Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin
of the previous amino acid. These amino acids in turn are attached to other amino acids by the same type of bond, making a chain. A short chain of amino acids is called an oligopeptide, and a long chain is called a polypeptide.
Figure 2.19 Two amino acids joined by a peptide bond. The bond connects the amino group on the second amino acid to the carboxyl group on the preceding amino acid. R is the side group of the amino acid that differs in each type of amino acid.
Like RNA and DNA, polypeptide chains have directionality and a way to distinguish the ends of the chain from each other. In polypeptides, the direction is defined by their amino and carboxyl groups. One end of the chain, the amino terminus, or N terminus, has an unattached amino group. The amino acid at this end is called the N-terminal amino acid. On the other end of the polypeptide, the final carboxyl group is called the carboxy terminus, or C terminus, and the amino acid is called the C-terminal amino acid. As we shall see, proteins are synthesized from the N terminus to the C terminus.
Protein structure terminology is the same as that for RNA structures. Proteins have primary, secondary, and tertiary structures, as well as quaternary structures. All of these are shown in Figure 2.20.
PRIMARY STRUCTURE
Primary structure refers to the sequence of amino acids and the length of a polypeptide. Because polypeptides are made up of 20 amino acids instead of just 4 nucleotides, as in RNA, many more primary structures are possible for polypeptides than for RNA chains. The sequence of amino acids in a polypeptide is dictated by the sequence of nucleotides in the mRNA used as the template for synthesis of that protein.
SECONDARY STRUCTURE
Also like RNA, polypeptides can have a secondary structure, in which parts of the chain are held together by hydrogen bonds. However, because many more types of interactions are possible between amino acids than between nucleotides, the secondary structure of a polypeptide is more difficult to predict. The two basic forms of secondary structures in polypeptides are α-helices, where a short region of the polypeptide chain forms a helix due to the interaction of each amino acid with the one before and the one after it, and β-sheets, in which stretches of amino acids interact with other stretches to form sheetlike structures (Figure 2.20). These types of structured regions are often joined together by more flexible regions known as linkers. Computer software is available to help predict which secondary structures of a polypeptide are possible on the basis of its primary structure. However, these programs are not entirely reliable, and techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy provide much more detailed information about the secondary structure of a polypeptide.
Figure 2.20 Primary, secondary, tertiary, and quaternary structures of proteins.
TERTIARY STRUCTURE
Polypeptides usually also have a well-defined tertiary structure, in which they fold up on themselves with hydrophobic amino acids (such as leucine and isoleucine), which are not very soluble in water, on the inside and charged amino acids (such as glutamate and lysine), which are more water soluble, or hydrophilic, on the outside. We discuss the structure of proteins in more detail in “Protein Folding and Degradation” below.
QUATERNARY STRUCTURE
Proteins made up of more than one polypeptide chain also have quaternary structure. Such proteins are called multimeric proteins. When the polypeptides are the same, the protein is a homomultimer. When they are different, the protein is a heteromultimer. Other names reflect the number of polypeptides in the protein. For example, the term homodimer describes a protein made of two identical polypeptides, whereas heterodimer describes a protein made of two different polypeptides. The names trimer, tetramer, and so on refer to increasing numbers of polypeptides. Hence, the ρ transcription termination factor is a homohexamer (see above).
The polypeptide chains in a protein are usually held together by hydrogen bonds. The only covalent chemical bonds in most proteins are the peptide bonds that link adjacent amino acids to form the polypeptide chains. As a result, if a multimeric protein is heated, it falls apart into its individual polypeptide chains. However, some proteins are unusually stable; these include extracellular enzymes, which must be able to function in the harsh environment outside the cell. Such proteins are often also held together by disulfide bonds between cysteine amino acids in the protein.
Translation
The translation of the sequence of nucleotides in mRNA into the sequence of amino acids in a protein occurs on the ribosome. The overall process of translation is highly conserved in bacteria, archaea, and eukaryotes, and the machinery is also highly conserved. As mentioned in “rRNAs and tRNAs” above, the ribosome is one of the largest and most complicated structures in cells, consisting of three different RNAs and over 50 different proteins in bacteria. It is also one of the major constituents of the bacterial cell, and much of the biosynthetic capacity of the cell goes into making ribosomes. Each cell contains thousands of ribosomes, with the actual number depending on the growth conditions. It is also one of the most evolutionarily highly conserved structures in cells, having remained largely unchanged in shape and structure from bacteria to humans. The key role of protein synthesis in the cell has led to the development of important antibiotics that target the translational machinery (Box 2.3).
The ribosome is an enormous enzyme that performs the complicated role of polymerizing amino acids into polypeptide chains, using the information in mRNA as a guide. As such, a better name for it might have been protein polymerase, by analogy to DNA and RNA polymerases. The historical name “ribosome” was coined before its function was known, because it is large enough to have been visualized under the electron microscope and so it was called a “some” (for body) and “ribosome” because it contains ribonucleotides. The recent determination of the structure of the ribosome (see below) has led to important insights into how it performs its function of polymerizing amino acids.
Structure of the Bacterial Ribosome
Figure 2.21 shows the components of a bacterial ribosome. The complete ribosome, called the 70S ribosome in bacteria, consists of two subunits, the 30S subunit, which contains one molecule of 16S rRNA, and the 50S subunit, which contains one molecule each of 23S and 5S rRNA. Each subunit also contains ribosomal proteins; the 30S subunit contains approximately 21 different proteins (S1, S2, etc., where S indicates small subunit proteins), while the 50S subunit contains approximately 31 different proteins (L1, L2, etc., where L indicates large subunit proteins). Ribosomes from different bacterial species have very similar compositions, with small differences in the number of ribosomal proteins. Like the names for the different types of rRNA, the names of ribosomal subunits are derived from their sedimentation rates during ultracentrifugation. The 30S and 50S subunits normally exist separately