Proteins and amino acids

Category: Cellular biology

Proteins are the most complex and abundant of the macromolecules. Within cells, many proteins function as enzymes in the catalysis of metabolic reactions, while others serve as transport molecules, storage proteins, electron carriers, and structural components of the cell. They are especially important in seeds, where they make up as much as 40 percent of the seed’s weight and serve to store amino acids for the developing embryo. Proteins are also important structural components of the cell wall. Because proteins and their building blocks, amino acids, form such a large component of plant life, plants serve as an important dietary source of the eight to ten essential amino acids for humans and other animals.

Amino Acids

Amino acids are the molecular building blocks of proteins. Amino acids all share a structure, with a central carbon atom, the alpha carbon, covalently bonded to a hydrogen atom, an amino group, a carboxylic acid group, and a group designated as an R group, which varies in structure from amino acid to amino acid. It is the diverse nature of the R group that provides the protein with many of its structural and functional characteristics. Some R groups are either polar or electrically charged at physiological pH, making the R groups hydrophilic (water-loving). Other R groups are nonpolar and hydrophobic (water-avoiding). The twenty standard amino acids the cell uses to synthesize its proteins are alanine, arginine, aspartate (aspartic acid), asparagine, cysteine, glutamate (glutamic acid), glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine.

Each of the twenty amino acids differs from the other nineteen in the structure of its R group. Once incorporated into a protein, a standard amino acid may undergo modification to create nonstandard amino acids and an even greater diversity of protein structures. One of the more common nonstandard amino acids found in proteins is hydroxyproline, which is commonly found in plant cell-wall proteins. In addition to the twenty amino acids that build proteins, many nonstandard amino acids occur free in the cell and are not found in proteins. Canavanine, for example, occurs in the seeds of many legumes.

Based on the information in cellular deoxyribonucleic acid (DNA), the cell joins the twenty standard amino acids by peptide bonds in specific sequences, resulting in chains ranging from as few as two amino acids to many thousands. Shorter chains of amino acids are referred to as peptides or oligopeptides, while longer chains are referred to as polypeptides. The term “protein” is usually reserved for those oligopeptides and polypeptides that have biological functions, because single polypeptides often do not have biological functions unless associated with other polypeptides.

Primary Structure

Proteins differ from one another in the sequences of their amino acids. The sequence of amino acids of a protein is called its primary structure. Mutations have been shown to result in the change of as few as one amino acid in a protein. Because DNA specifies a protein’s primary structure, protein sequence information is often used to study the evolutionary relationships among organisms.

Proteins are often complexed with other compounds in their biologically active state. These proteins are called conjugated proteins. Proteins complexed with metals, lipids, sugars, and riboflavin are called metalloproteins, lipoproteins, glycoproteins, and flavoproteins, respectively. Glycoproteins (literally, “sugar proteins”) are important constituents of the plasma membrane. These sugar molecules can occur singly or in short, simple branched chains.

A protein chain may be folded into a variety of three-dimensional shapes. The three-dimensional shape a protein assumes is called its conformation and is determined by its amino acid sequence. In order for a protein to be active, it must assume a certain conformation. Any alteration in its conformation may result in reduced activity. Denaturing agents alter the structure of a protein so that it loses its conformation, biological function, and activity.

Secondary Structure

The secondary structure refers to the local folding or conformation of the polypeptide chain over relatively short (fifty amino acids or so) stretches. Two common secondary structures, the alpha helix and the beta sheet, occur regularly in proteins. On average, only about half of the polypeptide chain assumes the alpha or beta conformation, while the remainder exists in turns and random structures. Some proteins show only alpha structure, others only the beta structure, while still others show either a mixture of the two structures or neither secondary structure. Both the alpha and the beta structures increase the structural stability of the protein. The amino acid sequence determines whether a particular sequence of amino acids in a protein will assume the alpha or beta structure.

Tertiary Structure

The overall spatial orientation of the entire polypeptide chain in space is referred to as its tertiary structure. Generally, two tertiary structures are recognized. Fibrous or filamentous proteins are arranged as fibers or sheets, while globular proteins are arranged roughly as spherical or globular structures. The amino acid sequence determines the overall folding of the protein tertiary structure. Fibrous proteins are primarily involved with structural functions, whereas globular proteins function as enzymes, transport molecules, electron carriers, and regulatory proteins.

Quaternary Structure

Some proteins are composed of more than one polypeptide chain. A protein composed of only one polypeptide is called a monomer, while proteins composed of two, three, four, and so on are referred to as dimers, trimers, and tetramers, and so on, respectively.

Bibliography

Dey, P. M., and J. B. Harborne, eds. Plant Biochemistry. San Diego: Academic Press, 1997. Describes various topics in plant biochemistry, each covered by a different specialist. Illustrated and referenced, the text emphasizes plant metabolism but also includes enzymes, functions, regulation, and molecular biology.

Mathews, Christopher K., K. E. Van Holde, and Kevin G. Ahern. Biochemistry. 3d ed. New York: Addison Wesley Longman, 2000. Covers all aspects of biochemistry for the advanced student. Profusely illustrated and referenced.

Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 3d ed. New York: Worth, 2000. Covers general biochemistry, from structures to metabolism. Excellently illustrated and referenced. Comes with a CD of art and animations.

Zubay, Geoffrey L. Biochemistry. 4th ed. Boston: Wm. C. Brown, 1998. General, advanced biochemistry text has especially good coverage of proteins. Includes illustrations and references and comes with a CD of art and animations.