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The nature of proteins.

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The nature of proteins Proteins consist of carbon, hydrogen, oxygen and also nitrogen. Proteins are macromolecules. They are constructed from one or more unbranched chains of amino acids; that is, they are polymers (Compound whose molecule consists of many repeated units linked together). A typical protein contains 200-300 amino acids but some are much smaller (the smallest are often called peptides) and some much larger. Amino Acids Amino acids are the building blocks (monomers) of proteins. 20 different amino acids are used to synthesize proteins. The shape and other properties of each protein is dictated by the precise sequence of amino acids in it. Each amino acid consists of an alpha carbon atom to which is attached a hydrogen atom an amino group (hence "amino" acid) A carboxyl group (-COOH). This gives up a proton and is thus an acid (hence amino "acid") One of 20 different "R" groups. It is the structure of the R group that determines which of the 20 it is and its special properties. The amino acid shown here is Alkaline. Amino acids contain an amino or NH2 group and a carboxyl (acid) or COOH group. The ionization of water Amino-acids at physiological pH values predominate at an ionization state where the alpha-amino group is positively charged (a cation) ...read more.


The most common of these are the alpha helix and the beta conformation. Alpha Helix * The R groups of the amino acids all extend to the outside. * The helix makes a complete turn every 3.6 amino acids. * The helix is right-handed; it twists in a clockwise direction. * The carbonyl group (-C=O) of each peptide bond extends parallel to the axis of the helix and points directly at the -N-H group of the peptide bond 4 amino acids below it in the helix. A hydrogen bond forms between them [-N-H�����O=C-] . Beta Conformation * consists of pairs of chains lying side-by-side and * stabilized by hydrogen bonds between the carbonyl oxygen atom on one chain and the -NH group on the adjacent chain. * The chains are often "anti-parallel"; the N-terminal to C-terminal direction of one being the reverse of the other. Tertiary Structure Tertiary structure refers to the three-dimensional structure of the entire polypeptide chain. Where the entire protein or parts of a protein are exposed to water (e.g., in blood or the cytosol), hydrophilic R groups - including R groups with sugars attached - are found at the surface; hydrophobic R groups are buried in the interior. The function of a protein depends on its tertiary structure. If this is disrupted, the protein is said to be denatured A mutation in the gene encoding a protein is a frequent cause of altered tertiary structure. ...read more.


The other 15 types are probably equally important but they are much less abundant. Primary Structure of Collagens The basic unit of collagens is a polypeptide consisting of the repeating sequence (glycine (Gly) - X - Y)n where X is often proline (Pro) and Y is often hydroxyproline (proline to which an -OH group is added after synthesis of the polypeptide). Secondary and Tertiary Structure The resulting molecule twists into an elongated, left-handed helix (NOT an alpha helix). When synthesized, the N- terminal and C- terminal of the polypeptide have globular domains, which keep the molecule soluble. As they pass through the endoplasmic reticulum (ER) and Golgi apparatus, * The molecules are glycosylated. * Hydroxyl (-OH) groups are added to the "Y" amino acid. * S-S bonds link three chains covalently. * The three molecules twist together to form a triple helix. In some collagens (e.g., Type II), the three molecules are identical (the product of a single gene). In other collagens (e.g., Type I), two polypeptides of one kind (gene product) assemble with a second, quite similar, polypeptide, that is the product of a second gene. When the triple helix is secreted from the cell (usually by a fibroblast), the globular ends are cleaved off. The resulting linear, insoluble molecules assemble into collagen fibers. They assemble in a staggered pattern that gives rise to the striations seen in this electron micrograph (courtesy of Dr. Jerome Gross). (Type IV collagens are an exception; they form a meshwork rather than striated fibers.) ...read more.

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