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Transcript
Amino Acids Introduction Amino acids are the building blocks of proteins. The sequence of amino acids in individual proteins is encoded in the DNA of the cell. The physical and chemical properties of the 20 different naturally occurring amino acids dictate the shape of the protein and its interactions with its environment. Certain short sequences of amino acids in the protein also dictate where the protein resides in the cell. Proteins are composed of hundreds to thousands of amino acids. As you can imagine, protein folding is a complicated process and there are many potential shapes due to the large number of combinations of amino acids. By understanding the properties of the amino acids you will gain an appreciation for the limits of protein folding and will learn how to predict the potential higher-order structure of the protein. All amino acids have the same backbone structure, with an amino group, a carboxyl group, an alpha- hydrogen, and a variety of functional groups (R) all attached to the alpha-carbon. If all of the amino acids have the same basic structure with an amino, a carboxyl and hydrogen fixed to the alpha-carbon, then the large variation in the properties and structure of the amino acids must come from the fourth group attached to the alpha carbon. This group is referred to as the side chain of the amino acid or the R group. The structures of the 20 common amino acids are shown on the chart below. The simplest amino acid, glycine, is shown in the upper left. The main-chain atoms of glycine are highlighted in yellow and its side chain (H) is highlighted in green. All amino acids have the same main-chain atoms, but differ in the side chains. For clarity, the alpha- proton is omitted in the remaining drawings. The side-chain groups of these amino acids contain many common groups of atoms called functional groups. The majority of functional groups, such as the hydroxyl group (–OH), are commonly polar, allowing them to interact with water. Details of the functional groups can be found in the functional groups interactive chart, which can be accessed by clicking on the Learn by doing link below. Peptide Bonds Proteins are polymers of amino acids. The amino acids are joined together by a condensation reaction. Each amino acid in the polymer is referred to as a "residue." Individual amino acids are joined together by the attachment of the nitrogen of an amino group of one amino acid to the carbonyl carbon (C=O) of the carboxyl group of another amino acid, to create a covalent peptide bond and yield a molecule of water, as shown below. The resulting peptide chain is linear with defined ends. Short polymers (less than 50 residues or amino acids) are usually referred to as peptides, and longer polymers as polypeptides. Several polypeptides together can form some large proteins. Because the synthesis takes place from the alpha-amino group of one amino acid to the carboxyl group of another amino acid, the result is that there will always be a free amino group on one end of the growing polymer (the N-terminus) and a free carboxyl group on the other end (the C-terminus). Note that after the amino acid has been incorporated into the protein, the charges on the amino and carboxyl termini have disappeared, thus the main-chain atoms have become polar functional groups. Since each residue in a protein has exactly the same main-chain atoms, the functional properties of a protein must arise from the different sidechain groups. By convention, the sequences of peptides and proteins are written with the N-terminus on the left and the C-terminus on the right. The name of the N-terminal residue is always the first amino acid. The name of each amino acid then follows. The primary sequence of a protein refers to its amino acid sequence.