Protein Structure and Genetics Help (page 2)
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.
The linear sequence of amino acids forms the primary structure of proteins (Fig. 3-6).
Some portions of many proteins have a secondary structure in the form of an alpha helix in which the carbonyl group (C=O) next to one peptide bond forms a hydrogen bond with an imino group (NH) flanking a peptide bond a few amino acids further along the polypeptide chain. The protein chain may fold back upon itself, forming weak internal bonds (e.g., hydrogen bonds, ionic bonds) as well as strong covalent disulfide bonds that stabilize its tertiary structure into a precisely and often intricately folded pattern. Two or more tertiary structures may unite into a functional quaternary structure. For example, hemoglobin consists of four polypeptide chains (two identical α-chains and two identical β-chains). A protein cannot function until it has assumed its full tertiary or quaternary configuration. Any disturbance of its normal co nfiguration may inactivate the function of the protein. For example, if the protein is an enzyme, heating may destroy its catalytic activity because weak bonds that hold the protein in its secondary or higher structural forms are ruptured. The shape of an active enzyme molecule fits its substrate (the substance that is catalyzed by the enzyme) in a manner analogous to the way a key fits a lock (Fig. 3-7). An enzyme that is altered, either genetically (by mutation of the respective gene), physically (e.g., heat), or chemically (e.g., pH change) may not fit the substrate and therefore would be incapable of catalyzing the conversion of substrate to normal product.
Factors Governing Structural Levels
Relatively weak bonds such as hydrogen bonds and ionic bonds (attraction of positively and negatively charged ionic groups) are mainly responsible for the secondary and higher structural levels of protein organization. Enzymes are not involved in the formation of weak bonds. The extent to which a protein contains alpha-helical regions is dependent upon at least three factors. The most important factor governing tertiary protein structure involves formation of the most favorable energetic interactions between atomic groupings in the side chains of the amino acids. A second factor is the presence of proline, which cannot participate in alpha-helical formation because it is an imino acid rather a true amino acid. Proline is therefore often found at the "corners," or "hairpin turns," of polypeptide chains. Finally, the formation of intrastr and (on the same chain) disulfide bridges tends to distort the alpha helix.
Formation of Quaternary Structure
The ionized side chains of some amino acids readily interact with water and therefore are called hydrophilic ("water-loving") amino acids. Hydrophobic ("water-fearing") amino acids contain nonionized side chains that tend to avoid contact with water. When a polypeptide chain folds into its tertiary shape, these forces cause amino acids with hydrophilic groups to predominate on the outside and hydrophobic segments of the chain to predominate in the interior of globular proteins. The multiple polypeptide chains of quaternary proteins are usually joined by hydrophobic forces. Nonpolar groups of the individual polypeptide chains come together as a way of excluding water. Hydrogen bonds, ionic bonds, and possibly interstr and (between chains) disulfide bonds may also participate in forming quaternary protein structures. Some quaternary proteins consist of two or more identical polypeptide chains (e.g., the bacterial enzyme β-galactosidase consists of four identical polypep ide chains). Such proteins are called homopolymers.Other quaternary proteins (such as hemoglobin) consist of non-identical chains and are called heteropolymers. In order to become functional proteins, some polypeptide chains must be subject to modifications after they have been synthesized. For example, the protein chymotrypsinogen must be cleaved at one specific position by an enzyme to produce the active split-product chymotrypsin.
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