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

m
Metabolism of Lipids  38

co
o.
Amino Acids : Part 1  49

ho
Amino Acids : Part 2  ya 61
5@
s1

Molecular Biology : Part 1  72

im
ai
r

Molecular Biology : Part 2  83

ee
m

Micronutrients: Vitamins and Minerals  89

sa
|
w

Miscellaneous Topics in Biochemistry  100

ro
ar
M
©
©
M
ar
ro
w
|
sa
m
ee
rai
im
s1
5@
ya
ho
o.
co
m
 Enzymes : Part 1 1

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

Basics of Enzymes [Link]

Definition : Specialized proteins that act as biological catalyst.

• Exception : Ribozymes (RNA).

Ribozyme Location Function

Peptidyl transferase 28 Sr RNA Translation
Sn RNA Spliceosome
RNA splicing
Group II introns -

m
Post-translational

co
Ribonuclease P -

o.
modification of tRNA

ho
Properties of Enzymes : ya
5@
s1

1. Made of protein. 4. Precipitated by protein precipitating

im

2. 16% by weight : Nitrogen. agents.

r ai
ee

3. Heat labile.
m
sa

Types of Enzymes :
|
w
ro
ar
M

Simple enzyme Complex enzyme

©

(Only protein : Apoenzyme) (Holoenzyme)

components

Protein part Non-protein part

(Apoenzyme)

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

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
• ALA synthase

m
• Glycogen phosphorylase

co
o.
Folic acid THFA All 1 Carbon reactions

ho
Methyl B12 ya Methionine synthase
5@
Cobalamin
Adenosyl B12 Methyl malonyl CoA mutase
s1
im

Lipoate Lipoamide Oxidative decarboxylation

rai

Ascorbic acid - Hydroxylation (Prolyl & lysyl)

ee
m
sa

Cofactors :
|
w

Metal Reaction catalysed Zn deficiency features

ro
ar

• Carbonic anhydrase • Acrodermatitis enteropathica

M
©

• Carboxypeptidase A & B • Visual disturbances

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

Class Class name Details & examples.

Oxidoreductases :

m
co
NAD+ FAD required as election acceptor (Oxidative
a. Dehydrogenase

o.
decarboxylation)

ho
ya
• Monooxygenase : Phenylalanine/Tyrosine/Tryptophan
5@
I b. Oxygenase hydroxylase, Cytochromes
s1

• Dioxygenase : Homogentisate oxidase

im

c. Oxidase Complex IV ETC

rai
ee

d. Peroxidase Glutathione peroxidase (H2O2 H2O)

m
sa

e. Catalase H2O2 H2O; Enzyme marker of peroxisome

|

Transfers functional group

w
ro

II Transferase Eg Kinases (Hexo/glucokinase)

ar
M

Phosphorylases (Glycogen phosphorylase)

©

• Breaks covalent bonds by adding H2O

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

m
co
Enzyme Mechanism of Action [Link]

o.
ho
• Substrate binding : Active site. ya
5@

• Site for regulator/modifier Allosteric site.

s1
im
ai

Free energy change (DG) :

r
ee

• Free energy change =

m
sa

ΔG = Energy of reactants - Energy of products.

|
w

• Enzyme ↓ activation energy.

ro
ar

No change in ΔG.
M
©

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Enzymes : Part 2 5

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

Enzyme Kinetics  [Link]

Equilibrium Constant (Keq) :

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

Factors Affecting Rate of Reaction :

1. Substrate concentration :
• Hyperbolic curve.

m
Velocity Active sites saturated

co
Vmax • Michaelis Menten equation :

o.
ho
Zero order V x [S]
V1 = max
kinetics ya km + [S]
5@
s1

Vmax/2 ↑ [S] ≠ ↑rate • Km (Michaelis constant) :

im

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

rai

kinetics
ee

-∝ 1
m

∝ [S] Enzyme affinity

sa
|

km [S] to substrate
w
ro

• Ideal substrate : ↓Km.

ar
M
©

2. Enzyme concentration : 3. Temperature & pH :

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 6 Biochemistry

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

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

Competitive inhibition Non-competitive inhibition Uncompetitive inhibition

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

m
V0 Vmax

co
Vmax

o.
Vmax1

ho
Vmax1
Effect on Vmax1 ya
5@
Vmax/2
Vmax/2
s1

Vmax & km Vmax1/2

im

Vmax1/2
r ai
ee
m

Km Km1 [S] Km= Km1 [S] Km1 Km

sa
|
w

1/V0
ro
ar
M

Line
©

weaver
1/Vmax1 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
Allopurinol Xanthine oxidase

m
co
Difluoromethyl ornithine Ornithine decarboxylase

o.
ho
Aspirin Cyclooxygenase
ya
5@
s1

Regulation of Enzyme Activity  [Link]

im
rai

Enzyme Quantity :
ee
m

• Heme Represses
sa

ALA synthase gene.

|
w

• Dietary cholesterol Represses HMG CoA reductase gene.

ro
ar
M

Porphyria : Take detailed drug history

©

Drugs metabolized by cytochrome

↓Heme levels

↑ALA synthase (Gene induction)

Accumulation of intermediates
Aggravates porphyria.

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 8 Biochemistry

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

2. Phosphorylation - dephosphorylation (Reversible) :

Phosphorylated state Dephosphorylated state

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

Allosteric Regulation :
• Substrate : Binds to catalytic site.

m
• Modifier :

co
o.
- Not structural analogue of substrate.

ho
- Binds to allosteric site. ya
5@
s1

Velocity Myoglobin
Allosteric enzymes :
im
ai

• Multi-subunit. Hb :
r
ee

Effect of
• Quaternary structure.
m

allosteric enzyme
sa

• Cooperative binding Sigmoid curve.

|
w

• Usually rate limiting step.

ro
ar

[S]
M

Allosteric activator & inhibitor :

©

Velocity Allosteric + Allosteric + Allosteric

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 -

Serine Proteases & Markers of Cell Organelles [Link]

m
co
Serine Proteases : Marker Enzymes of Cell Organelles :

o.
ho
Serine present in active site.
ya Cell organelle Marker
5@
Enzymes • 5’-nucleotidase
s1

1. Chymotrypsin : Bulky amino acids.

im

Plasma membrane • Adenylyl cyclase

Breaks protein
ai

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

r
ee

at this site.
3. Elastase : Small amino acids.
m

Smooth endoplasmic
sa

4. Thrombin. Glucose-6-phosphate
reticulum
|
w

5. Plasmin.
ro

Galactosyl
ar

6. Factor X. Golgi apparatus

M

transferase
©

7. Factor XI.
Mitochondria ATP synthase
Lysosome Cathepsin
Peroxisome Catalase

Clinical Enzymology  [Link]

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

m
α-2-ALP (Heat stable) Placenta

co
Marker of bone formation :

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

ho
Gamma ALP Intestinal cells ya Ulcerative colitis
5@

Leukocyte ALP Leukocytes Leukemia

s1
im
rai
ee
m

Cardiac Biomarkers in MI :
sa
|
w

Name Starts to rise Peak Return to baseline

ro
ar

CK-MB
M

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

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

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

Enzyme Markers  [Link]

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Enzymes : Part 2 11

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

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

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

Acute Kidney Injury :

• Kidney Injury Molecule 1 (KIM 1). • GGT.
• Neutrophil Gelatin • Microalbumin.

m
Associated Lipocalin (NGAL). • Osteopontin.

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

ho
• ALT. • ya
Sodium hydrogen exchange isoform.
5@

• Glutathione S-transferase. • Exosomal fetuin.

s1
im
rai
ee
m
sa
|
w
ro
ar
M
©

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 12

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

Chemistry of Carbohydrates [Link]

Carbohydrates : Aldose or keto derivatives of polyhydroxy alcohol.

Monosaccharides :

No. of carbon atoms Aldoses Ketoses

Triose (Simplest carbohydrates) Glyceraldehyde Dihydroxy acetone
Tetrose Erythrose Erythrulose
Pentose Ribose Epimer Xylose Ribulose Epimer Xylulose

m
co
Hexose Glucose, galactose, Mannose Fructose

o.
ho
Disaccharides : ya
5@
s1

Reducing disaccharides :
im
ai

Name Monomer units Linkage

r
ee

Maltose Glucose + glucose α 1, 4

m
sa

Isomaltose Glucose + glucose α 1, 6

|
w
ro

Lactose Galactose + glucose b 1, 4

ar

Lactulose Galactose + fructose a 1, b4

M
©

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

Polysaccharides :

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Carbohydrates : Introduction 13

Dietary Fibres & Glycosaminoglycans [Link] ----- Active space -----

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

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

m
• Cellulose, AKA non-starch polysaccharide :

co
- Made of beta-D-glucose.

o.
ho
- Resistant to digestion d/t b-linkage and lack of cellulase in human
ya
5@
intestine.
s1

• Hemicellulose.
im
ai

• Lignin : Neither digested nor fermented.

r
ee
m

Note :
sa
|

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

w
ro

digests lactose).
ar
M
©

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 14 Biochemistry

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

Unbranched heteropolysaccharides made of repeating disaccharide units

Aminosugar Acidic sugar

Glucosamine Galactosamine Glucuronic acid Iduronic acid

Synthesis Site :
Rough endoplasmic reticulum & golgi apparatus.

Properties :
1. Negatively charged : Confers consistency of mucus & enables mobility at joints.
2. Absorbs water : Provides cushioning effect at weight bearing joints.

m
co
Composition :

o.
ho
GAG ya
Repeating disaccharide unit
5@

Hyaluronic acid N-acetyl glucosamine + glucuronic acid

s1
im

Keratan sulphate N-acetyl glucosamine + galactose (No uronic acid)

rai
ee

Heparin Glucosamine + iduronic acid

m
sa

Significance :
|
w

1. Chondroitin sulphate :
ro
ar

- Most abundant.
M
©

- Found in bones & cartilage : Enables compressibility of cartilage.

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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 [Link]

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

m
(Mucopolysaccharides)

co
o.
ho
ya
Belongs to lysosomal storage disorder.
5@
s1

General Features :
im
rai
ee

Gargoylic facies : Coarse facial features.

m

• Frontal bossing.
sa
|

• Depressed nasal bridge.

w
ro
ar
M
©

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 :
All are AR except Hunter's.

m
co
Enzyme defect Features

o.
ho
• Visual disturbances +
Hurler's disease (MPS-I H) L-iduronidase ya • Mental retardation
5@
s1

• Hirsutism
im

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

• Normal intelligence
rai
ee

• X-linked recessive
m
sa

Hunter's disease (MPS II) Iduronate sulfatase • Intellectual disability

|

• Clear vision
w
ro
ar
M

Other Mucopolysaccharidoses :
©

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.
• Resembles MPS : Accumulation of GAG in lysosomes.
• Enzyme defect : N-acetyl glucosamine phosphotransferase

m
co
o.
ho
↓Mannose-6-phosphate : Signal for proteins tagged with it to get degraded in
the lysosome. ya
5@
s1
im

Glucose Transporters [Link]

rai
ee

SGLT
m
sa

• Sodium dependent.
|
w

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

ro
ar

absorption.
M
©

• Unidirectional.
• Against concentration gradient.
• Secondary active transport.

Types of SGLT :

Type Location Function

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

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 18 Biochemistry

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

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

GLUTs Simple diffusion

• Sodium independent.

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

m
co
Solute concentration

o.
ho
Location :
ya
5@

GLUT Location Important points

s1
im

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

• b cells of pancreas
ee
m

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

sa

GLUT-2
|

• Serosal side of intestine • Active in the fed state

w
ro

• Proximal renal tubules

ar
M

GLUT-3 Neurons, placenta, kidney Lowest Km

©

• Heart
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  [Link]

Well Fed State :

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

High insulin/glucagon ratio

m
co
Via Glut-2 glucose enters

o.
ho
Liver ya
5@

Glucose
s1

ss
im

Glycolysis
Ex c e

ai

Pyruvate PDH Acetyl CoA Exce

r
ee

ss
m

Glycogen
sa
|

TCA cycle Fatty acid synthesis

w
ro
ar
M

VLDL
©

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 [Link]

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

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

m
co
Aerobic Glycolysis :

o.
ho
Preparatory phase : Stage of ATP utilization (2 ATPs used).
ya
5@
s1

Glucose
im
ai

ATP
r
ee

Irreversible Hexokinase
m

ADP
sa
|

Glucose-6-phosphate
w
ro
ar
M

Phosphohexose isomerase
©

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

PEP

m
1 ADP

co
Pyruvate kinase (PK) Substrate level 2 x 1 ATP 2 ATP

o.
ho
1 ATP
phosphorylation Total : 9 ATP
Pyruvate. ya
5@
s1

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

im
rai

Applied biochemistry :
ee
m
sa

S. no Compound Enzyme inhibited Reason/Application

|
w

Blood glucose estimation : Gray

ro
ar

1. Fluoride Enolase vacutainer containing fluoride

M

oxalate used
©

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.

Significance of 2,3-BPG :
• Maintains taut state of hemoglobin.

m
co
• Responsible for unloading of O2 at tissue site S hifts oxygen dissociation

o.
ho
curve to the right.
ya
5@

Regulation of Glycolysis :
s1
im
ai

1. Fed state : 2. Fasting state :

r
ee

Low insulin glucagon ratio

m

High insulin glucagon ratio

sa
|
w

Dephosphorylation of enzymes Phosphorylation of enzymes

ro
ar
M
©

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

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 :
Even in the presence of ample 02, Glucose Lactate (Used in biosynthetic
pathways).

m
co
o.
Metabolic reprogramming :

ho
Normal cell : ya
Cancer cell : Uses glucose via aerobic glycolysis.
5@
s1
im

Glucose Glucose
rai
ee
m

PEP PEP
sa

PKM 1 (Pyruvate kinase) : PKM2 :

|
w

• Tetramer • Dimer
ro

• High catalytic activity

ar

• Low catalytic activity

M

Pyruvate Pyruvate
©

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) [Link]

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

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

Significance of PDH :

m
• Irreversible & cannot be circumvented by another enzyme.

co
• Fat : Never converted to glucose :

o.
ho
Exceptions :
ya
5@
a. Glycerol.
s1

b. Odd chain fatty acid (Propionyl CoA).

im
r ai
ee

NAD+ NADH (2-5 ATP)

m
sa

Pyruvate Acetyl CoA

|
w

b oxidation
ro
ar

Fatty acid
M
©

Hydrolysis
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 [Link]

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

Site :
Cytoplasm of liver & skeletal muscles.

Stages :
1. Formation of UDP glucose :

m
co
Hexokinase Phosphoglucomutase
Glucose-1-PO4

o.
Glucose Glucose-6-PO4

ho
UDP glucose UTP
ya
5@
pyrophosphorylase PPi
s1

UDP glucose
im
ai

2. Formation of linear polymer :

r
ee
m

UDP glucose Glucose

sa

Glycogenin 4 glucose residues added

|
w
ro

• Polypeptide primer Glycogen synthase :

ar

• Tyrosine residues + • RLE

M
©

• Active in dephosphorylated state

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
Glu-6-PO4 Glu-1-PO4

m
H2O

co
Glucose-6-phosphatase

o.
Phosphoglucomutase
Pi (In SER)

ho
Glucose Glu-6-PO4 ya
Pyruvate Lactate
5@
s1

- α (1-4) glycosidic linkage.

im

- α (1-6) glycosidic linkage.

rai
ee

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

m
sa

Note :
|
w

• Phosphoglucomutase : Common to glycogen synthesis & glycogenolysis.

ro
ar
M

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

©

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 :
• Allosteric activator of glycogen phosphorylase.

m
co
• Activated in extreme state of anoxia.

o.
ho
ALLOSTERIC REGULATION ya
5@
Inhibitors of Glycogenolysis : Activator of Glycogenesis :
s1

• Glu-6-PO4.
im

Glu-6-PO4.
ai

• Glucose (Only in liver).

r
ee
m

• ATP.
sa
|

Glycogen Storage Disorder (GSD)

w

[Link]
ro
ar
M

Liver GSD :
©

Prominent feature : Fasting hypoglycemia.

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

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

Biochemistry Revision • v4.0 • 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
• Thin extremities • S. glucose↓
• Convulsions, coma on fasting • Rothera’s test : Positive

m
• O/E : Massive hepatomegaly •

co
S. Uric acid ↑↑

o.
• S. Lactate ↑↑ (Lactic acidosis)

ho
Von Gierke’s
• AST & ALT : Normal
disease ya •
5@
Liver biopsy : Accumulation of normal
glycogen.
s1
im

• Ketosis
ai

• Hyperlipidemia
r
ee
m
sa
|

• Floppy infant
w
ro

• Generalized hypotonia
ar

• Fatal : Death within 2 years d/t

M
©

cardiac failure.

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

m
co
McArdle’s • Second wind phenomena : Exercise • S. Lactate : ↓

o.
intolerance • AST & ALT : Normal

ho
disease
Pain in calf Rest Resume activity • Creatine kinase : ↑↑
ya
5@
during exercise with more ease
s1

• Rhabdomyolysis Myoglobinuria • Burgundy coloured urine

im
ai

• Exercise intolerance (No 2 wind

nd
r

• S. Glucose : ↓ during exercise

ee

phenomena)
m

Tarui’s disease • S. Lactate : ↓

• Myoglobinuria
sa

• Creatine kinase : ↑
|

• Hemolysis
w
ro

Fanconi Bickel
ar

GLUT 2 defect -
syndrome
M
©

• No glycogen accumulation
Type 0 GSD Glycogen synthase defect
• No hepatomegaly

Gluconeogenesis [Link]

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
• Only mitochondrial step

m
3. Pyruvate kinase (PK)

co
• OAA : Transported to cytoplasm via Malate

o.
ho
Aspartate shuttle
ya
PEP carboxykinase
5@
b. OAA PEP
s1
im

CO2 GTP GDP

rai
ee

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

m
sa

• Pyruvate carboxylase : 2 ATP.

|

• PEP carboxykinase : 2 ATP.

w
ro

• 1,3-BPG kinase : 2 ATP.

ar
M
©

Galactose & Fructose [Link]

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
Trigger Breastfeeding Fruit juices

m
• Intellectual disability

co
o.
• Convulsions, vomiting, jaundice, failure to thrive
C/f

ho
• Hepatomegaly, liver failure
ya
• Feeding difficulty, poor weight gain
5@
s1

+ Fructose Low renal

im

threshold
rai
ee

Cataract Fructosuria
m
sa
|

No cataract
w
ro

Galactose-1-PO4 :
ar
M

• Hepatotoxic & neurotoxic

©

• ↓Inorganic PO4 Fructose-1-PO4 :

Accumulated
• ↓Activity of glycogen phosphorylase • Hepatotoxic & neurotoxic
compound
• Eye : Converted to dulcitol • ↓Inorganic PO4

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 32 Biochemistry

----- Active space ----- HMP Shunt & Uronic Acid Pathway [Link]

HMP SHUNT PATHWAY

AKA Pentose phosphate pathway.

Site :
Cytoplasm of liver.

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

m
Glu-6-PO4 dehydrogenase : RLE

co
NADPH (G6PD)

o.
ho
6 Phosphogluconate
ya
5@
NADP+
6-Phosphogluconate dehydrogenase
s1
im

NADPH CO2
rai

Ribulose-5-PO4
ee
m
sa

Functions of NADPH :
|
w

1. Free radical scavenging :

ro

Glutathione
ar
M

reductase
H2O2 Reduced glutathione
©

NADP+

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.

m
• Hemolysis Anemia, jaundice.

co
o.
• Methemoglobinemia Cyanosis.

ho
Aggravating factor : Drugs, fava beans, infections. ya
5@
s1

Protective against : Plasmodium falciparum.

im
rai
ee

Peripheral smear : Bite cells, Heinz body.

m
sa
|
w

URONIC ACID PATHWAY Bite cells

ro
ar

Oxidative pathway for glucose.

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) [Link]

Lipid : Soluble in non-polar solvents only.

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

m
double bonds • Unsaturated FA (Double bonds) • Mitochondrial membrane damage

co
• Essential FA :

o.
Docosahexaenoic acid (DHA)/

ho
Based on - Linoleic acid : Safflower oil
Cervonic acid :
diet - α-linolenic acid ya
5@
• Can cross placenta
• Non-essential FA
s1

• Deficiency : Retinitis pigmentosa

im

Unsaturated FA
ai

↑Trans FA :
r

Based on • Monounsaturated FA : Mustard/Rapeseed oil

ee

• ↓Fluidity of membrane
m

no. of double bonds • Polyunsaturated FA : Safflower oil

sa

• Insulin resistance
Polyunsaturated FA
|

• Dyslipidemia, CV risk
w

• Omega - 3 FA :
ro

• ↑Inflammation
ar

- α-linolenic acid : Flax - seed oil

M

- Timnodonic acid
©

Significance of omega - 3 FA :
Based on position - Cervonic acid : Breast milk, Fish & algal oil • Decreases :
of final double bond • Omega - 6 FA : - Cardiovascular risk (↓TG)
- Gamma linolenic acid - Platelet aggregation
- Linoleic acid - Mental illness, degenerative
- Arachidonic acid disease risk
• Cis FA - Inflammation
Based on • Trans FA : Vanaspati • Infant brain development
isomer (Partially hydrogenated vegetable oil) • Benefits in Type 2 DM, ADHD,
• RDA : 2 to 7 g/d Non-alcoholic fatty liver disease

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Chemistry of Lipids and Phospholipids 35

Phospholipids (PL) & Glycolipids [Link] ----- Active space -----

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

m
co
o.
ho
Cardiolipin
ya
5@
• Alw Barth syndrome (Cardioskeletal myopathy) :
s1

- Cardiomegaly + myopathy
im
ai

- Mitochondrial disease
r
ee

• Only antigenic PL
m
sa

• Cross reacts with Treponema pallidum :

|
w

False positive syphilis test

ro
ar
M
©

Sphingophospholipids :
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
• No hepatosplenomegaly
Sandhoff's disease β-hexosaminidase A & B • Hyperacusis

m
• CRS on macula

co
o.
Globoid cell

ho
ya
5@
Galactocerebrosidase/ • Gross developmental delay
s1

β-galactosidase • Opisthotonus posture

Krabbe’s disease (AR)
im

(Galactocerebroside accu- with clenched fists

rai

mulation in neural tissue) • No hepatosplenomegaly

ee
m
sa

White matter of brain

|
w
ro
ar

Lysosomal storage disease Enzyme defect Features

M
©

• Protruding abdomen • Erlenmeyer

• 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.
(Lysosomal storage disease)

m
co
• Calcification of adrenal gland.

o.
• Watery green diarrhoea.
ho
ya
5@
DIAGNOSTIC ALGORITHM
s1

Check for organomegaly

im

+ -
rai
ee

Check for cherry red (CR) spot on Check for CR spot & MR
m
sa

macula & mental retardation (MR)

|
w

+ - CRS - MR -
CRS + MR + CRS - MR +
ro
ar
M

Neimann-Pick Gaucher’s disease :

©

disease. Crumpled tissue paper

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  [Link]

Lipolysis :
Hydrolytic cleavage of TAG.

Site : Adipose tissue.

Steps :
Hormone Sensitive Lipase (HSL) HSL
TAG 2,3-DAG 2-MAG
Fatty acid (Diacyl glycerol) Fatty acid (Monoacyl glycerol)

m
co
o.
2 MAG esterase Fatty acid

ho
ya
5@
Glycerol
s1
im

Activators :
ai

Applied biochemistry :
• Glucagon
r
ee

1. Insulin resistance ↑Hydrolysis of stored TAG

m

• Epinephrine
sa

• ACTH
|

↑Free fatty acid level in blood

w

• TSH
ro
ar

• Thyroxine Fatty liver disease.

M
©

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

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

Starvation ketosis

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Metabolism of Lipids 39

Beta Oxidation [Link] ----- Active space -----

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

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

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

m
(2 ATP equivalents)

co
o.
ho
2. Carnitine transport : Transports Acyl CoA into mitochondria.
ya
5@
FA Acyl CoA
s1

Outer Mitochondrial
im

Thiokinase
ai

Membrane (OMM)
r
ee
m

AcylCoA + Carnitine
sa
|

CAT 1/CPT 1 :
w

• RLE
ro
ar

• Gateway of β oxidation
M

Acyl Carnitine Transported

©

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
C16 β oxidation = C16 - 1 = 7 β oxidation 7 x 4 = 28 ATP.
2

m
co
Activation : Utilizes 2 ATP equivalents - 2 ATP.

o.
ho
Total : 108 - 2 = 106 ATP
ya
5@

Regulation :
s1
im

CPT-1 gateway : Inhibited by Malonyl CoA.

ai
r

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

ee

• Fasting
m
sa

(RLE for FA synthesis)

|
w

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

(RLE for FA synthesis)

M
©

Other Oxidation Pathways & Disorders of Fatty Acid Oxidation [Link]

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 -

m
2. Jamaican Vomiting Sickness :

co
D/t consumption of unripe Ackee fruit Containe hypoglycin.

o.
ho
Acyl Co A
ya
- Hypoglycin
5@
Acyl CoA
s1

dehydrogenase
im
ai

↓β oxidation
r
ee
m
sa

↓Acetyl CoA
|

↓ATP
w
ro
ar

Ketone bodies absent :

M

↓Gluconeogenesis
©

Rothera’s test -
Fasting hypoglycemia
3. Refsum’s Disease :
Defect : Phytanoyl CoA oxidase (Hydroxylase) Alpha oxidation
Features :
• Asymptomatic > Symptomatic.
(Aggravates on consuming
curd/milk)
• Retinitis pigmentosa.
• Ichthyosis
• Peripheral neuropathy.
• Cardiac arrhythmias.
Rx : Restrict dairy products & green
Ichthyosis (Scaly skin) Retinitis pigmentosa
leafy vegetables.
Biochemistry Revision • v4.0 • 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.

m
Zellweger Syndrome : Resembles Down’s syndrome

co
Diagnosis :

o.
ho
• Peroxisomal (Vacant) ghost.
• Accumulation of VLCFA & phytanic acid. ya
5@
s1
im

Ketone Body Synthesis [Link]

rai
ee
m

Site :
sa

Exclusively liver mitochondria.

|
w
ro

Steps :
ar

Acyl CoA
M
©

β oxidation

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:
skeletal muscle, adipocytes • ↑Glycogenolysis

m
(GLUT 4 : Insulin dependent) ↑Hydrolysis of TAG • ↑Gluconeogenesis

co
o.
ho
↑↑Blood glucose Acetyl CoA ya
5@
+ Depletion of OAA ↑↑Blood glucose
s1
im

KB synthesis
r ai

Lab Diagnosis :
ee
m

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

sa
|

2. Ketostix : Detects urine ketone bodies.

w
ro
ar
M
©

Rothera’s test : Purple ring

Metabolism in Fed State [Link]

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 -
Steps : HMG CoA reductase
2 x Acetyl CoA

m
co
↓Coenzyme Q

o.
Acetoacetyl CoA + Acetyl CoA

ho
(Derived from Farnesyl)
HMG CoA synthase ya
5@

Myopathy
s1

HMG CoA
im
ai

HMG CoA reductase : RLE

r
ee
m

Mevalonate Cholesterol (27C)

sa
|
w
ro

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

ar
M

Compounds Derived from Cholesterol :

©

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

2. Steroid hormones.
Bile Acid Synthesis :
Site :
• Liver (Primary bile acid). • Intestine (Secondary bile acid).
Steps : Cholesterol
Vit C 7 α hydroxylase : RLE
7 OH cholesterol
Conjugation by
1˚ bile acids Cholic acid Taurine + Glycine Chenodeoxycholic acid
Undergoes least
2˚ bile acids Deoxycholic acid Lithocholic acid Enterohepatic
circulation
Enterohepatic circulation
Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 Metabolism of Lipids 45

Lipoproteins [Link] ----- Active space -----

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

m
• Carry endogenous TAG to peripheral organs : VLDL.

co
o.
• Carry cholesterol from peripheral tissue to adrenals : HDL.

ho
ya
5@
Electrophoretic Pattern :
s1
im
ai

Origin Chylomicron
r
ee
m
sa

LDL (β-Lipoprotein)
|
w
ro

Mobility VLDL (Pre β-Lipoprotein)

ar
M

IDL (Broad β)
©

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

Excreted via bile Risk of thrombosis

m
co
o.
ho
3. HDL : Facilitates reverse cholesterol transport.
ya
5@
Liver & intestine Spherical HDL3 :
s1

Receives cholesterol from Spherical HDL2

im

Discoidal HDL
peripheral tissues via
ai

• Phospholipid
r

• ABCA 1
ee

• Cholesterol
• SRB 1
m

Cholesterol dislodged to
• Apo A 1 Cholesterol
sa

• ABCG 1 liver
+
|

LCAT
w
ro
ar

Cholesterol
M

ester Spherical HDL3

©

Disorders of Lipoprotein [Link]

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
on CRISPR cas9.

m
co
o.
ho
Corneal arcus Tendon xanthoma :
ya M/c achilles tendon
5@
s1

Remnant
• TAG : ↑↑
im

AR Apo E chylomicron &

• Cholesterol : ↑↑
ai

VLDL
r
ee
m

C/f
sa
|
w
ro

Familial dysbetalipoproteinemia
ar

(Type III HL)

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 :

m
co
o.
ho
ya
5@
s1
im

Pigmentary retinopathy Petechial rash

rai
ee
m
sa
|
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 [Link]

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

m
co
Valine

o.
ho
• Serine
OH group containing • Threonine ya
5@

• Tyrosine
s1
im

• Cysteine
ai

Sulphur containing
• Methionine
r
ee
m

• Aspartic acid (Aspartate)

Acidic
sa

• Glutamic acid (Glutamate)

|
w

• Asparagine
ro

Amides
• Glutamine
ar
M

• Histidine
©

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

Based on Side Chain Characteristics :

Polar Non - polar :

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

Biochemistry Revision • v4.0 • 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.
• Tryptophan. • Histidine.

m
• Phenylalanine. • Isoleucine.

co
o.
• Threonine.

ho
DERIVED AMINO ACIDS ya
5@

Properties :
s1
im

• No codons.
rai

• Formation :
ee
m

- Post translational modification.

sa

- Intermediate of metabolic pathways.

|
w
ro

Classification :
ar
M
©

Seen in proteins : Not seen in proteins :

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

Mnemonic : Serina’s sister Selena from UGAnda.

Biochemistry Revision • v4.0 • 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.
• UV light absorption : Phenylalanine, tyrosine, tryptophan

m
Tryptophan : 280 nm (Maximum UV absorption).

co
o.
ho
3. Buffering :
ya
5@
Maximum with imidazole group of histidine (pH = pKa).
s1
im

4. Exist in Charged States :

rai

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

ee
m

• Maximum precipitability, minimum solubility.

sa
|

• Minimum buffering (pH = pI).

w
ro
ar

TITRATION CURVE
M
©

Compound with Single Ionizable Group :

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

Proteins [Link]

m
co
Peptide bond :

o.
ho
• B/w 2 amino acids Forms proteins.
ya
5@
• Uncharged.
s1

• Partial double bond.

im
ai

• Trans in nature.
r
ee
m

STRUCTURE OF PROTEINS
sa
|
w

Primary : Peptide (Covalent) bond.

ro
ar
M

Secondary : Coiling of linear structure. Primary structure Secondary structure

©

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 :

• Prion diseases.

m
• Amyloidosis.

co
o.
• Prion related protein diseases :

ho
7. Alzheimer’s disease. ya
11. Huntington’s disease.
5@

8. Parkinson’s disease. 12. Pick’s Disease (FTD).

s1
im

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

ai

10. Cystic fibrosis. 14. Lewy body dementia.

r
ee
m
sa

Pathology :
|
w

Mutation
ro

PrP : a helix PrP Sc : b sheet.

ar

• Hydrophobic amino acids exposed.

M
©

• Resistant to degradation.
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 [Link]

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 + .

Synthesis :

m
co
o.
Intracellular Extracellular

ho
Site RER of fibroblast ya ECM
5@
s1

Product Procollagen Tropocollagen

im

1. Hydroxylation : Prolyl & Lysyl hydroxylase 1. Cleavage

rai
ee

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

m
sa

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

|
w
ro

Types :
ar
M
©

Type Diseases associated

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Amino Acids : Part 1 55

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

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

Disorders a/w Elastin :

1. William Beuren syndrome.
2. Cutis laxa.

m
Keratin :

co
o.
• Component of outer layer of skin, nails & hair.

ho
• Rich in cysteine : Confers hardness to nails. ya
5@

• Associated disorder : Epidermolysis bullosa (Classical type).

s1
im
ai

Fibrillin :
r
ee

• Glycoprotein in scaffolding of elastin.

m
sa

• Fibrillin 1 mutation : Marfan’s syndrome.

|
w
ro
ar

Amino Acid Metabolism [Link]

M
©

Reactions : NH3
1. Deamination Ketoacid.
CO2
2. Decarboxylation Amines.

Toxic nature of ammonia :

↑GABA (Inhibitory neurotransmitter)
CO2

Glutamate + NH3 Glutamine : Causes cerebral edema.

α KG from TCA cycle

↑NH3 ↑Formation of Glutamine ↓α KG ↓ATP.
Biochemistry Revision • v4.0 • 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.
• Significance : Biosynthesis of non-essential amino acids.

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

co
o.
ho
Transamination of non-alpha amino acid :
ya Applied biochemistry
5@
Enzyme : δ ornithine aminotransferase.
Gyrate atrophy of retina & choroid :
s1
im

• Defect in δ ornithine aminotransferase

ai

• Treatment :
r
ee

- Restrict ornithine & arginine

m
sa

- Supplement PLP (B6)

|

Exceptions to transamination :
w
ro

1. Proline. 3. Lysine.
ar
M

2. Hydroxyproline. 4. Threonine.
©

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 [Link]

AKA Kreb’s Henseleit/Ornithine cycle.

Note : Reactions occurring in
Site : Exclusively in liver.
both cytoplasm & mitochondria
Organelle : Cytoplasm + mitochondria.
Mnemonic : PUBG
Contributions to Structure : • Pyrimidine synthesis
• 1st Nitrogen : Ammonia. • Urea cycle

m
• 2nd Nitrogen : Aspartate. • Blood : Heme synthesis

co
o.
• Carbon atom : Respiratory CO2. • Gluconeogenesis

ho
ya
5@
Urea Bicycle : Aspartate
s1
im
rai

TCA cycle Urea cycle

ee
m
sa
|
w

Fumarate
ro
ar
M

Reactions of Urea Cycle :

CO2 + NH3
©

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 :
• M/c Urea cycle disorder.
• X-linked recessive.

m
co
• Defect : OTC.

o.
ho
ya
Carbamoyl phosphate accumulates Shunted for Pyrimidine synthesis
5@
s1
im
ai

Excretion of Accumulation
r
ee

pyrimidines of orotic acid

m
sa

in urine
|
w

Orotic aciduria.
ro
ar
M

HHH syndrome :
©

• Defect : Ornithine transporter Hyperornithinemia.

• Carbamoyl phosphate + lysine Homocitrulline Homocitrullinemia.
• Accumulation of NH3 Hyperammonemia.

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

Spastic Diplegia Scissoring gait

Biochemistry Revision • v4.0 • 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

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

m
co
Management of Urea Cycle Disorders :

o.
ho
Investigations :
ya
5@
↑/Normal : Urea cycle disorders.
1. pH of blood
s1
im

↓Organic aciduria.
rai

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

ee
m

metabolic disorders.
sa
|
w

Interpretation :
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.

m
co
o.
ho
ya
5@
s1
im
rai
ee
m
sa
|
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 [Link]

Phenylalanine Tyrosine

Catabolic pathway Anabolic pathway

Ketogenic + glucogenic. • Melanin.

• Catecholamine.
• Thyroid hormones.

m
co
o.
Phenylalanine hydroxylase

ho
Phenylalanine Tyrosine.
ya
5@
BH4 BH2
s1
im

Dihydrobiopterin reductase
rai
ee

NADP+ NADPH
m
sa
|
w

Catabolic Fate :
ro

Tyrosine transaminase
ar

Phenylalanine Tyrosine Para/4 hydroxy phenyl pyruvate

M
©

PHPP hydroxylase/
4HPP dioxygenase

Homogentisic acid/dihydroxyphenyl acetate

Homogentisate oxidase/dioxygenase
OR
Dihydroxyphenylacetate dioxygenase

Maleyl acetoacetate (MAA)

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

Biochemistry Revision • v4.0 • 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
PHPP Tyrosinemia type 3

m
co
Classic Phenylketonuria :

o.
ho
Clinical features : X Melanin : Hypopigmentation.
ya
5@

Phenylalanine X Tyrosine X Catecholamine : Agitation, hyperactivity,

s1
im

mental retardation, intractable vomiting.

rai
ee

Phenyl pyruvate X T3, T4.

m
sa
|

Phenyl acetate Mousy/musty/barny odour.

w
ro
ar

Note :
M
©

Persistence of neurological symptoms after

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

Urine turns black

IV disc Skin. Cartilage. on air exposure/

m
co
alkalinization.

o.
Ochronotic arthritis.

ho
ya
5@

Clinical features :
s1
im

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

ai

disc, cartilage.
r

• Present with back pain.

ee
m

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

sa
|
w

Lab diagnosis :
ro

• X-ray :
ar

• FeCl3 test.
M

• AgNO3 test. - Bamboo spine.

©

• 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 [Link]

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

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

m
co
Pheochromocytoma :

o.
ho
Palpitations
ya
5@
s1
im

Triad
Profuse sweating Headache
r ai
ee
m

Lab diagnosis :
sa

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

|
w
ro

• VMA : Highest specificity. • Catecholamines.

ar

• Catecholamines. • Free metanephrines : Highest

M
©

• Fractionated metanephrines : sensitivity.

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 [Link] ----- Active space -----

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

3-OH kynurenine
PLP
Kynurinase Alanine Glucogenic

m
3-OH anthranilic acid Ketogenic

co
o.
Quinolinate phosphoribosyl

ho
transferase (QPRTase) : RLE
ya
5@
Vitamin B6 deficiency :
s1

• 3-OH kynurenine Xanthurenic acid. Niacin.

im
ai

• ↓Synthesis of niacin Pellagra.

r
ee
m

Niacin :
sa
|

• Endogenously synthesized vitamin.

w
ro

• 60 mg tryptophan 1 mg niacin.
ar
M
©

Derivatives :
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.

C/f :
• Asymptomatic.

m
co
• Accumulation of Bacterial

o.
Indoxyl compounds Excreted in urine

ho
tryptophan in intestine decomposition
ya
5@
• Ataxia. Bluish discoloration of diaper.
s1

• Wide based gait.

im
ai

• Cutaneous photosensitivity : M/c symptom.

r
ee
m

Test : Obermeyer test.

sa
|

Rx : Lipid soluble esters of tryptophan.

w
ro
ar
M

Derivatives of Tyrosine [Link]

©

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 :

B12 deficiency : N5 methyl THFA X THFA.

m
co
Functional deficiency

o.
↓DNA synthesis Nucleocytoplasmic synchrony

ho
of THFA
ya
5@
Megaloblastic anemia.
s1
im

Homocysteinuria :
rai

Clinical features : Resembles Marfan’s syndrome.

ee
m

• Developmental delay.
sa
|

• Mental retardation.
w
ro

• Tall & thin extremities.

ar
M

• Skeletal deformities.
©

• Visual disturbances : Ectopia

lentis (M/c : Inferomedial).
• Muscular hypotonia.
• H/o CAD.
Ectopia lentis Thromboembolism
• Thromboembolism.

Arachnodactyly Tall stature High arched palate

Skeletal deformities in homocysteinuria

Biochemistry Revision • v4.0 • 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 + .

Classic homocysteinuria Non-classic homocysteinuria

m
co
Methyl B12 formation ;

o.
Enzyme Cystathione β synthase

ho
Methylene THF reductase
ya
5@
Defect in Formation of cysteine Remethylation of homocysteine to methionine
s1

Homocysteine ↑ ↑
im
ai

Cysteine ↓ Normal
r
ee

Methionine Normal
m

↓
sa

• Cysteine supplementation
|
w

• High dose Vit B6 • Methionine supplementation

ro

Rx
ar

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

M
©

• Vit B12 & folic acid

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.

Other Amino Acids [Link]

m
co
Glycine :

o.
ho
Derivatives :
ya
5@
1. Purine (C4, C5, N7). 3. Heme.
s1

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

im
ai

methionine. 5. Collagen.
r
ee
m

Hyperoxaluria :
sa
|

Primary : Defect in glyoxylate amino transferase.

w
ro

Secondary : D/t
ar
M

• Vit C excess. • Ethylene glycol poisoning.

©

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

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

BASIC AMINO ACIDS Histidine

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

BCAA
PLP Transamination.

m
co
o.
BC ketoacid

ho
BC ketoacid NAD+
dehydrogenase CO2 NADH ya Oxidative decarboxylation.
5@

Acyl group
s1
im

FAD
ai

FADH2 FAD dependent dehydrogenation.

r
ee
m

Product.
sa
|

Maple Syrup Urine Disease

w
ro

Defect : Branched chain ketoacid dehydrogenase.

ar
M

Features :
©

• Age of onset : Neonate.

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Amino Acids : Part 2 71

Revision Tables [Link] ----- Active space -----

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

Disorder Defective enzyme

Albinism Tyrosinase

m
MSUD Branched chain keto acid dehydrogenase

co
o.
Isovaleryl CoA dehydrogenase

ho
Isovaleric acidemia
(A/w leucine catabolism)
ya
5@
ENZYME DEFECTS Homocystinuria Cystathionine β synthase
s1
im

Phenylalanine hydroxylase/DHB
Phenylketonuria
ai

reductase/Defect in THB synthesis

r
ee

Alkaptonuria Homogentisate oxidase

m
sa

Tyrosinemia type I Fumaryl acetoacetate hydrolase

|
w

Tyrosinemia type II Tyrosine transaminase

ro
ar

Tyrosinemia type III PHPP hydroxylase

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 [Link]

Steps to Identify Nucleotide :

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

m
c. PO43- group

co
o.
ho
Types of Nitrogenous Bases :
ya
5@
s1

Double ring : Purine Single ring : Pyrimidine

im

Adenine (6-amino purine)

rai
ee
m
sa
|
w
ro
ar
M
©

Guanine (2-amino, 6-oxopurine)

Cytosine Deamination Uracil Methylation Thymine
(2-oxo, 4-amino (2,4-dioxo (2,4-dioxo,
pyrimidine) pyrimidine) 5-methyl pyrimidine)

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

Nucleic Acids :
• Formed by 31-51 phosphodiester bond b/w nucleotides.
• Exhibit polarity.
• Sequenced from 51 31.
Biochemistry Revision • v4.0 • 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 -
(Only in RNA)
Hypoxanthine Inosine Inosine monophosphate (IMP) -

m
co
Xanthine Xanthosine Xanthine monophosphate (XMP) -

o.
ho
Cytosine Cytidine Cytidine monophosphate (CMP) d CMP
Thymine Thymidine - ya
d Thymidine monophosphate (Only in DNA)
5@
s1
im

Metabolism of Nucleotides [Link]

rai
ee

PURINE SYNTHESIS
m
sa

De-novo Purine Synthesis :

|
w

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

ro
ar

Contributors of purine ring :

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

Disorders of Purine Synthesis :

m
co
Lesch Nyhan Syndrome :

o.
ho
Defect : HGPRTase.
ya
5@
• Hypoxanthine IMP
↑Purine catabolism ↑Uric acid.
s1

• Guanine GMP
im
rai

C/f : Rx :
ee
m

• Compulsive self-mutilation. • Allopurinol

sa

• Hyperuricemia • High fluid intake.

|
w
ro

• Neurological defects. • Alkalization of urine.

ar
M
©

Kelley Seegmiller syndrome :

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 :

m
co
Aspartic acid

o.
Glutamine

ho
ya
5@
s1

Respiratory CO2
im
r ai
ee

Pathway :
m

Aspartate
CO2 + Glutamine CPS II Carbamoyl transcarbamoylase Carbamoyl aspartic acid
sa
|
w

phosphate Dihydroorotase
ro
ar

Dihydro orotic acid

M
©

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

Disorder : Hereditary Orotic Aciduria :

Defect : De novo synthesis of pyrimidines.

Type 1 orotic aciduria :

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

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 [Link]

Watson & Crick Model :

• Right handed antiparallel double helical structure.
A T
• Base pairing rule
G C
• Chargaff’s rule : A + G = C + T (Purines = Pyrimidines)
• Base stacking :
- Vertical force of interaction b/w base pairs.

m
co
- D/t hydrophobic interactions & Van der Waals forces.

o.
ho
Organization of DNA : ya
5@

Nucleosome : Histone octamer + ds DNA.

s1
im
ai

• Basic proteins.
r
ee

• Rich in arginine & lysine.

m
sa

• Positively charged.
|
w

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

ro
ar
M
©

DNA Replication :
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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Molecular Biology : Part 1 77

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

Binding of SSB (Single Strand Binding) protein :

Prevents local reannealing of DNA.

3. Helicase : Further unwinding of DNA.

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

m
co
5. Lagging strand synthesis :

o.
ho
a. Lagging strand template : 51 31.
ya
b. Multiple RNA primers added & DNA polymerase III adds short segments of
5@
s1

nucleotides (Okazaki fragments).

im

c. DNA polymerase I : Removes the RNA primer.

rai
ee

d. Ligase fills the gap on RNA primer removal.

m
sa

DNA Polymerase (DNAP) :

|
w
ro

Enzyme Function Enzyme Function

ar
M

Prokaryotic DNAP Eukaryotic DNAP

©

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 + .

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

m
Prevents telomere shortening

co
(No Hayflick limit.)

o.
ho
Applied Biochemistry
Properties : ya
5@
Cancer
1. Contains an intrinsic RNA template.
s1

+
im

2. Reverse transcriptase activity + .

Telomerase activity
rai
ee

Absent in : Somatic cells. -

m

Premature aging.
sa

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

|
w

cancer cells, lymphocytes.

ro
ar
M

DNA Repair Defects :

©

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 [Link] ----- Active space -----

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

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

m
co
RNAP-I RNAP-II RNAP-III

o.
ho
Sensitivity to α-amantin Least Highest Intermediate
ya
5@
• mRNA
• miRNA • tRNA
s1

rRNA
Major products
im

(Most abundant) • snRNA • 5S rRNA

ai

• lncRNA
r
ee
m

Promoters of Transcription :
sa
|

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

w
ro

• Gene-specific
ar

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

m
co
Functions :

o.
ho
• Stabilizes mRNA : Prevents the attack of 31 51 exonuclease.
ya
5@
• Facilitates exit of mRNA from nucleus Cytoplasm for translation.
s1

• Recruitment of 40s ribosome.

im
rai

3 Splicing Of Exons & Removal Of Introns :

ee
m
sa

Sn RNA (Ribozyme) : Rich in uracil +

SnRNP/
|
w

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

ro

Snurps
ar

Primary transcript
M
©

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

Alternate RNA Processing/Differential RNA Processing :

Linking of exons in different sequences

Different proteins formed

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

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 [Link]

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

m
• Histone mRNA : Poly A tail - .

co
o.
• hnRNA for histone gene : No introns.

ho
• SLE : D/t autoimmune response to snurps. ya
5@
• Nucleus : M/c site of post-transcriptional processing.
s1

• Nucleolus : Site of post-transcriptional processing of rRNA

im
rai
ee

tRNA :
m
sa

Non-coding RNA made of 74-91 nucleotides.

|
w
ro

Structure :
ar

• 2˚ structure : Clover leaf shape.

M
©

• 3˚ structure : Inverted L shape.

• 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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 82 Biochemistry

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

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

Function : Post-transcriptional regulation of gene expression.

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

Formation :
Pri miRNA gene

Precursor miRNA
Drosha DGCR8

m
co
Transported out of

o.
ho
nucleus via Exportin
ya
Dicer
5@
s1

ss miRNA
im
rai
ee

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

m
sa
|

Bind with 31 UTR of mRNA

w
ro
ar
M

mRNA mRNA Translation

©

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  [Link]

Point mutation (Base substitution) : M/c.

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

Missense mutation

C C A

m
co
(Codon for proline)

o.
ho
Frame shift mutation :
ya
5@
Insertion/deletion of nucleotide Distorted reading frame.
s1
im

Nonsense suppressor tRNA (Suppressor tRNA mutation) :

rai

Base substitution
ee

mRNA : Coding codon Stop codon

m

(UAC)
sa

(UAG)
|

tRNA can bind with stop codon on mRNA

w

tRNA : AUG Counter mutation AUC

ro

(No translation arrest).

ar

(On anticodon arm)

M
©

Epigenetics [Link]

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 [Link]

Salient Features of Genetic Code :

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

m
STEPS OF TRANSLATION

co
o.
Charging of tRNA :

ho
ya
Process of amino acid (AA) attaching on acceptor arm of tRNA.
5@

tRNA
s1
im
ai

+ Specific amino acid Aminoacyl tRNA synthetase Aminoacyl tRNA.

r
ee

A A A (Phenylalanine)
m
sa

U U U ATP AMP
mRNA
|
w
ro

Initiation :
ar
M

GTP + eIF-2 (initiation factor) + tRNAi

©

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 [Link]

BLOTTING TECHNIQUES
Southern blot Northern blot Western blot/Immuno blot
Target molecule DNA RNA Protein
Transfer medium Nitrocellulose/Nylon membrane Nitrocellulose membrane
Labelled DNA probe : Complimentary DNA :
Probe used Complimentary sequence to Complimentary to RNA Labelled antibody
target sequence. (By reverse transcriptase)

m
co
• RNA detection Detect specific protein/

o.
Application DNA detection

ho
• Study of gene expression antigen
ya
5@
South-Western blot : For DNA - protein interaction.
s1
im

MICROARRAY
rai

DNA identification :
ee
m

Chip with known oligonucleotide + Fluorescent labelled

sa

Unknown DNA
|
w

RNA identification :
ro
ar

Chip with known cDNA + Fluorescent labelled Fluorescence

M

Unknown RNA
©

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 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

m
co
o.
ho
ya
5@
s1
im
ai

• Non-dividing cells.
r
ee

• Rapid results & more sensitivity.

m
sa

Recombinant DNA Technology

|

[Link]
w
ro

Restriction endonuclease (RE) :

ar
M

• Present in bacteria : Restrict phage entry.

©

• 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
DNAase

m
Breakdown of DNA areas not bound to protein.

co
o.
On gel electrophoresis.

ho
- Only broken fragments seen. ya
5@

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

s1
im
ai

POLYMERASE CHAIN REACTION

r
ee

• Exponential amplification of target DNA.

m
sa

• No. of DNA after n cycles = 2n.

|
w
ro
ar
M
©

(90 to 94°C)

(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 &
dye displaced emitting fluorescence.

m
• ↑Fluorescence Amount of DNA

co
o.
quantified real time.

ho
DNA SEQUENCING ya
5@
s1

Sanger’s Sequencing :
im
ai

First sequencing method : Frederick Sanger.

r
ee
m

Components :
sa
|

• Dideoxy NTs (ddNT).

w
ro

• Klenow polymerase.
ar
M

• dNTs.
©

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.

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024
 Micronutrients : Vitamins and Minerals 89

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

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

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

Water soluble vitamins : B complex & C.

Vitamin A vs Vitamin D

m
[Link]

co
o.
Vitamin A Vitamin D

ho
• Retinal ya • Ergocalciferol (D2) : Plant sources
5@
Forms • Retinoic acid • Cholecalciferol (D3) : Animal sources/Self
s1

• Retinol synthesised
im
ai

7-dehydrocholesterol
r
ee

UVB rays (290-315 nm)

m

Intestine b-carotene (Diet) Retinol Skin

sa

Cholecalciferol
|

+ D-binding protein 25-hydroxylase

w
ro
ar

25-hydroxycholecalciferol
M

Metabolism Liver : Stored C arried in Retinyl ester PTH

Liver
©

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

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

Biochemistry Revision • v4.0 • 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
- Hepatomegaly

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

co
- Bony exostoses

o.
ho
- Hepatomegaly (Cirrhosis)
3. Pregnancy : Teratogenic ya
5@
s1

• Halibut liver oil (Richest)

im
ai

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

r

Sources
ee

vegetables • Fortified food

m

• Animal sources : Egg, milk, fish, meat

sa
|

• ↑Dark adaptation time • Vit. D assay

w

Assessment
• Carr & Price reaction : Direct assay • S. osteocalcin
ro
ar

• Children (1 to 6 y) : 400
M

• Children : 400
• Men & women : 600
©

RDA (IU/d) • Adults : 200

• Pregnancy : 800
• Pregnancy : 400
• Lactation : 950

Wald’s visual cycle :

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

Nerve impulse generated.

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

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

 Micronutrients : Vitamins and Minerals 91

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

Conjunctival & corneal dryness Bitot’s spot Corneal ulcer

m
co
o.
ho
Genu valgum & Genu varum Windswept deformity
ya Rachitic rosary
5@
s1
im

Vitamin E vs. Vitamin K

ai

[Link]
r
ee
m

Vitamin E Vitamin K
sa
|

• K1 : Phylloquinone (Dietary Source)

w
ro

• K2 : Menaquinone (Bacterial flora)

Forms Alpha tocopherol
ar

• K3 : M enadione (Synthetic; Water

M

soluble)
©

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 -
• Pregnancy : 10 mg/d
• Lactation : 12 mg/d

m
co
o.
Note :

ho
ya
• Vit. K epoxidase inhibitors : Warfarin & dicumarol (Anticoagulants).
5@
• Breast milk : Poor source of Vit. K.
s1
im

Hematopoetic Vitamins
ai

[Link]
r
ee
m

Folic Acid v/s Vitamin B12 :

sa
|
w

Folic acid (Vit. B9) Vit B12

ro
ar

Tetrahydrofolic acid : • Adenosyl B12 :

M

Carrier of 1 carbon groups : Methyl malonyl CoA mutase

©

• Formyl Methyl malonyl CoA Succinyl CoA

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

Biochemistry Revision • v4.0 • 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

Megaloblast in bone marrow

Macrocytes in peripheral sinear

m
co
Causes of Vit. B12 deficiency :

o.
ho
1. Nutritional : Strict vegans. 3. Intestinal :
ya
5@
2. Gastric : ↓Intrinsic Factor (IF) from - Crohn’s disease.
s1

parietal cells - Fish tapeworm (Diphyllobothrium

im
ai

- Autoimmune pernicious anemia. latum).

r
ee

- Gastrectomy. - Stagnant loop syndrome.

m
sa
|

Energy Releasing Vitamins

w

[Link]
ro
ar
M

Vitamin B1 vs. Vitamin B2 :

©

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
- Peripheral edema

m
Deficiency - Dyspnea

co
- Cardiomegaly

o.
ho
- Pulmonary edema
- High output cardiac failure ya
5@
s1

3. Wernicke’s Encephalopathy (WE) :

im

- Horizontal nystagmus
ai

4. Corneal vascularisation : Difficulty in

r

- Ophthalmoplegia
ee

vision, lacrimation
m

- Ptosis
sa

- Truncal ataxia
|

- Global confusion
w
ro
ar
M

4. Wernicke Korsakoff’s :
©

Features of WE + dementia +
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.
5. Gastric irritation.
6. Fulminant hepatitis.

m
co
o.
Note :

ho
Pellagra-like symptoms. ya
5@

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

s1
im

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

rai

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

ee
m

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

sa
|
w

Vitamin B5 (Pantothenic Acid) :

ro
ar

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

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

©

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.
Vitamin B6 :

m
Active form : Pyridoxal phosphate.

co
o.
Function : Coenzyme role.

ho
• Transamination ya • Heme synthesis : ALA synthase
5@

• Simple decarboxylation. • Glycogenolysis : Glycogen

s1
im

• Transsulfuration phosphorylase.
rai

• Tryptophan metabolism :
ee
m

Kynureninase.
sa
|
w

Deficiency manifestations :
ro
ar

• Pyridoxine dependent seizures.

M

• Sideroblastic anemia.
©

• 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
b. Iron deficiency anemia.

m
c. Scorbutic rosary.

co
o.
ho
ya
5@
Hemarthrosis Splinter hemorrhages Petechial rashes
s1
im
rai
ee
m

• Barlow’s disease (Infantile scurvy)

sa

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

|
w

• Treatment : Supplement Vit. C.

ro
ar
M

Minerals
©

[Link]

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 :

m
co
o.
ho
ya
5@
s1
im

Selenium, Zinc & Chromium :

rai
ee

Selenium Zinc Chromium

m
sa

• Anti-oxidant
|

• Metalloenzymes Potentiates action of

w

• Selenocysteine containing
ro

Functions • Stabilise human insulin insulin in impaired glucose

ar

enzymes : Glutathione
M

• Spermatogenesis tolerance.
©

peroxidase.
• 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
Copper 1.5-3 mg

m
co
Sodium 5-10 g

o.
Acrodermatitis enteropathica :

ho
Potassium 3-4 g Perioral & perianal rashes
ya
5@
s1

Miscellaneous Topics on Nutrition [Link]

im
rai

Energy available from macronutrients (in kCal/g) :

ee
m

• Carbohydrate : 4.
sa
|

• Protein : 4.
w
ro

• Fat : 9.
ar
M

• Alcohol : 7.
©

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 [Link]

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

m
H20

co
Fumarate Fe2+

o.
ho
H20 Aconitase
dehydrogenase

FADH2
ya
Succinate

5@
Isocitrate
s1

FAD NAD +
im

Isocitrate
ai

decarboxylation
r

NADH + H dehydrogenase
ee

+
Succinate

Oxidative
m

ATP/GTP
sa

CoA-sh Oxalosuccinate
SLP
|

ADP + Pi/GDP + Pi
w

Succinate Isocitrate
ro

thiokinase Co2
ar

dehydrogenase
M

Succinyl-CoA
©

a-Ketoglutarate
NADH + H+ NAD

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

Biochemistry Revision • v4.0 • 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) [Link]

m
Series of redox couples seen in inner mitochondrial membrane.

co
o.
Succinate
complex

ho
II
ya
NADH 4H NAD
+ + Fumarate 2H+ Intermembrane
5@
e - 4H+ space(IMS)
s1

e- complex (Final e- Fo
e -
im

complex I e -
complex III IV O2 acceptor) complex
e-
1mm
ai

CoQ Cyt c e- V
r

H2O
ee

F1
m

4H+ 4H+ 2H+

sa

Confirmational change Matrix

|

in b subunit
w
ro
ar

ADp + Pi ATP
M
©

Complexes :

Complex Name Protons pumped Inhibitors

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

Biochemistry Revision • v4.0 • 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 [Link]

Heme containing proteins :

m
1. Hemoglobin. 5. Catalase.

co
o.
2. Myoglobin. 6. Tryptophan pyrrolase.

ho
3. Cytochrome c. ya 7. Nitric oxide synthase.
5@

4. Cytochrome P450.
s1
im
ai

HEME SYNTHESIS
r
ee

Site :
m
sa

Liver, erythrocyte precursors.

|
w
ro

Organelle :
ar
M

Partly cytoplasmic & partly mitochondrial.

©

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

m
• Congenital Erythropoietic Porphyria (CEP).

co
o.
• ALAD enzyme deficiency (ADP).

ho
• Erythropoeitic Protoporphyria (EPP). ya
5@

• X-Linked Protoporphyria (XLP).

s1
im
ai

Types :
r
ee
m

Porphyria Defective enzyme C/F

sa

ADP ALA dehydratase -

|
w
ro

Neuro visceral manifestations

ar

HMB synthase (M/C : Abdominal pain)

M

Acute intermittent
©

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

m
4. Soret band at 400 nm.

co
5. Wood's lamp : Red fluorescence.

o.
ho
Note : Ehrilch's test + in hemolytic jaundice also.
ya
5@

Differentiation of Jaundice :
s1
im
ai

Test Prehepatic Hepatic Obstructive

r
ee
m

Direct bilirubin (Conjugated) Normal Normal/↑ ↑

sa

Indirect bilirubin (Unconjugated) ↑ Normal/↑ Normal

|
w

Urine bile salt - +

ro

+/-
ar

- +
M

Urine bile pigment +/-

©

Urine UBG + +/- -

ALT Normal ↑↑ Normal
AST Normal ↑↑ Normal
ALP Normal ↑ ↑↑↑

Biochemistry Revision • v4.0 • Marrow 8.0 • 2024

©
M
ar
ro
w
|
sa
m
ee
rai
im
s1
5@
ya
ho
o.
co
m
©
M
ar
ro
w
|
sa
m
ee
rai
im
s1
5@
ya
ho
o.
co
m