Biochemistry

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Contents

Anatomy
1. Enzymes1

2. Chemistry and Metabolism of Carbohydrates : Part 1 7

3. Chemistry and Metabolism of Carbohydrates : Part 2 14

4. Glycogen Metabolism 19

5. Alternative Methods for Glucose Oxidation 23

6. Chemistry of Proteins and Amino Acids 27

7. Metabolism of Amino Acids 31

8. Chemistry of Lipids 40

9. Metabolism of Lipids 44

10. Electron Transport Chain 48

11. Molecular Biology 50

12. Vitamins57

13. Heme Metabolism 62

 ENZYMES --------- My space ---------

• Biocatalyst which ↑ the rate of biochemical reaction by lowering activation energy.

Enzyme Catalyzed Reaction

• Enzyme (E) + Substrate (S) Enzyme substrate complex (ES) Enzyme + Product (P)
• Substrate binds to the active site of enzyme.

Ribozymes
• Enzymes where RNA has catalytic activity.
• Example - Peptidyl transferase, telomerase.

Note
• All enzymes are proteins except for ribozymes.

CO-FACTOR, CO-ENZYME AND HOLOENZYME

• Protien part of the enzyme - Apo enzyme

Co-Factor Co-Enzyme
• Inorganic molecule attached • Organic molecules (vitamin
to apo enzyme. B-complex) attached to apo enzyme.
Co-factor Enzyme Co-enzyme Reaction

Fe2+ Biotin / B7 Carboxylation

Cytochrome oxidase
Cu2+ Transamination
Peridoxylphosphate (PLP) / B6
Zn2+ Carbonic anhydrase Decarboxylation

Thiamine pyrophosphate (TPP) / B1 Oxidative decarboxylation

Holoenzyme
• Apo-enzyme + co-factor / co-enzyme → Holoenzyme
• Highly specific.
ENZYME ACTIVITY
• Conversion of 1 µmol of substrate in a second.
Optima
Enzyme Activity

Factors Affecting Enzyme Activity

• Temperature
- Optima is 35 to 40°C.
- Bell shaped graph.

Temperature

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 Biochemistry

--------- My space --------- • pH

- Optima is 5-8. Optima

Enzyme Activity
- Exception : Pepsin - pH 2,
ALP - pH 11
- Bell shaped graph.

pH
• Substrate concentration
- Initially, active sites are free.

Enzyme Activity
As concentration of substrate ↑, Saturation
active sites deplete & saturation
is achieved.
- Hyperbolic graph
- AKA saturation kinetics /
steady state kinetics / zero order kinetics. Substrate Concentration
Enzyme Kinetics
• Given by Michaelis and Menten.
K1 K2
• E + S ES E + P
K-1
- K1 - Rate of formation of enzyme substrate
- K-1 - Rate of disassociation of enzyme substrate
- K2 - Rate of formation of product

Michaelis Menten Equation

VMax x S VO = Initial velocity
• VO =
KM + S VMax = Maximum velocity
KM = Michaelis Menten constant
• When initial velocity is half of final velocity, KM is equal to substrate concentration.
- VO = 1/2 VMax KM = S

Significance of KM

• KM ∝ 1
(E) affinity with the (S)
• ↑ KM → ↓ Affinity with S KM
- Glucokinase catalyzing 1st step of glycolysis. 1 VMax
• ↓ KM → ↑ Affinity with S Vo
- Hexokinase catalyzing 1st step of glycolysis.
Lineweaver Burk Plot 1
• Reciprocal of Michaelis Menten equation. VMax
• Plotted as a straight line (y = mx + c) :
1
1 KM
= + 1 S
Vo VMax x S VMax Lineweaver Burk Plot

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 Enzymes

CLASSIFICATION OF ENZYMES 
[Link] --------- My space ---------

Mnemonic - Our Teacher Has Lied In the Lecture

• Oxidoreductases • Lyases
• Transferases • Isomerases
• Hydrolases • Ligase

Oxidoreductases
Mneumonic - DOOP
• Dehydrogenases • Oxygenases
- LDH, PDH, xanthine oxidase • Peroxidases
• Oxidases

Transferases
• Aminotransferases / transaminases - Transfer of amino groups (ALT, AST).
• Hexokinase, glucokinase - Transfer of inorganic phosphate.

Hydrolyases Lyases
• All digestive enzymes. • Enzymes that split up molecules.
• Eg., Fumarase, Aldolase
Isomerases
• Mutase - Phosphoglucomutase Ligase
• Isomerases - Phosphohexoisomerase • Enzyme that combines molecules.
• Racemase • Eg., DNA ligase, glutamine synthetase

SYNTHASE VS. SYNTHETASE

Synthase Synthetase
• No ATP involvement. • ATP is involved.
• Eg., Citrate synthase • Eg., Glutamine synthetase, Carbamoyl
phosphate synthetase (CPS) 1 & II
KINASE VS. PHOSPHATASE

Kinase Phosphatase
• Attaches phosphate to substrate. • Removes phosphate from substrate.
• Eg., Hexokinase, Glucokinase • Eg., Gluco-6-phosphatase

INHIBITION 
[Link]

COMPETITIVE INHIBITION
• Competition between the inhibitor & substrate to bind to the active site.
• E + [S] ES E + P Key :
+ I - Inhibitor
I EI EI - Enzyme inhibitor complex
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 Biochemistry

--------- My space --------- • VMax = same, KM = increase.

Vmax : Without enzyme inhibition
V Vmax' : With enzyme inhibition 1/V0
Uninhibited
Vmax Km : Without enzyme inhibition
Inhibited Km' : With enzyme inhibition 1/Vmax = constant
V 'max

'X - shaped' graph

Km K'm -1/Km -1/Km' 1/[s]
[s]
Michaelis-Menten Equation Lineweaver Burk Plot

• Examples
- Statins inhibit HMG CoA reductase.
- Anti-cancerous drugs inhibit folate reductase.
- Malonate inhibits succinate dehydrogenase (SDH). SDH binds with malonate
instead of succinate.
NON COMPETITIVE INHIBITION
ES E + P Key :
• E + [S]
+ + ESI - Enzyme substrate inhibitor complex
I EI I ESI
• Binds with either enzyme to form enzyme inhibitor complex or with enzyme
substrate to form enzyme substrate inhibitor complex.
• VMax = decreased, KM = same

1/V0
V 1/Vmax'

1/Vmax

[s] -1/Km' = -1/Km 1/[s]

Michaelis-Menten Equation Lineweaver Burk Plot

• It is an irreversible inhibition.
• Examples
- Fluoride inhibits enolase.
- Fluoroacetate inhibits oxaloacetate.
UNCOMPETITIVE INHIBITION
• E + [S] [ES] E + P
+
I ESI
• Binds with enzyme substrate complex to form enzyme substrate inhibitor
complex.
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 Enzymes

• Vmax = decrease, Km = decrease --------- My space ---------

V 1/Vmax'

Vmax 1/V0
V 'max 1/Vmax

K'm Km [s] -1/Km' -1/Km 1/[s]

Michaelis-Menten Equation Lineweaver Burk Plot

ALLOSTERIC INHIBITION / MODULATION

• Does not follows Michalis Menten kinetics. With positive modifier
• Modulator binds to any site on enzyme. V

• If effect is positive - Activator / modulator With negative modifier

- Binding of O2 to heme.
Sigmoid curve
- Acetyl CoA for pyruvate caroxylase.
- N Acetyl Glutamate (NAG) for CPS I Allosteric Modulation [S]
• If effect is negative - Inhibitor
- AKA feedback inhibition.
SUICIDE INHIBITION
• Inhibitor forms a more potent complex than the enzyme substrate complex.
• Example
- Allopurinol inhibits xanthine oxidase.
IRREVERISBLE INHIBITION
• Blocks the active site of the enzyme.
• Example
- Cyanide inhibits Cytochrome a1 a3 oxidase.

ISOENZYMES 
[Link]

• Forms of the enzyme catalysing the same reaction but differentiated :

- Structurally - Immunologically
- Electrophoretically
Examples
LDH
• 5 isoenzymes
• Tetrameric enzyme
• In normal individuals : LDH 2 > LDH 1
• In MI : LDH 1 > LDH 2 (flipping ratio)
LDH
• Catalyses : Lactate Pyruvate
NAD NADH + H+
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 Biochemistry

--------- My space --------- Creatine Phospokinase (CPK)

- Dimeric enzyme
- 3 isoenzymes
CPK
- Catalyses : Creatine Creatine PO4
ATP ADP
- CPK 1 : Rises in brain diseases.
- CPK 2-MB : Most sensitive and reliable indicator of MI.
ENZYMES IMPORTANT FOR DIAGNOSIS

Enzyme Diagnosis

SGOT / AST Heart & liver diseases

SGPT / ALT Liver diseases

ALP Obstructive jaundice, bone disease

Acid Phosphatase Prostate carcinoma

GGT Chronic alcoholism

Lipase, amylase Acute pancreatitis

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 CHEMISTRY AND METABOLISM --------- My space ---------

OF CARBOHYDRATES : PART 1

CHEMISTRY OF CARBOHYDRATES 
[Link]

• Carbohydrates - Polyhydroxy derivatives of aldehydes and ketones.

• Produce aldehydes and ketones on hydrolysis.
• Universal sources of energy.
CLASSIFICATION OF CARBOHYDRATES

Based on Functional Groups

Carbohydrates

Aldoses Ketoses

Carbon Atoms Nomenclature Aldoses Ketoses

3 Trioses Gyceraldehyde Dihydroxyacetone
4 Tetroses Erythrose Erythrulose
5 Pentoses Ribose Ribulose
6 Hexoses Glucose Fructose
7 Heptoses Sedoheptulose

Based on Units Attached

• Monosaccharide : Single unit
• Disaccharide : 2 units
2 sugars connected
• Oligosaccharide : 3-10 units
with glycosidic bond.
• Polysaccharide : > 10 units

Isomers

Stereoisomers (D & L)
• Non superimposable mirror images of each other.
• Glucose : Stable in 'D' form.
- Glucose is a.k.a Dextrose.
• Fructose in human body : D-fructose

Diastereomers
• Non mirror images of each other.
• Eg : Galactose and Mannose
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 Biochemistry

--------- My space --------- Optical Isomers (d & l)

• Optically active.
• (dl) : Optically inactive.

Anomers
• Sugars which differ at C-1 (anomeric C-atom).

CH2-OH CHO
O CH2-OH
O
H-C-OH
H OH H H
OH-C-H
OH OH H H H-C-OH OH OH H OH

H OH H-C-OH H OH
β-D-glucose (Haworth) CHO α-D-glucose
Fischer

Note
• Reducing sugars : Sugars with free anomeric carbon atom.
• All sugars are reducing except Sucrose and Trehalose.

Epimers
• Differ at any other position except C-1.
• Examples :
- Galactose : C4 epimer of glucose.
- Mannose : C2 epimer of glucose.
• Undergo reduction → amino alcohols.
- Glucose → Sorbitol
- Galactose → Galactitol
• Undergo oxidation → corresponding acids.
- Glucose (in vivo) → Glucuronic acid.

Disaccharides

Disaccharide Components Linkage Characteristics

Lactose (Milk sugar) Glucose (β) + Galactose (β) β1 → 4 Reducing sugar
Maltose Glucose (α) + Glucose (α) α1 → 4 Reducing sugar
Sucrose (Invert sugar) Glucose + Fructose α 1 → 2 Non-reducing sugar
Lactulose Galactose + Fructose β 1 → 4 Laxative
Trehalose Glucose + Glucose α 1 → 1 Non-reducing sugar

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 Chemistry and Metabolism of Carbohydrates : Part 1

Polysaccharides --------- My space ---------

Polysaccharides

Homopolysaccharides Heteropolysaccharides

Glucosans Fructosans Uronic acid Amino sugars

Eg : Starch Eg :
Glycogen Inulins
Dextrins
Dextrans
Cellulose

Heteropolysaccharides
• A.K.A Mucopolysaccharides (MPS) | Glycosaminoglycans (GAGs)
• Examples :
- Hyaluronic acid : Only MPS without sulphate.
- Keratan sulphate : Only MPS lacking uronic acid (has galactose).
- Chondroitin sulphate : MC MPS.
- Heparan sulphate : Lining of basement membrane.
• Mucopolysaccharidoses : L
 ysosomal storage disorders caused d/t deficiency of
hydrolases.
MPS Inheritance Enzyme Defect Manifestation
MPS I-H AR α-L-Iduronidase Hurler's syndrome
MPS I-S AR α-L-Iduronidase Schie's syndrome
MPS II X linked Iduronate sulfatase Hunter's syndrome
MPS III AR Heparin sulfatase Sanfilippo syndrome
- Individuals with Sanfilippo's syndrome and Hunter's syndrome have clear
vision.
- Treatment : Enzyme replacement therapy.

METABOLISM OF CARBOHYDRATES 
[Link]

Anabolic Pathway Catabolic Pathway

Energy utilised Energy released
A + B C C A + B
Site : Cytoplasm Site : Mitochondria
Always occur in well fed state. Occur in fasting state.

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 Biochemistry

--------- My space --------- TRANSPORT OF GLUCOSE

Glucose Transport
• Transport of glucose / fructose / galactose (anabolic pathway).
Glucose transporters

Insulin dependent Insulin independent

(GLUT - 4, GLUT - 8 (includes rest of the
and GLUT 12) glucose transporters)

GLUT Site Characteristics

GLUT - 1 RBC's , Blood brain barrier Low km, high affinity for glucose.
GLUT - 2 β cells of pancreas, intestine
GLUT - 3 Neurons Low km, high affinity for glucose.
GLUT - 4 Heart, adipose tissue, skeletal muscle Insulin dependent
GLUT - 5 Sperms Fructose (facilitative mode)

Sodium Dependent Glucose Transport

• 2˚ Co-transport.
• Active transport

SGLUT Site Characteristics

SGLUT - 1 Glucose, Galactose
Reabsorption of glucose.
SGLUT - 2 Glucose

Note
• Composition of ORS : Na+ and glucose given together → ↑ absorption of glucose.

Bidirectional Glucose Transport

• Glucose, fructose and galactose enter the cell, but their outward movement is
prevented by Kinase enzyme (by attaching inorganic phosphate).
PATHWAYS OF GLUCOSE METABOLISM
Pathways

Major pathways Minor pathways

• Glycolysis • HMP shunt
• Gluconeogenesis • Uronic acid
• Glycogenolysis
• Glycogenesis
• TCA
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 Chemistry and Metabolism of Carbohydrates : Part 1

Glycolysis --------- My space ---------

• Partial / incomplete breakdown of glucose (6C).
• 1 molecule of glucose (6C) → 2 molecules of pyruvate (3C).
• In aerobic medium : Produces 7 ATP..
• In anaerobic medium : Produces 2 ATP
- Dead end of anaerobic glycolysis : Lactate

Regulation of Glycolysis
Irreversible steps of glycolysis :
• Hexokinase
Glucose Glucose-6-Phosphate

ATP ADP

• Phosphofructokinase I
Fructose-6-Phosphate Fructose 1, 6 Bisphosphate
- ATP, Citrate
ATP + AMP ADP

• Phosphoenol pyruvate Pyruvate kinase

Pyruvate

ADP ATP

• Rate limiting enzymes : Inhibited by feedback inhibition.

• Examples :
- Hexokinase
- Phosphofructokinase 1
- Pyruvate kinase
• Rate committed enzymes : Phosphofructokinase 1

Inhibitors of Glycolysis
• Fluoride ions :
- Inhibit enolase enzyme (convert 2PGA → PEP).
- Clinical correlation : Fluoride ions (to stop glycolysis) are added along with
anticoagulant to assess glucose in serum.
• Arsenate : Inhibit glyceraldehyde-3-phosphate dehydrogenase.

Substrate Level Phosphorylation

• Synthesis of ATP at the expense of the substrate.
- Kinase
1, 3 BPGA 3 PGA

ADP ATP

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 Biochemistry

--------- My space --------- - Pyruvate kinase

Phosphoenol pyruvate Pyruvate

ADP ATP
Rapoport - Leubering Shunt (RLS)
Glucose

90% Glycolysis 10% RLS

• No formation of end product.
• 2, 3 BPG (byproduct) : ↑ in hypoxia (unload maximum O2 to tissues).
• Net gain of ATP : Zero
3 PGA

1, 3 BPGA
ADP
2, 3 BPGA

ATP
H2O
3 PGA
iP
2 PGA
Warburg Effect
• Aerobic glycolysis in cancer cells.

Pasteur Effect
• ↓ in glycolysis in the presence of oxygen.

Fate of Pyruvate
Pyruvate
Lactate dehydrogenase Pyruvate dehydrogenase complex
(Skeletal
muscle)
NAD+ O2 NADH + H+
Lactate Acetyl CoA (2 C
(Reversible reaction) (Irreversible reaction)

• Pyruvate dehydrogenase complex : Multi enzyme complex

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 Chemistry and Metabolism of Carbohydrates : Part 1

Components --------- My space ---------

Co - Enzymes Enzymes (Sub-units)

• B1 : TPP • E1 : Pyruvate
• B2 : FAD dehydrogenase complex
• B3 : NAD • E2 : Dihydrolipoyl
• B5 : HSCoA transacetylase
• Lipoate • E3 : Dihydrolipoyl
dehydrogenase

- TPP : Most important co-enzyme as it removes CO2 (decarboxylation).

- Decarboxylation occuring in the presence of O2 : Oxidative decarboxylation
- B1 deficiency → lactic acidosis.

Energetics
• 1 molecule of pyruvic acid → 2.5 ATP (NAD)
• 2 molecules of pyruvic acid → 5 ATP.
1 molecule of glucose
7 ATP
2 molecule of pyruvate 12 ATP
5 ATP
2 molecule of acetyl CoA
• Respiratory enzyme : PDH
Active form (Dephosphorylated)
- PDH
Inactive form (Phosphorylated)
- Insulin prevents PDH in active form (↑ insulin/glucagon → ↑ PDH → ↑
glycolysis (exception).
• Site : Mitochondria
• Carbohydrates can be converted into fats, but vice versa is not possible directly.

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--------- My space ---------
CHEMISTRY AND METABOLISM
OF CARBOHYDRATES : PART 2

TCA (TRICARBOXYLIC ACID) CYCLE 

[Link]

• A.K.A Kreb's cycle / Citric acid cycle.

Acetyl CoA (2C) HSCoA

Citrate synthase
Citrate (6C)

Oxaloacetic acid / OAA (4C)

Kreb's Cycle Iso-citrate (6C)

1 CO2

α-Ketoglutarate (5C)

Succinyl CoA (4C)

1 CO2

Site
• Matrix of mitochondria

Energetics
• 1 molecule of Acetyl CoA → 3 NADH+H+ + 1 FADH2 + 1 GTP
- 3 NADH + H+ = 3 × 2.5 = 7.5
- 1 FADH2 = 1 × 1.5 = 1.5
- 1 GTP = 1 × 1.0 = 1.0
• Total : 10 ATP
• 2 molecules of Acetyl CoA → 20 ATP

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 Chemistry and Metabolism of Carbohydrates : Part 2

1 Molecule of glucose --------- My space ---------

Glycolysis 7 ATP
2 Molecule of pyruvate
Link reaction 5 ATP
2 Molecule of acetyl CoA
20 ATP
TCA cycle
• 1 molecule of glucose on complete oxidation → 32 ATP

Regulation
• Regulated by 3 enzymes :
- Citrate synthase : Irreversible step
- Isocitrate dehydrogenase : Rate limiting enzyme
- α -ketoglutarate dehydrogenase : Catalyse physiologically unidirectional step.
• TPP is the major coenzyme.

Note
• PDH : Present in active and inactive form.
• α-KGDH : Not present in active and inactive form.

Substrate Level Phosphorylation

Succinate thiokinase
Succinyl CoA Succinate
GDP GTP

ATP ADP

Inhibitors of TCA
• Fluoroacetate (MC) : Fluorocitrate produced instead of citrate.

Salient Features
• First substrate of TCA : Oxaloacetate
• All the enzymes of TCA are present in the mitochondrial matrix.
- Except SDH (Succinate dehydrogenase) : Present in inner mitochondrial
membrane.
• TCA is the only amphibolic pathway.
Amphibolic pathway

Catabolic Anabolic
• CO2 + H2O produced • Lipogenesis : Fatty acid synthesis.
• Related to amino acid pathway.
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 Biochemistry

--------- My space --------- GLUCONEOGENESIS 

[Link]

• Synthesis of glucose from non-carbohydrate precursors like :

- Alanine (Most potent glucogenic amino acid)
- Lactate
- Propionate (from odd chain fatty acids)
- Glycerol (from hydrolysis of TGs)
• Acetyl CoA is not a glucogenic substrate.
• Site : Mitochondria → cytoplasm → ER
- Heme synthesis
- Urea cycle In mitochondria and cytoplasm
- Gluconeogenesis
• Occurs in liver and kidney in fasting state.
• 3 irreversible steps of glycolysis are made reversible.
- Glucose → Glucose 6 phosphate
- Fructose-6-phosphate → Fructose 1,6 bisphosphate
- PEP → Pyruvate
Pyruvate PEP
+CO2
B7 Pyruvate PEP CK
Mitochondria
2 ATP carboxylase 2 GTP

OAA OAA

Malate Malate

• Fructose 1, 6 Bisphosphate F 1, 6 Bisphosphatase

Fructose-6-Phosphate

• G-6-Phosphatase
Glucose-6-Phosphate Glucose

• Pyruvate carboxylase is the only enzyme in mitochondria.

• Carboxylation requires : ATP, Biotin, CHCO3-

Regulation
• Anabolic process
• Consumes 4 ATP and 2 GTP molecules.
• Glucagon :
- Accelerate gluconeogenesis.
- Makes pyruvate kinase inactive.
- Activate F-2,6 Bisphosphatase.

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 Chemistry and Metabolism of Carbohydrates : Part 2

Cahill's Cycle --------- My space ---------

• Converts alanine → glucose
- Alanine : Most potent glucogenic amino acid.
• Involves liver and muscle.

Muscle
Liver

Glucose

PA Glucose
Cahil's Cycle

Alanine Pyruvate

Alanine

Cori's Cycle
Muscle
Liver

Glucose

PA Glucose
Cori's Cycle
Lactate Pyruvate

Lactate

Propionyl CoA
• Obtained from degradation of odd chain fatty acids.
Propionyl CoA
B7 ATP
D-methylmalonyl CoA
Racemase
L-methylmalonyl CoA
B12 Mutase
Succinyl CoA

TCA
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 Biochemistry

--------- My space --------- • B12 deficiency → Methylmalonic aciduria.

Glycerol
• Obtained from hydrolysis of TG's.
Glycerol
ATP
α-Glycerokinase
ADP
Glycero-1-phosphate
Dehydrogenase
DHAP

Glucose

• α-Glycerokinase : Absent in adipose tissue.

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 GLYCOGEN METABOLISM --------- My space ---------

• Body stores glycogen as glycogen can be broken down in absence of O2 whereas

- Fats require O2 for their breakdown.
• Sites of glycogen storage : Liver and muscle

Anabolism Catabolism
Glycogenesis Glycogenolysis
Occurs in well fed state. Occurs in fasting state.
RLE : Glycogen synthase RLE : Glycogen phosphorylase
Insulin promote glycogenesis. Insulin inhibit glycogenolysis.
Epinephrine promote glycogenolysis (in liver and muscle).
Glucagon inhibit glycogenesis.
Glucagon promote glycogenolysis (in liver).

• Products of glycogenolysis :
- In liver : Glucose
- In muscle : Glucose-6-phosphate (d/t absence of glucose-6-phosphatase in
the muscle).
- Glucose-6-phosphate present in the ER.

METABOLIC PATHWAYS 
[Link]

GLYCOGENESIS
• Activation of C-1 of glucose by UTP.
• Synthesis of primer : Glycogenin (synthesised on the backbone of proteins).
• Glycogen synthase initiate the pathway.
• Branching enzyme : Synthesise α (1,6) linkage.
GLYCOGENOLYSIS
• Phosphorylitic splitting : Catalyzed by enzyme Glycogen phosphorylase.
• Limit dextrin : Point of cessation of phosphorylitic splitting.

• Debranching enzyme : Bifunctional enzyme

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 Biochemistry

--------- My space --------- - Cut α 1 → 6 linkage.

- Transfer α 1 → 4 linkage.
• Glycogen phosphorylase (RLE) acts again.
In muscle
Glucose-6-phosphate ↑ G6P Lactate
Glucose-6-phosphatase (Liver) G-6-phosphatase (Absent in muscle)

Glucose No glucose
Note
• Common enzyme of glycogenesis and glycogenolysis : Phosphoglucomutase.
Phosphoglucomutase
Glucose-6-phosphate Glucose-1-phosphate

REGULATION
• Insulin promote glycogen synthase (active in dephosphorylated form).
• Glucagon promote glycogen phosphorylase (active in phosphorylated form).
Adenylate Phospho
ATP C-AMP 5I-AMP
Cyclase Diesterase

Protein kinase Kinase Protein kinase

(Inactive) (Active)

O O O O

H H Phosphatase P P P
Dephosphorylated Phosphorylated
form form

Covalent modification
• Ca2+ promotes glycogenolysis.
• Epinephrine promotes glycogenolysis in liver and muscle.
• Glucagon promotes glycogenolysis only in liver.

Note
• Insulin promote enzymes that are active in dephosphorylated form.

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 Glycogen Metabolism

GLYCOGEN STORAGE DISORDERS 

[Link] --------- My space ---------

GSD Type Deficient Enzyme

Von Gierke's Type Ia Glucose-6-phosphatase
Pompe's Type II Lysosomal α 1-4 acid maltase
Cori's Type III Debranching enzyme
Anderson's Type IV Branching enzyme
McArdle's Type V Muscle phosphorylase
Her's Type VI Liver phosphorylase
Tarui's Type VII Phosphofructokinase

Liver GSD Muscle GSD

• Von Gierke's
• Pompe's
• Cori's
• McArdle's
• Anderson's
• Tarui's
• Her's

Von Gierke's Disease (Type 1a)

G-6-Phosphate

↑ Lactic acid ↑ Acetyl CoA ↑ Uric acid

↓ Glucose

↑ TG ↑ KB
• Diagnostic features :
- Hypoglycemia (fasting) - Hepatomegaly
- Hyper triglyceridemia - Renomegaly
- Hyperuricemia - Ketosis
• Clinical features :
- Chubby cheeks (d/t ↑ TGs)
- Thin extremities

Type 0
• Deficient enzyme : Glycogen synthase
• Fatal disease (d/t no synthesis of glycogen).

Type Ib
• Deficient enzyme : ER translocase
• Clinical features (similar to type Ia) : ↑ Risk of infections.

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 Biochemistry

--------- My space --------- Pompe's Disease (Type II)

• Deficient enzyme : Lysosomal α 1 → 4 acid maltase.
• Clinical features :
- Cardiomegaly
- Hypotonia
- Macroglossia (feeding difficulties)
- Floppy infant appearance.
- Death (d/t cardiac failure)

Cori's Disease (Type II)

• Deficient enzyme : Debranching enzyme
• A.K.A Limit dextrinosis.
• Clinical features :
- Hypoglycemia
- Deranged liver enzymes.

Anderson's Disease (Type IV)

• Deficient enzyme : Branching enzyme / Amylopectinose
• Clinical features :
- ↑ Portal vein tension → esophageal varices.
- Liver cirrhosis

McArdle's Disease (Type V)

• Deficient enzyme : Muscle phosphorylase.
• MC GSD
• Clinical features :
- Exercise intolerance. - Burgundy color of urine.
- Pain in calf muscles. - 2nd wind phenomenon.
- ↑ Degradation of myoglobin.

Hers's Disease (Type VI)

• Deficient enzyme : Liver phosphorylase
• Clinical features : Hepatomegaly

Tarui's Disease (Type VII)

• Deficient enzyme : Phosphofructokinase
• Clinical features :
- Similar to McArdle's disease.
- 2nd wind phenomenon absent
- ↑ Intake of fruit juice → worsens the condition.

22 Biochemistry • v1.0 • DBMCI one • 2024

 ALTERNATIVE METHODS FOR GLUCOSE OXIDATION --------- My space ---------

• HMP shunt
• Uronic acid pathway
• Galactose metabolism
• Fructose metabolism
• Qualitative tests for carbohydrates

HMP SHUNT & URONIC ACID PATHWAY 

[Link]

HMP SHUNT

Salient Features
• No end product.
• Site : Liver > RBCs > Adipose tissue
• Anabolic process
• Insulin stimulates HMP shunt.
• Significance
Generate

NADPH Ribose sugars

• Synthesis of : (precurssor of purine
- Lipogenesis and pyrimidines)
- Cholesterol
- Bile acids

Shunt

Oxidative phase : Uses Non oxidative phase :

• G-6-Phosphate • 2 Transketolase (require TPP)
dehydrogenase (RLE) • 1 Transaldolase
• Generates 2 molecules of F-6-
Phosphate and 1 molecule of
Glyceraldehyde 3 phosphate.

• Multicyclic process.
• Sedoheptulose 7 phosphate : Important intermediate of the shunt.

Biochemistry • v1.0 • DBMCI one • 2024 23

 Biochemistry

--------- My space --------- Role of HMP Shunt in RBCs

• Maintains cell membrane of RBCs (keeping it intact) by not letting free radicals
to multiply.

H2O HMP Shunt

+ GSSG (Oxidised glutathione) NADPH G-6-PDH
1
/2 O2 deficiency
Glutathione Glutathione
peroxidase (Se) reductase ( B2 )

GSH (Reduced glutathione) NADP+

↑H2O2
• ↑ H2O2 → Peroxide free radicals → Hemolytic anemia.
• G-6-PDH deficiency → Hemolytic anemia.
- X-linked
- Heinz bodies present.
• ↓ Glutathione reductase : Measure of B2 (riboflavin) deficiency.
• ↓ Transketolase : Measure of B1 (TPP) deficiency.
• ↓ Glutathione peroxidase : Measure of Se abnormality.
URONIC ACID PATHWAY
• Site : Liver
• Produces glucouronic acid.
- Required for heme degradation (liver).
- Synthesis of mucopolysaccharides.
• In non-primates, ascorbic acid is produced.
- In humans, L-gulonolactone oxidase is required for its synthesis.
• Clinical correlation : Absence of xylitol dehydrogenase → Essential pentosuria →
excretion of xylulose in the urine.

GALACTOSE & FRUCTOSE METABOLISM 

[Link]

GALACTOSE METABOLISM
• Galactose : 100% faster absorption.
- Component of milk sugar.
Galactitol/ Aldol Galactokinase (GALK)
Galactose Gal-1-PO4 UDPG (activated glucose)
Dulcitol reductase
Gal-1-PO4 uridyl transferase
ATP ADP (GALT)
UDPGal Glucose-1-PO4

Glucose-6-PO4

Glucose
24 Biochemistry • v1.0 • DBMCI one • 2024
 Alternative Methods for Glucose Oxidation

Clinical Correlation --------- My space ---------

• GALT / GALK absent → Galactosemia.

Parameters Classical Galactosemia Non - Classical Galactosemia

Enzyme deficient GALT GALK
• Vomiting
• Diarrhoea
Clinical features • Cataract
• Jaundice
• Cataract (↑ Dulcitol)

Biochemical Findings
• Benedicts test : Positive • Mucic acid test : Positive
• GOD - POD test : Negative • Enzyme assay
FRUCTOSE METABOLISM
• Fructose
- Sweeter than glucose
- Transport : Facilitative mode
- Most lipogenic sugar
Fructokinase
Fructose Fructose-1-PO4

ATP ADP Aldolase B

Glyceraldehyde DHAP (Dihydroxy

Acetone Phosphate)

Glycolysis
Clinical Correlation
• Aldolase B deficiency → Hereditary fructose intolerance.
• Clinical features :
- Asymptomatic at birth.
- When fruit juice given → condition worsens → vomiting, diarrhoea, jaundice,
no cataract.
• Fructokinase deficiency → Fructosuria

Biochemical Findings
• Benedict's test : Positive • GOD-POD test : Negative
• Seliwanoff's test : Positive

Biochemistry • v1.0 • DBMCI one • 2024 25

 Biochemistry

--------- My space --------- QUALITATIVE TESTS FOR CARBOHYDRATES 

[Link]

Tests Carbohydrates
Molisch's test All carbohydrates
Iodine test Only polysaccharides (Starch)
Barfoed's test Differentiates b/w monosaccharides and disaccharides.
Benedict's test Differentiates b/w reducing sugars and non-reducing sugars.
Mucic acid test Only galactose
Seliwanoff's test Ketohexoses (Fructose, Sucrose).

Differentiate between reducing and non-reducing sugars

• Benedict's test : Red precipitate of CuO present in reducing sugars.
• Osazone test :
- Glucose & fructose → Needle like crystals.
- Lactose → Powdery puff crystals.
- Maltose → Sunflower petals.
• Mutarotation : α and β forms.

Note
• None of the above three tests are given by sucrose (non-reducing sugar).

26 Biochemistry • v1.0 • DBMCI one • 2024

 CHEMISTRY OF PROTEINS AND AMINO ACIDS --------- My space ---------

• Proteins are polymers of amino acids (AAs).

• Amino acids - Molecules that exist as zwitter ion.
• Structure : α carbon atom + carboxylic group + amino group
• Amphoteric substance : Can donate & accept a proton.
H H

HOOC C NH2 OOC

-
C NH3+

R R
Structure of Amino Acid Structure of Zwitter Ion
• Iso-electric point : Point when there is no net migration / movement of amino acid.
- Amino acids are seperated at iso electric point.
- Net charge of AA is zero / neutral / amount of negative charge = positive
charge.
• pH and pI
- pH < pI : Protonated - pH = pI : Zwitter ion
- pH > pI : Deprotonated

CLASSIFICATION 
[Link]

BASED ON SIDE CHAIN (R GROUP)

Type Amino Acid
• Glycine
• Alanine
Aliphatic (straight chain) • Leucine
• Isoleucine
• Valine
• Phenylalanine
Aromatic • Tyrosine
• Tryptophan
• Cysteine
Sulphur containing
• Methionine
• Aspartate
Acidic
• Glutamate
• Lysine
Basic • Arginine
• Histidine
• Proline
Imino acids
• Hyroxyproline

Biochemistry • v1.0 • DBMCI one • 2024 27

 Biochemistry

--------- My space --------- BASED ON POLARITY

Type Amino Acid
• Cysteine
• Acidic AAs
Polar & soluble
• Basic AAs
• -OH group containing AAs (Serine, Threonine)
• Leucine
Non-polar & insoluble
• Isoleucine

BASED ON NUTRITIONAL REQUIREMENT

Type Amino Acid

• Tryptophan
• Valine
• Threonine
Essential • Isoleucine
(Mneumonic - TV TILL 8 PM) • Leucine
• Lysine
• Phenylalanine
• Methionine
• Arginine
Semi-essential
• Histidine
• Glycine
Non-essential • Serine
• Alanine & 7 other AAs.

Note
• Total number of standard AAs : 20
• 21st AA : Selenocysteine - Coded by non-sense codon UGA.
• 22nd AA : Pyrrolysine - Coded by UAG.

BASED ON METABOLIC FATE

Type Amino Acid

• 14 amino acids
Glucogenic
• Alanine (most potent)
• Leucine (most potent)
Ketogenic
• Lysine
• Phenylalanine
Both glucogenic & ketogenic • Isoleucine
(Mnemonic - PITT) • Tyrosine
• Tryptophan

28 Biochemistry • v1.0 • DBMCI one • 2024

 Chemistry of Proteins and Amino Acids

CHEMISTRY OF PROTEINS 
[Link] --------- My space ---------

• AA + AA → forms a peptide bond by losing a water molecule.

• Monosaccaride + monosaccaride → forms a glycosidic bond by losing a water
molecule.
Note
• AA + AA → Dipeptide
• AA + AA + AA → Tripeptide
• AA + AA + AA + AA +...... → Polypeptide

• Polypeptides have N-terminal & C-terminal.

Dipeptide
• Aspartame - Artificial sweetener
- Phenalyalanine + Aspartate
- Contraindicated in phenylketonuria.

Tripeptide
• Glutathione - Antioxidant
- Consists of glycine, cysteine, glutamate (G-C-G).
- Cysteine gives the sulphydryl group (reducing function).
• Creatine - Energy reservoir of muscles.
- Consists of glycine, arginine, methionine (G-A-M).
- When it loses a molecule of H2O → Creatinine is formed (anhydride of
creatine).

Polypeptide
Insulin, glucagon - Peptide hormones
STRUCTURAL ORGANISATION OF PROTEINS

Primary
• Linear sequence of AAs.
• Bonds present : Peptide bond.
- Strongest bond & is not broken by denaturation.

Secondary
• Bonds present : Peptide bond, hydrogen bonds, disulfide bonds.
Intramolecular
- Hydrogen bond
Intermolecular
Types
• α-helix
- Proline destabilizes the helix, hence absent.
- Glycine produces bends.
Structure of α-helix Protiens

Biochemistry • v1.0 • DBMCI one • 2024 29

 Biochemistry

--------- My space --------- • β-pleated

- Parallel & anti-parallel
Parallel Anti-parallel
Super Secondary Structures
• βαβ • β-Meander
• Greek key
Tertiary Structure
• Most stable.
• Best visualised by X-ray crystallography.
• Bonds : Peptide bond, hydrogen bond, disulphide bond, covalent bond, ionic bond
& Van der Waals forces, hydrophobic bond.
- Hyrophobic bond provides stability → forms domains (characteristic feature).
Quarternary Structure
• Polypeptide units with all the bonds present in tertiary structure.

Note
• Other bonds that provide stability :
- Reverse bends - Reverse turns

BREAKDOWN OF PEPTIDE BONDS

N-terminal Residue Analysis
• Reagents involved :
- Sanger's reagent - 2, 4 dinitrofluoro benzene (2,4 DNFB)
- Edman degradation - Phenyl isothiocyanate (PITC)
C-terminal Residue Analysis
• Treat the polypeptide with the following enzymes
- Carboxypeptidase - Chymotrypsinogen
NITROGEN BALANCE
• Proteins are the only macromolecules with nitrogen.
• Rate of input of protein synthesis = rate of output of protein degradation.
• Zero nitrogen balance : Synthesis = degradation
- Seen in healthy individuals.
• Positive nitrogen balance : Synthesis > degradation
- Seen in growing children, lactating mothers.
• Negative nitrogen balance : Synthesis < degradation
- Seen in starvation, trauma, diabetes mellitus.
Note
• Nitrogen is present as an amino group → transported in the form of ammonia
(NH3) → eliminated in the form of urea.
• Humans are ureotelic organisms.

30 Biochemistry • v1.0 • DBMCI one • 2024

 METABOLISM OF AMINO ACIDS --------- My space ---------

Metabolism of amino acids

As per N - Skeleton As per C - Skeleton

H2N-CH-COOH
R

METABOLISM AS PER NITROGEN SKELETON 

[Link]

Transamination

Deamination

Urea cycle

TRANSAMINATION
• Definition : Transfer of amino group from an amino acid to a keto acid → form
a new amino acid and a new keto acid.
• Alanine (3C) + α-KG (5C) PLP Glutamate (5C) + Pyruvate (3C)
ALT
- ALT / SGPT : Indicator of liver diseases.
• Aspartate (3C) + α- KG (5C) PLP Glutamate (5C) + Oxaloacetate (3C)
AST
- AST / SGOT : Indicator of heart diseases.
• Enzyme : Aminotransferase / Transaminases.
- Co-enzyme : PLP (Pyridosal phosphate) / Vit B6
• Only 17 AAs (out of 20 AAs) undergo transamination.
• AAs which cannot undergo transamination :
- Proline - Threonine
- Lysine

DEAMINATION
• Definition : Removal of -NH2 group.
• Types :
- Oxidative - Non-oxidative

Oxidative Decarboxylation
• Enzyme : L-amino acid oxidase
• Dependent on auto oxidisable flavoproteins.
Biochemistry • v1.0 • DBMCI one • 2024 31
 Biochemistry

--------- My space --------- - Alanine Pyruvate

NH2
- Aspartate Oxaloacetate

NH2

Oxidative Deamination of Glutamate / Transdeamination

• Site : Liver and kidney.
• Enzyme : Glutamate dehydrogenase
- Requires NAD / NADP
Glutamate α-Ketoglutarate

NH2
TCA
Ammonia
• Released after final step of deamination.
• NH3 cannot move in free form.
↑ NH3

↓ α-KG Glutamate Glutamine

H2O
↓TCA GABA
Cerebral edema
Affect CNS Affect CNS
function function
• Brain is the most affected organ d/t increased NH3.
- Blurring of vision.
- Speech : Repetition, slurring
- Coma
- Flapping tremors
• Transporter from brain to the liver : Glutamate
NH3
Glutaminase
Glutamate Glutamine Glutamate
Glutamine
synthetase NH3 to liver
ATP ADP

• Transporter from skeletal muscle to the liver : Alanine

Alanine Pyruvate

NH3

32 Biochemistry • v1.0 • DBMCI one • 2024

 Metabolism of Amino Acids

UREA CYCLE 
[Link] --------- My space ---------

• Site : Liver
- Exist in 2 compartments : Mitochondria and cytoplasm.
• Takes place in 5 steps :
- I, II steps occur in mitochondria.
- III, IV, V steps occur in cytoplasm.
• RLE : CPSI (Carbamoyl phosphate Synthetase I).
• Anabolic process.
• Energetic : 3 ATP required to 4 iP.
• Regulation : NAG (N-acetyl glutamate) enzyme (modulator of CPS I).
• Structure of urea : O HCO3

H2N NH2
Amino acids
Aspartate
Mitochondria

HCO3- + NH4+ Citrin transporter

2 ATP Citrulline Aspartate
2. OTC
1. CPS 1 + NAG
ATP 3. ASS
2 ADP + 2 iP
AMP + PPi
Carbamoyl phosphate
Ornithine Arginosuccinate

Transporter
4.
Arginosuccinase
Urea 5.
Arginase
Arginine Fumarate (Goes to TCA cycle)
H2O

Urea Cycle
CLINICAL CORRELATION

Enzyme Deficiency Disorder

CPS I Hyperammonemia type I
OTC Hyperammonemia type II
ASS Citrullinemia type I
Citrin transporter Citrullinemia type II
Arginosuccinase Arginosuccinic aciduria
NAG synthase Hyperammonemia type VI
Ornithine transporter HHH syndrome

Biochemistry • v1.0 • DBMCI one • 2024 33

 Biochemistry

--------- My space --------- Treatment

Phenyl butyrate (Scavenger of ammonium ions)

Phenyl acetyl glutamine

Excreted in urine
METABOLISM AS PER CARBON SKELETON 
[Link]

PHENYLALANINE
• Essential AA (syntesises tyrosine).
• Act as glucogenic and ketogenic.
• Aromatic AA.

Metabolism
PAH Catabolic fate
Fumarate
Phenylalanine Tyrosine
Acetyl CoA
Specialized anabolic products

Melanin (Skin pigment) Thyroid hormone (T3, T4) Catecholamines

PAH : Phenylalanine hydroxylase

Anabolic Fate of Tyrosine

Synthesis of Tyrosine
PAH
↑ Phenylalanine Tyrosine
BH4 BH2
Phenyl acetate DHPR
Ketoacids Phenyl lactate
Phenyl pyruvate NADP
+
NADPH + H+

Ketonuria
Phenylketonuria
• D/t PAH deficiency :
- Pale skin - Low IQ
- Musty odor of urine (d/t phenyl acetate).
• Investigations :
- Guthrie's test : Positive (Bacillus subtilis)
- FeCl3 test : Positive
• Treatment :
- Restricted diet in phenylalanine.
- Tyrosine supplementation.
- Cassava based diet.
34 Biochemistry • v1.0 • DBMCI one • 2024
 Metabolism of Amino Acids

Albinism --------- My space ---------

• Tyrosinase
Tyrosine Melanin

- Tyrosine deficiency → Albinism

- Vitiligo and leukoderma : Not d/t ↓ tyrosine.

Pheochromocytoma
• Tyrosine is required for dopamine :
Dopamine

Nor epinephrine
Methylation (-CH3)
Epinephrine
• Overproduction of catecholamines → Pheochromocytoma (cancer of adrenal
gland)
- ↑ Homovanillic acid - ↑ Metanephrine
• Clinical features : Profuse sweating, palpitations.

Cheese Reaction
Tyrosine
MAO
Dopamine HVA

Catecholamines
• People on MAO inhibitor on consumption of aged cheese, wine, beer → ↑
Dopamine → ↑ Catecholamines → Hypertensive crisis.

Catabolic Fate of Tyrosine

Tyrosine
Transaminase
p-OH phenylpyruvate
Dioxygenase
Homogentisate
Oxidase

4-Malelylacetoacetate
Isomerase

4-Fumarylacetoacetate
Fumarylacetoacetate hydrolase

Fumarate Acetoacetate
(Glucogenic) (Ketogenic)
Biochemistry • v1.0 • DBMCI one • 2024 35
 Biochemistry

--------- My space --------- Defective Enzyme Disorder Clinical Features

Fumarylacetoacetate hydrolase Tyrosinemia type I Cabbage odor of urine
Transaminase Tyrosinemia type II Oculocutaneous syndrome
p-OH phenylpyruvate dioxygenase Tyrosinemia type III Swimming pool odor of urine
• Coke coloured urine (urine turns
black on exposure to air).
Homogentisate oxidase Alkaptonuria • Alkapton bodies → Ochronosis &
ochronotic arthritis.
• Benedict's test positive.

• Treatment : Nitisone (inhibitor of p-OH phenyl pyruvate deoxygenase enzyme).

TRYPTOPHAN
• Essential AA.
• Structure : Heterocyclic (Indole ring)
• Both glucogenic and ketogenic.

Specialized Products Synthesized

• Niacin
- 60 mg of Tryptophan → I mg of Niacin
• Serotonin
- Biogenic amine Serotonin (neurotransmitter): Stimulates the cerebral activity
MAO
Serotonin 5HI AA

Melatonin
• Melatonin
- Diurinal variation : Helps in sleep and awake cycle.
- Hormone secreted from pineal gland.

Metabolic Errors of Tryptophan

Hartnup's Disease
• D/t defective tubular absorption of tryptophan.
• Mimic pellagra.
• ↑ Excretion of indolacetic/indole derivatives in urine.
• Investigations : Obermeyer's test

Pellagra
• 3D's :
- Diarrhoea - Dementia
- Dermatitis (Photo sensitive : Casal necklace)
• If untreated → Death

36 Biochemistry • v1.0 • DBMCI one • 2024

 Metabolism of Amino Acids

Carcinoid Syndrome --------- My space ---------

• Overproduction of serotonin in Argentaffin cells.
• Clinical features :
- Profuse Sweating - Palpitation
- Pellagra like symptoms (d/t ↓ Niacin).

SULPHUR CONTAINING AA 
[Link]

1. Methionine : Essential, insoluble 2. Cysteine : Non essential, soluble

METHIONINE

Functions
• Production of cysteine. • Nor epinephrine → Epinephrine
• Transmethylation reactions • Serotonin → Melatonin

Metabolism
MAT
Methionine SAM (Active form of methionine) SAHC
Donates CH3 (methyl
Adenosyl
group) to acceptor
Methionine synthase
Homocysteine
Serine Adenosyl
Methyl B12 B12
Cystathione β-synthase
Vitamin B6
MAT : Methionine adenosyl transferase.
THFA Methyl THFA Cystathionine SAM : S- Adenosyl methionine.
HS Cystathionase SAHC : S- Adenosyl homocysteine.
MTHFR
MTHFR : Methyl tetrahydrofolate reductase.
Homoserine Cysteine THFA : Tetrahydro folic acid.

Succinyl CoA (Glucogenic)

Metabolic Errors

Homocystinuria
• Deficiency of B6 / Cystathionine β-synthase
• Findings :
- ↑ homocysteine. - Normal methionine levels.
- ↓ cysteine.
• Investigations : Cyanide nitroprusside test.
• Clinical features :
- Developmental delay - Low IQ
- Ectopia lentis (lens disoriented) - Fingers : Long
- Sternum: Deformed
Biochemistry • v1.0 • DBMCI one • 2024 37
 Biochemistry

--------- My space --------- • Non classic homocystinuria (d/t deficiency of B9 /B12)

- ↑ homocysteine levels - ↓ methionine levels
- Normal cysteine
• B12 deficiency → Folate trap (↑ methyl malonate levels).

Cystinuria
• Defective tubular reabsorption of the basic amino acids.
• Excretion of :
- Cysteine - Lysine
- Ornithine - Arginine
• Garrod's tetrad :
- Cystinuria - Pentosuria
- Alkaptonuria - Albinism
GLYCINE
• Simplest AA.
• Optically inactive (lacks a chiral C atom).

Special Products Synthesised by Glycine

Heme
Succinyl CoA

Cystine C4, C5, N-7 of

Glutathione Glutamate Glycine
purines
e
i o nin e
h i n
et in
M Arg

Creatine Bile acids

BASIC AMINO ACIDS 

[Link]

• Lysine • Histidine
• Arginine

Lysine
• Essential AA.
• Ketogenic in action.
• Required for the synthesis of :
- Polyamines - Carnitine (β-oxidation)
- Histones

Arginine
• Semi essential AA.
• Required for the synthesis of :
- Citrulline
38 Biochemistry • v1.0 • DBMCI one • 2024
 Metabolism of Amino Acids

- Nitric oxide (vasodilator, EDRF : Endothelial Derived Relaxation Factor) --------- My space ---------
- Urea
- Polyamines

Histidine
• Essential AA.
• Contains imidazole ring.
• Required for the synthesis synthesis of :
Histidine Histamine
Histidase
Urocanate CO2

FIGLU (Formiminoglutamate)
B9
Formimino (One carbon metabolism)
Glutamate
• B9 deficiency → FIGLU in urine.

BRANCHED CHAIN AMINO ACIDS (BCAA) 

[Link]

• Leucine : Ketogenic
• Isoleucine : Both ketogenic & glucogenic
• Valine : Glucogenic

Metabolic Errors

Maple Syrup Urine Disease (MSUD)

• Urine smells like burnt sugar.
• Enzyme deficient : α Keto acid dehydrogenase
• Treatment : B1 supplementation.

Isovaleric Acidemia
• A.K.A Sweaty feet odor syndrome.
• Enzyme deficient : Isovaleryl dehydrogenase

Disease Odor
PKU Musty smell
Tyrosinemia type I Cabbage like odor
Tyrosinemia type II Swimming pool odor
MSUD Burnt sugar smell
Isovaleric acidemia Sweaty feet odor
Multiple carboxylase defect Tom cat urine odor

Biochemistry • v1.0 • DBMCI one • 2024 39

--------- My space ---------
CHEMISTRY OF LIPIDS

• Lipids / Triglycerides - Tri-esters of fatty acid & glycerol.

• Fatty acid - Has a hydrophobic & a hydrophilic part.

Classification
• Given by Bloor.
Lipids

Simple lipids Conjugate lipids Derived lipids

• Neutral fat • Protein - Lipoprotein • Eicosanoids
• Waxes • Phosphate - Phospholipid • Cholesterol
• Carbohydrate - Glycolipid
• Sulphate - Sulfolipid

CONJUGATE LIPIDS 
[Link]

Fatty acid + Protein / Phosphate / Carbohydrate / Sulphate

PHOSPHOLIPID
Lipid + PO4- + Nitrogenous base

Classification Based on Alcohol Attached

Phospholipid

Glycerophospholipid - Glycerol Sphingophospholipid -

Spingosine (unsaturated alcohol)
Glycerophospholipid
• Phosphatidylcholine / Lecithin DPL - Lung surfactant.
- Used in lung maturation test when a child is born.
- Lecithin / sphingomyelin ratio should be >2:1.
• Phosphatidylinositol - 2nd messenger
• Cardiolipin - Only phospholipid with antigenic properties.
• Phosphatidylethanolamine
• Phosphatidylserine

Sphingophospholipid
• Spingomyelin - Lines the myelin sheath.
GLYCOLIPID
• Lipid + Carbohydrate
40
 Chemistry of Lipids

• Alcohol : Sphingosine --------- My space ---------

- Sphingosine + Fatty acid → Ceramide
• Types : Cerebrosides, Gangliosides.
LIPOPROTEINS
• Lipid + Protein
• Protein part : Apo protein.

Types
• Chylomicrons - Highest concentration of exogenous TGs and least amount of
protein.
• VLDL - Highest concentration of endogenous TGs.
• LDL - Maximum concentration of cholesterol.
• IDL - Intermediate produced during the conversion of VLDL to LDL.
• HDL - Maximum amount of protein.

Electrophoretic Movement of Lipoprotiens

• Chylomicrons (stay at the origin)
• LDL / β
• VLDL / Pre β
• IDL / Broad β
• HDL / α-1 (Fastest)

Anode

Ultracentrifugal Separation
• HDL (Most dense)
• LDL
• VLDL
• Chylomicrons (Least dense)

• Density is directly proportinal to protein content & inversely proportional to lipid

content.

Chylomicrons
• Undergoes metabolism via exogenous pathway.
• Apo-proteins :
- Apo-B-48 : Synthesized by RNA editing (specific for chylomicrons).
- Apo-C-II : Activator of LPL.
- Apo-E : Responsible for receptor mediated endocytosis.

VLDL
• Responsible for endogenous pathway.
• Apo-protien :
- Apo-B-100 (major carrier) : Synthesized by RNA editing
Biochemistry • v1.0 • DBMCI one • 2024 41
 Biochemistry

--------- My space --------- - Apo-C-II : Activator of LPL

- Apo-E : Responsible for receptor mediated endocytosis.

HDL
• Responsible for reverse cholesterol transport.
• Apo-proteins :
- Apo-A-I : Activator of LCAT enzyme
- Apo-A-E : Responsible for receptor mediated endocytosis.
- Apo-H

SPHINGOLIPIDOSES 
[Link]

• Class of lysosomal storage disorders d/t deficiency of hydrolase enzymes.

• MC - Gaucher's disease
• All sphingolipidosis :
- Are autosomal recessive except Fabry's (X-linked).
- Have cherry red spot on macula except Gaucher's.
- Have mental retardation except Gaucher's.
• Lipid inclusions
- Zebra bodies : Niemann Pick disease.
- Gaucher's cells : Gaucher's diseases
• Sphingolipidoses & the enzyme deficient
Sphingolipidoses Deficient Enzyme

Tay-Sach's disease Hexosaminidase A

Niemann Pick disease Sphingomyelinase

Gaucher's disease β glucocerebrosidase

Fabry's disease α galactosidase

Wolman's Disease
• Not a sphingolipdoses.
• Deficient enzyme : Acid lipase / Cholesteryl ester hydrolase.
• Clinical features :
- Relentless vomiting. - Calcification of adrenals.
- Watery green diarrhoea.

DERIVED LIPIDS AND FATTY ACIDS 

[Link]

Cholesterol
• Cholesterol - C27H45OH
• Amphipathic lipid.

42 Biochemistry • v1.0 • DBMCI one • 2024

 Chemistry of Lipids

• 70% is in ester form (LCAT enzyme) --------- My space ---------

• Deficiency of LCAT → Norum's disease.

Eicosanoids
• Synthesis of prostanoids (prostaglandins, prostacyclins, thromboxanes) &
leukotrienes from arachidonic acid (polyenoic fatty acid).

Fatty Acids
• Omega 3 fatty acids are cardioprotective.
• 5 essential fatty acids :
- Linoleic acid : Required for synthesis of arachidoinc acid (most essential).
- Linolenic acid
- Arachidonic acid
- DHA : Present in breast milk.
- EPA : Present in fish / cod liver oil.
• Trans fatty acids are harmful to the body as they ↑ the levels of TGs &
cholesterol.

Biochemistry • v1.0 • DBMCI one • 2024 43

--------- My space ---------
METABOLISM OF LIPIDS

Anabolism Catabolism

AKA Lipogenesis Lipolysis / β oxidation

Occurs in Well fed state Fasting state

Site Cytoplasm Mitochondria

Rate limiting enzyme Acetyl CoA Carboxylase Carnitine Palmitoyltransferase I

LIPOGENESIS 
[Link]

LIPOGENESIS
• De novo synthesis - Precursor is a 2 carbon compound (Acetyl CoA).

Step 1 : Transport of Acetyl CoA from Mitochondria to Cytoplasm

• Citrate shuttle is needed to facilitate transport as Acetyl CoA is impermeable.
Mitochondria Cytoplasm

Acetyl CoA ATP citrate lyase

Oxaloacetic acid Citrate Citrate Acetyl CoA + Oxaloacetic acid

CYS-SH
Step 2 : Carboxylation of Acetyl CoA
1 6
Acetyl CoA Malonyl CoA Pan-SH
Carboxylase, 2 ACP 5
ATP, Biotin, HCO3-
3 4
Step 3 : Fatty Acid Synthase (FAS) Complex Acyl Carrier Protein

• FAS complex has 3 sub-units containing the following enzymes :

Condensing Unit Reducing Unit Releasing Unit
• Ketoenoyl reductase
• Malonyl CoA Acyl Transferase (MAT)
• Ketoacyl reductase • Thioesterase
• Ketoenoyl / ketoacyl synthase
• Dehydratase

Pan-SH : Accepts malonyl CoA

• Acyl carrier protein (ACP) has 2 active sites
Cysteine-SH : Accepts Acetyl CoA
Note
• Palmitic acid is the most abundant fatty acid in the body.

44
 Metabolism of Lipids

REGULATION --------- My space ---------

• Rate limiting enzyme : Acetyl CoA carboxylase

Active form Inactive form

(Dephosphorylated) (Phosphorylated)
• Insulin helps acetyl CoA stay in the active form.
ELONGATION
• Occurs in Endoplasmic Reticulum (ER).

LIPOLYSIS 
[Link]

• Depends on carbon atom position - α, β, ω

• Occurs in mitochondria.
Pathways

Major Minor
• β-oxidation • α-oxidation
• ω-oxidation

Step 1 : Activation of Fatty Acid

• Fatty acid Acyl CoA synthetase Acyl CoA

ATP AMP + Pi
Step 2 : Carnitine Shuttle
• Transports FA from cytoplasm to mitochondria to undergo lipolysis.
• Enzymes invovled :
- Carnitine palmitoyl transferase I (CPT-I) - Present in outer mitochondrial
membrane.
- Carnitine palmitoyl transferase II (CPT-II) - Present in inner mitochondrial
membrane.
- Carnitine palmitoyl translocase present in between the membranes.

Step 3 : β Oxidation
• 4 steps : Oxidation → Hydration → Oxidation → Thiolytic cleavage
• To calculate number of cycles needed for oxidation : (n/2)-1
(n = number of carbon atoms)
• To calculate number of acetyl CoA produced : n/2

Palmitic Acid
• 1 molecule of palmitic acid (16C) produces 8 molecules of acetyl CoA from
7 cycles.

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 Biochemistry

--------- My space --------- • Energetics :

- 7 FADH2
- 7 NADH + H+ = 108 ATP - 2 ATP required for activation → Total = 106 ATP
- 8 Acetyl CoA
RLE & REGULATION
• Rate limiting enzyme : CPT 1
• Regulated by lipoprotein lipase (anabolic) & hormone sensitive lipase (catabolic).
OXIDATION OF FATTY ACIDS BASED ON LENGTH
• Short chain FA Does not require carnitine
• Medium chain FA
• Long chain FA - Requires carnitine
Peroxisome
Very Long Chain FA (VLCFA)
• Oxidised in peroxisomes & Carrier Protein
is transported VLCFA Acetyl CoA +
VLCFA Octanoyl CoA
by a carrier protein.
• VLCFA → Octanoyl CoA + acetyl CoA
• Octanoyl CoA is sent to
mitochondria for β oxidation Mitochondria
β oxidation of Octanoyl CoA

METABOLIC ERRORS OF LIPOLYSIS

Medium Chain Acyl CoA Dehydrogenase (MCAD) Deficiency
• Deficient enzyme : Medium chain acyl CoA dehydrogenase.
• Absence of MCAD causes lipids to undergo ω oxidation to produce dicarboxylic
acid.
• ↓ β-oxidation leads to ↓ concentration of acetyl CoA & ketone bodies →
↓ gluconeogenesis → Hypoglycemia.
• Leads to death of the infant.
Zellweger Syndrome
• AKA cerebrohepatorenal syndrome.
• It is a peroxisome biogenesis disorder (PBD).
• ↑ concentration of VLCFA d/t deficiency of carrier protein / mutation of the
gene coding the carrier protein.
Refsum’s Disease
• Deficient enzyme : α-phytate oxidase
• ↑ concentration of phytanic acid (present in milk & green leafy vegetables).
Jamaican Vomiting Sickness
• Caused d/t consumption of unripe Ackee fruit.
• Toxin : Hypoglycin

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 Metabolism of Lipids

• Clinical features : Sudden onset of vomiting, fever, diarrhea, convulsions, --------- My space ---------
hypoglycemia.

KETOGENESIS 
[Link]

• Ketogenesis : Formation of ketone bodies in the mitochondrial fraction of liver.

• Three types :
- Acetoacetate : Primary
- Acetone Secondary
- β hydroxy butyrate
• Normal concentration of ketone bodies : 1 mg/dL
• ↑ during starvation, diabetes mellitus (causes diabetic ketoacidosis).
• Precursor : Acetyl CoA
• RLE : HMG CoA Synthase present in mitochondria
• Investigation : Rothera's test
- Appearance of violet ring at the junction.
- Positive only for acetone, acteoacetate.
• Most predominant ketone body in DKA - β hydroxy butyrate
• Main source of energy for heart & brain during starvation.
• Organs not using ketone bodies for energy : Liver (lacks thiophorase enzyme) &
RBC (lacks mitochondria).

Fed Fasting Starvation

Brain Glucose Glucose Ketone bodies

Heart Fatty acids Fatty acids Ketone bodies

RBCs Glucose Glucose Glucose

CHOLESTEROL BIOSYNTHESIS 
[Link]

• 70% moves in esterified form & LCAT enzyme is required.

• Syntesised by de novo method.
- Precursor : Acetyl CoA
- Site : Cytoplasm
- Rate limiting enzyme : HMG CoA reductase (inhibited by statins).

Fate of Cholesterol
• Excreted in feces.
• Required for the synthesis of bile acids - Primary & secondary bile acids.
- Rate limiting enzyme : 7 alpha hydroxylase.
• Required for the synthesis of steroid hormones & vitamin D.
• Regulated by feedback inhibition : Blocking HMG CoA reductase.

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--------- My space ---------
ELECTRON TRANSPORT CHAIN

Carbohydrate Fats Protein

Acetyl CoA

Oxaloacetic acid Citric acid

TCA cycle in
mitochondrial matrix
• Carbohydrates, fats & proteins are metabolised to form acetyl CoA → Enters
TCA cycle.
• 3 NADH + H+ & 1 FADH2 is released.
• Site : Inner membrane of mitochondria.
Complex I Complex II
NADH CoQ reductase Succinate CoQ reductase

Combines to form
CoQ (Ubiquinone)
Transfers to
Complex III
Cytochrome D, cytochrome C

Transfers to
Complex IV
Cytochrom a1, a3 oxidase
F1-Fo ATP
O2 ADP synthetase ATP

H+ + e- H2O
• Energy released at each step of transfer of electrons is
- Dissipated as heat.
- Forms ATP by oxidative phosphorylation.
H+
Biological Oxidation
Oxysomes
• H+ are impermeable to inner membrane of mitochondria.
• Hence, oxysomes carry H+ to F1-Fo synthetase to form ATP.
• ETC coupled with ATP oxidative phosphorylation is biological oxidation.

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 Electron Transport Chain

INHIBITORS AND UNCOUPLERS 

[Link] --------- My space ---------

INHIBITORS
Block complexes / processes

Complex / Process Inhibitor

Complex I Rotenone, phenobarbital

Complex II Carboxin, malonate, thionyl trifluoroacetone

Complex III Hypoglycemic drugs, British Anti Lewisite (BAL)

Complex IV Cyanide, H2S, azide, CO

ATP synthesis Oligomycin

UNCOUPLERS
Release energy in the form of heat.

Type Uncoupler

Physiological Thermogenin, thyroxine

Synthetic 2,4 dinitrophenol (2,4 DNP)

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--------- My space ---------
MOLECULAR BIOLOGY

• DNA : Deoxyribonucleic acid

• RNA : Ribonucleic acid
• Protein : Polymer of AAs.
Transcription Translation
DNA RNA Proteins
Reverse transcription

Replication

• Nucleotide : Base + Sugar + PO4

• Nucleoside : Base + Sugar

NITROGENOUS BASES 
[Link]

Nitrogenous bases

Purines Pyrimidines

N9 N

O O

N-9 Glycosides N-1 Glycosides

• Adenine • Thymine
• Guanine • Cytosine
• Urasil
PURINES
Synthesised by 2 pathways.

De-Novo Pathway
• Precursor Ribose-5-P

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 Molecular Biology

CO2 Glycine --------- My space ---------

C6 Glycine N7
Aspartate N1
C5 C8 Methylene THF

C2 C4
Formyl THF N9
N3 Glycine
Glutamine Glutamine

• Operative in all of areas except :

- Brain - WBCs
- RBCs - Bone marrow
• RLE :
- PRPP synthetase - PRPP glutamine amidotransferase
• RCE : PRPP glutamine amidotransferase
NMP Ribonucleotide reductase dNMPs
AMP (B12, Selenocysteine reductase) dAMPs
Salvage Pathway
• Operative in :
- Brain - WBCs
- RBCs - Bone marrow

Purine Catabolism
• Product : Uric acid
• Normal concentration of uric acid :
- Males : 3-7 mg/dl
- Females : 2-6 mg/dl

Metabolic Errors

Gout
• D/t hyperuricemia.
• Metatarsophalangeal joint : 1st joint affected.
• Tophi : Sodium-urate crystals
• Treatment :
- Uricosuric drugs - Allopurinol
- NSAIDs

Lesch Nyhan Syndrome

• D/t deficiency of HGPRT enzyme.
• X-linked
• Clinical features :
- Aggressive behaviour
- Self mutilation
- Hyperuricemia
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 Biochemistry

--------- My space --------- Kelley Seegmiller Syndrome

• D/t partial deficiency of HGPRT enzyme.
• Less severe than Lesch Nyhan Syndrome.
PYRIMIDINES
• Site of synthesis : Cytoplasm
- Dihydroorotic acid (dehydrogenase) : Only mitochondrial enzyme.
• RLE : CPS I
- CPSI : RLE of Urea cycle
• 1st pyrimidine : Uracil
Uracil

TMP CH3 (Folate) CMP

• Catabolic products :
- Harmless
- Produces β alaline & CO2 → utilized by body.

Metabolic Errors

Orotic Aciduria
Types

Type I Type II
• Deficient enzyme : OPRT • Deficient enzyme :
(Oratate phospho ribosyl transferase) OMP decarboxylase

DNA 
[Link]

• Structure of DNA :
- Proposed by Watson & Crick (B-type DNA).
- Double stranded.
- Antiparallel strands.
3.4 A°
- Complementary to each other. 34 A°
- Diameter : 20 Å
- Pitch : 34 Å
- 10 base pairs per turn.
• Composition of DNA : 20 A°
- Proposed by Chargaff. Structure of DNA
- Adenine = Thymine
- Guanine = Cytosine
- Purines = Pyrimidines

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 Molecular Biology

DNA REPLICATION --------- My space ---------

• Selection of ori of replication.

Enzyme Function
Helicases Unwinding
Topoisomerases Stress releasing
Gyrases (in prokaryotes) Helicases and topoisomerases
DNA polymerase Fidelity enzyme
Single strand binding protein (SSB)
Stabilize helix
(in prokaryotes)

3I
5I
Leading strand
3I

5I
Primer

3I 5I
3I 5I
3I 5I
Filled by DNA ligase 3I 5I Lagging strand
3I (Okazaki fragments)

Prokaryotes
• DNA polymerase I :
- Gap filling - Proof reading
- Primer removal
• DNA polymerase II : Repair
• DNA polymerase III
- Leading & lagging strand - Proof reading

Eukaryotes
• DNA polymerase (5 subunits) :
- α : Primase enzyme
- β : Repair
- γ : Mitochondrial DNA synthesis
- δ : Lagging strand synthesis
- ε : Leading strand synthesis
• Proof reading : To check copying errors.
• Defect in DNA repair mechanisms.

Disease Defect
Xeroderma Pigmentosum Nucleotide excision repair
HNPCC Mismatch repair

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 Biochemistry

--------- My space --------- Transcription

• Transcription : Formation of RNA from DNA.
• Enzyme : DNA dependent RNA polymerase.
• Selection of Promoter sequences :
- In prokaryotes (TATAA) : Pribnow box
- In eukaryotes : Hogness box
• No primer is required
• RNA polymerase in prokaryotes have 5 subunits :
Recognises promoter
sequence
σ
α α1 Holoenzyme
Catalytic Core
activity polymerase
β β1

• RNA polymerase in eukaryotes :

- RNA polymerase I : Synthesis of rRNA
- RNA polymerase II : Synthesis of mRNA
- RNA polymerase III : Synthesis of tRNA
• New strand is always synthesized in 5' → 3' direction.
- 5' ATTGA 3' (Non template / coding strand).
- 3' TAACT 5' (Template / non coding strand).

5I A U U G A 3I

3I

5I

Hair pin / Cruciform RNA

5I 3I
hnRNA

Exons (Coding) Introns (Non coding) → Removed

• hn RNA is trimmed : Splicing / Post transcription modification.

• Steps of post-transcriptional modification :
- Poly G capping (by Methyl transferase → 5'-3' exonuclease cannot act).
- Poly A tailing (3'-5' exonuclease cannot act).
- Splicing : Produces spliceosome.

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TRANSLATION --------- My space ---------

• Site : Cytoplasm
• mRNA is exported from the nucleus
• rRNA : 2 subunits

Peptidyl transferase site P A Acceptor site

• In prokaryotes : 70s (50S, 30s)

• In eukaryotes : 80s (60s, 40s)
• t-RNA : Clover leaf structure.
51 31 Activated AA

Pseudouridine site

Dihydrouracil site

Anticodon binding site

t-RNA

• mRNA : Only codons which are recognized by tRNA.

Steps
• Initiation
- AUG : Start codon
- Ternary complex produced.
- Activation of amino acid.
- Charging of tRNA.
• Elongation
- Peptide bond formation.
- Translocation
• Termination : Non sense codon (UAA, UAG, UGA)
• Post translational modification
- Hydroxylation → collagen
- Carboxylation → clotting factors II, VII, IX, X (by Vit K)

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 Biochemistry

--------- My space --------- Genetic Code

• Information is translated in the form of genetic code.
• Degeneracy (Wobble hypothesis) : No change in the AA produced even on
changing the 3rd position on codon.
• Triplets : Code for 64 AAs.

GENETIC TECHNIQUES 
[Link]

Blotting Techniques
• Southern Blotting : DNA
• Northern Blotting : RNA
• Western Blotting : Protein

Polymerase Chain Reaction (PCR)

• Steps : Denaturation → Annealing → Extension → Detection.
• Requirements : Thermostable Taq DNA polymerase, Mg2+

Fluorescent In Situ Hybridization (FISH)

• Detect deletions, translocation, amplification.
• Multicolor FISH : In metaphase stage.
• Nuclear FISH :
- In interphase stage
- More rapid
- Tumor cells are used as sample.

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 VITAMINS --------- My space ---------

Classification
Vitamins

Fat souble Water soluble

• Vitamin A, D, E, K • Vitamin B and C
• Stored in the body. • Not stored in the body (except B12).
• Vitamin K acts as coenzyme. • All act as coenzymes.

WATER SOLUBLE VITAMINS 

[Link]

VITAMIN B
Vitamin B

Hematopoietic Non-hematopoietic
• Vitamin B9, B12 • Vitamin B1, B2, B3, B5, B6, B7

Vitamin B1
• Active form : Thiamine pyrophosphate (TPP)
• Source : Aleurone layer of grains (rice polishings).
• Biochemical function : Co-enzyme for oxidative decarboxylation for the enzymes :
- PDH - Enzyme of link reaction
- Alpha-Keto Glutarate Dehydrogenase (α-KGDH) - Enzyme of TCA cycle.
- Alpha-Keto Acid Dehydrogenase (α-KADH) - Enzyme of MSUD.
- Transketolase - Enzyme of HMP shunt.
• Deficiency manifestations - Beriberi
• Investigation - ↓ transketolase activity in RBC

Beriberi
Beriberi

Wet beriberi Dry beriberi Infantile beriberi

• Characterised by edema • No edema

• Alcoholic & B1 deficient → Wernicke's encephalopathy Global confusion

• Clinical features (Mnemonic - GOA)
- If untreated, it leads to
Korsakoff psychosis - Amnesia, confabulation.
Ophthalmoplegia Ataxia

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 Biochemistry

--------- My space --------- Vitamin B2

• Active form : Riboflavin, FMN, FAD (function is related to active forms)
• AKA Warburg's yellow enzyme.
• Deficiency manifestations
- Chelosis - Corneal vascularization
- Glossitis - Seborrheic dermatitis
- Angular stomatitis
• Investigation - Check glutathione reductase acitivity in RBC.

Vitamin B3 / Niacin
• The only endogeously synthesized vitamin.
• Active form : NAD, NADH, NADP, NADPH.
• 60mg of trypthophan synthesizes 1mg of niacin.
• Deficiency manifestations : Pellagra
• Maize eaters are prone to B3 deficiency as maize contains Zein protein which
lacks tryptophan. Diarrhoea

Pellagra
• 3 Ds - Diarrhoea, dermatitis, dementia
• Characteristic feature : Casal necklace
Dermatitis Dementia
Vitamin B5 / Panthothenic Acid
• A β-alanine component.
• Active form : HSCoA
• Functions : In fatty acid metabolism (acetyl CoA, propionyl CoA, malonyl CoA,
HMG CoA)
• Deficiency manifestiation : Gopalan burning feet syndrome.

Vitamin B6 / Panthothenic Acid

• Active form - PLP, B6
• Functions - Transamination, decarboxylation, transulfuration. component of
glycogen phosphorylase, ALA synthase.
• Deficiency manifestations : ↓synthesis of GABA (neurological manifestations seen)
- In B12 deficiency, megalobastic anemia is seen but no anemia in B6 deficiency.
• Investigation - Xanthurenic acid estimation by tryptophan load test.

Vitamin B6 / Biotin
• AKA Anti egg injury factor.
- Avidin present in raw egg inhibits biotin.
- Eating raw eggs ↑ chances of biotin deficiency.
• Functions : Carboxylation reactions involving
- Pyruvate carboxylase - Propionyl CoA carboxylase
- Acetyl CoA carboxylase
• Deficiency manifestation - Multiple carboxylase defect.

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 Vitamins

Vitamin B9 / Folate --------- My space ---------

• Active form : Tetrahydrofolate (THF), Dihydrofolate (DHF)
• Functions : One carbon metabolism
• Carbon is in the form of -CH3, -CH2, -CH, -HCHO.
• Deficiency manifestation - Megaloblastic anemia (d/t decreased DNA synthesis),
spina bifida.
- D/t defect in one carbon metabolism.
• Investigations : FIGLU, AICAR

Vitamin B12 / Folate

• Active form : Cobalamin
- Cyanocobalamin - If central molecule is cyano.
- Methyladenocobalamin - If central molecule is methyl.
• AKA extrinsic factor of castle.
- Absorbebd in ileum & produces intrinsic factor of Castle.
• Function - Component of :
- Riboneucleotide reductase
- Mutase (forms succinyl CoA by propionyl CoA)
- Involved in conversion of homocysteine to methionine.
• Deficiency manifestations
- Peripheral neurological manifestations.
- Subacute axonal degeneration (d/t ↑ concentration of methyl malonyl CoA).
- Homocystinuria
• Investigation : Shilling's test - Radioactive isotope Co60 used.
VITAMIN C
• Cannot be synthesised endogenously d/t absence of L-gulonolactone oxidase.
• Active form : Ascorbic acid
• Function
- Anti-oxidant
- Hydroxylation - Post translational modification of collagen
- Iron absorption
• Source : Amla (richest source)
• Forms : Ascorbic acid & dehydroascorbic acid.
- Reversible forms
• Deficiency manifestions
- Delay in wound healing
- Scurvy - D/t defective formation of collagen
- Petechial hemorrhages

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 Biochemistry

--------- My space --------- FAT SOLUBLE VITAMINS 

[Link]

VITAMIN A
• Forms : Retinol, retinal, retinoic acid
- Interconvertible forms.
- Retinal - Involved in vision.
- Retinol & retinoic acid - Involved in reproduction & vision.
• Storage : ITO cells of liver.
Function
• Vision
dim Rhodopsin Dim
→ br
r i g ht → ight
B
Wald's Visual Cycle
11-cis retinal 11-trans retinal

Enters liver
11-cis retinol 11- trans retinol

• Maintains the epithelial layer.

Deficiency Manifestations
• Loss of sensitivity towards green light (earliest sign).
• Night blindness (earliest symptom).
• Xerophthalmia - Leads to Bitot spots.
Hypervitaminosis
• ↑ vitamin A levels.
• D/t consumption of liver of polar bear in arctic regions.
• Consequence : Damaged organelle (lysosome).
• Clinical features :
- Pseudotumour cerebri - Increased triglycerides
- Hepatomegaly - Alopecia
VITAMIN D
• Active form : 1, 25 dihydroxycholecalciferol / calcitriol
• AKA sunshine vitamin.
• Synthesis
Sun rays 7-dehydrocholesterol
25-hydroxylation in liver by 25-hydroxylase

25-hydroxycholecalciferol
1-hydroxylation in kidney by 1-α-hydroxylase (activated by PTH)

1,25-dihydroxycholecalciferol / Calcitriol / Vitamin D

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 Vitamins

• Function : In bones, intestine, kidney. --------- My space ---------

- ↓ excretion of calcium, ↑ reabsorbtion of calcium → ↑ calcium.
• Deficiency manifestations :
- Rickets (in children)
- Osteomalacia (in adults)
VITAMIN E
• AKA vitamin in search of disease : Cause of many diseases but not a specific
one.
• Most potent chain breaking anti-oxidant.
• Active form : Tocopherol
• Functions : Antioxidant activity
- Lowers risk of atherosclerosis - ↓ peroxidation of fats
• Deficiency manifestations
- Hemolytic anaemia - Peripheral neuropathy
- Cerebral ataxia
VITAMIN K
• 3 forms : Phylloquinone (Vit. K1), menaquinone (Vit. K2), menadione (Vit K3)
- Phylloquinone & menaquinone - Fat soluble
- Menadione - Water soluble
• Only fat souluble vitamin acting as coenzyme.
• Function : Carboxylation of glutamate present on prothrombin.
- Post translational modification of II, VII, IX, X clotting factors.
- Biotin independent reaction.
γ carboxylation
Glutamate of glutamate

Prothrombin

Vit K Vit K epoxide

inhibits
Epoxide reductase Warfarin, Dicoumarol
• Deficiency manifestation : ↑ bleeding time

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--------- My space ---------
HEME METABOLISM

Heme synthesis (anabolic)

• Heme metabolism
Heme breakdown (catabolic)
Structure of Hemoglobin
• Heme is an iron porphyrin.
- Iron (Fe2+ form) present in the centre, surrounded by 4 pyrrole rings.
• Globin - Gives globular structure.

HEME SYNTHESIS, REGULATION AND BREAKDOWN 

[Link]

HEME SYNTHESIS
• Site : Mitochondria & cytoplasm.
- Begins in mitochondria → moves to cytoplasm → moves back to
mitochondria
• Steps :
Succinyl CoA + Glycine
α-ALA synthase α-ALA Synthase
Mitochondria • Rate limiting enzyme.
α-Aminolevulinic acid (α-ALA)
• B6 acts as a co-enzyme
α-ALA dehydratase • Two types : ALA synthase I & ALA synthase II

Porphobilinogen (PBG)
PBG deaminase

Hydroxylmethylbilane (HMB)
UPG III cosynthase
Cytoplasm
Uroporphyrinogen III (UPG)
UPG decarboxylase
CO2

Coproporphyrinogen III (CPG)

CPG oxidase

Protoporphyrinogen IX
Protoporphyrinogen oxidase

Mitochondria Protoporphyrin IX
Fe2+ Ferrochelatase+

Heme

62
 Heme Metabolism

REGULATION --------- My space ---------

• Regulate feedback inhibition.

↑ concentration of heme

Blocks the activity of ALA synthase

Limits the production of heme

HEME BREAKDOWN / CATABOLISM

Heme Heme oxygenase Biliverdin

degrades
Reductase

Bilirubin (Lipophilic)

Transported into the liver via albumin

Liver
Glucuronyl Conjugation of
transferase glucuronic acid

Biliverdin
diglucuronide

Porphyria
• ↑ conc. of porphyrins due to absence of specific enzymes.
Deficient Enzyme Porphyria Manifested
ALA dehydratase Plumboporphyria (lead poisoning)
PBG deaminase Acute intermittent porphyria
UPG synthase Congenital erythropoietic porphyria
UPG decarboxylase Porphyria cutanea tarda
CPG oxidase Hereditary coproporphyria
PPP oxidase Variegate porphyria
Heme synthase / Ferrochelatase Erythropoietic protoporphyria
Types
• Hepatic • Erythropoetic
Note
• Lead inhibits ALA dehydratase and ferrochelatase

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 Biochemistry

--------- My space --------- Clinical Feature

• Jaundice (d/t increased bilirubin)

Investigation - Vandenberg's Reaction

• Used to differentiate the type of jaundice
• Serum is treated with diazotised sulphanilic acid which changes colour on
detecting bilirubin.

Direct Positive Reaction Indirect Positive Reaction

Conjugated bilirubin is soluble & Unconjugated bilirubin is not soluble &
colour appears immediately needs methyl alcohol for dissolving

Seen in obstructive jaundice Seen in hemolytic jaundice

• Biphasic reaction - Hepatic jaundice

Pre-hepatic Hepatic Post-hepatic

• Excessive breakdown of RBCs
Cause • Malaria Infective liver damage Bile duct obstruction
• HS Gilbert syndrome

Serum bilirubin Unconjugated Both conjugated & unconjugated Conjugated

Urine bilirubin Absent + (deep yellow urine) ++

Urine urobilinogen ↑ because of ↑ stercobilinogen ↓ because of ↓ stercobilinogen Absent

• ↑↑↑ • ↓ • Absent
Fecal stercobilinogen
• Dark brown stool • Pale coloured stool • Clay coloured stool

Vandenberg test Indirect positive Biphasic Direct positive

64 Biochemistry • v1.0 • DBMCI one • 2024