Introduction into biochemistry

Biochemistry is the science concerned with the various molecules that occur in living cells and organisms and with their chemical reactions. Anything more than a superficial comprehension - demands a knowledge of biochemistry.

Biochemistry has advanced rapidly with the development, from the mid-20-th century, of such techniques as chromatography, x-ray diffraction, radioscopic labeling, electron microscopy, and amplificators, secvinators and etc. Using these techniques to separate and analyze biologically important molecules, the steps of the metabolic pathways in which they are involved (glycolysis, Krebs cycle, structure of genome) have been determined. This has provide some knowledge of how organisms obtain and store energy, how they manufacture and degrade their biomolecules, how they sense and respond to their environment, and how all this information is carried and expressed by their genetic material. Biochemistry forms an important part of many other disciplines, especially physiology, nutrition, and genetics, and its discoveries have made a profound impact in medicine, agriculture, industry, and many other areas of human activity.

Biochemistry can be defined more formally as the science concerned with the chemical basis of life (Greek - bios “life”).

The cell is the structural unit of living systems. Consideration of this concept leads to a functional definition of biochemistry as the science concerned with he reactions and processed that they undergo. By this definition, biochemistry encompasses large areas of cell biology, of molecular biology, and of molecular genetics.

The major objective of biochemistry is the complete understanding at the molecular level of all of the chemical processes associated with living cells.

A father objective of biochemistry is to attempt to understand how life began. Knowledge of this fascinating subject is still embryonic.

Enzyme A protein that acts as a catalyst in biochemical reactions. They greatly increases (by a factor of up to 10²⁰) the rate at which the reaction proceeds to form the product.

Medical students who acquire a sound knowledge of biochemistry will be in strong position to deal with two central concerns of the health sciences: 1) the understanding and maintenance of health and 2) the understanding and effective treatment of disease.

Immunology –

Molecular biology

Molecular pharmacology

Molecular genetic (Genetic engineering, Biotechnology, Genetic therapy)

Proteins structure, functions and classification

Proteins is the higher molecular biopolymers, which constructed from amino acids. Protos - first, important. This term was proposed by Mulder in 1838.

It is notable that the different types of proteins are synthesized as polymers of only 20 amino acids. These common amino acids are defined as those for which at least one codon exists in the genetic code Transcription and translation of DNA code result in polymerization of amino acids into a specific linear sequence characteristic for protein. Proteins may also contain derived amino acids, which are usually formed by an enzymatic reaction on a common amino acid after that amino acid have been incorporated into a protein structure. Examples of derived amino acids are cystine, desmosine, and isodesmosine found in elastine, hydroxyproline and hydroxylysine in collagen, and γ-carboxyglutamate in prothrombin.

Common amino acids contain a central alpha (α)-carbon atom to which a carboxylic acid group, an amino group, and a hydrogen atom are covalently bonded. In addition, the (α)-carbon atom is bound to a specific chemical group, designed R and called the side chain, that uniquely defines each of the 20 common amino acids (F).

Alkyl amino acids have alkyl group side chains and include glycine, alanine, leucine, and isoleucine. Glycine has the simplest structure, with R=H. Alanine contains a methyl (CH₃-) group. Valine has an isopropyl R group. The leucine and isoleucine R groups are butyl groups that are structural isomers of each other. In leucine the branching in the isobutyl side chain occurs on the gamma (γ) carbon and in isoleucine is branched at the beta (β)-carbon of the amino acid.

The aromatic acids are phenylalanine, tyrosine, and tryptophan. Phenilalanine contains a benzene ring, Tyrosine has a phenol group, and tryptophan has the heterocyclic structure, named indole. In each case the aromatic moiety is attached to (α)-carbon through a methylen (-CH₂-) carbon (F).

Sulfur-containing amino acids are cysteine and methionine. The cysteine side chain group is a thiomethyl (HSCH₂-). In methionine the side chain is a methyl ethyl thiol ether (CH₃SCH₂CH₂-).

The two hydroxyl (alcohol)-containing amino acids are serine and threonine. The serine side chain is a hydroxymethyl (HOCH₂-). an ethanol structure In threonine is connected to the (α)-carbon through the carbon containing the hydroxyl substituent, resulting in a secondary alcohol structure (CH₃ -CHOH-CH_α-).

Proline is unique aminoacid in that the amino group is incorporated in its side chain and more accurately classified as an (α)-amino acid, since its α-amine is a secondary amine with its α nitrogen having two covalent bonds to carbon (to the α-amino nitrogen into five-membered ring contains the rotation freedom around the – N-α- C-α -bond in praline to specific rotational angle, which limits participation of proline in polypeptide chain conformations.

The amino acids discussed so far contain side chain that are uncharged at physiological pH. The dicarboxylic monoamino acids contain a carboxylic group in their side chain. Aspartate contains a carboxylic acid group separated by a methylene carbone (-CH₂-) from the α carbone. In glutamate the carboxylic acid group is separated by two methylene (-CH₂-CH₂-) carbon atoms from the α carbone. Dibasic monocarboxylic acids include lysine, arginine, and histidine (F). In these structures, the R group contains one or two nitrogen atoms that act as a base by binding a proton. The lysine side chain is an N-butyl amine. In arginine, the side chain contains a quanidino group separated from the α carbone by three methylene carbone atoms. Both the quanidino group of arginine and the ε-amino group of lysine are protonated at physiological pH (~7) and in their positively charged form. In histidine the side chain contains a five-membered heterocyclic structure, the imidazole. The pK’_α of the imidazole group is approximately 6,0 in water, physiological solutions contain relatively high concentrations of both basic (imidazole) and acidic (imidazolium) forms of the histidine side chaun.

Glutamine and asparagines are structural analogs of glutamic acid and aspartic acid with their side chain carboxylic acid group amidated. The amide side chains of glutamine and asparagines cannot be protonated and are uncharged at physiological pH.

Isoelectric point of proteins dependends on amino acids (on their charge). Isoelectric point is pH in which peptide uncharged and precipitated.