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. Valinehas an isopropyl R group. The leucine and isoleucine R groups are butyl groups that are structural isomers of each other. In leucinethe 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 tryptophanhasthe 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 cysteineside 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-).

Prolineis 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. Aspartatecontains 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 lysineside 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.

General properties

1) precipitation’s reactions. When the charge of protein molecule disappears the proteins lose their hydratic cover, the solubility of proteins decreases and proteins precipitate. The salts of heavy metall remove the charge of protein molecule and such proteins can not to keep hydratic cover and are precipitated. The concentrate acids removal the hydratic cover and precipitate of protein. The precipitation of protein by neutral salts called the saltingout. The possibility of precipitation of proteins for some cations is following: LiàNaàKàRbàCs. Li remove hydratic cover because have high density of electric charge.

All proteins have complicated construction. All proteins have three levels of organization their molecules – primary, secondary and tertiary structures. Some proteins also possess a fourth structure called the quaternary structure. Primary structure – is aminoacid composition and the sequence of different aminoacid’s residues, along the polipeptides chain, the quantity and quality of aminoacid’s residues of polipeptide chain. The bond of this structure is peptide bond. There are 20 aminoacids which enter into the formation of peptide molecules through peptide lincage between successive aminoacid molecules. An unlimited number of peptide molecules are possible from 20 aminoacids. These peptides will differ from each other in the number, quality and the sequence of aminoacids in their molecules. The number of aminoacids in a peptide molecule varies from few tens to several hundreds, thousands. There are two terminal aminoacid’s residues in a peptide chain – N-terminal residues containing a free NH2group and C-terminal residues containing a free carbocylgroup. The numbering of the aminoacid residues in a peptide chain starts from N-terminal aminoacid. For example, N-arginyl-alanyl-glycyl-arginyl-glutamyl-alanyl-methionyl-lysine. The sequence aminoacids C terminus along the polypeptide chain causes the arrangement the different functional groups along polypeptide chain (-SH, -COOH, -NH2, -OH, -CH3). Every protein have unique primary structure and all properties of protein depend from its primary structure. The primary structure of proteins is regulated by the respective genes on specific chromosomes. The substitution of a single aminoacid by another in a peptide chain may result in a dramatic change in its properties and functions. For example, the HbA has glutamatic acid in 6-th position in the βchains. When glutamine is changed by valine – the solubility and possibility of Hb to bound oxygen change and such Hb called HbS. This Hb precipitate and because the form of erythrocyte is changed and become same as letter S. In 1953 Sanger founded the primary structure of polypeptide chain of insulin (151 a/a) and he was awarded Nobel prize for chemistry. Ten years later Edelman and Porter were awarded Nobel prize also for pr. str. of ribonuclease (1300a/a). The method of acid hydrolis of protein and electrophoresis and chromatography had been used. This method called “finger print” – double chromatography. Sanger did this research about ten years. Now there are aminoacid analysator and aminoacid composition is opened for 24 hours. If the peptide chain has only the primary structure it has not any function. It is innative secondary structure of proteine. The foldind of the polypeptide chain into a specific coiled structure hed together by the hydrogen bonds is called the secondary structure of protein. Method of x-ray diffraction was used by Linus Pauling and Corey for discover this structure and they were awarded Nobel prize for this discovery. The secondary structure has two forms. 1) α-helix. It is a clockwise (a right handed) spiral and is formed by intrachain hydrogen bonding between the carboxyl group of each aminoacid and the aminogroup of the aminoacid that is situated 4 residues ahead in the linear sequence. The percentage of α-helix content in globular proteins varies from 5-10% to 80-90%. The largest consecutive stretch of α-helix in a globular p/p spans about 36 residues or about ten complete turns of α-helix a minimum stretch of α-helix spiral requires four residues for turn, because there are 3,6 aminoacid residues (aar) per turn of the helix. The distance traveled per turn is 0,54 nm. The main features of the α-helix: 1) each peptide bond participates in the H-bonding. This confers maximum stability. Proteins containing α-helix show great strength and elasticity, beel they can be easily stretched because they are in the form of a tight coil. 2) All of the main chain peptide amino and carbonyl oxygen residues are hydrogen bonded. Thus greatly reducing the hydrophilic nature of the α-helical region. 3) An α-helix forms spontaneously since it is the lowest energy most stable conformation for a PPC. Two factors that definitely interrupt the α-helix orientation are 1) the presence of proline (the N-atom is part of a rigid ring) and aa with charged or bulky rgroupe, 2) the electrostatic repulsion due either to a cluster of positively charged R-groups from lys and arg, or a cluster of negatively charged R-groups from glu and asp. Second form of secondary structure is β-sheet structure. In this case the hydrogen bonds exist between peptide chains running parallel and closer to each other. Proteins containing this structure are inelastic because H-bonds are at the right augle to the direction of stretching. Thus the β-pleated sheet cannot be further exteded as it is already almost fully extended. Various proteins have α-helix and β-pleated structures but one of these structures may predominate. Myoglobin and hemoglobin show a predominantly α-helix structure, α-keratine has a highly developed α-helix, while collagen and fibroin of silks and spider’s web show a beta pleated structure. Tertiary structure of proteins. Protein’s molecule is folded and refolded on itself to give rise to a definite three –dimensional conformation which makes it rounded, this is called its tertiary structure. The proteins, which have tertiary structure, are native. The tertiary structure of proteins is mainly maintained by S-S covalent linkages between cystein residues and by ester linkages between carboxyl group and a hydroxyl group on two different aminoacids. H-bonds, ionic bonds and hydrophobic bonds attraction between the negatively charged carboxyl groups and positively charged aminogroups Van der Waal’s forces (exist between non polar side chains of aa) also provide stability the tertiary structure. Quaternary structure of proteins. If proteins molecule is made up of more than one peptide chain subunits with (1, 2, 3 str), the interaction of these chains maintained quaternary structure. 1) Decreases the mistake during of protein synthesis, 2) economize the genetic materials, 3) give the possibility of regulation. Denaturation. The weak forces responsible for maintaining secondary, tertiary and quaternary structure of proteins are readily disrupted with resulting loss of biological activity. This disruption of native structure is termed denaturation. The primary structure isn’t disrupted. The biological activity of most proteins is destroyed by exposure to strong mineral acids or bases, heat, ionic detergents, chaotropic agents (urea, guanidine), heavy metals (Ag, Pb, Hg) or organic solvent (acetone, alcohole, butanol). Generally are less soluble in water, and they often precipitate from solution (boiled eggs for example). Denaturating agents:

A - The high temperature (example – blow dry of the hair) disrupts hydrogen bonds

B - Strong acids and bases (polirized connections) cause dehydratation

C - Urea and guanidine (promote the formation of extra hydrogen bonds)

D - The salts of heavy metals disrupt ionic bonds and derange charge of protein

E - Alkaloids causes neutralization of charge of proteins

3) They consist of elements of constant concentration: C – 53%, O – 22%, N – 16%, H – 7%, S – 2%.

4) High molecular weight – from 6000 to mil. Daltons (D).

5) Determinated size and forms of their moleculs.

Proteins

Globullars Fibrillars

Watersoluble waterunsoluble

Myosin, fibrinogen scleroproteins

Fibrinogen (6 p/p chains) + Ca + trombeen-------------à fibrin (2 p/p chains); scleroproteins – keratin and collagen (connective tissues).

6) Common products of distruction - proteins -à hydrolisis-à a/acids

7) Common plan of the structure - connections – covalent with energy 84-840 kJ/M, noncovalent (week) – 1) hydrogen, 2) ionns’s, 3) hydrophobic

8) Some common color’s reactions – biuretic (peptide bonds), nynhydrate (α a/a), Fole, nitroprusside (thio a/a), Millone (tyr), ksantoproteinic (tyr, try).

9) Proteins having amphoteric characteristic – their charge depend from their aminoacid composition and from pH solution

10) Сolloidal character of water solution of proteins. This means presence of Tyndal effect, proteins forms gels, they don’t pass through semipermeable membrane, proteins have a small velocity of diffusion and high viscosity