Collagen (previous page) is the most abundant protein in the human body and is the 'glue' that literally sticks us together. Proline, which is the least flexible amino acid, due to attachment of the side chain to the alpha-amino grip, is less likely to be found in alpha helices, but curiously it is found abundantly in the fibrous protein known as collagen. Beta-keratin is a harder fibrous protein found in nails, scales, and claws. Alpha keratin has primary structure and secondary structure, but little tertiary or quaternary structure.Ĭonsequently, alpha keratin exists mostly as long fibers, such as are found in hair. (As we shall see, these last two levels of structure arise from 'bends' in polypeptide chains and interactions between separate polypeptide chains, respectively.)Īlpha keratin, for example, is what we refer to as a fibrous protein (also called scleroprotein). Not all proteins have significant amounts of tertiary or quaternary structure. Figure 3.2.2: An image of the primary structure of a protein. For transmembrane proteins, which project through both sides of the membrane, the hydrophilics are found at each point where the polypeptide chain emerges from the membrane.
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For a protein like porin, which provides an interior channel through which water can pass, this is where the hydrophilics are found. When one examines the structure of proteins in non-aqueous environments, such as the interior of a lipid bilayer, the arrangement is flipped – hydrophobics predominate on the outside where they can interact with the hydrophobic side chains of membrane fatty acids and the hydrophilic amino acids are arranged anyplace where they can contact water. The hydrophobic amino acids in these proteins are found predominantly on the interior. Proteins that are in aqueous environments, such as the cytoplasm of the cell, have their amino acids arranged so that those with hydrophilic side chains (such as threonine or lysine) predominate on the exterior of the protein so as to interact with water. This introduces a slight simplifying aspect to the structure of proteins – one need only consider the positioning of the R-groups around each peptide bond when determining protein structure schematically. Amino acids are joined to each other by peptide bonds. Note also that biochemistry books vary in how they organize amino acids into categories. Note that tyrosine has a hydroxyl group and fits into two categories. Hydroxyl/Sulfhydryl (threonine, serine, tyrosine, cysteine).
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Aliphatic (leucine, isoleucine, alanine, methionine, valine).Aromatic (phenylalanine, tyrosine, tryptophan).Based on side chains, we can group the 20 amino acids found in proteins as follows: This is important, because it is only in the side chains (R-groups) that amino acids differ from each other. Though all of the amino acids are, in fact, soluble in water, the interactions of their side chains with water differ significantly. Whereas nucleotides all are water soluble and have the same basic composition (sugar, base, phosphate) and the sugars also are water soluble and mostly contain 5 or 6 carbons (a few exceptions), the amino acids (general structure below) are structurally and chemically diverse.