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  Chemistry of Amino Acids and Proteins, Biology tutorial

Introduction:

Proteins, from Greek proteios, meaning first, are class of organic compounds that are present in and very important to each living cell. In form of hair, skin, callus, ligaments muscles, tendons and cartilage proteins hold together, protect, and give structure to body of multi-celled organism. In form of enzymes, antibodies, hormones, and globulins, they catalyze, control, and protect body chemistry. In form of hemoglobin, myoglobin and different lipoproteins, they affect transport of oxygen and other substances within organism.

Proteins are usually considered as helpful, and are essential part of diet of all animals. Humans can become critically ill if they don't eat sufficient appropriate protein, disease kwashiorkor being the tremendous form of protein deficiency. Protein based antibiotics and vaccines assist to fight disease.

Deadly properties of protein toxins and venoms are less extensively appreciated. Botulinum toxin A, from Clostridium botulinum, is considered as most powerful poison known. Toxins produced by tetanus and diphtheria microorganisms are almost as poisonous. The list of highly toxic proteins or peptides would also comprise venoms of several snakes, and ricin, toxic protein found in castor beans.

Proteins can also be classified by chemical reactions. Many proteins are soluble in water, in alcohol, in dilute base or in different concentrations of salt solutions. Proteins have characteristic coiled structure that is determined by sequence of amino acids in primary polypeptide chain and stereo configuration of radical groups attached to alpha carbon of every amino acid. Proteins are heat labile showing different degrees of lability relying upon kind of protein, solution and temperature profile.

Despite diversity of physiological function and differences in physical properties--silk is flexible fiber, horn tough rigid solid, and enzyme pepsin water soluble crystals--proteins are adequately similar in molecular structure to warrant treating them as the single chemical family. When compared with carbohydrates and lipids, proteins are visibly different in fundamental composition. Lipids are mainly hydrocarbon in nature, usually being 75 to 85% carbon. Carbohydrates are about 50% oxygen, and like lipids, frequently have less than 5% nitrogen (frequently none at all). Proteins and peptides, on the other hand, are made up of 15 to 25% nitrogen and about equal amount of oxygen.

Amino acids play main roles both as building blocks of proteins and as intermediates in metabolism. 20 amino acids which are found in proteins convey huge array of chemical versatility. Tertiary Structure of protein. Exact amino acid content, and sequence of those amino acids, of specific protein, is found out by sequence of bases in gene which encodes that protein. Chemical properties of amino acids of proteins find out biological activity of protein. Proteins not only catalyze all (or most) of reactions in living cells, they manage virtually all cellular process. Additionally, proteins have within their amino acid sequences essential information to find out how that protein will fold in three dimensional structure, and stability of resulting structure. Field of protein folding and stability has been vitally significant area of research for years, and remains today one of the great unsolved mysteries.

Necessary amino acids:

Humans can generate 10 of the 20 amino acids. Others should be supplied in food. Failure to get enough of even 1 of 10 necessary amino acids, those that we can't make, results in degradation of body's proteins-muscle and so forth-to get one amino acid which is required. Unlike fat and starch, human body doesn't store excess amino acids for later use-amino acids should be in food every day.

The 10 amino acids which we can generate are glycine, alanine, aspartic acid, cysteine, asparagine, glutamic acid, proline, glutamine, serine and tyrosine. Tyrosine is generated from phenylalanine, so if diet is deficient in phenylalanine, tyrosine will be needed as well. Essential amino acids are methionine, arginine, histidine, threonine, lysine, isoleucine, leucine, phenylalanine, tryptophan, and valine. Amino acids are needed in diet. Plants, of course, should be able to make all amino acids. Humans, conversely, don't have all enzymes needed for biosynthesis of all of amino acids.

Amino acids comprise of primary amine bound to aliphatic carbon atom (so-called α-carbon), that in turn is bound to carboxylic acid group. At least one hydrogen atom is bound to α-carbon; additionally, α-carbon bears side chain that is different for different amino acids. In the neutral aqueous solution, amino acids exist in 2 forms. The extremely small fraction of amino acid molecules will be neutral, with the deprotonated amino group and protonated carboxylic acid group. Though, overwhelming majority of molecules will be in a Zwitterion tautomer, with the positive charge on (protonated) amino group and negative charge on (deprotonated) carboxylate group.

Amino acids are linked via Peptide bond. The peptide bond comprises of carbonyl group's carbon atom directly bound to nitrogen atom of the secondary amine. The peptide chain will contain unbound amino group free at one end (known as N-terminus) and single free carboxylate group at other end (known as the C-terminus).

Peptide bond is planar, as resonance between carbonyl group and amino nitrogen lends C-N bond a partial double-bond character. This prevents rotation around C-N bond, locking peptide bond in trans conformation, and holding six atoms in plane: α-carbon of one amino acid, carbonyl carbon and oxygen atoms, amino nitrogen and hydrogen atoms, and &alpha-carbon of second amino acid are all co-planar.

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