PART 1 Introduction
2.2. CELL CONSTRUCTION 1. Introduction
2.2.2. Amino Acids and Proteins
Proteins are the most abundant organic molecules in living cells, constituting 40% to 70%
of their dry weight. Proteins are polymers built from amino acid monomers. Proteins typi- cally have molecular weights of 6000 to several hundred thousand. The a-amino acids are the building blocks of proteins and contain at least one carboxyl group and one a-amino group, but they differ from each other in the structure of their R groups or side chains.
26 An Overview of Biological Basics Chap. 2
Although the sequence of amino acids determines a protein’s primarystructure, the secondaryand tertiarystructure are determined by the weak interactions among the vari- ous side groups. The ultimate three-dimensional structure is critical to the biological ac- tivity of the protein. Two major types of protein conformation are (1) fibrous proteins and (2) globular proteins. Figure 2.9 depicts examples of fibrous and globular proteins. Pro- teins have diverse biological functions, which can be classified in five major categories:
1. Structural proteins: glycoproteins, collagen, keratin 2. Catalytic proteins: enzymes
3. Transport proteins: hemoglobin, serum albumin
4. Regulatory proteins: hormones (insulin, growth hormone) 5. Protective proteins: antibodies, thrombin
The enzymes represent the largest class of proteins. Over 2000 different kinds of en- zymes are known. Enzymes are highly specific in their function and have extraordinary catalytic power. Each enzyme’s molecule contains an active siteto which its specific sub- strate is bound during catalysis. Some enzymes are regulated and are called regulatoryen- zymes. Most enzymes are globular proteins.
Figure 2.9. Fibrous and globular proteins. (With permission, from A. Lehninger, Bio- chemistry, 2d ed., Worth Publishing, New York, 1975, p. 61.)
The building blocks of proteins are a-amino acids, and there are 20 common amino acids. Amino acids are named on the basis of the side (R) group attached to the a-carbon.
Amino acids are optically active and occur in two isomeric forms.
28 An Overview of Biological Basics Chap. 2
Only L-amino acids are found in proteins. D-amino acids are rare in nature; they are found in the cell walls of some microorganisms and in some antibiotics.
Amino acids have acidic (—COOH) and basic (—NH2) groups. The acidic group is neutral at low pH (—COOH) and negatively charged at high pH (—COO-). At intermedi- ate pH values, an amino acid has positively and negatively charged groups, a dipolar mol- ecule called a zwitterion.
The pH value at which amino acids have no net charge is called the isoelectric point, which varies depending on the R group of amino acids. At its isoelectric point, an amino acid does not migrate under the influence of an electric field. Knowledge of the isoelectric point can be used in developing processes for protein purification. A list of 21 amino acids that are commonly found in proteins is given in Table 2.4.
The proteins are amino acid chains. The condensation reaction between two amino acids results in the formation of a peptide bond.
The peptide bond is planar. Peptides contain two or more amino acids linked by pep- tide bonds. Polypeptides usually contain fewer than 50 amino acids. Larger amino acid chains are called proteins. Many proteins contain organic and/or inorganic components other than amino acids. These components are called prosthetic groups, and the proteins containing prosthetic groups are named conjugated proteins. Hemoglobin is a conjugated protein and has four heme groups, which are iron-containing organometallic complexes.
(2.1)
TABLE 2.4 Chemical Structure of 21 Amino Acids of the General Structure
R Group Name Abbreviation Symbol Class
—H Glycine GLY G Aliphatic
—CH3 Alanine ALA A
—CH(CH3)2 Valine VAL V
—CH2CH(CH3)2 Leucine LEU L
—CHCH3CH2CH3 Isoleucine ILU I
—CH2OH Serine SER S Hydroxyl or sulfur containing
—CHOHCH3 Threonine THR T
—CH2SH Cysteine CYS C
—(CH2)2SCH3 Methionine MET M
—CH2COOH Aspartic acid ASP D Acids and corresponding amides
—CH2CONH2 Asparagine ASN N
—(CH2)2COOH Glutamic acid GLU E
—(CH2)2CONH2 Glutamine GLN Q
—(CH2)3CH2NH2 Lysine LYS K Basic
—(CH2)3NHCNHNH2 Arginine ARG R
Histidine HIS H
Phenylalanine PHE F Aromatic
Tyrosine TYR Y
Tryptophan TRP W
Proline PRO P Imino acid
—CH2—S—S—CH2— Cystine — Disulfide
The three-dimensional structure of proteins can be described at four different levels.
1. Primary structure:The primary structure of a protein is its linear sequence of amino acids. Each protein has not only a definite amino acid composition, but also a unique sequence. The one-dimensional structure of proteins (the amino acid sequence) has a profound effect on the resulting three-dimensional structure and, therefore, on the function of proteins.
2. Secondary structure: This is the way the polypeptide chain is extended and is a result of hydrogen bonding between residues not widely separated. Two major types of secondary structure are (a) helixes and (b) sheets. Helical structure can be either a-helical or triple helix. In an a-helical structure, hydrogen bonding can occur between the a-carboxyl group of one residue and the —NH group of its neighbor four units down the chain, as shown in Fig. 2.10. The triple-helix structure present in collagen consists of three a-helixes intertwined in a superhelix. Triple-helix structure is rigid and stretch resistant.
The a-helical structure can be easily disturbed, since H bonds are not highly stable. How- ever, the sheet structure (b-pleated sheet) is more stable. The hydrogen bonds between par- allel chains stabilize the sheet structure and provide resistance to stretching (Fig. 2.11).
3. Tertiary structure:This is a result of interactions between R groups widely sepa- rated along the chain. The folding or bending of an amino acid chain induced by interaction between R groups determines the tertiary structure of proteins. R groups may interact by covalent, disulfide, or hydrogen bonds. Hydrophobic and hydrophilic interac- tions may also be present among R groups. The disulfide bond can cross-link two polypeptide chains (for example, insulin). Disulfide bonds are also critical in proper chain folding, as shown in Fig. 2.12. The tertiary structure of a protein has a profound effect on its function.
4. Quaternary structure:Only proteins with more than one polypeptide chain have quaternary structure. Interactions among polypeptide chains determine the quaternary structure (Fig. 2.9). Hemoglobin has four subunits (oligomeric), and interaction among
30 An Overview of Biological Basics Chap. 2
Figure 2.10. The a-helical structure of fi- brous proteins.
these subunits results in a quaternary structure. The forces between polypeptide chains can be disulfide bonds or other weak interactions. The subunit structure of enzymes has an important role in the control of their catalytic activity.
Antibodiesor immunoglobulinsare proteins that bind to particular molecules or por- tions of large molecules with a high degree of specificity. Antibody (Ab) molecules ap- pear in the blood serum and in certain cells of a vertebrate in response to foreign macromolecules. The foreign macromolecule is called the antigen (Ag). The specific anti- body molecules can combine with the antigen to form an antigen–antibody complex. The complex formation between Ag and Ab is called the immune response. In addition to their obvious clinical importance, antibodies are important industrial products for use in diag- nostic kits and protein separation schemes. Antibodies may also become a key element in the delivery of some anticancer drugs. Antibodies have emerged as one of the most impor- tant products of biotechnology.
Antibody molecules have binding sites that are specific for and complementary to the structural features of the antigen. Antibody molecules usually have two binding sites and can form a three-dimensional lattice of alternating antigen and antibody molecules.
This complex precipitates from the serum and is called precipitin. Antibodies are highly specific for the foreign proteins that induce their formation.
Figure 2.11. Representation of an antiparallel b-pleated sheet. Dashed lines indicate hy- drogen bonds between strands.
Figure 2.12. Structure of the enzyme ribonuclease. (a) Primary amino acid sequence, showing how sulfur-sulfur bonds between cysteine residues cause folding of the chain. (b) The three-dimensional structure of ribonuclease, showing how the macromolecule folds so that a site of enzymatic activity is formed, the active site. (With permission, from T. D. Brock, K. M. Brock, and D. M. Ward, Basic Mi- crobiology with Applications, 3d ed., Pearson Education, Upper Saddle River, NJ, 1986, p. 56.)
The five major classes of immunoglobins in human blood plasma are: IgG, IgA, IgD, IgM, and IgE, of which the IgG globulins are the most abundant and the best under- stood. Molecular weights of immunoglobulins are about 150 kilodaltons (kD) except for IgM, which has a molecular weight of 900 kD. A daltonis a unit of mass equivalent to a hydrogen atom. Immunoglobulins have four polypeptide chains: two heavy (H) chains (about 430 amino acids) and two light (L) chains (about 214 amino acids). These chains are linked together by disulfide bonds into a Y-shaped, flexible structure (Fig. 2.13). The heavy chains contain a covalently bound oligosaccharide component. Each chain has a re- gion of constant amino acid sequence and a variable-sequence region. The Ab molecule has two binding sites for the antigen; the variable portions of the L and H chains
Figure 2.13. Structure of immunoglobulin G (IgG). Structure showing disulfide link- ages within and between chains and antigen binding site. (With permission, adapted from T. D. Brock, D. W. Smith, and M. T. Madigan, Biology of Microorganisms, 4th ed., Pear- son Education, Upper Saddle River, NJ, 1984, p. 524.)
contribute to these binding sites. The variable sections have hypervariable regions in which the frequency of amino acid replacement is high. The study of how cells develop and produce antibodies is being actively pursued worldwide. Recent developments have also led to insights on how to impart catalytic activities to antibodies. These molecules have been called abzymes. Coupling new developments in protein engineering to antibod- ies promises the development of extremely specific catalytic agents.