidine (pH = pKa).
l.c
ai

4. Exist in Charged States :

gm
s@

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

jb

• Maximum precipitability, minimum solubility.

lra
ni

• Minimum buffering (pH = pI).

bi
|
w

TITRATION CURVE
ro
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 • v4.2 • 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

Proteins 00:25:00

Peptide bond :
• B/w 2 amino acids Forms proteins. om
• Uncharged.
l.c

• Partial double bond.

ai
gm

• Trans in nature.
s@
jb

STRUCTURE OF PROTEINS
lra
ni
bi

Primary : Peptide (Covalent) bond.

|
w
ro

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 • v4.2 • 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 :

• Prion diseases.
• Amyloidosis.
• Prion related protein diseases :
7. Alzheimer’s disease. 11. Huntington’s disease.
om
8. Parkinson’s disease. 12. Pick’s Disease (FTD).
l.c
ai

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

gm

10. Cystic fibrosis. 14. Lewy body dementia.

s@
jb
lra

Pathology :
ni
bi

PrP : a helix Mutation PrP Sc : b sheet.

|
w

• Hydrophobic amino acids exposed.

ro
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 • v4.2 • 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 + .

Synthesis :

Intracellular Extracellular
Site RER of fibroblast ECM
om
l.c

Product Procollagen Tropocollagen

ai
gm

1. Hydroxylation : Prolyl & Lysyl hydroxylase 1. Cleavage

s@

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

jb
lra

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

ni
bi

Types :
|
w
ro
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

Biochemistry Revision • v4.2 • Marrow 8.0 • 2025

 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.

Keratin :
• Component of outer layer of skin, nails & hair.
• Rich in cysteine : Confers hardness to nails.
om

• Associated disorder : Epidermolysis bullosa (Classical type).

l.c
ai
gm

Fibrillin :
s@

• Glycoprotein in scaffolding of elastin.

jb
lra

• Fibrillin 1 mutation : Marfan’s syndrome.

ni
bi
|

Amino Acid Metabolism

w

00:47:40
ro
ar

NH3
M

Reactions :
©

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 • v4.2 • 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.
• Significance : Biosynthesis of non-essential amino acids.
• Ping pong mechanism/Bibi reaction : 2 substrate 2 product reaction.

Transamination of non-alpha amino acid :

Applied biochemistry
om
Enzyme : δ ornithine aminotransferase.
Gyrate atrophy of retina & choroid :
l.c
ai

• Defect in δ ornithine aminotransferase

gm

• Treatment :
s@

- Restrict ornithine & arginine

jb
lra

- Supplement PLP (B6)

ni

Exceptions to transamination :
bi
|

1. Proline. 3. Lysine.
w
ro

2. Hydroxyproline. 4. Threonine.
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.

Biochemistry Revision • v4.2 • Marrow 8.0 • 2025

 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
• 1st Nitrogen : Ammonia. • Urea cycle
• 2nd Nitrogen : Aspartate. • Blood : Heme synthesis
• Carbon atom : Respiratory CO2. • Gluconeogenesis
om
Urea Bicycle : Aspartate
l.c
ai
gm

TCA cycle Urea cycle

s@
jb
lra
ni
bi

Fumarate
|
w
ro

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 synthetase : 2 x PO4
Fumarate (C ) Total required : 4 PO4
4

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 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.
• X-linked recessive.
• Defect : OTC.

Carbamoyl phosphate accumulates Shunted for Pyrimidine synthesis

om
l.c
ai
gm

Excretion of Accumulation
s@

pyrimidines of orotic acid

jb
lra

in urine
ni
bi

Orotic aciduria.
|
w
ro

HHH syndrome :
ar

• Defect : Ornithine transporter Hyperornithinemia.

M
©

• Carbamoyl phosphate + lysine Homocitrulline Homocitrullinemia.

• Accumulation of NH3 Hyperammonemia.

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

Spastic Diplegia Scissoring gait

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 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

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

Management of Urea Cycle Disorders :

Investigations : om
↑/Normal : Urea cycle disorders.
1. pH of blood
l.c
ai

↓Organic aciduria.
gm

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

s@
jb

metabolic disorders.
lra
ni
bi

Interpretation :
|
w
ro
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
s@
jb
lra
ni
bi
|
w
ro
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.
• Thyroid hormones.
Phenylalanine hydroxylase
Phenylalanine om Tyrosine.
BH4 BH2
l.c
ai

Dihydrobiopterin reductase
gm
s@

NADP+ NADPH
jb
lra
ni
bi

Catabolic Fate :
|

Tyrosine transaminase
w

Phenylalanine Tyrosine Para/4 hydroxy phenyl pyruvate

ro
ar

PHPP hydroxylase/
M
©

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

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 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

Classic Phenylketonuria :
Clinical features : X Melanin : Hypopigmentation.
om

Phenylalanine X Tyrosine X Catecholamine : Agitation, hyperactivity,

l.c
ai

mental retardation, intractable vomiting.

gm
s@

Phenyl pyruvate X T3, T4.

jb
lra
ni

Phenyl acetate Mousy/musty/barny odour.

bi
|
w

Note :
ro
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

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 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

IV disc Skin. Cartilage. on air exposure/
Ochronotic arthritis. alkalinization.
om

Clinical features :
l.c
ai

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

gm

• Present with back pain. disc, cartilage.

s@
jb

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

lra
ni
bi

Lab diagnosis :
|

• FeCl3 test. • X-ray :

w
ro

• AgNO3 test. - Bamboo spine.

ar
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.

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 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).
• Epinephrine

Pheochromocytoma :
Palpitations
om
l.c
ai

Triad
gm

Profuse sweating Headache

s@
jb

Lab diagnosis :
lra

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

ni
bi

• VMA : Highest specificity. • Catecholamines.

|
w

• Catecholamines. • Free metanephrines : Highest

ro
ar

• Fractionated metanephrines : sensitivity.

M
©

Highest sensitivity.
• Total metanephrines.

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

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

Albinism
Biochemistry Revision • v4.2 • 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
Kynurinase Alanine Glucogenic

3-OH anthranilic acid Ketogenic

Quinolinate phosphoribosyl
transferase (QPRTase) : RLE
om
Vitamin B6 deficiency :
l.c

• 3-OH kynurenine Xanthurenic acid. Niacin.

ai
gm

• ↓Synthesis of niacin Pellagra.

s@
jb

Niacin :
lra
ni

• Endogenously synthesized vitamin.

bi

• 60 mg tryptophan
|

1 mg niacin.
w
ro
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 • v4.2 • 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 :
• Asymptomatic.
• Accumulation of Bacterial
Indoxyl compounds Excreted in urine
tryptophan in intestine decomposition om
• Ataxia. Bluish discoloration of diaper.
l.c

• Wide based gait.

ai
gm

• Cutaneous photosensitivity : M/c symptom.

s@
jb

Test : Obermeyer test.

lra
ni

Rx : Lipid soluble esters of tryptophan.

bi
|
w
ro

Sulphur Containting Amino Acids 00:33:10

ar
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.

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 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.

Functional deficiency Nucleocytoplasmic asynchrony

↓DNA synthesis
of THFA om
Megaloblastic anemia.
l.c
ai

Homocysteinuria :
gm
s@

Clinical features : Resembles Marfan’s syndrome.

jb

• Developmental delay.
lra
ni

• Mental retardation.
bi

• Tall & thin extremities.

|
w
ro

• Skeletal deformities.
ar

• Visual disturbances : Ectopia

M
©

lentis (M/c : Inferomedial).

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

Arachnodactyly Tall stature High arched palate

Skeletal deformities in homocysteinuria

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 68 Biochemistry

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

Pectus carinatum Pectus excavatum Pes cavus Genu valgum/varus

Skeletal deformities in homocysteinuria

Test : Cyanide nitroprusside test + .

Classic homocysteinuria Non-classic homocysteinuria
Methyl B12 formation ;
Enzyme Cystathione β synthase
om Methylene THF reductase
Defect in Formation of cysteine Remethylation of homocysteine to methionine
l.c

Homocysteine ↑ ↑
ai
gm

Cysteine ↓ Normal
s@

Methionine Normal ↓
jb
lra

• Cysteine supplementation
ni
bi

• High dose Vit B6 • Methionine supplementation

|

Rx
w

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

ro
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.

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 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.

Other Amino Acids 00:49:55

Glycine :
Derivatives : om
1. Purine (C4, C5, N7). 3. Heme.
l.c

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

ai
gm

methionine. 5. Collagen.
s@
jb

Hyperoxaluria :
lra
ni

Primary : Defect in glyoxylate amino transferase.

bi
|

Secondary : D/t
w
ro

• Vit C excess. • 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.
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 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
PLP Transamination.
BC ketoacid
BC ketoacid NAD+
dehydrogenase CO2 Oxidative decarboxylation.
om
NADH
l.c

Acyl group
ai

FAD
gm

FADH2 FAD dependent dehydrogenation.

s@
jb

Product.
lra
ni

Maple Syrup Urine Disease

bi
|

Defect : Branched chain ketoacid dehydrogenase.

w
ro

Features :
ar

• Age of onset : Neonate.

M
©

• 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.

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 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
MSUD Branched chain keto acid dehydrogenase
Isovaleryl CoA dehydrogenase
Isovaleric acidemia
om (A/w leucine catabolism)
ENZYME DEFECTS Homocystinuria Cystathionine β synthase
l.c

Phenylalanine hydroxylase/DHB
ai

Phenylketonuria
gm

reductase/Defect in THB synthesis

s@

Homogentisate oxidase/Dihydro phenyl

Alkaptonuria
jb

acetate dioxygenase
lra
ni

Tyrosinemia type I Fumaryl acetoacetate hydrolase

bi
|

Tyrosinemia type II Tyrosine transaminase

w
ro

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

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 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
b. Pentose sugar
c. PO43- group

Types of Nitrogenous Bases : om

l.c

Double ring : Purine Single ring : Pyrimidine

ai
gm

Adenine (6-amino purine)

s@
jb
lra
ni
bi
|
w
ro
ar

Guanine (2-amino, 6-oxopurine)

M

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 • v4.2 • 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)
Hypoxanthine Inosine Inosine monophosphate (IMP) -
Xanthine Xanthosine Xanthine monophosphate (XMP) -
Cytosine Cytidine Cytidine monophosphate (CMP) d CMP
Thymine Thymidine - d Thymidine monophosphate (Only in DNA)
om
l.c
ai

Metabolism of Nucleotides 00:13:20

gm
s@

PURINE SYNTHESIS
jb
lra

De-novo Purine Synthesis :

ni
bi

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

|
w

Contributors of purine ring :

ro
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 • v4.2 • 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

Disorders of Purine Synthesis :

Lesch Nyhan Syndrome :
Defect : HGPRTase. om
• Hypoxanthine IMP
l.c

↑Purine catabolism ↑Uric acid.

• Guanine GMP
ai
gm

C/f : Rx :
s@
jb

• Compulsive self-mutilation. • Allopurinol

lra

• Hyperuricemia • High fluid intake.

ni
bi

• Neurological defects. • Alkalization of urine.

|
w
ro
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 :

Aspartic acid
l.c
om Glutamine

Respiratory CO2
ai
gm
s@

Pathway :
jb

Aspartate
CO2 + Glutamine CPS II Carbamoyl transcarbamoylase Carbamoyl aspartic acid
lra
ni
bi

phosphate Dihydroorotase
|
w

Dihydro orotic acid

ro
ar

Dihydroorotate NAD+
M

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 :
- Vertical force of interaction b/w base pairs.
- D/t hydrophobic interactions & Van der Waals forces.

Organization of DNA :
om

Nucleosome : Histone octamer + ds DNA.

l.c
ai
gm

• Basic proteins.
s@

• Rich in arginine & lysine.

jb
lra

• Positively charged.
ni
bi

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

|
w
ro
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.
d. DNA polymerase I : Removes the RNA primer.
5. Lagging strand synthesis :
a. Lagging strand template : 51 31.
b. Multiple RNA primers added & DNA polymerase III adds short segments of
om
l.c

nucleotides (Okazaki fragments).

ai
gm

c. DNA polymerase I : Removes the RNA primer.

s@

d. Ligase fills the gap on RNA primer removal.

jb
lra

DNA Polymerase (DNAP) :

ni
bi
|

Enzyme Function Enzyme Function

w
ro

Prokaryotic DNAP Eukaryotic DNAP

ar
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

Prevents telomere shortening

(No Hayflick limit.)
Properties :
om Applied Biochemistry
Cancer
1. Contains an intrinsic RNA template.
l.c

+
ai

2. Reverse transcriptase activity + .

gm

Telomerase activity
s@

Absent in : Somatic cells. -

jb

Premature aging.
lra

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

ni
bi

cancer cells, lymphocytes.

|
w
ro

DNA Repair Defects :

ar
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.
• Eukaryotic RNAP
RNAP-I RNAP-II RNAP-III
Sensitivity to α-amantin Least Highest
om Intermediate
• mRNA
• miRNA • tRNA
l.c

rRNA
Major products
ai

(Most abundant) • snRNA • 5S rRNA

gm

• lncRNA
s@
jb

Promoters of Transcription :
lra
ni

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

bi

• Gene-specific
|
w

-3 -2 -1 +1 +2 +3
ro
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.
• Enzyme : Polyadenylate polymerase.

Functions :
• Stabilizes mRNA : Prevents the attack of 31 om51 exonuclease.
• Facilitates exit of mRNA from nucleus Cytoplasm for translation.
l.c

• Recruitment of 40s ribosome.

ai
gm
s@

3 Splicing Of Exons & Removal Of Introns :

jb
lra

Sn RNA (Ribozyme) : Rich in uracil +

SnRNP/
ni
bi

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

Snurps
|

Primary transcript
w
ro
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

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

• Histone mRNA : Poly A tail - .
• hnRNA for histone gene : No introns.
• SLE : D/t autoimmune response to snurps.
om
• Nucleus : M/c site of post-transcriptional processing.
l.c

•
ai

Nucleolus : Site of post-transcriptional processing of rRNA

gm
s@

tRNA :
jb
lra

Non-coding RNA made of 74-91 nucleotides.

ni
bi

Structure :
|
w

• 2˚ structure : Clover leaf shape.

ro
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
Drosha DGCR8

Transported out of
nucleus via Exportin
Dicer
om
l.c

ss miRNA
ai
gm
s@

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

jb
lra
ni

Bind with 31 UTR of mRNA

bi
|
w
ro
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

C C A
(Codon for proline)
Frame shift mutation : om
Insertion/deletion of nucleotide Distorted reading frame.
l.c
ai

Nonsense suppressor tRNA (Suppressor tRNA mutation) :

gm
s@

mRNA : Coding codon Base substitution Stop codon

jb

(UAC)
lra

(UAG)
ni

tRNA can bind with stop codon on mRNA

bi

tRNA : AUG Counter mutation AUC

(No translation arrest).
|
w

(On anticodon arm)

ro
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.
STEPS OF TRANSLATION
Charging of tRNA :
Process of amino acid (AA) attaching on acceptor arm of tRNA.
om

tRNA
l.c
ai
gm

+ Specific amino acid Aminoacyl tRNA synthetase Aminoacyl tRNA.

s@

A A A (Phenylalanine)
jb
lra

U U U ATP AMP
mRNA
ni
bi

Initiation :
|
w
ro

GTP + eIF-2 (initiation factor) + tRNAi

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 • v4.2 • 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
target sequence. (By reverse transcriptase)

• RNA detection Detect specific protein/

Application DNA detection
• Study of gene expression
om antigen

South-Western blot : For DNA - protein interaction.

l.c
ai

MICROARRAY
gm
s@

DNA identification :
jb

Chip with known oligonucleotide + Fluorescent labelled

lra

Unknown DNA
ni
bi

RNA identification :
|

+ Fluorescent labelled
w

Chip with known cDNA Fluorescence

ro

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

• Non-dividing cells.
s@

• Rapid results & more sensitivity.

jb
lra

Recombinant DNA Technology

ni

00:34:59
bi
|

Restriction endonuclease (RE) :

w
ro

• 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
DNAase
Breakdown of DNA areas not bound to protein.
On gel electrophoresis.
- Only broken fragments seen.
om

- Fragments bound to proteins not visualized (Footprint regions).

l.c
ai
gm

POLYMERASE CHAIN REACTION

s@

• Exponential amplification of target DNA.

jb
lra

• No. of DNA after n cycles = 2n.

ni
bi
|
w
ro
ar

(90 to 94°C)
M
©

(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 &
dye displaced emitting fluorescence.
• ↑Fluorescence Amount of DNA
quantified real time. om
DNA SEQUENCING
l.c

Sanger’s Sequencing :
ai
gm

First sequencing method : Frederick Sanger.

s@
jb

Components :
lra
ni

• Dideoxy NTs (ddNT).

bi
|

• Klenow polymerase.
w
ro

• dNTs.
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.

Vitamin A vs Vitamin D 00:01:25

Vitamin A Vitamin D
• Retinal • Ergocalciferol (D2) : Plant sources
om
Forms • Retinoic acid • Cholecalciferol (D3) : Animal sources/Self
l.c

• Retinol synthesised
ai
gm

7-dehydrocholesterol
s@

UVB rays (290-315 nm)

jb

Intestine b-carotene (Diet) Retinol Skin

lra

Cholecalciferol
ni

+ D-binding protein 25-hydroxylase

bi
|

25-hydroxycholecalciferol
w
ro

Metabolism Liver : Stored C arried in Retinyl ester PTH

ar

Liver
in Ito cells chylomicron (↑Ca2+, ↓PO4)
M

+
©

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

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 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
- Hepatomegaly
Toxicity 2. Chronic toxicity (> 50,000 IU/d) : • Calcinosis : Ca2+ deposited in blood Vessels
- Bony exostoses
- Hepatomegaly (Cirrhosis)
3. Pregnancy : Teratogenic
om
l.c

• Halibut liver oil (Richest)

ai
gm

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

Sources
s@

vegetables • Fortified food

jb

• Animal sources : Egg, milk, fish, meat

lra
ni

• ↑Dark adaptation time • Vit. D assay

bi

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

• Children (1 to 6 y) : 400
ro

• Children : 400
ar

• Men & women : 600

RDA (IU/d) • Adults : 200
M

• Pregnancy : 800
©

• Pregnancy : 400
• Lactation : 950

Wald’s visual cycle :

Inactive phosphodiesterase.
Rhodopsin Transducin : cGMP
Active phosphodiesterase
• Opsin + Cis retinal. • 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

Genu valgum & Genu varum Windswept deformity Rachitic rosary

om
l.c
ai
gm

Vitamin E vs. Vitamin K 00:20:28

s@
jb

Vitamin E Vitamin K
lra
ni

• K1 : Phylloquinone (Dietary Source)

bi

• K2 : Menaquinone (Bacterial flora)

|

Forms Alpha tocopherol

w

• K3 : M enadione (Synthetic; Water

ro

soluble)
ar
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

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 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
• Lactation : 12 mg/d

Note :
• Vit. K epoxidase inhibitors : Warfarin & dicumarol (Anticoagulants).
om
• Breast milk : Poor source of Vit. K.
l.c
ai
gm

Hematopoetic Vitamins 00:27:02

s@
jb

Folic Acid v/s Vitamin B12 :

lra
ni
bi

Folic acid (Vit. B9) Vit B12

|
w

Tetrahydrofolic acid : • Adenosyl B12 :

ro

Methyl malonyl CoA mutase

ar

Carrier of 1 carbon groups :

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.

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 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

Megaloblast in bone marrow

Macrocytes in peripheral sinear

Causes of Vit. B12 deficiency :

1. Nutritional : Strict vegans. 3. Intestinal :
om
2. Gastric : ↓Intrinsic Factor (IF) from - Crohn’s disease.
l.c

parietal cells - Fish tapeworm (Diphyllobothrium

ai
gm

- Autoimmune pernicious anemia. latum).

s@

- Gastrectomy. - Stagnant loop syndrome.

jb
lra
ni

Energy Releasing Vitamins

bi

00:40:36
|
w
ro

Vitamin B1 vs. Vitamin B2 :

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 • v4.2 • 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
- Peripheral edema
Deficiency - Dyspnea
- Cardiomegaly
- Pulmonary edema
- High output cardiac failure
om
l.c

3. Wernicke’s Encephalopathy (WE) :

ai
gm

- Horizontal nystagmus
4. Corneal vascularisation : Difficulty in
s@

- Ophthalmoplegia
vision, lacrimation
jb

- Ptosis
lra

- Truncal ataxia
ni

- Global confusion
bi
|
w
ro

4. Wernicke Korsakoff’s :
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 • v4.2 • 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.
6. Fulminant hepatitis.

Note :
Pellagra-like symptoms.
om

• Hartnup’s disease : ↓Absorption of tryptophan ↓Niacin.

l.c
ai

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

gm

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

s@
jb

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

lra
ni
bi

Vitamin B5 (Pantothenic Acid) :

|
w

Function : Present in CoA & Acyl carrier protein (FA synthase complex).
ro
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 • v4.2 • 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.

Vitamin B6 :
Active form : Pyridoxal phosphate.
Function : Coenzyme role.
• Transamination • Heme synthesis : ALA synthase
om

• Simple decarboxylation. • Glycogenolysis : Glycogen

l.c
ai

• Transsulfuration phosphorylase.
gm

• Tryptophan metabolism :
s@
jb

Kynureninase.
lra
ni
bi

Deficiency manifestations :
|

• Pyridoxine dependent seizures.

w
ro

• Sideroblastic anemia.
ar
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.

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 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
b. Iron deficiency anemia.
c. Scorbutic rosary.
om
Hemarthrosis Splinter hemorrhages Petechial rashes
l.c
ai
gm
s@

• Barlow’s disease (Infantile scurvy)

jb
lra

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

ni
bi

• Treatment : Supplement Vit. C.

|
w
ro

Minerals
ar

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 • v4.2 • Marrow 8.0 • 2025

 98 Biochemistry

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

Absorption :

om
l.c
ai
gm

Selenium, Zinc & Chromium :

s@

Selenium Zinc Chromium

jb
lra

• Anti-oxidant
ni

• Metalloenzymes Potentiates action of

bi

• Selenocysteine containing
|

Functions • Stabilise human insulin insulin in impaired glucose

w

enzymes : Glutathione
ro

• 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 • v4.2 • 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
Copper 1.5-3 mg
Sodium 5-10 g Acrodermatitis enteropathica :
Potassium 3-4 g om Perioral & perianal rashes
l.c

Miscellaneous Topics on Nutrition 01:15:09

ai
gm
s@

Energy available from macronutrients (in kCal/g) :

jb

• Carbohydrate : 4.
lra
ni

• Protein : 4.
bi

• Fat : 9.
|
w
ro

• Alcohol : 7.
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 • v4.2 • 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
Fumarase Cis-aconite
H20
Fumarate Fe2+
H20 Aconitase
dehydrogenase

FADH2
Succinate

om
Isocitrate
l.c

FAD NAD +
ai
gm

Isocitrate

decarboxylation
s@

Succinate NADH + H+ dehydrogenase

Oxidative
jb

ATP/GTP
lra

CoA-sh Oxalosuccinate
SLP
ni

ADP + Pi/GDP + Pi
bi

Succinate Isocitrate
|

thiokinase Co2 dehydrogenase

w
ro

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 • v4.2 • 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

Series of redox couples seen in inner mitochondrial membrane.

Succinate
complex
II Fumarate Intermembrane
NADH 4H NAD
+ +
2H+
om
e - 4H+ space(IMS)
l.c

e- complex (Final e- Fo
e -
ai

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

CoQ e-
1mm
Cyt c e- H2O V
s@

F1
jb

4H+ 4H+ 2H+

lra

Confirmational change Matrix

ni

in b subunit
bi
|
w

ADp + Pi ATP
ro
ar

Complexes :
M
©

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 • v4.2 • 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

Heme containing proteins :

1. Hemoglobin. 5. Catalase.
2. Myoglobin. 6. Tryptophan pyrrolase.
3. Cytochrome c. 7. Nitric oxide synthase.
om

4. Cytochrome P450.
l.c
ai
gm

HEME SYNTHESIS
s@

Site :
jb
lra

Liver, erythrocyte precursors.

ni
bi

Organelle :
|
w
ro

Partly cytoplasmic & partly mitochondrial.

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.

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 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 :
Mode of inheritance : M/c is autosomal dominant except
• Congenital Erythropoietic Porphyria (CEP).
• ALAD enzyme deficiency (ADP).
• Erythropoeitic Protoporphyria (EPP).
om

• X-Linked Protoporphyria (XLP).

l.c
ai
gm

Types :
s@
jb

Porphyria Defective enzyme C/F

lra

ADP ALA dehydratase -

ni
bi

Neuro visceral manifestations

|
w

HMB synthase (M/C : Abdominal pain)

ro
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 • v4.2 • 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.
3. Watson Schwartz test : Differentiates b/w UBG & PBG.
4. Soret band at 400 nm.
5. Wood's lamp : Red fluorescence.
Note : Ehrilch's test + in hemolytic jaundice also.
om

Differentiation of Jaundice :
l.c
ai
gm

Test Prehepatic Hepatic Obstructive

s@

Direct bilirubin (Conjugated) Normal Normal/↑

jb

↑
lra

Indirect bilirubin (Unconjugated) ↑ Normal/↑ Normal

ni
bi

Urine bile salt - +/- +

|
w

- +
ro

Urine bile pigment +/-

ar
M

Urine UBG + +/- -

©

ALT Normal ↑↑ Normal

AST Normal ↑↑ Normal
ALP Normal ↑ ↑↑↑

Biochemistry Revision • v4.2 • Marrow 8.0 • 2025

©
M
ar
ro
w
|
bi
ni
lra
jb
s@
gm
ai
l.c
om
©
M
ar
ro
w
|
bi
ni
lra
jb
s@
gm
ai
l.c
om