Draft:Proteins

A protein is one or more polypeptides held together by peptide bonds.

Theoretical proteins
Here's a theoretical definition:

Def. any naturally occurring complex combinations of amino acids that contain at least the elements: carbon (C), hydrogen (H), nitrogen (N), and oxygen (O) are called proteins.

Def. any "of numerous large, complex naturally-produced molecules composed of one or more long chains of amino acids, in which the amino acid groups are held together by peptide bonds" is called a protein.

Def. a "large, complex molecule composed of one or more long chains of amino acids, in which each chain is held together by peptide bonds" is called a protein.

Def. a "large, complex molecule composed of long chains of amino acids linked by a peptide bond" is called a protein.

Def. "any of numerous naturally occurring extremely complex combinations of amino acids that contain the elements carbon, hydrogen, nitrogen, oxygen, usually sulfur, occasionally phosphorus, iron, or other elements, are essential constituents of all living cells, and are synthesized from raw materials by plants but assimilated as separate amino acids by animals" is called a protein.

Biochemistry
Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids, have a great variety of chemical structures and properties; it is the combined effect of all of the amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity.

The amino acids in a polypeptide chain are linked by peptide bonds. Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone.

The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar; the other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone.

Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three-dimensional structure; however, the boundary between the two is not well defined and usually lies near 20–30 residues.

Proteins can interact with many types of molecules, including with other proteins, with lipids, with carboyhydrates, and with DNA.

Amino acids
Def. "[a]ny organic compound containing both an amino and a carboxylic acid functional group" is called an amino acid.

Def. any amino acid "having the amino, and carboxylic acid groups on the same carbon atom" is called an α-amino acid.

Def. "[a] functional group formally derived from ammonia by replacing one, two or three hydrogen atoms" is called an amine, or amino group.

Def. "[a] univalent functional group consisting of a carbonyl [-CO] and a hydroxyl [·OH] functional group" is called a carboxyl, or carboxylic acid group.

Notation: let the symbol COOH represent the carboxylic acid group.

Def. "amino acids that are precursors to proteins, and are produced by cellular machinery coded for in the genetic code of any organism" are called proteinogenic amino acids.

"The proteinogenic amino acids have been found to be related to the set of amino acids that can be recognized by ribozyme auto-aminoacylation systems. "

Peptides
Def. a "covalent bond [amide bond] formed between the amino and carboxyl functional groups of separate amino acids" is called a peptide bond.

Def. "various numbers of amino acids in which the amine of one is reacted with the carboxylic acid of the next to form an amide bond" is called a peptide.

Def. "two amino acids joined by a peptide bond" is called a dipeptide.

Def. "three amino acids joined by peptide bonds" is called a tripeptide.

Def. four amino acids joined by peptide bonds is called a tetrapeptide.

Def. five amino acids joined by peptide bonds is called a pentapeptide.

Def. a "peptide containing a relatively small number of amino acids" is called an oligopeptide.

Def. "[a]ny polymer of (same or different) amino acids joined via peptide bonds" is called a polypeptide.

In the diagram at top right, the remainder of the carboxyl group (C = O) has been bonded to the the remainder of the amino group (NH) of an adjacent amino acid by a peptide bond. The remainder of the carbonyl group and amino group has been formed into H2O ← OH (from -C=O·OH) + H (from $$NH_2^-$$).

The second from the top diagram shows the amino group end (or N-terminus) in green and the carboxyl group end (or C-terminus) in blue of a tetrapeptide ([Valine] Val-[Glycine] Gly-[Serine] Ser-[Alanine] Ala).

"The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus."

Preproteins
Def. any protein or polypeptide containing a signal sequence that specifies its insertion into or through membranes is called a preprotein.

Def. any preprotein of a proprotein is called a preproprotein.

Proproteins
Def. "[a]ny protein that is cleaved by a convertase to form a smaller protein or biologically-active polypeptide" is called a proprotein.

Proteoses
Def. a "mixture of peptides produced by the hydrolysis of proteins" is called a proteose.

Peptones
Def. any "water-soluble product, a mixture of polypeptides and amino acids formed by the partial hydrolysis of protein" is called a peptone.

Albumins
Def. a "class of monomeric proteins that are soluble in water, and are coagulated by heat; they occur in egg white, milk etc; they function as carrier protein for steroids, fatty acids, and thyroid hormones and play a role in stabilizing extracellular fluid volume" is called albumins.

Globulins
Def. any "of a group of simple proteins, soluble in water only in the presence of salts, that are coagulated by heat; one of the two parts of hæmoglobin" is called a globulin.

Prolamins
Def. any "of a group of plant storage proteins, that have a high proline content, found in cereals" is called a prolamin.

Histones
Def. any "of various simple water soluble proteins that are rich in the basic amino acids lysine and arginine and are complexed with DNA in the nucleosomes of eukaryotic chromatin" is called a histone.

Protamines
Def. "any of a class of proteins, rich in arginine, found in the sperm of fish; used medicinally to control the action of insulin" is called a protamine.

Conjugated proteins
Def. any "protein that consists of both a polypeptide and a prosthetic group such as a lipid (in lipoproteins), sugar (in glycoproteins) or porphyrins and metals (in hemoglobin etc)" is called a conjugated protein.

Cytochromes
Def. any "of various related hemoproteins found in the cells of most organisms, which are an important part of cell respiration" is called a cytochrome.

Flavoproteins
Def. "any of a group of enzymes, containing flavin, that act as dehydrogenases" is called a flavoprotein.

Glycoproteins
Def. a "protein with covalently bonded carbohydrates" is called a glycoprotein.

Hemeproteins
Def. any "conjugated protein containing heme as the prosthetic group" is called a hemeprotein.

Lipoproteins
Def. any "of a large group of complexes of protein and lipid with many biochemical functions" is called a lipoprotein.

Metalloproteins
Def. "a protein, such as haemoglobin or chlorophyll, that contains a metal atom as a cofactor" is called a metalloprotein.

Opsins
Def. any "of a group of light-sensitive proteins in the retina" is called an opsin.

Phosphoproteins
Def. "any protein containing bound phosphate" is called a phosphoprotein.

Phytochromes
Def. any "of a class of pigments that control most photomorphogenic responses in higher plants" is called a phytochrome.

Scleroproteins
Def. any "of many fibrous proteins found in connective tissue etc" is called a scleroprotein.

Hypotheses

 * 1) Amino acids in addition to the critical 22 are also coded genetically.