1. Subcellular Organelles Cells contain various organised structures, collectively called as cell organelles. When the cell membrane is disrupted, the organised particles inside the cell are homogenised. They could then be separated by applying differential centrifugal forces. Fig. 1.1.

2. Amino Acids and Proteins Table 2.1. Classification of amino acids A . Aliphatic amino acids a. Mono amino mono carboxylic acids: Simple amino acids: 1. Glycine 2. Alanine Branched chain amino acids: 3. Valine 4. Leucine 5. Isoleucine Hydroxy amino acids: 6. Serine 7. Threonine Sulphur containing: 8. Cysteine 9. Methionine Having amide group: 1 0 . Asparagine 1 1 . Glutamine b . Mono amino dicarboxylic acids 1 2 . Aspartic acid 1 3 . Glutamic acid c . Di basic mono carboxylic acids 1 4 . Lysine 1 5 . Arginine Contd...

3. Enz ymes Table 3.2. Examples of co-enzymes Co-enzyme Group transferred Thiamine pyrophosphate (TPP) Hydroxy ethyl Pyridoxal phosphate (PLP) Amino group Biotin Carbon dioxide Coenzyme-A (Co-A) Acyl groups Tetrahydrofolate (FH4) One carbon groups Adenosine triphosphate (ATP) Phosphate Table 3.1. Classification of enzymes Class 1. Oxidoreductases: Transfer of hydrogen; e.g. alcohol dehydrogenase. Class 2. Transferases: Transfer of groups other than hydrogen (Subclass: Kinase, transfer of phosphoryl group from ATP; e.g., hexokinase) Class 3. Hydrolases: Cleave bond; add water; e.g., acetyl choline esterase Class 4. Lyases: Cleave without adding water, e.g., aldolase. (Subclass: Hydratase;add water to double bond) Class 5. Isomerases: Intramolecular transfers. Example, triose phosphate isomerase. Class 6. Ligases: ATP dependent condensation of two mole- cules, e.g.

4. Carbohydrate Chemistr y Table 4.1. Common monosaccharides No. of Generic Aldoses (with Ketoses carbon atoms name aldehyde group) (with keto group) 3 Triose Ex: Glyceralde- Ex: Dihydroxy- hyde acetone 4 Tetrose Erythrose Erythrulose 5 Pentose Arabinose Xylulose Xylose Ribulose Ribose 6 Hexose Glucose Fructose Galactose Mannose Table 4.2. Hexoses of physiological importance Glucose Blood sugar.

5. Chemistr y of Lipids Table 5.1. Classification of lipids I. Simple lipids a . Triacyl glycerol or triglycerides or neutral fat b . Waxes I I . Compound lipids A . Phospholipids, containing phosphoric acid. 1. Nitrogen containing glycerophosphatides: i . Lecithin (phosphatidyl choline) i i . Cephalin (phosphatidyl ethanol amine) iii. Phosphatidyl serine 2 . Non-nitrogen glycerophosphatides i . Phosphatidyl inositol i i . Phosphatidyl glycerol iii. Diphosphatidyl glycerol (cardiolipin) 3. Plasmalogens, having long chain alcohol i . Choline plasmalogen i i . Ethanolamine plasmalogen 4. Phosphosphingosides, with sphingosine Sphingomyelin Contd...

6 . Glycolysis Table 6.1. Glucose transporters Transporters Present in Properties GluT1 RBC, brain, Glucose uptake kidney in most of cells GluT2 Serosal surface Glucose uptake in of intestinal cells, liver; Glucose beta cell pancreas sensor in beta cells GluT3 Neurons, brain Glucose into brain GluT4 Skeletal, heart Insulin mediated muscle, adipose tissue glucose uptake Fig. 6.1. SGluT.

G LUCONEOGENESIS 71 Table 7.1. Regulatory enzymes of gluconeogenesis (compare with Table 6.6) Enzyme Activation Inhibition P C Cortisol, Insulin, ADP Glucagon PEPCK D o Insulin Fructose-1,6-bis- D o F-1,6-BP, AMP phosphatase G-6-phosphatase D o Insulin Fig. 7.4.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 74 Table 8.1. Functions of glycogen 1. Glycogen is the storage form of carbohydrates in the human body. 2. The major sites of storage are liver and muscle. The major function of liver glycogen is to provide glucose during starvation. 3. The function of muscle glycogen is to act as reserve fuel for muscle contraction. Fig. 8.3.

9. Minor Pathways of Carbohydrates Table 9.1. Significance of the pathway Hexose monophosphate (HMP) pathway is also known as: Pentose phsophate pathway; Dickens-Horecker pathway; Shunt pathway; or Phospho-gluconate oxidative pathway 1 . Tissues It is seen in organs where fatty acid or steroid synthesis is taking place, such as in liver, mammary glands, testis, ovary, adipose tissue 2 . Generation of reducing equivalents The major role of the pathway is to provide cytoplasmic NADPH for reductive biosynthesis of fatty acids, cholesterol and steroids. 3 . Erythrocyte membrane NADPH is required by the RBC to preserve the integrity of RBC membrane. 4 . Lens of eye For preserving the transparency of lens, NADPH is required. 5 . Availability of ribose Ribose and deoxy-ribose are required for DNA/RNA synthesis. 6 . What about ATP ATP is neither utilised nor produced by the HMP shunt pathway.

I NSULIN AND D IABETES M ELLITUS 87 Fig. 10.2.

11. Metabolism of Fatt y Acids Fig. 11.1. Partial hydrolysis of triglyceride Table 11.1. Six steps of lipid absorption 1 . Minor digestion of triacylglycerols in mouth and stomach by lingual (acid-stable) lipase. 2 . Major digestion of all lipids in the lumen of the duodenum/ jejunum by pancreatic lipolytic enzymes. 3 . Bile acid facilitated formation of mixed micelles. 4 . Passive absorption of the lipolytic products from the mixed micelle into the intestinal epithelial cell. 5 . Re-esterification of 2-monoacylglycerol with free fatty acids inside the intestinal enterocyte. 6 . Assembly of chylomicrons containing Apo B48, triacylglycerols esters and phospholipids and export from intestinal cells to the lymphatics.

12. Cholesterol Metabolism Fig. 12.1: Structure of cholesterol Table 12.1. Significance of cholesterol 1 . Heart diseases: The level of cholesterol in blood is related to the development of atherosclerosis. 2 . Cell membranes: Cholesterol has a modulating effect on the fluid state of the membrane. 3 . Nerve conduction: Cholesterol is used to insulate nerve fibers. 4 . Bile acids and bile salts: The 24 carbon bile acids are derived from cholesterol. 5 . Steroid hormones: Cholesterol is the precursor of 21carbon glucocorticods, 19 carbon androgens and 18 carbon estrogens. 6 . Vitamin D: It is synthesised from choles terol.

13. PUF A and Prostaglandins Table 13.1. Fatty acids Fatty acids having carbon atoms 4 to 6 are called small chain fatty acids (SCFA); those with 8 to 14 carbon atoms are known as medium chain fatty acids (MCFA); those with 16 to 18 carbon atoms are long chain fatty acids (LCFA); and those carrying 20 or more carbon atoms are named as very long chain fatty acids (VLCFA) (Table 8.1). The important polyunsaturated fatty acids (PUFA) are: 1 . Linoleic acid (18 C, 2 double bonds) 2 . Linolenic acid (18 C, 3 double bonds) 3 . Arachidonic acid (20 C, 4 double bonds) Significance of PUFA are: 1. PUFAs are used for esterification and excretion of cholesterol . 2. They are nutritionally essential; and are called Essential Fatty Acids . 3 . Prostaglandins , thromboxanes and leukotrienes are produced from arachidonic acid. 4. They are components of membrances . As PUFAs are easily liable to undergo peroxidation, the membranes containing PUFAs are more prone for damage by free radicals.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 160 Table 14.1. Proteolytic enzymes Proteolytic enzymes are secreted as inactive zymogens which are converted to their active form in the intestinal lumen. This would prevent autodigestion of the secretory acini. 1 . Endopeptidases. They act on peptide bonds inside the protein molecule, so that the protein becomes successively smaller and smaller units, e.g. Pepsin, Trypsin, Chymotrypsin, and Elastase. 2 . Exopeptidases, which act at the peptide bond only at the end region of the chain. 2-A. Carboxypeptidase acts on the peptide bond only at the carboxy terminal end on the chain. 2-B. Amino peptidase, which acts on the peptide bond only at the amino terminal end on the chain. Table 14.2.

G L YCINE M E T ABOLISM 177 Fig. 15.3. Glycine cleavage system. Glycine is completely degraded to CO 2 , ammonia and one-carbon unit methylene THFA.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 182 Table 16.1. Transmethylation reactions Methyl acceptors Methylated products Guanido acetic acid Creatine Nicotinamide N-methyl nicotinamide Norepinephrine Epinephrine Epinephrine Metanephrine Norepinephrine Normetanephrine Ethanolamine Choline Carnosine Anserine Acetyl serotonin Melatonin Serine Choline Histidine Methyl histidine tRNA Methylated tRNA Fig. 16.2.

17. Acidic, Basic and Branched Chain Amino Acids Table 17.1. Functions of glutamic acid 1 . Transamination reactions: (Fig. 14.8). 2. Glutamic acid is also formed during the metabolism of histidine, proline and arginine. 3 . Deamination: Glutamic acid is deaminated to form alpha ketoglutarate by the enzyme glutamate dehydrogenase with the help of NAD + (Fig. 14.9). 4 . Glucogenic: Glutamic acid enters the TCA cycle, becomes oxaloacetate and goes to glucogenic pathway. 5 . N-acetyl glutamate (NAG) is a positive modifier of carbamoyl phosphate synthetase-I in the mitochondria. Glutamic acid + Acetyl CoA  NAG + CoASH 6 . Ammonia trapping and glutamine (Fig.14.10): 7. Gamma carboxy glutamic acid (GCGA) is present in prothrombin. The gamma carboxyl group is added as a post-translational modification, which needs vitamin K. 9 . Glutathione: Glutamate is a constituent of the tripeptide glutathione (Fig. 16.4). 10. Gamma amino butyric acid (GABA): Glutamic acid on decarboxylation gives rise to gamma amino butyric acid ( GABA ). It is an inhibitory neurotransmitter.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 196 Fig. 18.1. Catabolism of phenyl alanine and tyrosine 1 = Phenyl alanine hydroxylase 1A = NADPH dependent reductase 2 = Tyrosine transaminase 3 = parahydroxy phenylpyruvate hydroxylase 4 = Homogentisic acid oxidase 5 = Maleyl acetoacetate isomerase 6 = Fumaryl acetoacetate hydrolase Contd...

19. Citric Acid Cycle Fig. 19.1. Sources and utilisation of acetyl CoA Table 19.1. Functions of the citric acid cycle 1. It is the final common oxidative pathway that oxidises acetyl CoA to CO 2 . 2. It is the source of reduced co-enzymes that provide the substrate for the respiratory chain. 3. It acts as a link between catabolic and anabolic pathways (amphibolic role). 4. It provides precursors for synthesis of amino acids and nucleotides. 5. Components of the cycle have a direct or indirect controlling effects on key enzymes of other pathways.

20. Electron Transpor t Chain Fig. 20.1. Oxidation of foodstuffs in three stages Table 20.1. Redox Oxidation is defined as the loss of electrons and reduction as the gain in electrons. When a substance exists both in the reduced state and in the oxidised state, the pair is called a redox couple .

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 230 Fig. 21.2. Normal electrophoretic pattern Table 21.1. Functions of albumin 1 . Colloid osmotic pressure of plasma Proteins exert the effective osmotic pressure'. It is about 25 mm Hg, and 80% of it is contributed by albumin. (See Fig. 21.3). 2 . Transport function; Albumin is the carrier of: i. Bilirubin and non-esterified fatty acids are specifically transported by albumin. i i . Drugs (sulpha, aspirin, salicylates, dicoumarol, phenytoin). iii. Hormones: steroid hormones, thyroxine. i v . Metals: calcium, copper and heavy metals are non- specifically carried by albumin.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 242 Table 22.1. Porphyrins of biological importance. See also Fig. 22.2 for the structure of heme Name of Order of substituents porphyrin from 1st to 8th positions Uroporphyrin I A,P, A,P, A,P, A,P Uroporphyrin III A,P, A,P, A,P, P,A Coproporphyrin I M,P, M,P, M,P, M,P Coproporphyrin III M,P, M,P, M,P, P,M Protoporphyrin III M,V, M,V, M,P, P,M (A = acetyl; P = propionyl; M = methyl; V = vinyl) Fig. 22.3.

23. Lipid Soluble Vitamins Table 23.1.

2 4 . Water Soluble Vitamins Fig. 24.1. Structure of thiamine pyrophosphate Table 24.1. Nutrition of thiamine (vitamin B 1 ) Sources Cereals (whole wheat flour and unpolished handpound rice) are rich sources of thiamine. Yeast is also a very good source. Physiological role of thiamine i Pyruvate dehydrogenase: The co-enzyme form is thiamine pyrophosphate (TPP). It is used in oxidative decarboxylation of alpha keto acids, e.g. pyruvate decarboxylase, a component of the pyruvate Contd...

25. Mineral Metabolism Table 25.1. Important minerals Major elements Trace elements 1 . Calcium 1 . Iron 2 . Magnesium 2 . Iodine 3 . Phosphorus 3 . Copper 4 . Sodium 4 . M a n g a n e s e 5 . Potassium 5 . Zinc 6 . Chloride 6 . Molybdenum 7 . Sulphur 7 . Selenium 8 . Fluoride Table 25.2.

26. Energy Metabolism Table 26.1. Energy yield from nutrients Nutrients Calorific values in kilocalories/g Carbohydrates 4 Fats 9 Proteins 4 Alcohol 7 Table 26.2. Basal metabolic rate (BMR) Definition: The basal metabolic rate is the energy required by an awake individual during physical, emotional and digestive rest. Factors: Affecting BMR: Age: In old age BMR is lowered. Sex: Males have a higher BMR than females. Temperature: BMR increases in cold climate. Exercise: increases BMR Fever: 12% increase in BMR is noticed per degree centigrade rise in temperature. Thyroid hormones: Since thyroid hormones have a general stimulant effect on rate of metabolism and heat production, BMR is raised in hyperthyroidism and lowered in hypothyroidism.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 324 Fig. 27.2. Common pyrimidines Table 27.1. Nucleosides and nucleotides Nucleosides are formed when bases are attached to the pentose sugar, D-ribose or 2-deoxy D-ribose. When the nucleoside is esterified to a phosphate group, it is called a nucleotide or nucleoside mono-phosphate. When a second phosphate gets esterified to the existing phosphate group, a nucleoside diphosphate is generated. The attachment of a 3rd phosphate group results in the formation of a nucleoside triphosphate. The nucleic acids (DNA and RNA) are polymers of nucleoside monophosphates.

J A YPEE G OLD S T ANDARD M INI A TLAS S ERIES B IOCHEMISTR Y 336 Table 28.1. Watson-Crick model of DNA structure 1 . Right handed double helix DNA consists of two polydeoxy ribonucleotide chains twisted around one another in a right handed double helix similar to a spiral stair case. The sugar and phosphate groups comprise the handrail and the bases jutting inside represent the steps of the staircase. 2 . The base pairing rule Always the two strands are complementary to each other. The base pairing ( adenine with thymine; guanine with cytosine ) is called Chargaff's rule , so, the number of purines is equal to the number of pyrimidines. 3 . Hydrogen bonding The DNA strands are held together mainly by hydrogen bonds between the purine and pyrimidine bases. There are two hydrogen bonds between A and T while there are three hydrogen bonds between C and G. 4 . Antiparallel The two strands in a DNA molecule run antiparallel. One strand runs in the 5' to 3' direction, while the other is in the 3' to 5' direction. 5. The spiral has a pitch of 3.4 nanometers per turn. 6. Within a single turn, 10 base pairs are seen. Thus, adjacent bases are separated by 0.34 nm.

29. Transcription and Translation Fig. 29.1. Central dogma of molecular biology Table 29.1. Differences between RNA and DNA RNA DNA 1. Mainly seen in cytoplasm Mostly inside nucleus 2. Usually 100-5000 bases Millions of base pairs 3. Generally single stranded Double stranded 4. Sugar is ribose Sugar is deoxyribose 5. Purines: Adenine, guanine Adenine, guanine Pyrimidines: Cytosine, uracil Cytosine, thymine 6. Guanine content is not equal Guanine is equal to to cytosine and adenine cytosine and adenine is is not equal to uracil equal to thymine 7.

30. Recombinant DNA T echnology and other Molecular Biology T echniques Fig. 30.1. Eco RI enzyme cuts the bonds marked with red arrow. This results in the sticky ends Table 30.1.