VASUDEVAN BIOCHEMISTRY BOOK

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Vasudevan Biochemistry Book

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Accordingly, we have made elaborate changes in the order of chapters, old chapters on clinical chemistry have been extensively updated and clinically relevant points were further added. Secondly, rapid progress has been made in the area of molecular biology during past few years, and these advances are to be reflected in this book also. The major change in this sixth edition is that advanced knowledge has been added in almost all pages, a few sentences were added here and there in almost all pages; sometimes, a few pages are newly incorporated; while it became necessary to include a few new chapters also.

From the first edition onwards, our policy was to provide not only basic essentials but also some of the advanced knowledge. A lot of students have appreciated this approach, as it helped them to pass the PG entrance examinations at a later stage.

However, this asset has paved the way for a general criticism that the extra details are a burden to the average students. Especially when read for the first time, the student may find it difficult to sort out the essential minimum from the desirable bulk.

So, in the fifth edition, we have promised that we shall make two different books, one for MBBS and another one for postgraduate courses in Biochemistry. Thus, the content has been reduced substantially in the last edition. But, due to various reasons, most of which beyond the control of the authors, the postgraduate book could not be published.

This led to the criticism that the content is sub-optimal. Many PG students were enquiring about the advanced book. The advanced students felt that they were neglected. This 6th edition is a compromise. It is present in postsynaptic membrane. It is a complex of 5 subunits, consisting of acetyl choline binding site and the ion channel. This generates an action potential in the postsynaptic nerve.

The channel opens only for a millisecond, because the acetyl choline is rapidly degraded by acetyl cholinesterase. Calcium channels: Under appropriate stimuli calcium channels are opened in the sarcoplasmic reticulum membrane, leading to an elevated calcium level in the cytosol of muscle cells. Calcium channel blockers are therefore widely used in the management of hypertension. Amelogenin, a protein present in enamel of teeth has hydrophobic residues on the outside.

A 27 amino acid portion of amelogenin functions as a calcium channel. Chemical Basis of Life Phosphorylation of a serine residue of the protein opens the calcium channel, through which calcium ions zoom through and are funnelled to the mineralization front. The amelogenin is used for the formation of calcium hydroxy apatite crystals.

Voltage Gated Channels Voltage gated channels are opened by membrane depolarization Fig. The channel is usually closed in the ground state. The membrane potential change voltage difference switches the ion channel to open, lasting less than 25 milliseconds. In voltage gated channels, the channels open or close in response to changes in membrane potential. They pass from closed through open to inactivated state on depolarization. Once in the inactivated state, a channel cannot re-open until it has been reprimed by repolarization of the membrane.

Voltage gated sodium channels and voltage gated potassium channels are the common examples. These are seen in nerve cells and are involved in the conduction of nerve impulses. Ion channels allow passage of molecules in accordance with the concentration gradient.

Ion pumps can transport molecules against the gradient. The active transport is unidirectional. It requires specialized integral proteins called transporters. The transport system is saturated at higher concentrations of solutes. The transporters are susceptible to inhibition by specific organic or inorganic compounds.

General reaction is depicted in Figure 2. Sodium Pump It is the best example for active transport. Cell has low intracellular sodium; but concentration of potassium inside the cell is very high. This is maintained by the sodiumpotassium activated ATPase, generally called as sodium pump.

The ATPase is an integral protein of the membrane Fig. It has binding sites for ATP and sodium on the inner side and the potassium binding site is located outside the membrane. It is made up of two pairs of unequal subunits 2 2. Both subunits of the pump alpha and beta span the whole thickness of membrane. Details are shown in Fig. Clinical applications of sodium pump are shown in Box 2. This would trigger muscle contraction. The function of calcium pump is to remove cytosolic calcium and maintain low.

Ionophores They are membrane shuttles for specific ions. They transport antibiotics. Ionophores increase the permeability of membrane to ions by acting as channel formers. The two types of ionophores are; mobile ion carriers e. Valinomycin and channel formers e. They are produced by certain microorganisms and are used as antibiotics. When cells of higher organisms are exposed to ionophores, the ion gradient is dissipated.

Valinomycin allows potassium to permeate mitochondria and so it dissipates the proton gradient; hence it acts as an uncoupler of electron transport chain Chapter Active Transport The salient features of active transport are: This form of transport requires energy.

Clinical Applications of Sodium Pump Cardiotonic drugs like digoxin and ouabain bind to the alpha-subunit and act as competitive inhibitor of potassium ion binding to the pump. This would enhance the contractility of the cardiac muscle and so improve the function of the heart. Chapter 2; Subcellular Organelles and Cell Membranes 17 against a concentration gradient is coupled with movement of a second substance down the concentration gradient; the second molecule being already concentrated within the cell by an energy requiring process.

The co-transport system may either be a symport or an antiport. In symport , Fig. Phlorhizin, an inhibitor of sodium-dependent co-transport of glucose, especially in the proximal convoluted tubules of kidney, produces renal damage and results in renal glycosuria.

Amino acid transport is another example for symport. The antiport system Fig. Features of different types of transport modalities are summarized in Table 2. Clinical Applications In Hartnup's disease, transport mechanisms for amino acids are defective in intestine and renal tubules Chapter In cystinuria , renal reabsorption of cysteine is abnormal Chapter Renal reabsorption of phosphate is decreased in vitamin D resistant rickets Chapter Diseases due to abnormalities of transport systems include familial hypercholesterolemia, cystic fibrosis, congenital long QT syndrome, Wilson disease, I-cell disease, hereditary spherocytosis and paroxysmal nocturnal hemoglobinuria, etc.

Exocytosis cytosolic concentration, so that muscle can receive the next signal. Uniport, Symport and Antiport Transport systems are classified as uniport, symport and antiport systems Fig.

Uniport system carries single solute across the membrane, e. Calcium pump is another example. If the transfer of one molecule depends on simultaneous or sequential transfer of another molecule, it is called co-transport system. The active transport may be coupled with energy indirectly. Here, movement of the substance. Different types of endocytosis. Left side, phagocytosis; middle, pinocytosis; right side, receptor mediated endocytosis.

Secretory Vesicles and Exocytosis Under appropriate stimuli, the secretory vesicles or vacuoles move towards and fuse with the plasma membrane. This movement is created by cytoplasmic contractile elements; the microtubule system.

The inner membrane of the vesicle fuses with outer plasma membrane, while cytoplasmic side of vesicle fuses with cytoplasmic side of plasma membrane. Thus the contents of vesicles are externalized. This process is called exocytosis or reverse pinocytosis. Release of trypsinogen by pancreatic acinar cells; release of insulin by beta cells of Langerhans and release of acetyl choline by presynaptic cholinergic nerves are examples of exocytosis Fig.

Often, hormones are the signal for exocytosis, which leads to calcium ion changes, triggerring the exocytosis. Endocytosis Endocytosis is the mechanism by which cells internalize extracellular macromolecules, to form an endocytic vesicle. This requires energy in the form of ATP as well as calcium ions in the extracellular fluid.

Cytoplasmic contractile elements take part in this movement. In general, plasma membrane is invaginated, enclosing the matter.

This forms the endocytic vesicle. The endocytosis may be pinocytosis or phagocytosis or receptor mediated endocytosis Fig. Pinocytosis Pinocytosis literally means drinking by the cell'. Cells take up fluid by this method Fig. The fluid phase pinocytosis is a nonselective process. Receptor Mediated Endocytosis The selective or adsorptive pinocytosis is receptor mediated; also called as absorptive pinocytosis. The cytoplasmic side of these vesicles are coated with filaments; mainly composed of Clathrin.

These are called Clathrin coated pits Fig. Absorption of cholesterol by clathrin coated pit is shown in Figure After the LDL-receptor complex is internalized, the receptor molecules are released back to cell surface; but the LDL is degraded by lysosomal enzymes. Several hormones are also taken up by the cells by receptor-mediated mechanism.

TEXT BOOK OF BIOCHEMISTRY FOR MEDICAL STUDENTS By: DM Vasudevan & Kannam Vidyanathan

The protein, Dynamin which has GTPase activity, is necessary for the internalisation of clathrin coated pits. Many viruses get attached to their specific receptors on the cell membranes. They are taken up by caveolae mediated processes. Caveolae mediated endocytosis is also known as potocytosis. Phagocytosis The term is derived from the Greek word "phagein" which means to eat.

It is the engulfment of large particles such as bacteria by macrophages and granulocytes. They extend pseudopodia and surround the particles to form phagosomes Fig. Phagosomes later fuse with lysosomes to form phagolysosomes, inside which the particles are digested. The biochemical events accompanying phagocytosis is described as respiratory burst Chapter Classification of amino acids based on structure 2.

Based on side chain character 3. Based on metabolic fate 4. Based on nutritional requirements 5. Iso electric point 6. Reactions due to carboxyl group 7. Reactions due to amino group 8. Reactions of SH group 9. Peptide bond formation. Proteins are of paramount importance for biological systems. All the major structural and functional aspects of the body are carried out by protein molecules.

All proteins are polymers of amino acids. Proteins are composed of a number of amino acids linked by peptide bonds. Although about amino acids occur in nature, only 20 of them are seen in human body. Most of the amino acids except proline are alpha amino acids, which means that the amino group is attached to the same carbon atom to which the carboxyl group is attached Fig. Based on Structure 1-A. Aliphatic amino acids a. Mono amino mono carboxylic acids: Simple amino acids: Glycine, Alanine Fig.

Valine, Leucine, Isoleucine Fig. Serine, Threonine Fig. Sulphur containing amino acids: Cysteine, Methionine Fig. Asparagine, Glutamine Fig. Mono amino dicarboxylic acids: Aspartic acid, Glutamic acid Fig.

Table 3. Di basic mono carboxylic acids: Lysine, Arginine Fig. Aromatic amino acids: Phenylalanine, Tyrosine Fig. Heterocyclic amino acids: Tryptophan Fig. Imino acid: Proline Fig. Derived amino acids: Derived amino acids found in proteins: After the synthesis of proteins, some of the amino acids are modified, e.

Gamma carboxylation of glutamic acid residues of proteins is important for clotting process Fig. In ribosomal proteins and in histones, amino acids are extensively methylated and acetylated.

Derived amino acids not seen in proteins Non-protein amino acids: Some derived amino acids are seen free in cells, e. Ornithine Fig. These are produced during the metabolism of amino acids. Thyroxine may be considered as derived from tyrosine.

Non-alpha amino acids: Gamma amino butyric acid GABA is derived from glutamic acid. Beta alanine, where amino group is in beta position, is a constituent of pantothenic acid vitamin and co-enzyme A.

Each amino acid will have three-letter and oneletter abbreviations which are shown in Table 3. Special Groups in Amino Acids In the figures, special groups are shaded. Arginine contains guanidinium group; Phenyl alanine benzene ; Tyrosine phenol ; Tryptophan Indole ; Histidine imidazole ; and Proline pyrrolidine Table 3. Proline has a secondary amino group, and hence it is an imino acid.

Amino acids having nonpolar side chains: Chapter 3; Amino Acids: Structure and Properties 21 Box 3. Arginine and Histidine are semi-essential amino acids; while others are essential 3. Purely Ketogenic Leucine is purely ketogenic because it is converted to ketone bodies Fig. Histidine and proline These groups are hydrophobic water repellant and lipophilic. Therefore, the parts of proteins made up of these amino acids will be hydrophobic in nature.

Amino acids having uncharged or nonionic polar side chains: These amino acids are hydrophilic in nature. Tyrosine and Cysteine may show hydrophobic character when present in the interior of the protein. Amino acids having charged or ionic polar side chains hydrophilic: Acidic amino acids: They have a negative charge on the R group: Aspartic acid and Glutamic acid Tyrosine is mildly acidic.

Basic amino acids: They have a positive charge on the R group: Lysine, Arginine and Histidine. Ketogenic and Glucogenic Lysine, Isoleucine, Phenylalanine, Tyrosine and Tryptophan are partially ketogenic and partially glucogenic.

How ever in humans lysine is predominantly ketogenic. During metabolism, part of the carbon skeleton of these amino acids will enter the ketogenic pathway and the other part to glucogenic pathway see Fig.

Purely Glucogenic All the remaining 14 amino acids are purely glucogenic as they enter only into the glucogenic pathway See Chapter Essential or Indispensable The amino acids may further be classified according to their essentiality for growth. Their carbon skeleton cannot be synthesized by human beings and so preformed amino acids are to be taken in food for normal growth. See memory aid in Box 3.

Partially essential or Semi-essential Histidine and arginine are semi-indispensable amino acids. Growing children require them in food. But they are not essential for the adult individual. Non-essential or Dispensable The remaining 10 amino acids are non-essential, because their carbon skeleton can be synthesized. Box 3. Selenocysteine as the 21st amino acid 21st century witnesses the addition of selenocysteine as the 21st amino acid present in human proteins. An amino acid is given the individual status, when it is incorporated as such into proteins during protein biosynthesis, and having a separate codon.

Selenocysteine is present in some enzymes. Instead of SH sulfhydryl group in cysteine, SeH selenium is present in selenocysteine. It is abbreviated as SeCys or SeC. Details are given in Chapter 15, under serine. Similarly pyrrolysine Pyl is known as the 22nd amino acid. Pyrrolysine is a lysine in an amide linkage to substituted-pyrrolinecarboxylate. It is present in methyl transferase enzymes of certain bacteria. Both SeC and Pyl are encoded by codons that normally function as stop signals.

However, they are also required for normal protein synthesis. All body proteins do contain all the non-essential amino acids. Naming Numbering of Carbon Atoms Carbon atoms in amino acids in sequence are named with letters of Greek alphabets, starting from the carbon atom to which carboxyl group is attached.

As examples, naming of glutamic acid is shown in figure 3. Sodium glutamate is a flavoring agent. Aspartame, an artificial sweetener contains aspartic acid and phenyl alanine.

All amino acids have high melting points more than C. All amino acids are soluble in water and alcohol polar solvents ; but insoluble in nonpolar solvents benzene. Ampholyte and Iso-electric Point 1. The pH at which the molecule carries no net charge is known as iso-electric point or isoelectric pH pI.

In acidic solution they are cationic in form and in alkaline solution they behave as anions Fig. At iso-electric point the amino acid will carry no net charge; all the groups are ionized but the charges will cancel each other. Therefore at isoelectric point, there is no mobility in an electrical field. Solubility and buffering capacity will be minimum at iso-electric pH. If more HCl is added, more molecules become cationic in nature and solubility increases. On the other hand, if we titrate the solution from iso-electric point with NaOH, molecules acquire the anionic form.

The iso-electric pH pI for mono amino mono carboxylic amino acids can be calculated:.

L and D amino acids B. Optical Activity 1.

Amino acids having an asymmetric carbon atom exhibit optical activity. Asymmetry arises when 4 different groups are attached to the same carbon atom Fig.

Glycine is the simplest amino acid and has no asymmetric carbon atom and therefore shows no optical activity. All others are optically active. The mirror image forms produced with reference to the alpha carbon atom, are called D and L isomers. The L-amino acids occur in nature and are therefore called natural amino acids.

D-amino acids are seen in small amounts in microorganisms and as constituents of certain antibiotics such as Gramicidin-S, Polymyxin, Actinomycin-D and Valinomycin, as well as bacterial cell wall peptidoglycans. Isoleucine and threonine have 2 optically active centers and therefore each has 4 diastereo isomers. Sorensen's Formal Titration Amino acids cannot be exactly titrated. If, for example, 1 ml of 1N solution of glycine is titrated against 1N sodium hydroxide, the alkali requirement will be less than 1 ml.

This is because hydrogen ions released by ionization of carboxyl group are partly taken up by the amino group. To circumvent this problem, excess formaldehyde is added to the solution, which converts amino group into neutral dimethylol derivative. Thereafter, titration can be completed to the end point. In the above example, after addition of formaldehyde, exactly 1 ml of 1N sodium hydroxide is utilized in the titration.

From the graph it is evident that the buffering action is maximum in and around pK1 or at pK2 and minimum at pI Fig. In the case of amino acids having more than two ionizable groups, correspondingly there will be more pK values, e. Aspartic acid Fig. The pK values of amino acids are given in Table 3. From these values, it can be seen that at physiological pH of 7. Thus to be very correct, zwitterion forms are to be shown as the structures of amino acids. The pK value of imidazolium group of histidine is 6.

The buffering capacity of plasma proteins and hemoglobin is mainly due to histidine residue. Due to Carboxyl Group 1.

The amino acids will undergo alpha decarboxylation to form the corresponding amine Fig. Thus some important amines are produced from amino acids. For example,. Transamination reaction In the body, Glutamic acid is the most common amino acid to undergo oxidative deamination.

Formation of carbamino compound: Carbon dioxide adds to the alpha amino group of amino acids to form carbamino compounds. The reaction occurs at alkaline pH and serves as a mechanism for the transport of carbon dioxide from tissues to the lungs by hemoglobin Chapter Reactions Due to Side Chains 6.

The methyl group of Methionine, after activation, may be transferred to an acceptor which becomes methylated Chapter Amide Formation: The -COOH group of dicarboxylic amino acids other than alpha carboxyl can combine with ammonia to form the corresponding amide.

These amides are also components of protein structure. The amide group of glutamine serves as the source of nitrogen for nucleic acid synthesis. Reactions Due to Amino Group 3. The alpha amino group of amino acid can be transferred to alpha keto acid to form the corresponding new amino acid and alpha keto acid Fig.

This is an important reaction in the body for the inter-conversion of amino acids and for synthesis of non-essential amino acids. Oxidative Deamination: The alpha amino group is removed from the amino acid to form the corresponding keto acid and ammonia Fig. Structure and Properties 25 Table 3. Color reactions of amino acids Reaction 1. Ninhydrin 2. Biuret reaction 3.

Xanthoproteic test 4. Millon's test 5. Aldehyde test 6. Sakaguchi's test 7. Sulphur test 8. Nitroprusside test 9. Peptide bond formation 7. Ester formation by the OH group: The hydroxy amino acids can form esters with phosphoric acid.

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In this manner the Serine and Threonine residues of proteins are involved in the formation of phosphoproteins. Similarly these hydroxyl groups can form O-glycosidic bonds with carbohydrate residues to form glycoproteins.

Reaction of the amide group: The amide groups of Glutamine and Asparagine can form Nglycosidic bonds with carbohydrate residues to form glycoproteins.

Reactions of SH group: Cysteine has a sulfhydryl SH group and it can form a disulphide S-S bond with another cysteine residue.

The two cysteine residues can connect two polypeptide chains by the formation of interchain disulphide bonds or links Fig. The dimer formed by two cysteine residues is sometimes called Cystine or Dicysteine.

Amino Acid Derivatives of Importance i.

Gamma amino butyric acid GABA, a derivative of glutamic acid and dopamine derived from iii. Gabapentin is clinically used to relieve pain. Histamine synthesized from histidine is the mediator of allergic reactions. Thyroxine from tyrosine is an important thyroid hormone.

Cycloserine , a derivative of serine is an antituberculous drug. Azaserine inhibits reactions where amide groups are added, and so acts as an anticancer drug. Histidine residues are important in the buffering activity of proteins. Ornithine and citrulline are derivatives of arginine, and are essential for urea synthesis. Proteins are made by polymerization of amino acids through peptide bonds.

Details of protein structures are given in Chapter 4. Color Reactions of Amino Acids and Proteins 1. All amino acids when heated with ninhydrin can form complexes; pink, purple or blue in color. The color complex is called Ruhemann's purple. Proline and. Chemical Basis of Life hydroxy proline will give yellow color with ninhydrin. Amino acids with amide group glutamine, asparagine produce a brown color. The ninhydrin reaction may be adopted for qualitative as well as quantitative estimation of amino acids.

It is often used for detection of amino acids in chromatography. Proteins do not give a true color reaction; but N-terminal end amino group of protein will also react with ninhydrin, to produce a blue color. Biuret Reaction: Cupric ions in an alkaline medium form a violet color with peptide bond nitrogen Schiff, This needs a minimum of two peptide bonds, and so individual amino acids and di-peptides will not answer this test.

This reaction can be used for quantitative estimation also. Magnesium and ammonium sulphates interfere with this reaction. Xanthoproteic test: The ring systems in phenyl alanine, tyrosine and tryptophan undergo nitration on treatment with concentrated nitric acid when heated Salkowski, The end product is yellow in color which is intensified in strong alkaline medium.

This reaction causes the yellow stain in skin by nitric acid. Millons Test: The phenol group of phenylalanine and tyrosine containing proteins, when heated with mercuric sulphate in sulphuric acid and sodium nitrite or, mercurous and mercuric nitrates in nitric acid form red colored mercury phenolate Millon, Chloride interferes with this reaction and so it is not suitable to test for tyrosine in urine samples. Both xanthoproteic and Millon's tests are negative for tapioca casava which is deficient in phenylalanine and tyrosine.

Aldehyde tests for tryptophan: In the Hopkins-Cole test, tryptophan containing protein is mixed with glyoxylic acid, and the mixture is layered over concentrated sulphuric acid. A violet ring at the interface of liquids shows the presence of the indole ring. Formaldehyde and mercuric sulphate is used similarly in Acree-Rosenheim reaction to get a violet color. Para-dimethyl-amino-benzaldehyde and strong hydrochloric acid give dark blue color Ehrlich's reaction.

Gelatin with limited tryptophan content will not answer these tests. Sakaguchis test for arginine: Free arginine or arginyl residues in proteins react with alpha-naphthol and alkaline hypobromite to give bright red color. This is due to the guanidinium group. Sulphur test for cysteine: When cysteine or cysteine containing proteins are boiled with strong alkali, organic sulphur splits and forms sodium sulphide, which on addition of lead acetate produces lead sulphide as a black precipitate. Methionine does not answer this test because sulphur in methionine is in the thio-ether linkage which is difficult to break.

Albumin and keratin will answer sulphur test positively; but casein will give a negative test. Nitroprusside reaction for SH groups: Proteins with free sulfhydryl groups give a reddish color with sodium nitroprusside, in ammoniacal solution.

Many proteins give a negative, reaction in the native state, but when denatured, reaction will be positive, showing the emergence of free SH groups. Pauly's test for histidine or tyrosine: Diazo benzene sulfonic acid reacts with imidazole group of Histidine to form a cherry-red colored diazotised product under alkaline conditions.

Textbook Biochemistry Medical Students by Vasudevan

The same reagent will give an orange red colored product with phenol group of Tyrosine. Color reactions of amino acids are shown as summary in Table 3. Quantitative estimation procedures of proteins are given in Chapter 4. Proteins are made by polymerisation of amino acids through peptide bonds. Two amino acids are combined to form a dipeptide; three amino acids form a tripeptide; four will make a tetrapeptide; a few amino acids together will make an oligopeptide; and combination of 10 to 50 amino acids is called as a polypeptide.

By convention, big polypeptide chains containing more than 50 amino acids are called proteins. In a tripeptide, there are 3 amino acids, but these 3 can be any of the total 20 amino acids.

An ordinary protein having about amino acids, will have different possibilities. This number is more than the total number of atoms present in the whole universe. Agegnehu rated it it was amazing Dec 21, Michael Igbudu rated it it was amazing Jun 19, Adya rated it liked it Feb 23, Manoj Porel rated it it was amazing Jun 06, Sajidur rated it it was amazing Feb 08, Hasaanbari rated it it was amazing Sep 05, Sreelekha rated it it was amazing Jan 29, Kiran rated it it was amazing Jan 31, Sneha Balu rated it it was amazing Dec 22, Nirmalkumar rated it liked it Oct 12, Joel Mwova rated it really liked it Jun 23, Sankaran rated it it was amazing Jan 30, Rousol rated it it was amazing Feb 20, Saira rated it it was amazing Dec 17, Nandhini rated it it was amazing Mar 30, Fayomi Damilola rated it it was amazing Apr 09, Monali rated it it was amazing Oct 15, Mihir Punjabi rated it really liked it Dec 01, Praveenkumar rated it it was amazing Oct 02, Prince rated it really liked it Oct 02, Mori Sneha rated it really liked it Nov 02, There are no discussion topics on this book yet.Prince rated it really liked it Oct 02, See the following example: These are formed by interactions between nonpolar hydrophobic side chains by eliminating water molecules.

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One carbon compounds, Generation and utilization of one carbon groups. Proline and. Detoxification and Biotransformation of Xenobiotics Voltage Gated Channels Voltage gated channels are opened by membrane depolarization Fig. Initially 5 molecules of NaR are added to the left compartment and 10 molecules of NaCl in the right compartment and both of them are ionized Fig.

After absorption, the small molecules are further broken down and oxidised to carbon dioxide.