01 Protein Structure

01 Protein Structure - Amino Acids of Proteins 20 different...

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Amino Acids of Proteins 20 different amino acids in proteins. All are α- amino acids. One – proline - is technically an imino acid, because the amino group forms a ring structure with the side chain. In all except glycine the α -carbon is chiral ie. the molecule has optical isomers. All naturally occurring amino acids are L- isomers. Side chains determine the properties and identities of the amino acids.
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Amino Acid Side Chains About half the amino acid side chains are hydrophobic, and half are hydrophilic (a few are difficult to classify and have intermediate properties). Side chains with electrical charges (acid, -ve, or basic, +ve), or with groups with a strong dipole, such as –OH, are hydrophilic. Hydrocarbon side chains, without a charge or dipole, are hydrophobic. Histidine, tyrosine and tryptophan have large hydrocarbon side chains which contain groups with a dipole. This makes them a little difficult to classify. Amino acid names are abbreviated to a three letter code, usually the first three letters of the name. For greater brevity a single letter code is now often used in papers. Where possible this is the first letter of the name, but some start with the same first letter (four As for example). Other letters are allocated in this case.
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Structure of Proteins Protein structure is complex and usually irregular. Proteins fold into complex three dimensional shapes, determined by interactions between all parts of their monomer constituents (amino acid residues ). To simplify description the structure of proteins is broken down into four levels, primary, secondary, tertiary and quaternary, each characterised by different types of bonding. In spite of this complexity and irregularity you should note that all similar protein molecules have the same structure under the same conditions. We may not be able to predict what that structure will be, but the interactions occurring are exact and repeatable.
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Primary Structure The linear sequence of amino acids in a protein chain forms its primary structure. Amino acids are covalently bonded by a bond formed between the α –COOH group of one amino acid and the α - NH2 group of the amino acid next in the chain. This bond is formed by loss of water and is chemically an anhydride bond. It is often known as the peptide bond. There are no rules about the order of amino acids in a chain, or their number. Chains can be of any length, often up to several thousand amino acids, and amino acid residues can be placed in any order, determined only by the base sequence of DNA coding for their synthesis. The first residue in a chain has a free (unbonded) –NH2 group and is called the N-terminus. The last residue has a free –COOH group and is called the C-terminus. During protein synthesis the chain is built up from N-terminus to C-terminus and when numbering the residues in the chain the N-terminal residue is numbered 1.
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Proteins and Peptides Note that a single chain of amino acids is technically a peptide. The term
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01 Protein Structure - Amino Acids of Proteins 20 different...

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