(Again, remember that the number of elementary particles in the universe is estimated to be 10 80.) Obviously, not all these potential proteins exist in nature. Even if limited to the smallest chain length, there would be 20 100, over 10 130-that is, 1 with 130 zeroes after it-possible primary structures. How many proteins are possible? Protein chains generally vary in size from 100 to 1,000 amino acids in length. The side chains of amino acids give them their different chemical properties and allow proteins to have so many different structures. Amino acids in water, therefore, have the general structure: Similarly, α‐amino groups (pK a greater than 9) are stronger bases than water and will accept a proton from water. Carboxyllic acids are stronger acids than water, so the carboxyl group of an amino acid (pK a near 2) will donate a proton to water. The strongest acid that can exist in water is the conjugate acid of water, the hydronium ion, H 3O +. The formation of zwitterions can be rationalized from the principles of acid‐base chemistry. This exchange happens simultaneously in solution so that the amino acids form doubly ionized species, termed zwitterions (from German zwei, meaning two) in solution. The carboxyll and amino groups of the amino acids can respectively donate a proton to and accept a proton from water. (The D comes from dextro, meaning right.) For example, some peptide antibiotics, such as bacitracin, contain D‐amino acids. (Biochemists, being creatures of habit, usually do not refer to amino acid stereochemistry in the R and S nomenclature.) A few D‐amino acids are found in nature, although not in cellular proteins. Thus, the amino acids found in proteins are L‐alpha amino acids.
In organic chemistry, this stereochemistry is referred to as L (for levo, meaning left). In the structure illustrated in Figure, the amino group is always to the left side of the alpha carbon. The amino acids found in proteins have a common stereochemistry. The side chains that distinguish one amino acid from another are attached to the alpha carbon, so the structures are often written as shown in Figure, where R stands for one of the 20 side chains: In organic chemistry, the carbon directly attached to a carboxyl group is the alpha (α) position, so the amino acids in proteins are all alpha‐amino acids. These groups are joined to a single (aliphatic) carbon. Amino acids, as the name implies, have two functional groups, an amino group (–NH 2) and a carboxyl group (–COOH). The naturally occurring amino acids have a common structure.
Metabolism: A Collection of Linked Oxidation and Reduction Processes.Biosynthetic versus Catabolic Reactions.Chemical Mechanisms of Enzyme Catalysis.Physiological Conditions and Hemoglobin.Oxygen Binding by Myoglobin and Hemoglobin.Overview of Biological Information Flow.Water: Properties and Biomolecular Structure.United Strength of Biochemical Structures.
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