Contents

Enzymes : Part 1  1

Enzymes : Part 2  5

Carbohydrates : Introduction  12

Metabolism of Carbohydrates : Part 1  19

Metabolism of Carbohydrates : Part 2  25

Chemistry of Lipids and Phospholipids  34

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Metabolism of Lipids  38

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Amino Acids : Part 1  49

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

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Molecular Biology : Part 2  83

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Micronutrients: Vitamins and Minerals  89

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Miscellaneous Topics in Biochemistry  100

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 Enzymes : Part 1 1

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

Basics of Enzymes 00:01:00

Definition : Specialized proteins that act as biological catalyst.

• Exception : Ribozymes (RNA).

Ribozyme Location Function

Peptidyl transferase 28 Sr RNA Translation
Sn RNA Spliceosome
RNA splicing

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Group II introns -

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Post-translational

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Ribonuclease P -

p
modification of tRNA

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Properties of Enzymes : la
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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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 2 Biochemistry

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

Vitamin Active form Reaction involved

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

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• ALA synthase

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• Glycogen phosphorylase

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Folic acid THFA All 1 Carbon reactions

ap
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Methyl B12 re
laMethionine synthase
Cobalamin
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Adenosyl B12 Methyl malonyl CoA mutase

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Lipoate Lipoamide Oxidative decarboxylation

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Ascorbic acid - Hydroxylation (Prolyl & lysyl)

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Cofactors :
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Metal Reaction catalysed Zn deficiency features

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• Acrodermatitis enteropathica
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• Carbonic anhydrase
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• Visual disturbances
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• Carboxypeptidase A & B
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Zinc • Alcohol dehydrogenase (↓Retinol dehydrogenase)

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• 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
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 Enzymes : Part 1 3

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

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

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

Classification of Enzymes 00:17:14

Class Class name Details & examples.

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Oxidoreductases :

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NAD+ FAD required as election acceptor (Oxidative

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a. Dehydrogenase

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decarboxylation)

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

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c. Oxidase Complex IV ETC

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d. Peroxidase Glutathione peroxidase (H2O2 H2O)

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e. Catalase H2O2 H2O; Enzyme marker of peroxisome

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Transfers functional group

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Eg Kinases (Hexo/glucokinase)
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II Transferase
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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/atom elimination
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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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.

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- Avidin (Raw egg) inhibits biotin (Vit. B7) & hence, all carboxylase reactions.

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Enzyme Mechanism of Action

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00:41:42

ap
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• Substrate binding : Active site. la
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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 :

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1. Substrate concentration :

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• Hyperbolic curve.

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Velocity Active sites saturated

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• Michaelis Menten equation :

p
Vmax

ap
V x [S]
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Zero order
V1 = max
kinetics la km + [S]
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Vmax/2 ↑ [S] ≠ ↑rate • Km (Michaelis constant) :

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

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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.

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as substrate • Usually irreversible

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V0 Vmax

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Vmax

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Vmax1 Vmax1

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Vmax1 la
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Effect on Vmax/2
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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
1/Vmax1
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1/Vmax
Burk plot
1/Vmax 1/Vmax1
1/V max
1

-1/Km - 1/Km1 1/[S] -1/Km1 = - 1/Km -1/Km - 1/Km1

InhibitorEnzyme Inhibitor Enzyme
Dihydrofolate Cyanide Cytochrome c
Methotrexate
reductase CO oxidase
HMG CoA
Statins Fluoride Enolase Phenylalanine inhibits
reductase
Examples placental alkaline
Glyceraldehyde
Dicumarol Vit K epoxide Iodoacetate phosphatase
3-P-DH
Ethanol Alcohol DH
Malonate Fluoroacetate Aconitase
Succinate DH
(Poison)
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 Enzymes : Part 2 7

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

Applied biochemistry

1. Folic acid supplemented when patient is on methotrexate.

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

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

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Allopurinol Xanthine oxidase

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Difluoromethyl ornithine Ornithine decarboxylase

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ap
Aspirin Cyclooxygenase
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Regulation of Enzyme Activity  00:22:53

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Enzyme Quantity :
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• Heme Represses ALA synthase gene.

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• Dietary cholesterol Represses HMG CoA reductase gene.

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Porphyria : Take detailed drug history

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Drugs metabolized by cytochrome

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↓Heme levels

↑ALA synthase (Gene induction)

Accumulation of intermediates
Aggravates porphyria.

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

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 8 Biochemistry

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

2. Phosphorylation - dephosphorylation (Reversible) :

Phosphorylated state Dephosphorylated state

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

Allosteric Regulation :

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• Substrate : Binds to catalytic site.

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• Modifier :

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- Not structural analogue of substrate.
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- Binds to allosteric site. la
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Velocity Myoglobin
Allosteric enzymes :
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• Multi-subunit.
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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)

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Enzymes : Part 2 9

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

Enzyme Allosteric Inhibitor (Products) Allosteric Activator (Substrates)

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

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

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Serine Proteases : Marker Enzymes of Cell Organelles :

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Serine present in active site.
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la
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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.
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• Na+-K+ ATPase
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at this site.
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3. Elastase : Small amino acids. Smooth endoplasmic

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Glucose-6-phosphate
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4. Thrombin. reticulum
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5. Plasmin. Galactosyl
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Golgi apparatus
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6. Factor X. transferase
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7. Factor XI.
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
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 10 Biochemistry

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

Isoenzyme Subunits Electrophoretogram Tissue localization % in serum Clinical significance

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

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

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

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α-2-ALP (Heat stable) Placenta

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Marker of bone formation :

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

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Gamma ALP Intestinal cells la Ulcerative colitis
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Leukocyte ALP Leukocytes Leukemia

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Cardiac Biomarkers in MI :
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pm
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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.

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• Neutrophil Gelatin • Microalbumin.

.c
id
Associated Lipocalin (NGAL). • Osteopontin.

p le
ap
• IL-8. • Liver fatty acid binding protein.

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• ALT. • la
Sodium hydrogen exchange isoform.
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• Glutathione S-transferase. • Exosomal fetuin.
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Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 12

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

Chemistry of Carbohydrates 00:01:25

Carbohydrates : Aldose or keto derivatives of polyhydroxy alcohol.

Monosaccharides :

No. of carbon atoms Aldoses Ketoses

Triose (Simplest carbohydrates) Glyceraldehyde Dihydroxy acetone
Tetrose Erythrose Erythrulose

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Pentose Ribose Epimer Xylose Ribulose Epimer Xylulose

id
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Hexose Glucose, galactose, Mannose Fructose

p
ap
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Disaccharides : la
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Reducing disaccharides :
iv
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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.

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Insoluble (Crude fibres) :

.c
• Cellulose, AKA non-starch polysaccharide :

id
p le
- Made of beta-D-glucose.

ap
y.
- Resistant to digestion d/t b-linkage and lack of cellulase in human
la
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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.
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Energy released per gram : 2 kcal/g.

Uses :
• Adds bulk to the stool.
• Regulates bowel movements.
• Improves satiety.
• Prebiotic (Fibre) : Promote colonisation of probiotic bacteria.
• Sequesters bile salts ↓Cholesterol.
• Improves glucose tolerance.

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 14 Biochemistry

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

Unbranched heteropolysaccharides made of repeating disaccharide units

Aminosugar Acidic sugar

Glucosamine Galactosamine Glucuronic acid Iduronic acid

Synthesis Site :
Rough endoplasmic reticulum & golgi apparatus.

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

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

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Composition :

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

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Heparin Glucosamine + iduronic acid

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

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2. Keratan sulphate (KS) :

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

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

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

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 Carbohydrates : Introduction 15

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

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

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

Mucopolysaccharidoses 00:37:15

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

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id
(Mucopolysaccharides)

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ap
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Belongs to lysosomal storage disorder.la
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General Features :
iv
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Gargoylic facies : Coarse facial features.

ip
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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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 16 Biochemistry

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

Bullet shaped
middle phalanx Beaking of
vertebra

Dysostosis multiplex

MPS I & II :

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All are AR except Hunter's.

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id
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Enzyme defect Features

p
ap
• Visual disturbances +
y.
Hurler's disease (MPS-I H) L-iduronidase
la • Mental retardation
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• Hirsutism
iv

Sheie's disease (MPS-I S) L-iduronidase (Partial defect)

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• Normal intelligence
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• X-linked recessive
ip
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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 -

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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.

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• Resembles MPS : Accumulation of GAG in lysosomes.

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• Enzyme defect : N-acetyl glucosamine phosphotransferase

id
p le
ap
↓Mannose-6-phosphate : Signal for proteins tagged with it to get degraded in
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la
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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

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process (Passive).

.c
id
le
Solute concentration

p
ap
y.
Location :
la
ere
GLUT Location Important points
at
iv

GLUT-1 Brain, placenta, kidney, RBC, retina, colon Low km (High affinity for glucose)
pr
@

• b cells of pancreas
j9
ip

• Sinusoidal cells of liver • High km (Low affinity)

fz

GLUT-2
pm

• Serosal side of intestine • Active in the fed state

ua

• Proximal renal tubules

|
w
ro

GLUT-3 Neurons, placenta, kidney Lowest Km

ar

• Heart
M
©

GLUT-4 • Skeletal muscle Insulin dependent

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 1 19

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

Fed & Fasting State Metabolism  00:00:10

Well Fed State :

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

om
High insulin/glucagon ratio

.c
id
le
Via Glut-2 glucose enters

p
ap
y.
Liver re
la
e

Glucose
at

ss
iv

Glycolysis
pr
Ex c e

Pyruvate PDH Acetyl CoA Exce

j9

ss
ip
fz

Glycogen
pm

TCA cycle Fatty acid synthesis

ua
|
w
ro

VLDL
ar
M

Peripheral tissues
©

Stored as Triacyl glycerol

(TAG)
- Insulin hSL
Fatty acid
Fasting State :
Stage Duration post food intake Source of energy

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

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

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 20 Biochemistry

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

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

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

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

.c
id
le
Aerobic Glycolysis :

p
ap
y.
Preparatory phase : Stage of ATP utilization (2 ATPs used).
re
la
e
at

Glucose
iv
pr
@

ATP
j9

Irreversible Hexokinase
ip

ADP
fz
pm

Glucose-6-phosphate
ua
|
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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 1 21

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

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

om
PEP

.c
id
1 ADP

p le
Pyruvate kinase (PK) Substrate level 2 x 1 ATP 2 ATP

ap
1 ATP

y.
Pyruvate. phosphorylation Total : 9 ATP
la
ere
at

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

iv
pr
@

Applied biochemistry :
j9
ip
fz

S. no Compound Enzyme inhibited Reason/Application

pm
ua

Blood glucose estimation : Gray

|

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 • v4.0 • Marrow 8.0 • 2024

 22 Biochemistry

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

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

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

om
Significance of 2,3-BPG :

.c
• Maintains taut state of hemoglobin.

id
le
• Responsible for unloading of O2 at tissue site S hifts oxygen dissociation

p
ap
curve to the right.
y.
la
ere
Regulation of Glycolysis :
at
iv
pr

1. Fed state : 2. Fasting state :

@
j9
ip

High insulin glucagon ratio Low insulin glucagon ratio

fz
pm
ua

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 • v4.0 • Marrow 8.0 • 2024

 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 :

om
Even in the presence of ample 02, Glucose Lactate (Used in biosynthetic

.c
pathways).

id
p le
ap
Metabolic reprogramming :

y.
la
re
Normal cell : Cancer cell : Uses glucose via aerobic glycolysis.
e
at
iv

Glucose Glucose
pr
@
j9
ip

PEP PEP
fz
pm

PKM 1 (Pyruvate kinase) : PKM2 :

ua

• 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 • v4.0 • Marrow 8.0 • 2024

 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).

om
Significance of PDH :

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

id
p le
• Fat : Never converted to glucose :

ap
y.
Exceptions :
la
re
a. Glycerol.
e
at

b. Odd chain fatty acid (Propionyl CoA).

iv
pr
@
j9

NADH (2-5 ATP)

ip

NAD+
fz

Pyruvate Acetyl CoA

pm
ua

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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 2 25

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

Glycogen Metabolism 00:00:10

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

Site :
Cytoplasm of liver & skeletal muscles.

Stages :

om
1. Formation of UDP glucose :

.c
id
le
Hexokinase Phosphoglucomutase

p
Glucose Glucose-6-PO4 Glucose-1-PO4

ap
y.
UDP glucose UTP
la
re
pyrophosphorylase PPi
e
at

UDP glucose
iv
pr

2. Formation of linear polymer :

@
j9
ip

UDP glucose Glucose

fz
pm

Glycogenin 4 glucose residues added

ua

• Polypeptide primer Glycogen synthase :

|
w

• Tyrosine residues + • RLE

ro

• Active in dephosphorylated state

ar
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 • v4.0 • Marrow 8.0 • 2024

 26 Biochemistry

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

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

om
.c
Glu-6-PO4 Glu-1-PO4

id
le
H2O Glucose-6-phosphatase

p
Phosphoglucomutase

ap
Pi (In SER)

y.
Glucose Glu-6-PO4 la
Pyruvate Lactate
ere
at

- α (1-4) glycosidic linkage.

iv
pr

- α (1-6) glycosidic linkage.

@
j9

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

ip
fz
pm

Note :
ua

• 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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 2 27

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

Insulin : cAMP 5’ AMP ↓↓cAMP

Dephosphorylation

Activation of : Inactivation of :
Glycogen synthase Glycogen phosphorylase

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

om
.c
• Allosteric activator of glycogen phosphorylase.

id
le
• Activated in extreme state of anoxia.

p
ap
y.
ALLOSTERIC REGULATION re
la
Inhibitors of Glycogenolysis : Activator of Glycogenesis :
e
at
iv

• Glu-6-PO4. Glu-6-PO4.
pr
@

• Glucose (Only in liver).

j9
ip

• ATP.
fz
pm

Glycogen Storage Disorder (GSD)

ua

00:19:20
|
w

Liver GSD :
ro
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 • v4.0 • Marrow 8.0 • 2024

 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

om
• Thin extremities • S. glucose↓

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

id
• O/E : Massive hepatomegaly

le
• S. Uric acid ↑↑

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

y.
• AST & ALT : Normal
disease la
re
• Liver biopsy : Accumulation of normal
e
at

glycogen.
iv

• Ketosis
pr
@

• Hyperlipidemia
j9
ip
fz
pm

• Floppy infant
ua

• 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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 2 29

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

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

• Adolescent male

om
• Pain in calf muscle on exercise

.c
• No hemolysis • S. Glucose : ↓ during exercise

id
le
McArdle’s • Second wind phenomena : Exercise • S. Lactate : ↓

p
ap
disease intolerance • AST & ALT : Normal

y.
Pain in calf Rest Resume activity • Creatine kinase : ↑↑
la
re
during exercise with more ease
e
at

• Rhabdomyolysis Myoglobinuria
iv

• Burgundy coloured urine

pr
@

• Exercise intolerance (No 2 wind

nd
• S. Glucose : ↓ during exercise
j9

phenomena)
ip

Tarui’s disease • S. Lactate : ↓

fz

• Myoglobinuria
pm

• Creatine kinase : ↑
• Hemolysis
ua

Fanconi Bickel
|

GLUT 2 defect -
w

syndrome
ro
ar

• No glycogen accumulation
Type 0 GSD Glycogen synthase defect
M

• 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 • v4.0 • Marrow 8.0 • 2024
 30 Biochemistry

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

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

om
.c
• Only mitochondrial step

id
3. Pyruvate kinase (PK)

le
• OAA : Transported to cytoplasm via Malate

p
ap
Aspartate shuttle
y.
la
PEP carboxykinase
re
b. OAA PEP
e
at
iv

CO2 GTP GDP

pr
@
j9

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

ip
fz

• Pyruvate carboxylase : 2 ATP.

pm

• PEP carboxykinase : 2 ATP.

ua
|

• 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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 2 31

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

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

Galactosemia vs Hereditary Fructose Intolerance (HFI) :

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

om
Trigger Breastfeeding Fruit juices

.c
id
• Intellectual disability

p le
• Convulsions, vomiting, jaundice, failure to thrive

ap
C/f
• Hepatomegaly, liver failure
y.
la
• Feeding difficulty, poor weight gain
ere
at

+ Fructose Low renal

iv
pr

threshold
@
j9

Cataract Fructosuria
ip
fz
pm

No cataract
ua
|

Galactose-1-PO4 :
w

• Hepatotoxic & neurotoxic

ro
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 • v4.0 • Marrow 8.0 • 2024

 32 Biochemistry

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

HMP SHUNT PATHWAY

AKA Pentose phosphate pathway.

Site :
Cytoplasm of liver.

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

om
NADP+

.c
id
Glu-6-PO4 dehydrogenase : RLE

le
NADPH (G6PD)

p
ap
y.
6 Phosphogluconate
la
re
NADP+
e

6-Phosphogluconate dehydrogenase
at
iv

NADPH CO2
pr
@

Ribulose-5-PO4
j9
ip
fz
pm

Functions of NADPH :
ua

1. Free radical scavenging :

|

Glutathione
w

reductase
ro

H2O2 Reduced glutathione NADP+

ar
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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Carbohydrates : Part 2 33

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

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

C/f : Defect in G6PD ↓NADPH.

om
.c
id
• Hemolysis Anemia, jaundice.

p le
ap
• Methemoglobinemia Cyanosis.

y.
Aggravating factor : Drugs, fava beans, infections. la
ere
at
iv

Protective against : Plasmodium falciparum.

pr
@
j9

Peripheral smear : Bite cells, Heinz body.

ip
fz
pm
ua

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 • v4.0 • Marrow 8.0 • 2024

 34

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

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

Lipid : Soluble in non-polar solvents only.

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

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

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

p le
• Essential FA :

ap
Docosahexaenoic acid (DHA)/
Based on - Linoleic acid : Safflower oil
y.
Cervonic acid :
diet - α-linolenic acid la
re
• Can cross placenta
e
• Non-essential FA
at

• Deficiency : Retinitis pigmentosa

iv

Unsaturated FA
pr
@

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

j9

• ↓Fluidity of membrane
ip

no. of double bonds • Polyunsaturated FA : Safflower oil

fz

• Insulin resistance
pm

Polyunsaturated FA
• Dyslipidemia, CV risk
ua

• Omega - 3 FA : • ↑Inflammation
|

- α-linolenic acid : Flax - seed oil

w
ro

- Timnodonic acid
ar

Significance of omega - 3 FA :
Based on position - Cervonic acid : Breast milk, Fish & algal oil
M

• 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 • v4.0 • Marrow 8.0 • 2024

 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

om
Phosphatidyl inositol
PA + Inositol Cell membrane

.c
(2nd messenger in hormonal pathways)

id
p le
ap
y.
Cardiolipin
la
re
• Alw Barth syndrome (Cardioskeletal myopathy) :
e
at
iv

- Cardiomegaly + myopathy
pr
@

- Mitochondrial disease
j9
ip

• Only antigenic PL
fz
pm

• Cross reacts with Treponema pallidum :

ua

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 • v4.0 • Marrow 8.0 • 2024
 36 Biochemistry

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

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

Disorder Enzyme defect Features

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

om
• No hepatosplenomegaly

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

id
• CRS on macula

p le
ap
Globoid cell

y.
la
re
Galactocerebrosidase/ • Gross developmental delay
e
at

β-galactosidase • Opisthotonus posture

iv

Krabbe’s disease (AR)

pr

(Galactocerebroside accu- with clenched fists

@

mulation in neural tissue) • No hepatosplenomegaly

j9
ip
fz

White matter of brain

pm
ua
|
w

Lysosomal storage disease Enzyme defect Features

ro
ar

• Protruding abdomen • Erlenmeyer

M

• Crumpled tissue paper appearance flask deformity

©

β-glucocerebrosidase/ • Massive hepatosplenomegaly

β-glucosidase (Glucocere- • Thrombocytopenia
Gaucher’s disease (AR)
broside accumulation in bone • Pain & pathological fractures of long bones
marrow, liver) • 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 • v4.0 • Marrow 8.0 • 2024

 Chemistry of Lipids and Phospholipids 37

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

Lysosomal storage disease Enzyme defect Features

• Angiokeratoma • No CR spot or MR
• Lenticular opacities

Fabry’s disease (X-linked

a-galactosidase
recessive)

• Maltese cross : Urinary sediments

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

om
.c
(Lysosomal storage disease)

id
le
• Calcification of adrenal gland.

p
ap
• Watery green diarrhoea.
y.
la
re
DIAGNOSTIC ALGORITHM
e
at

Check for organomegaly

iv

-
pr

+
@
j9

Check for CR spot & MR

ip

Check for cherry red (CR) spot on

fz

macula & mental retardation (MR)

pm
ua

+ - CRS - MR -
CRS + MR + CRS - MR +
|
w

Neimann-Pick Gaucher’s disease :

ro
ar

disease. Crumpled tissue paper

M

appearance Krabbe’s disease

©

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

Opisthonus posture
with clenched fists

Gaucher cell Check for Maltese cross

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

Maltese cross

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 38

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

Metabolism in Fasting State  00:00:22

Lipolysis :
Hydrolytic cleavage of TAG.

Site : Adipose tissue.

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

om
(Diacyl glycerol) Fatty acid (Monoacyl glycerol)

.c
Fatty acid

id
p le
ap
2 MAG esterase Fatty acid

y.
la
re
Glycerol
e
at
iv

Activators :
pr

Applied biochemistry :
@

• Glucagon
j9

1. Insulin resistance ↑Hydrolysis of stored TAG

ip

• Epinephrine
fz
pm

• ACTH ↑Free fatty acid level in blood

ua

• TSH
|
w

• Thyroxine Fatty liver disease.

ro
ar

• MSH (Melanocyte Stimulating 2. Niacin : Locks TAG in the adipose tissue

M
©

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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Lipids 39

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

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

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

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

om
1 ATP 1 AMP

.c
id
(2 ATP equivalents)

p le
ap
2. Carnitine transport : Transports Acyl CoA into mitochondria.
y.
la
re
FA Acyl CoA
e
at
iv

Outer Mitochondrial Thiokinase

pr
@

Membrane (OMM)
j9
ip

AcylCoA + Carnitine
fz
pm

CAT 1/CPT 1 :
ua

• 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 • v4.0 • Marrow 8.0 • 2024

 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

om
C16 β oxidation = C16 - 1 = 7 β oxidation 7 x 4 = 28 ATP.

.c
2

id
le
Activation : Utilizes 2 ATP equivalents - 2 ATP.

p
ap
Total : 108 - 2 = 106 ATP
y.
la
e re
Regulation :
at
iv

CPT-1 gateway : Inhibited by Malonyl CoA.

pr
@

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

j9

• Fasting
ip
fz

(RLE for FA synthesis)

pm
ua

• 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 • v4.0 • Marrow 8.0 • 2024

 Metabolism of Lipids 41

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

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

↓β oxidation

↓Acetyl CoA ↓ATP Enters omega oxidation

No ketone bodies synthesis : Fasting hypoglycemia Dicarboxylic acid

Rothera’s test -

om
.c
id
2. Jamaican Vomiting Sickness :

p le
D/t consumption of unripe Ackee fruit Containe hypoglycin.

ap
y.
Acyl Co A
- Hypoglycinla
re
Acyl CoA
e
at

dehydrogenase
iv
pr

↓β oxidation
@
j9
ip
fz
pm

↓Acetyl CoA ↓ATP

ua
|
w

↓Gluconeogenesis Ketone bodies absent :

ro
ar

Rothera’s test -
M
©

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 • v4.0 • Marrow 8.0 • 2024
 42 Biochemistry

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

Defect : Peroxisome Targeting Sequence (PTS)

Defective phytanic acid & very long chain FA oxidation.

C/f : Resembles Down’s syndrome

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

om
.c
Zellweger Syndrome : Resembles Down’s syndrome

id
le
Diagnosis :

p
ap
• Peroxisomal (Vacant) ghost.
y.
• Accumulation of VLCFA & phytanic acid. la
ere
at
iv

Ketone Body Synthesis

pr

00:33:38
@
j9
ip

Site :
fz
pm

Exclusively liver mitochondria.

ua
|

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 • v4.0 • Marrow 8.0 • 2024
 Metabolism of Lipids 43

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

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

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

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

+
↓Glucose uptake by heart, HSL Liver:

om
skeletal muscle, adipocytes • ↑Glycogenolysis

.c
id
(GLUT 4 : Insulin dependent) ↑Hydrolysis of TAG • ↑Gluconeogenesis

le
p
ap
y.
↑↑Blood glucose Acetyl CoA la
re
+
e

Depletion of OAA ↑↑Blood glucose

at
iv

KB synthesis
pr
@

Lab Diagnosis :
j9
ip

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

fz
pm

2. Ketostix : Detects urine ketone bodies.

ua
|
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 • v4.0 • Marrow 8.0 • 2024

 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 -

om
Steps : HMG CoA reductase

.c
2 x Acetyl CoA

id
p le
↓Coenzyme Q

ap
Acetoacetyl CoA + Acetyl CoA (Derived from Farnesyl)

y.
HMG CoA synthase la
ere
Myopathy
at

HMG CoA
iv
pr

HMG CoA reductase : RLE

@
j9
ip

Mevalonate Cholesterol (27C)

fz
pm
ua

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

|
w

Compounds Derived from Cholesterol :

ro
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 • v4.0 • Marrow 8.0 • 2024
 Metabolism of Lipids 45

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

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

om
• Carry exogenous TAG to peripheral organs : Chylomicron.

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

p le
ap
• Carry cholesterol from peripheral tissue to adrenals : HDL.

y.
la
re
Electrophoretic Pattern :
e
at
iv
pr
@

Origin Chylomicron
j9
ip
fz
pm

LDL (β-Lipoprotein)
ua

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 • v4.0 • Marrow 8.0 • 2024

 46 Biochemistry

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

Site : Intestine Adipose tissue 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
mediated
• Apo E
endocytosis LDL
• Apo CII
TAG via Apo E Enters
+ as ligand
Lipoprotein lipase
Liver (70%) Extrahepatic tissue (30%)
FA + glycerol
(Apo B100 :
Ligand) Enters circulation

om
Excreted via bile

.c
Risk of thrombosis

id
p le
ap
y.
3. HDL : Facilitates reverse cholesterol transport.
la
re
Liver & intestine Spherical HDL3 :
e
at

Receives cholesterol from Spherical HDL2

iv

Discoidal HDL
pr

peripheral tissues via

• Phospholipid
@

• ABCA 1
j9

• Cholesterol
ip

• SRB 1 Cholesterol dislodged to

• Apo A 1 Cholesterol
fz

• ABCG 1 liver
pm

+ LCAT
ua
|

Cholesterol
w

Spherical HDL3
ro

ester
ar
M
©

Disorders of Lipoprotein 01:03:43

Mode of inheritance Defect Lipoprotein accumulated Lipid levels

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

Eruptive xanthoma Milky white Lipemia retinalis

plasma

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Metabolism of Lipids 47

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

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

om
on CRISPR cas9.

.c
id
p le
ap
Corneal arcus Tendon xanthoma :

y.
la M/c achilles tendon
ere
at

Remnant
• TAG : ↑↑
iv

AR Apo E chylomicron &

pr

• Cholesterol : ↑↑
@

VLDL
j9
ip

C/f
fz
pm
ua

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 • v4.0 • Marrow 8.0 • 2024
 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
.c
id
p le
ap
y.
la
ere
at
iv

Pigmentary retinopathy Petechial rash

pr
@
j9
ip
fz
pm
ua
|
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 • v4.0 • Marrow 8.0 • 2024

 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

om
Aliphatic Leucine

.c
Branched chain Isoleucine

id
ple
Valine

ap
y.
• Serine
OH group containing • Threonine la
e re
• Tyrosine
at
iv

• Cysteine
pr

Sulphur containing
@

• Methionine
j9
ip

• Aspartic acid (Aspartate)

fz

Acidic
•
pm

Glutamic acid (Glutamate)

ua

• Asparagine
Amides
|

• Glutamine
w
ro

• Histidine
ar

Basic • Arginine
M
©

• 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 • v4.0 • Marrow 8.0 • 2024

 50 Biochemistry

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

Ketogenic : Ketogenic + glucogenic : Glucogenic :

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

Semi-essential : Essential : Non-essential :

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

om
• Tryptophan. • Histidine.

.c
id
• Phenylalanine. • Isoleucine.

p le
ap
• Threonine.

y.
DERIVED AMINO ACIDS la
e re
Properties :
at
iv

• No codons.
pr
@

• Formation :
j9
ip

- Post translational modification.

fz
pm

- Intermediate of metabolic pathways.

ua

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 • v4.0 • Marrow 8.0 • 2024
 Amino Acids : Part 1 51

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

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

PROPERTIES OF AMINO ACIDS

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

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

om
• UV light absorption : Phenylalanine, tyrosine, tryptophan

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

p le
ap
y.
3. Buffering :
la
re
Maximum with imidazole group of histidine (pH = pKa).
e
at
iv

4. Exist in Charged States :

pr
@

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

j9
ip

• Maximum precipitability, minimum solubility.

fz
pm

• Minimum buffering (pH = pI).

ua
|

TITRATION CURVE
w
ro

Compound with Single Ionizable Group :

ar
M
©

Completely ionized

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

Un-ionized

Alkali added

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 52 Biochemistry

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

pk2

pH pk1 + pk2
pI =
pk1 2

pH = pI : Point of minimum buffering capacity

Alkali added

om
Proteins

.c
00:25:00

id
p le
Peptide bond :

ap
y.
• B/w 2 amino acids Forms proteins.
la
re
• Uncharged.
e
at

• Partial double bond.

iv
pr

• Trans in nature.
@
j9
ip

STRUCTURE OF PROTEINS
fz
pm
ua

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 • v4.0 • Marrow 8.0 • 2024
 Amino Acids : Part 1 53

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

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

Protein misfolding diseases :

om
• Prion diseases.

.c
id
• Amyloidosis.

p le
ap
• Prion related protein diseases :

y.
7. Alzheimer’s disease. 11. Huntington’s disease.
re
la
8. Parkinson’s disease. 12. Pick’s Disease (FTD).
e
at
iv

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

pr
@

10. Cystic fibrosis. 14. Lewy body dementia.

j9
ip
fz
pm

Pathology :
ua

PrP : a helix Mutation PrP Sc : b sheet.

|
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• 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 • v4.0 • Marrow 8.0 • 2024
 54 Biochemistry

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

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

2. Triple helix 3a chain :

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

3. Quarter staggered arrangement :

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

om
.c
Synthesis :

id
p le
ap
Intracellular Extracellular
y.
Site RER of fibroblast la ECM
ere
at

Product Procollagen Tropocollagen

iv
pr

1. Hydroxylation : Prolyl & Lysyl hydroxylase 1. Cleavage

@
j9

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

ip
fz

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

pm
ua

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

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 Amino Acids : Part 1 55

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

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

Disorders a/w Elastin :

1. William Beuren syndrome.

om
2. Cutis laxa.

.c
id
Keratin :

p le
ap
• Component of outer layer of skin, nails & hair.

y.
• Rich in cysteine : Confers hardness to nails. la
ere
• Associated disorder : Epidermolysis bullosa (Classical type).
at
iv
pr

Fibrillin :
@
j9

• Glycoprotein in scaffolding of elastin.

ip
fz

• Fibrillin 1 mutation : Marfan’s syndrome.

pm
ua
|

Amino Acid Metabolism

w

00:47:40
ro
ar

Reactions : NH3
M
©

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 • v4.0 • Marrow 8.0 • 2024
 56 Biochemistry

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

Site : Cytoplasm of all organs.

Examples :
Alanine α Ketoglutarate Aspartate α Ketoglutarate

B6 ALT B6 AST

Pyruvate Glutamate Oxaloacetate Glutamate

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

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

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

p le
ap
y.
Transamination of non-alpha amino acid :
la Applied biochemistry
re
Enzyme : δ ornithine aminotransferase.
e

Gyrate atrophy of retina & choroid :

at
iv

• Defect in δ ornithine aminotransferase

pr
@

• Treatment :
j9
ip

- Restrict ornithine & arginine

fz

- Supplement PLP (B6)

pm

Exceptions to transamination :
ua

1. Proline. 3. Lysine.
|
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2. Hydroxyproline. 4. Threonine.
ro
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 • v4.0 • Marrow 8.0 • 2024

 Amino Acids : Part 1 57

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

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

AKA Kreb’s Henseleit/Ornithine cycle.

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

om
• 1st Nitrogen : Ammonia. • Urea cycle

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

p le
ap
• Carbon atom : Respiratory CO2. • Gluconeogenesis

y.
la
re
Urea Bicycle : Aspartate
e
at
iv
pr
@

TCA cycle Urea cycle

j9
ip
fz
pm
ua

Fumarate
|
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ro

Reactions of Urea Cycle :

CO2 + NH3
ar
M
©

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

Mitochondria NAG : Obligate allosteric activator
2 ADP
Carbamoyl phosphate TCA cycle
II. Ornithine
transcarbamylase (OTC) Aspartate
Ornithine Citrulline
Ornithine (VII) Citrin transporter (VI)
transporter
Citrulline + Aspartate
Ornithine
Urea Arginase (V) 1 ATP
1 AMP AS synthetase (III) Energetics :
H2O Argininosuccinate (AS)
Arginine CPS 1 : 2 x PO4
Cytoplasm AS lyase (1v)
AS lyase : 2 x PO4
Fumarate (C4) Total required : 4 PO4
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 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 :

om
• M/c Urea cycle disorder.

.c
• X-linked recessive.

id
le
• Defect : OTC.

p
ap
y.
la
Carbamoyl phosphate accumulates Shunted for Pyrimidine synthesis
ere
at
iv
pr

Excretion of Accumulation
@
j9
ip

pyrimidines of orotic acid

fz
pm

in urine
ua

Orotic aciduria.
|
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HHH syndrome :
ro
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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Amino Acids : Part 1 59

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

Trichorrhexis nodosa : Brittle hair.

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

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

.c
id
p le
Management of Urea Cycle Disorders :

ap
y.
Investigations :
la
re
↑/Normal : Urea cycle disorders.
e

1. pH of blood
at
iv

↓Organic aciduria.
pr
@

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

j9
ip

metabolic disorders.
fz
pm
ua

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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
.c
id
p le
ap
y.
la
ere
at
iv
pr
@
j9
ip
fz
pm
ua
|
w
ro
ar
M
©

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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.

om
• Catecholamine.

.c
• Thyroid hormones.

id
p le
Phenylalanine hydroxylase

ap
Phenylalanine Tyrosine.
y.
la
re
BH4 BH2
e
at
iv

Dihydrobiopterin reductase
pr
@
j9

NADP+ NADPH
ip
fz
pm
ua

Catabolic Fate :
Tyrosine transaminase
|

Phenylalanine Tyrosine Para/4 hydroxy phenyl pyruvate

w
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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

om
PHPP Tyrosinemia type 3

.c
id
le
Classic Phenylketonuria :

p
ap
Clinical features :
y.
X Melanin : Hypopigmentation.
la
ere
Phenylalanine X Tyrosine X Catecholamine : Agitation, hyperactivity,
at
iv

mental retardation, intractable vomiting.

pr
@
j9

Phenyl pyruvate X T3, T4.

ip
fz
pm

Phenyl acetate Mousy/musty/barny odour.

ua
|
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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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

om
Urine turns black

.c
IV disc Skin. Cartilage. on air exposure/

id
le
alkalinization.

p
Ochronotic arthritis.

ap
y.
la
ere
Clinical features :
at
iv

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

pr
@

• Present with back pain. disc, cartilage.

j9
ip

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

fz
pm
ua

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

om
Vanilyl Mandellic Acid (VMA).
• Epinephrine

.c
id
p le
Pheochromocytoma :

ap
y.
Palpitations
la
ere
at
iv

Triad
pr

Profuse sweating Headache

@
j9
ip

Lab diagnosis :
fz
pm

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

ua

• VMA : Highest specificity. • Catecholamines.

|
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• Catecholamines. • Free metanephrines : Highest

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ar

• Fractionated metanephrines : sensitivity.

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©

Highest sensitivity.
• Total metanephrines.

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

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

Albinism
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 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

om
Kynurinase Alanine Glucogenic

.c
id
le
3-OH anthranilic acid Ketogenic

p
ap
Quinolinate phosphoribosyl

y.
transferase (QPRTase) : RLE
la
re
Vitamin B6 deficiency :
e
at

• 3-OH kynurenine Xanthurenic acid. Niacin.

iv
pr

• ↓Synthesis of niacin Pellagra.

@
j9
ip

Niacin :
fz
pm

• Endogenously synthesized vitamin.

ua

• 60 mg tryptophan 1 mg niacin.
|
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ro

Derivatives :
ar
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 • v4.0 • Marrow 8.0 • 2024
 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.

om
C/f :

.c
• Asymptomatic.

id
le
• Accumulation of

p
Bacterial
Indoxyl compounds Excreted in urine

ap
tryptophan in intestine decomposition
y.
la
re
• Ataxia. Bluish discoloration of diaper.
e
at

• Wide based gait.

iv
pr

• Cutaneous photosensitivity : M/c symptom.

@
j9
ip
fz

Test : Obermeyer test.

pm

Rx : Lipid soluble esters of tryptophan.

ua
|
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Derivatives of Tyrosine
ro

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 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 :

om
B12 deficiency : N5 methyl THFA X THFA.

.c
id
le
Functional deficiency

p
↓DNA synthesis Nucleocytoplasmic synchrony

ap
of THFA
y.
la
re
Megaloblastic anemia.
e
at
iv

Homocysteinuria :
pr
@

Clinical features : Resembles Marfan’s syndrome.

j9
ip

• Developmental delay.
fz
pm

• Mental retardation.
ua

• Tall & thin extremities.

|
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• Skeletal deformities.
ro
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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 68 Biochemistry

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

Pectus excavatum Pectus carinatum Pes cavus Genu valgum/varus

Skeletal deformities in homocysteinuria

Test : Cyanide nitroprusside test + .

om
.c
Classic homocysteinuria Non-classic homocysteinuria

id
le
Methyl B12 formation ;

p
ap
Enzyme Cystathione β synthase
Methylene THF reductase
y.
la
re
Defect in Formation of cysteine Remethylation of homocysteine to methionine
e
at

Homocysteine ↑ ↑
iv
pr

Cysteine ↓ Normal
@
j9
ip

Methionine Normal ↓
fz
pm

• Cysteine supplementation
ua

• 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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Amino Acids : Part 2 69

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

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

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

om
Other Amino Acids

.c
00:49:55

id
p le
Glycine :

ap
y.
Derivatives :
la
re
1. Purine (C4, C5, N7). 3. Heme.
e
at

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

iv
pr

methionine. 5. Collagen.
@
j9
ip

Hyperoxaluria :
fz
pm

Primary : Defect in glyoxylate amino transferase.

ua

Secondary : D/t
|
w

• Vit C excess.
ro

• Ethylene glycol poisoning.

ar

• Vit B6 deficiency. • Methoxyflurane.

M

Oxalate stones : Envelope shaped

©

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

BASIC AMINO ACIDS Histidine

Histidine :
Derivatives : FIGLU (Formimino glutamic acid)
• FIGLU. THFA
• Histamine. Formimino THFA
Glutamic acid.
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 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)

om
BCAA

.c
PLP Transamination.

id
p le
BC ketoacid

ap
y.
BC ketoacid NAD+
dehydrogenase CO2 la Oxidative decarboxylation.
re
NADH
e
at

Acyl group
iv

FAD
pr
@

FADH2 FAD dependent dehydrogenation.

j9
ip

Product.
fz
pm

Maple Syrup Urine Disease

ua

Defect : Branched chain ketoacid dehydrogenase.

|
w

Features :
ro
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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

om
Albinism Tyrosinase

.c
id
MSUD Branched chain keto acid dehydrogenase

p le
ap
Isovaleryl CoA dehydrogenase
Isovaleric acidemia
y.
(A/w leucine catabolism)
la
re
ENZYME DEFECTS Homocystinuria Cystathionine β synthase
e
at
iv

Phenylalanine hydroxylase/DHB
pr

Phenylketonuria
reductase/Defect in THB synthesis
@
j9
ip

Alkaptonuria Homogentisate oxidase

fz
pm

Tyrosinemia type I Fumaryl acetoacetate hydrolase

ua

Tyrosinemia type II Tyrosine transaminase

|
w

Tyrosinemia type III PHPP hydroxylase

ro
ar
M
©

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

PECULIAR ODOURS Hypermethioninemia Boiled cabbage

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

om
Nucleoside
b. Pentose sugar

.c
id
c. PO43- group

p le
ap
y.
Types of Nitrogenous Bases :
la
ere
at

Double ring : Purine Single ring : Pyrimidine

iv
pr

Adenine (6-amino purine)

@
j9
ip
fz
pm
ua
|
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 • v4.0 • Marrow 8.0 • 2024
 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 -

om
(Only in RNA)

.c
Hypoxanthine Inosine Inosine monophosphate (IMP) -

id
le
Xanthine Xanthosine Xanthine monophosphate (XMP) -

p
ap
Cytosine Cytidine Cytidine monophosphate (CMP) d CMP

y.
Thymine Thymidine - la
d Thymidine monophosphate (Only in DNA)
e re
at
iv

Metabolism of Nucleotides
pr

00:13:20
@
j9

PURINE SYNTHESIS
ip
fz

De-novo Purine Synthesis :

pm
ua

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 • v4.0 • Marrow 8.0 • 2024
 74 Biochemistry

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

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

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

om
.c
Disorders of Purine Synthesis :

id
le
Lesch Nyhan Syndrome :

p
ap
y.
Defect : HGPRTase.
la
re
• Hypoxanthine IMP
e

↑Purine catabolism ↑Uric acid.

at

• Guanine GMP
iv
pr
@

C/f : Rx :
j9
ip

• Compulsive self-mutilation. • Allopurinol

fz
pm

• Hyperuricemia • High fluid intake.

ua

• 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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Molecular Biology : Part 1 75

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

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

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

om
.c
id
le
Aspartic acid

p
ap
Glutamine

y.
la
ere
at

Respiratory CO2
iv
pr
@
j9

Pathway :
ip

Aspartate
fz

CO2 + Glutamine CPS II Carbamoyl transcarbamoylase Carbamoyl aspartic acid

pm
ua

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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)

om
• Base stacking :

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

id
le
- D/t hydrophobic interactions & Van der Waals forces.

p
ap
y.
Organization of DNA : la
ere
Nucleosome : Histone octamer + ds DNA.
at
iv
pr

• Basic proteins.
@
j9

• Rich in arginine & lysine.

ip
fz

• Positively charged.
pm
ua

• 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.

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

.c
id
le
5. Lagging strand synthesis :

p
ap
a. Lagging strand template : 51 31.
y.
la
b. Multiple RNA primers added & DNA polymerase III adds short segments of
ere
at

nucleotides (Okazaki fragments).

iv
pr

c. DNA polymerase I : Removes the RNA primer.

@
j9

d. Ligase fills the gap on RNA primer removal.

ip
fz
pm

DNA Polymerase (DNAP) :

ua
|

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

om
.c
id
Prevents telomere shortening

p le
(No Hayflick limit.)

ap
y.
Properties : Applied Biochemistry
la
re
Cancer
1. Contains an intrinsic RNA template.
e
at

+
iv

2. Reverse transcriptase activity + .

pr

Telomerase activity
@
j9

Absent in : Somatic cells. -

ip
fz

Premature aging.
pm

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

ua

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Molecular Biology : Part 1 79

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

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

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

om
• Eukaryotic RNAP

.c
id
ple
RNAP-I RNAP-II RNAP-III

ap
Sensitivity to α-amantin Least Highest Intermediate
y.
la
re
• mRNA
e

• miRNA • tRNA
at

rRNA
Major products
iv

(Most abundant) • snRNA • 5S rRNA

pr
@

• lncRNA
j9
ip

Promoters of Transcription :
fz
pm

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

ua

• Gene-specific
|

-3 -2 -1
w

+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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 80 Biochemistry

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

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

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

om
• Enzyme : Polyadenylate polymerase.

.c
id
p le
Functions :

ap
y.
• Stabilizes mRNA : Prevents the attack of 31 51 exonuclease.
la
re
• Facilitates exit of mRNA from nucleus Cytoplasm for translation.
e
at

• Recruitment of 40s ribosome.

iv
pr
@

3 Splicing Of Exons & Removal Of Introns :

j9
ip
fz

Sn RNA (Ribozyme) : Rich in uracil +

pm

SnRNP/
ua

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

Snurps
|

Primary transcript
w
ro
ar

Steps :
M
©

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Molecular Biology : Part 1 81

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

Exception to central dogma.

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

RNA 01:27:28

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

.c
id
• Histone mRNA : Poly A tail - .

p le
• hnRNA for histone gene : No introns.

ap
y.
• SLE : D/t autoimmune response to snurps.
la
re
• Nucleus : M/c site of post-transcriptional processing.
e
at
iv

• Nucleolus : Site of post-transcriptional processing of rRNA

pr
@
j9

tRNA :
ip
fz

Non-coding RNA made of 74-91 nucleotides.

pm
ua

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

om
Drosha DGCR8

.c
id
le
Transported out of

p
ap
nucleus via Exportin
y.
la
Dicer
ere
at

ss miRNA
iv
pr
@
j9

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

ip
fz
pm

Bind with 31 UTR of mRNA

ua
|
w
ro

mRNA mRNA Translation

ar
M

degradation destabilization arrest

©

Gene silencing/Gene knockdown/RNA interference

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Molecular Biology : Part 2 83

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

Mutations  00:00:05

Point mutation (Base substitution) : M/c.

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

Missense mutation

om
.c
C C A

id
le
(Codon for proline)

p
ap
y.
Frame shift mutation :
la
re
Insertion/deletion of nucleotide Distorted reading frame.
e
at
iv

Nonsense suppressor tRNA (Suppressor tRNA mutation) :

pr
@

Base substitution
j9

mRNA : Coding codon Stop codon

ip
fz

(UAC) (UAG)
pm

tRNA can bind with stop codon on mRNA

ua

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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.

om
• Stop codons : UAA, UGA, UAG.

.c
id
STEPS OF TRANSLATION

p le
ap
Charging of tRNA :

y.
Process of amino acid (AA) attaching on acceptor arm of tRNA.
re
la
e

tRNA
at
iv
pr

+ Specific amino acid Aminoacyl tRNA synthetase Aminoacyl tRNA.

@
j9

A A A
ip

(Phenylalanine)
fz

U U U
pm

mRNA ATP AMP

ua

Initiation :
|
w

GTP + eIF-2 (initiation factor) + tRNAi

ro
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 • v4.0 • Marrow 8.0 • 2024
 Molecular Biology : Part 2 85

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

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

Hybridisation Techniques 00:17:00

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

om
target sequence. (By reverse transcriptase)

.c
id
le
• RNA detection Detect specific protein/

p
ap
Application DNA detection
• Study of gene expression antigen

y.
la
re
South-Western blot : For DNA - protein interaction.
e
at
iv

MICROARRAY
pr
@

DNA identification :
j9
ip

Chip with known oligonucleotide + Fluorescent labelled

fz
pm

Unknown DNA
ua

RNA identification :
|

Chip with known cDNA + Fluorescent labelled Fluorescence

w
ro

Unknown RNA
ar

detected.
Protein identification :
M
©

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
.c
id
p le
ap
y.
la
ere
at
iv
pr

• Non-dividing cells.
@
j9

• Rapid results & more sensitivity.

ip
fz
pm

Recombinant DNA Technology 00:34:59

ua
|

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.
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 Molecular Biology : Part 2 87

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

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

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

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

om
DNAase

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

p le
ap
On gel electrophoresis.

y.
- Only broken fragments seen. la
ere
- Fragments bound to proteins not visualized (Footprint regions).
at
iv
pr

POLYMERASE CHAIN REACTION

@
j9

• Exponential amplification of target DNA.

ip
fz

• No. of DNA after n cycles = 2n.

pm
ua
|
w
ro
ar

(90 to 94°C)
M
©

(50 to 60°C)

(72°C)
+ deoxynucleotide
+ Taq polymerase

Steps of PCR

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 88 Biochemistry

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

om
dye displaced emitting fluorescence.

.c
id
• ↑Fluorescence Amount of DNA

p le
ap
quantified real time.

y.
la
re
DNA SEQUENCING
e
at

Sanger’s Sequencing :
iv
pr

First sequencing method : Frederick Sanger.

@
j9
ip

Components :
fz
pm

• Dideoxy NTs (ddNT).

ua

• Klenow polymerase.
|
w

• dNTs.
ro
ar
M

Principle :
©

No functional No 3’-5’ phospho- Controlled chain

Dideoxy NT
3’-OH group diester bond termination.
Technique :
DNA for sequencing added to 4 test tubes with different ddNT.

ddNT in test tube : ddT ddG ddC ddA

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

Electrophoresis

Bands of different length for each test tube

Sequence of nucleotides can be found out.

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 Micronutrients : Vitamins and Minerals 89

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

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

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

Water soluble vitamins : B complex & C.

om
.c
Vitamin A vs Vitamin D 00:01:25

id
p le
ap
Vitamin A Vitamin D

y.
• Retinal
la • Ergocalciferol (D2) : Plant sources
re
Forms • Retinoic acid • Cholecalciferol (D3) : Animal sources/Self
e
at

• Retinol synthesised
iv
pr

7-dehydrocholesterol
@
j9

UVB rays (290-315 nm)

ip

Intestine b-carotene (Diet) Retinol Skin

fz
pm

Cholecalciferol
+ D-binding protein 25-hydroxylase
ua
|

25-hydroxycholecalciferol
w

Metabolism C arried in Retinyl ester

ro

Liver : Stored PTH

Liver
ar

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 90 Biochemistry

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

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

om
- Hepatomegaly

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

le
- Bony exostoses

p
ap
- Hepatomegaly (Cirrhosis)

y.
3. Pregnancy : Teratogenic la
ere
at
iv

• Halibut liver oil (Richest)

pr

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

@

Sources
j9

vegetables • Fortified food

ip

• Animal sources : Egg, milk, fish, meat

fz
pm

• ↑Dark adaptation time • Vit. D assay

ua

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

• Children (1 to 6 y) : 400
ro

• Children : 400
• Men & women : 600
ar

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 retinol. • Opsin + Trans retinal. 5’GMP
• Inactive GPCR. • Active GPCR
Hyperpolarisation of Na+ channels

Nerve impulse generated.

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Micronutrients : Vitamins and Minerals 91

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

Conjunctival & corneal dryness Bitot’s spot Corneal ulcer

om
.c
id
p le
ap
y.
Genu valgum & Genu varum Rachitic rosary
Windswept deformity
la
ere
at
iv
pr

Vitamin E vs. Vitamin K

@

00:20:28
j9
ip
fz

Vitamin E Vitamin K
pm

• K1 : Phylloquinone (Dietary Source)

ua

• 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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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 -

om
• Pregnancy : 10 mg/d

.c
• Lactation : 12 mg/d

id
p le
ap
Note :

y.
• Vit. K epoxidase inhibitors : Warfarin & dicumarol (Anticoagulants).
re
la
• Breast milk : Poor source of Vit. K.
e
at
iv
pr

Hematopoetic Vitamins
@

00:27:02
j9
ip

Folic Acid v/s Vitamin B12 :

fz
pm
ua

Folic acid (Vit. B9) Vit B12

|

• Adenosyl B12 :
w

Tetrahydrofolic acid :
ro

Carrier of 1 carbon groups : Methyl malonyl CoA mutase

ar

Methyl malonyl CoA Succinyl CoA

M

• Formyl
Form &
©

• Methyl • Methyl B12

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Micronutrients : Vitamins and Minerals 93

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

• Serum folate/Red cell folate

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

Bone marrow
& peripheral
smear

om
Megaloblast in bone marrow
Macrocytes in peripheral sinear

.c
id
ple
Causes of Vit. B12 deficiency :

ap
y.
1. Nutritional : Strict vegans. 3. Intestinal :
la
re
2. Gastric : ↓Intrinsic Factor (IF) from - Crohn’s disease.
e
at

parietal cells - Fish tapeworm (Diphyllobothrium

iv
pr

- Autoimmune pernicious anemia. latum).

@
j9

- Gastrectomy. - Stagnant loop syndrome.

ip
fz
pm

Energy Releasing Vitamins

ua

00:40:36
|
w

Vitamin B1 vs. Vitamin B2 :

ro
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 • v4.0 • Marrow 8.0 • 2024

 94 Biochemistry

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

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

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

2. Wet beri-beri

om
- Peripheral edema

.c
id
Deficiency - Dyspnea

le
- Cardiomegaly

p
ap
- Pulmonary edema

y.
- High output cardiac failure la
ere
at

3. Wernicke’s Encephalopathy (WE) :

iv
pr

- Horizontal nystagmus
@

4. Corneal vascularisation : Difficulty in

- Ophthalmoplegia
j9

vision, lacrimation
ip

- Ptosis
fz
pm

- Truncal ataxia
- Global confusion
ua
|
w

4. Wernicke Korsakoff’s :
ro
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 • v4.0 • Marrow 8.0 • 2024
 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.

om
5. Gastric irritation.

.c
6. Fulminant hepatitis.

id
p le
ap
Note :

y.
Pellagra-like symptoms. la
ere
• Hartnup’s disease : ↓Absorption of tryptophan ↓Niacin.
at
iv

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

pr
@

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

j9
ip

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

fz
pm
ua

Vitamin B5 (Pantothenic Acid) :

|

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

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

ar
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 • v4.0 • Marrow 8.0 • 2024

 96 Biochemistry

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

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

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

om
Vitamin B6 :

.c
id
Active form : Pyridoxal phosphate.

p le
ap
Function : Coenzyme role.

y.
• Transamination la • Heme synthesis : ALA synthase
ere
• Simple decarboxylation. • Glycogenolysis : Glycogen
at
iv

• Transsulfuration phosphorylase.
pr
@

• Tryptophan metabolism :
j9
ip

Kynureninase.
fz
pm
ua

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 Micronutrients : Vitamins and Minerals 97

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

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

om
b. Iron deficiency anemia.

.c
id
c. Scorbutic rosary.

p le
ap
y.
la
re
Hemarthrosis Splinter hemorrhages Petechial rashes
e
at
iv
pr
@
j9
ip

• Barlow’s disease (Infantile scurvy)

fz
pm

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

ua

• 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 • a-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 • v4.0 • Marrow 8.0 • 2024

 98 Biochemistry

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

Absorption :

om
.c
id
p le
ap
y.
la
ere
at
iv
pr

Selenium, Zinc & Chromium :

@
j9
ip

Selenium Zinc Chromium

fz
pm

• Anti-oxidant
• Metalloenzymes Potentiates action of
ua

• Selenocysteine containing
• Stabilise human insulin
|

Functions 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 • v4.0 • Marrow 8.0 • 2024

 Micronutrients : Vitamins and Minerals 99

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

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

om
.c
Copper 1.5-3 mg

id
le
Sodium 5-10 g

p
Acrodermatitis enteropathica :

ap
y.
Potassium 3-4 g Perioral & perianal rashes
la
ere
at

Miscellaneous Topics on Nutrition 01:15:09

iv
pr
@

Energy available from macronutrients (in kCal/g) :

j9
ip

• Carbohydrate : 4.
fz
pm

• Protein : 4.
ua

• Fat : 9.
|
w

• Alcohol : 7.
ro
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 • v4.0 • Marrow 8.0 • 2024

 100

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

TCA Cycle 00:00:10

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

om
Fumarase

.c
Cis-aconite

id
H20

p le
Fumarate Fe2+

ap
H20 Aconitase

y.
dehydrogenase

FADH2
la
Succinate

re
Isocitrate
e
at

FAD NAD +
iv
pr

Isocitrate

decarboxylation
@

NADH + H + dehydrogenase
j9

Succinate
ip

Oxidative
ATP/GTP
fz

CoA-sh Oxalosuccinate
pm

SLP ADP + Pi/GDP + Pi

ua

Succinate Isocitrate
Co2
|

thiokinase dehydrogenase
w
ro

Succinyl-CoA
ar

a-Ketoglutarate
NADH + H+
M

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 • v4.0 • Marrow 8.0 • 2024

 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)

om
00:06:00

.c
id
Series of redox couples seen in inner mitochondrial membrane.

le
p
Succinate

ap
complex

y.
II Fumarate Intermembrane
NADH 4H NAD la
+ + re2H+
e - 4H+ space(IMS)
e
at

e- complex (Final e- Fo
e -
iv

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

CoQ e-
1mm
@

Cyt c e- H2O V
j9

F1
ip

2H+
fz

4H+ 4H+ Confirmational change Matrix

pm

in b subunit
ua
|
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 • v4.0 • Marrow 8.0 • 2024

 102 Biochemistry

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

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

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

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

Heme Metabolism 00:16:16

om
Heme containing proteins :

.c
id
1. Hemoglobin. 5. Catalase.

p le
ap
2. Myoglobin. 6. Tryptophan pyrrolase.

y.
3. Cytochrome c. la 7. Nitric oxide synthase.
ere
4. Cytochrome P450.
at
iv
pr

HEME SYNTHESIS
@
j9

Site :
ip
fz

Liver, erythrocyte precursors.

pm
ua

Organelle :
|
w

Partly cytoplasmic & partly mitochondrial.

ro
ar
M

Steps :
©

Succinyl CoA + glycine

ALA Synthase B6
Lead ALA
ALA dehydratase Lead
Heme
Porphobilinogen Ferrochelatase
HMB synthase/PBG Protoporphyrin III
deaminase/Uroporphyrinogen
Protoporphyrinogen
I synthase
oxidase
Hydroxymethylbilane Protoporphyrinogen III
Uroporphyrinogen III
Uroporphyrinogen Coproporphyrinogen
synthase
decarboxylase oxidase
Uroporphyrinogen III Coproporphyrinogen III.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Miscellaneous Topics in Biochemistry 103

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

Drugs : Drugs utilizing cytochrome ↓Heme synthesis Aggravate porphyria.

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

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

.c
id
• Congenital Erythropoietic Porphyria (CEP).

p le
ap
• ALAD enzyme deficiency (ADP).

y.
• Erythropoeitic Protoporphyria (EPP). la
ere
• X-Linked Protoporphyria (XLP).
at
iv
pr

Types :
@
j9
ip

Porphyria Defective enzyme C/F

fz
pm

ADP ALA dehydratase -

ua

Neuro visceral manifestations

|
w

HMB synthase (M/C : Abdominal pain)

ro

Acute intermittent
ar
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 • v4.0 • Marrow 8.0 • 2024
 104 Biochemistry

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

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

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

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

.c
id
4. Soret band at 400 nm.

p le
5. Wood's lamp : Red fluorescence.

ap
y.
Note : Ehrilch's test + in hemolytic jaundice also.
la
ere
Differentiation of Jaundice :
at
iv
pr
@

Test Prehepatic Hepatic Obstructive

j9
ip

Direct bilirubin (Conjugated) Normal Normal/↑ ↑

fz
pm

Indirect bilirubin (Unconjugated) ↑ Normal/↑ Normal

ua

Urine bile salt - +/- +

|
w

Urine bile pigment - +/- +

ro
ar

+ -
M

Urine UBG +/-

©

ALT Normal ↑↑ Normal

AST Normal ↑↑ Normal
ALP Normal ↑ ↑↑↑

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

©
M
ar
ro
w
|
ua
pm
fz
ip
j9
@
pr
iv
at
ere
la
y.
ap
p le
id
.c
om
©
M
ar
ro
w
|
ua
pm
fz
ip
j9
@
pr
iv
at
ere
la
y.
ap
p le
id
.c
om