Protein Structure and Genetics Help
Proteins function in nearly every aspect of cellular life and there can be thousands (or tens of thousands) of different proteins in a single cell. Enzymes, which catalyze most chemical reactions within a cell, are made of protein chains. Some hormones, such as insulin, are also made of proteins. Other functions involving proteins are cell signaling, immune responses (e.g., antibodies), blood clotting factors, chromatin structure (e.g., histones), movement (e.g., molecular motors), cytoskeletal elements (e.g., tubulin), contractile proteins (e.g., myosin and actin of muscle fibers), extra cellular matrix (e.g., collagen), etc.
Knowledge of protein structure and bonding forces is essential for a keen understanding of how various genetic factors (mutations) and environmental factors (e.g., pH, temperature, salt concentrations, chemical treatments) can modify proteins and either reduce, destroy, or enhance their biological activities. Such knowledge is also important for developing techniques to extract functional proteins from genetically engineered cells.
Proteins are long polymers of amino acids, often referred to as "residues" (especially during degradation of proteins to ascertain their amino acid sequences), covalently held together by peptide bonds. Proteins are thus also referred to as polypeptides. Twenty different amino acids occur naturally in proteins. All completely ionized biological amino acids except proline have the general structure shown in Fig. 3-4. The α-carbon is the central atom to which an amino (NH3+) and a carboxyl (COO_) group are attached.
The Peptide Bond
The peptide bond that joins adjacent amino acids during protein synthesis is a strong covalent bond, in which atoms are coupled by sharing an electron. By the removal of water, the carboxyl group of one amino acid becomes joined to the amino group of an adjacent amino acid as shown in Fig. 3-5. This union, which is accompanied by the removal of water, is an example of dehydration synthesis. Each complete polypeptide chain thus has a free amino group at one end and a free carboxyl group at its other end. The amino end of the polypeptide corresponds to the 5' end of its respective mRNA. The carboxyl end of the polypeptide corresponds to the 3' terminus of the same mRNA. An enzymatic component of the ribosome, called peptidyl transferase, is responsible for peptide bond formation.
Each kind of amino acid differs according to the nature of the side chain or radical attached to the a-carbon. Glycine has the simplest side chain, consisting of a hydrogen atom. Other amino acids have hydrocarbon side chains of various lengths; some of these chains are ionized positively (basic proteins such as lysine and arginine), others are negatively charged (acidic amino acids such as aspartic and glutamic acids), and still others arenonionized (e.g., valine, leucine). Some amino acids, such as phenylalanine and tyrosine, have aromatics (ring structures) in their side chains. The amino acid proline does not contain a free imino group (NH) because its nitrogen atom is involved in a ring structure with its side chain. Only two amino acids (cysteine and methionine) contain sulfur in their side chains. The sulfurs of different cysteines can be covalently linked into a disulfide bond (S–S) that is responsible for helping to stabilize the tertiary and quaternary shapes of proteins containing them. Fig. 3-x shows the amino acids arranged by side chain type.
Table 3-1 shows amino acids and their three letter and single letter abbreviations.
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