BIOCHEMISTRY

Carbohydrate Metabolism:

- Glucose is central molecule for carbohydrate metabolism.

- Liver monitors blood glucose level, i.e., liver is considered as Glucose monitor.
- Standard blood glucose level = 70-105 mg/100 dl

Major Pathways:

1. Glucolysis (Embden-Meyerhof pathway /EMP)

2. TCA (Citric Acid Cycle/ Krebs cycle)
3. Hexose Monophosphate Shunt (HMP)
4. Gluconeogenesis
5. Glycogenesis
6. Glucogenolysis
7. Uronic Acid Pathway (Glucose to Glucoronic Acid)
8. Galactose Metabolism (Galactose to Glucose to Lactose)
9. Fructose Metabolism (Fructose to Pyruvate)
 Glycolysis / Embden-Meyerhof pathway (‘Glyco’-Sugar ; ‘Lysis’ – Dissolution)

Glucose

Hexokinase 1 ATP used

Glucose-6-phosphate

Isomerase 1 ATP used

Fructose-6-phosphate

Phospho fructo kinase

Fructose-1,6-diphosphate

Aldolase

Glyceraldehyde 3-phosphate + Dihydroxy acetone Phosphate

Glyceraldehyde 3-phosphate (2)

6 ATP formed Glyceraldehyde-3-phosphate dihydrogenase

1, 3-diphosphoglycerate

Phosphoglycerate mutase 2ATP formed

3-phosphoglycerate

Phosphoglycerate mutase
2-phosphoglycerate

Enolate
Phosphoenol pyruvate

Pyruvate kinase 2 ATP formed

Enol pyruvate

Ketopyruvate

Lactate dehydrgenase
Lactate
- Anaerobic as well as aerobic process
- Anaerobic - Lactate is end product (2 ATP formed).
- Aerobic - Pyruvate is end product. (8 ATP formed or sometime 6 ATP formed depend
upon shuttle pathway).
- 10 Step Process

- ATP formed- ATP used = Net ATP

(10) - (2) = 8 ATP

 TCA (Citric Acid Cycle / Krebs cycle)

2 Pyruvate Acetyl-CoA + Oxaloacetate

3 ATP formed Citrate Synthetase

Citrate

Aconitase

Isocitrate

3 ATP formed Isocitrate Dehydrogenase

Oxalosuccinate

Isocitrate Dehydrogenase

α-ketoglutarate

3 ATP formed α-ketoglutarate dehydrogenase

Succinyl -COA

1 ATP formed Succinate dehydrogenase

Succinate

2 ATP formed Succinate dehydrogenase

Fumarate

Fumarase

Malate

3 ATP formed Malate dehydrogenase

Oxaloacetate
☻P C C I O Kapil Shashtri Should Follow Mahendras Over

3 3 3 1 2 3

- Location of TCA: Mitochondrial Complex

- TCA has Amphibolic (Anabolic + Catabolic) role.
- Strictly Aerobic Process.
- Total ATP 15  2 (Molecules of Pyruvate) = 30 ATP
- Total ATP per mole of Glucose under Aerobic condition = 38
o i.e., Glycolysis = 8
TCA = 30
- Total ATP per mole of Glucose under Anaerobic condition = 2

 Urea Cycle: (Kreb-Henslet Cycle):

- - Location : Liver

- Ammonia (Toxic) Water-soluble Urea (non-toxic)

- 3 ATP utilized for synthesis of 1 molecule of urea.

 Hexose Monophosphate Shunt (HMP)

- Also called as Pentose Phosphate Shunt or Warburg-Dickens-Lipman Pathway or
Direct Oxidative Pathway.
- Alternative Metabolism to Glucose.
- Enzyme for HMP shunt located in Liver.
- Location: Liver, Testes, Erythrocyte, Ovary, Lens, Cornea, Cytosol, Adipose tissue.
- Lactonate intermediate formed in HMP shunt.
- Product of HMP shunt: Pentose and NADPH

 Gluconeogenesis = Amino Acid / Lactate / Pyruvate / Glycerol Glucose

- Location: Mostly in liver and to some extent in kidneys.
- About 1 kg Glucose is synthesized everyday in the liver.
- Cori Cycle: Lactic Acid (Lactate) Glucose

Location: Liver

 Glycogenesis: Glucose Glycogen

- Location: Cytosol
- Require ATP & UTP
OXIDATION
 Exergonic Reactions: Energy Releasing.
 Endergonic Reaction: Energy Consuming.
 β –oxidation of Fatty Acid:
- Removal of 2 Carbon atoms in the form of Acetyl CoA.
- Enzymes are present in mitochondria of liver and cytosol.
- Net ATP = 129
 Electron transport Chain (ETC)
- Also called as Respiratory Chain.
- Carbohydrate, fatty acids, Amino acids get oxidized to CO2 and H2O.
 Oxidative Phosphorylation:
- Process of synthesizing ATP from ADP and Pi coupled with ETC.
 Enzymes involved in biological Oxidation: Oxidoreductase are grouped into four
categories
1. Oxidases
2. Dehydrogenases
3. Hydroperoxidases
4. Oxygenases
 METABOLISM OF AMINO ACIDS
 Transamination:
- Transfer of an amino (-NH2) group from an amino acid to keto acid.
- Catalysed by enzyme Transaminase (Aminotrasferase).
- Transaminase require a coenzyme Pyridoxal Phosphate

NUCLEIC ACIDS

Nucleic acids play an important role in,

- Transmission of hereditary characteristics

- Biosynthesis of proteins

Classes of Nucleic Acids:

(i) DNA (deoxyribonucleic acid)

(ii) RNA (ribonucleic acid)

Nucleic acids are long polymers in which the monosteric units are nucleotides. The nucleotides
are made up of three chemical components. They are,

(a) A nitrogen-containing heterocyclic base,

(b) A five-carbon sugar,
(c) A phosphoric acid moiety

There are two classes of nitrogen-containing bases formed in nucleotides; purines and
pyrimidines.

(1) Purines: Adenine (A) and Guanine (G).

(2) Pyrimidines: Cytosine (C), Thymine (T) and Uracil (U).

- Uracil is present in nucleotides of RNA and Thymine is found in nucleotides of DNA.

- The second component of the nucleotides is the pentose sugar.
- RNA contains the sugar ribose and DNA contains a derivative of ribose viz. 2-
deoxyribose.
 DNA:
DNA is composed of monomeric units of,
deoxyadenylate (dAMP)
deoxyguanylate (dGMP)

deoxycytidylate (dCMP)
 deoxythymidylate (dTMP)

Chargaff’s Rule:

DNA had equal no. of Adenine and Thymine residues (A = T) and equal number of Guanine and
Cytosine (G = C).

Molar equivalence between Purine & Pyrimidines in DNA

 DNA Double Helix: (Watson and Crick model)

 Proposed by James Watson and Francis Crick.
 Structure compared to Twisted Ladder.

Salient Features:

 DNA is Right handed double helix.

 2 Strands are anti-parallel runs in 5’ to 3’ direction & other 3’ to 5’.
 Diameter of Double Helix is 20 Ao (2 nm).
 Each turn (Pitch) of Helix is 34 Ao (3.4 nm) with 10 pair of Nucleotides & each pair placed
at distance of 3.4 Ao.
 Forms of DNA: Double helical DNA exist in 6 diff. forms A, B, C, D, E, Z.
Z-DNA is Left Handed Helix and with 12 Base pairs.
A-DNA has 11 Base pairs.
 RNA:
Polymer of ribonucleotide held by 3′,5′-phosphodiester bridges.

Structure:

- Pentose: Sugar in RNA is ribose.

- Pyrimidine: RNA contains pyrimidine, uracil in place of thymine (in DNA).
- Single strand: RNA is usually Single stranded polynucleotide.
- Chargaff’s Rule not obeyed.
- RNAs can be histologically identified by Orcinol color reaction due to ribose.
Types: with cellular composition

1) Messenger RNA (mRNA) = 5-10 %

2) Transfer RNA (tRNA) = 10-20 %
3) Ribosomal RNA (rRNA) = 50-80 %

tRNA (Soluble RNA /Clover leaf model):

- Contain acceptor arm with sequence CCA (5’ to 3’)

- Anti-codon arm and D arm (Dihydrouridine)

RNA Polymerases:

Types of RNA Polymerase Used for synthesis of

RNA Polymerase 1 r-RNA
RNA Polymerase 2 m-RNA
RNA Polymerase 3 t-RNA

Protoplast fusion (Genetic transfusion):

1. Lysozyme (Mix)
2. Polyethylene glycol (Fused)

Codon

- Sequence of 3 bases in m-RNA molecule (triplet)

- 4 bases in DNA (Adenine, Guanine, Thymine, Cytosine)
- 64 triplet codon are possible
- Initiation codon:
AUG = inAUGurates protein synthesis
- Stopping codons:
UGA = U Go Away
UAA = U Are Away
UAG = U Are Gone
 ENZYMES

- Composed of protein – Apoenzyme

- Composed of non-protein – Coenzyme
- Composed of metal
- Coenzyme + Apoenzyme = Holoenzyme / Prosthetic group
- Holoenzyme is a complete enzyme.
- Unit of enzyme activity – Ketal (1 ketal = 6  107 IU)
- Aminocyclase – Resolution of DL amino acid

Source Name of enzyme Source Application

Plant Proteases Pineapple, Papaya Inflammation gastritis
Animal Hyaluronidase Animal testes Local anaesthesia
Bacteria α-Amylases Bacillus spp. Paper, textiles, baking industries
β-Amylases Bacillus cereus
Thromboembolic disease
Streptokinase Streptococcus spp.
 VITAMINS

Vit Name Coenzyme Chemical nucleus Deficiency Features

A Retinol β-carotene β-ionone Night Antioxidant,
(Provitamin) blindness, Teratogenic,
Xerophthalmi Heat stable
a
B
B1 Thiamine Thiamine Pyridine + thiazole Beriberi, -
(Aneurine) pyrophosphate (sulphur) Polyneuritis,
Wernicke-
Korsakoff
disease
B2 Riboflavin FMN and FAD Ribose + Cheilosis, Coenzyme for
Isoxazocine pharyngitis oxidation,
hypoplastic reduction
anemia
B3 Niacin NAD and Pyridine Pellagra, 4Ds Coenzyme for
(Nicotinamide) NADPH (dermatitis, oxidation,
(tryptophan) diarrhoea, reduction
dementia,
death),
Hartnup
disease,
hyperuricaemi
a (gout)
B4 Adenine NAD and FAD Purine - Cellular
respiration
B5 Pantothenic acid Coenzyme A Aliphatic structureAcne, -
Parasthesis,
Burning feet
syndrome
B6 Pyridoxine Pyridoxal Pyridine Microcytic Coenzyme in
pyrophosphate anemia, deamination
convulsions, and
kidney stone, decarboxylatio
sideroblastic n of amino
anemia acid
B7 Biotin - Imidazoline fused Impair the Coenzyme in
with carbohydrate carboxylation
tetrahydrothiophen and fat reaction
e metabolism
B8 Inositol - Cyclohexane - Intracellular
Ca2+ conc.
 control,
reducing
cholesterol
B9 Folic acid Tetrahydrofolic Pyridine GABA Megaloblastic Coenzyme in
acid (THFA) glutaryl acid anemia, transfer of
macrocytic carbon unit
anemia
B1 Paraamino - Benzene ring - Bacterial
0 benzoic acid substituted with an synthesis of
(PABA) amino and folate
carboxyl group
B1 Pteryl hepta Chick-growth factor, form of folic acid
1 glutamic acid
(Salicylic acid)
B1 Cyanacobolamin Methylcobalamin - Pernacious -
2 e e anemia,
macrocytic
anemia
B1 Orotic acid - Pyrimidine Orotic Mineral carrier
3 carboxylic acid aciduria
B1 Pterin phosphate Cell proliferant, anti-anemia, anti-tumor, rat-growth factor, isolated from
4 human urine at 0.33 ppm
B1 Pangamic acid - Hexanoic acid - Asthma,
5 (ester) cancer,
schizophrenia
etc.
B1 Dimethyl - Glycine - Athletic
6 glycine (DMG) performance
enhancer,
autism,
epilepsy
B1 Amygdalin - Glucopyranose - Anticancer
7 (Laetrile)
B2 Carnitine Biosynthesized from amino acids lysine and methionine
0
C Ascorbic acid - Ribose nucleus Scurvy Antioxidant,
Tautomeric,
used in
deodorants
D Calciferol
D2 Ergocalciferol - Steroidal nucleus Rickets, Absorption &
D3 Cholecalciferol - osteomalacia balance of
Ca++
E α-Tocopherol - Benzopyrone Neurological Antioxidant
disorder
G Riboflavin Same as Vit. B2
H Biotin Same as Vit. B7
K Phylloquinones - 1,4- Impairment in Clotting of
napthoquinones clot blood
(Haemorrhage
)
M Folic acid Same as Vit. B9
P Rutin - Benzopyrone - Anti-
inflammatory
R PABA Same as Vit. B10
S Pteryl hepta Same as Vit. B11
glutamic acid
(Salicylic acid)
NAD: Nicotinamide adenine dinucleotide; NADP: Nicotinamide adenine dinucleotide phosphate; FAD:
Flavin adenine dinucleotide; FADP: Flavin adenine dinucleotide phosphate
 IMPORTANT DEFINITIONS

- Transformation: Naked DNA is transferred from one bacteria to another

- Transduction: Transfer of genetic material from one cell to another by Bacteriophage.
- Conjugation: Natural process involves active passage of genetic material from one
cell to another by Sex pili.
- Transposition: Movement of genes from one chromosome to another.

IMPORTANT POINTS TO REMEMBER

- A highly sensitive semiquantitative method for detecting microbial antigens in

biological fluid is Counter Immune Electrophoresis.
- Emulsin protein break β-linkage.
- Average weight of amino acid – 110 dalton
- Glucose = Pyranose ring
- Chaperon – Shape of protein
- Enzyme translocase inhibitor – Erythromycin
- Degradation of protein / proteolysis – Ubiquitin
- Haemophilia (Sickle cell anaemia) – Glutamate replaced by valine (normally, the 6th
amino acid)
- Ramachandran Plot – Secondary structure of protein
- Highest efficient enzyme – Anticholinesterases
- Turnover number (TON) –Number of substrate / Enzyme efficiency is determined by
TON.
- Tears – Lysozyme (Muramidase)
- Bromelin – Pineapple
- Sodium Dodecyl Sulfate – Polyacrylamide Gel Electrophoresis (SDS-PAGE):
Separation of Proteins
- Histidine is the only common amino acid having an ionisable side chain with a pKa
near neutrality.
- Xanthine Oxidase – Molybdenum.

- Denaturation Renaturation DNA synthesis

(95oC for 1 min) (55oC for 1 min)

- Polysaccharide soluble in water Inulin

- Crown Gall disease Agrobacterium tumefaciens (cause)

- Inulin – Assessing of Kidney Function test

 - Serum bilirubin: 0.1-1.2 mg/dl. Increase in serum bilirubin results in jaundice.

- Bilirubin is excreted in urine in Obstructive and Hepatic jaundice.

IMPORTANT CHARTS TO REMEMBER

Enzyme elevated : Disease

Enzyme elevated Disease

Acid phosphatase Prostate cancer
Aldolase Muscular dystrophy
Amylase Pancreatitis
Serum Glutamate Oxaloacetate Transaminase Myocardial infarction
(SGOT) / Aspartate aminotransferase (AST)
Serum Glutamate Pyruvate Transaminase Hepatitis
(SGPT) / Alanine aminotransferase (ALT)
Creatinine kinase Acute hepatitis
Alkaline phosphatise Ricketts, Jaundice
LDH Heart attack, Liver disease

Biochemical Test:

Name of the test Performed for

Benedict test Glucose
Benzidine test Blood
Faber’s disease Ceramidase
Folin-Wu test Blood glucose estimation
Fouchet’s test Bile pigments
Gaucher’s disease β-glucosidase
Gerhardt’s test Ketone bodies
Gimelin’s test Bile pigments
Hay’s test Bile salts
Krabb’s disease β-galactosidase
Niemann-Pick disease Sphingomylinase
Rothera’s test Ketone bodies
Salkowitch test Calcium
Tay-Sach disease Sphingolipidoses

Disorders due to enzyme deficiency:

Disease Defective enzyme

Citrullinemia Arginosuccinate synthase
Cori’s disease Amylo 1,6-glucosidase
Favism Glucose-6-phosphate dehydrogenase
Her’s disease Phosphorylase
Lesch-Nyhan Hypoxanthine guanine phosphoribosyl transferase
syndrome (HGPRT)
McArdle’s disease Phosphorylase
Pompe’s disease α-1,4 glucosidase
T-cell Purine nucleoside phosphorylase
Immunodeficiency
Van Gierke’s Glucose-6-phosphatase
disease

Test for Amino acids:

Name of the test Amino acids

Biuret test Histidine
Hopkins-Cole reaction Tryptophan
Millon’s test Tyrosine
Pauli’s test Histidine
Xanthoproic test Aromatic amino acids (Tyrosine)

Symbol for Amino acids:

Amino acid One letter symbol Three letter symbol

Alanine A Ala
ARginine R Arg
AsparagiNe N Asn
Aspartic AciD D Asp
Cysteine C Cys
Glutamic Acid E Glu
Glutamine Q Gln
Glycine G Gly
Histidine H His
Isoleucine I Ile
Leucine L Leu
Lysine K Lys
Methionine M Met
Ph(F)enylalanine F Phe
Proline (imino
P Pro
acid)
Serine S Ser
Threonine T Thr
Tryptophan W Trp
TYrosine Y Tyr
Valine V Val
Blotting Tests: (SNoW = DRoP)

Test Applicable to
Western blotting HIV infection / Proteins
Southern blotting DNA testing
Northern blotting mRNA transmission
Helix:

One turn 3.6 amino acid

Space 5.4 Å
For one amino acid 1.5 Å

Water:

Volume of plasma water 3 litre

Extracellular water 14 litre
Total body water 42 litre

LDH Isoenzyme : Disease

LDH isoenzyme Disease

LDH 1 Acute myocardial infarction (MI)
LDH 2 Pulmonary embolus
LDH 3 Pulmonary embolus
LDH 4 Nephrotic syndrome
LDH 5 Severe myocardial infarction

Coenzymes:

Type of coenzyme Name of enzyme

Coenzyme A Pantothenic acid
Coenzyme I Nicotinic acid (Niacin)
Coenzyme Q Ubiquinone

Synthesis:

Type of CoA Used for synthesis of

Acetyl CoA Cholesterol
Succinyl CoA Heme
Unsaturated Fatty Acids:

Fatty acids No. of double bonds Position

Palmitene One 9
Oleic acid (Fat free) One 9
Linoleic acid (Fat free) Two 9, 12
Linolenic acid (Fat free) Three 9, 12, 15
Arachidonic acid Four 5, 8, 11, 14
Carbohydrates and derived products:

Sugars Hydrolysis product Linkage

Lactose Glucose + Galactose 1,4β-linkage
Maltose Glucose + Glucose 1,4α-linkage
Sucrose Glucose + Fructose -

Linkages:

Carbohydrates Linkage
Glycogen 1,4 and 1,6 linkages
Cellulose 1,4β + 1, 6β linkages
Amylose (water-soluble) 1,4β-linkage
Amylopectin (water-insoluble) 1,4α + 1,6α linkages

Other tests:

Test Applicable to
Coagulase test Virulent Staphylococcus aureus
Coombs test Non-agglutinating antibody

Mechanism of inhibiton:

Type of inhibition Features

Competitive Km increased ; Vmax constant
Non-competitive Vmax decreased ; Km constant
Uncompetitive Km, Vmax decreased

Gel Electrophoresis:

Mechanism DNA travels from cathode to anode

Dye Ethidium bromide (DNA intercalating agent)
Tracking agent Methylene blue
Antioxidants:

Antioxidants Examples
Super antioxidant Flavonoids
Universal antioxidant Lipoic acid