For all living entities, hereditary information resides or is encoded in nucleic acids. The two major classes include deoxyribonucleic acid (DNA), which is the most common macromolecule that encodes genetic information, and ribonucleic acid (RNA). In some forms, RNA encodes genetic information for various viruses; in other forms, RNA plays an essential role in several of the genetic processes to be discussed.
DNA consists of deoxyribose sugars connected by phosphodiester bonds (Figure 2-2, A). The bases that are covalently linked to each deoxyribose sugar are the key to the genetic code within the DNA molecule. The four bases include two purines, adenine (A) and guanine (G), and the two pyrimidines, cytosine (C) and thymine (T) (Figure 2-3). In RNA, uracil replaces thymine. Taken together, the sugar, the phosphate, and a base form a single unit referred to as a nucleotide. DNA and RNA are nucleotide polymers (i.e„ chains or strands), and the order of bases along a DNA or RNA strand is known as the base sequence. This sequence provides the information that specifies the proteins that will be synthesized by microbial cells (i.e., the sequence is the genetic code).
The intact DNA molecule usually is composed of two nucleotide polymers. Each strand has a 5' and a 3' hydroxyl terminus (see Figure 2-2, B). The two strands run antiparallel, with the 5' terminus of one strand opposed to the 3' terminal of the other. The strands are also complementary as the adenine base of one strand always binds, via two hydrogen bonds, to the thymine base of the other strand, or vice versa. Likewise, the guanine base of one strand always binds by three hydrogen
Energy and nutrients
Assembly of cell structure
Motion and other responses to environment
Figure 2-1 General overview of bacterial life processes.
bonds to the cytosine base of the other strand, or vice versa. The molecular restrictions of these base pairings, along with the conformation of the sugar-phosphate backbones oriented in antiparallel fashion, result in DNA having the unique structural conformation often referred to as a "twisted ladder" (see Figure 2-2, B). Additionally, the dedicated base pairs provide the format essential for consistent replication and expression of the genetic code. In contrast to DNA, RNA rarely exists as a double-stranded molecule and, whereas DNA carries the genetic code, the three major types of RNA (messenger RNA [mRNA], transfer RNA [tRNA], and ribosomal RNA [rRNA]) play other key roles in gene expression.
A DNA sequence that encodes for a specific product (RNA or protein) is defined as a gene. Thousands of genes within an organism encode messages or blueprints for production, by gene expression, of specific protein and RNA products that play essential metabolic roles in the cell. All genes taken together within an organism comprise that organism's genome. The size of a gene and an entire genome is usually expressed in the number of base pairs (bp) present (e.g., kilobases [103 bases], megabases [106 bases]).
Certain genes are widely distributed among various organisms while others are limited to particular species. Also, the base pair sequence for individual genes may be highly conserved (i.e., show limited sequence differences among different organisms) or be widely variable, As discussed in Chapter 8, these similarities and differences in gene content and sequences are the basis for the development of molecular tests used to detect, identify, and characterize clinically relevant microorganisms.
The genome is organized into discrete elements known as chromosomes. The set of genes within a given chromosome is arranged in a linear fashion, but the number of genes per chromosome is variable. Similarly, although the number of chromosomes per cell is consistent for a given species, this number varies considerably among species. For example, human cells contain 23 pairs (i.e., diploid) of chromosomes whereas bacteria contain a single, unpaired (i.e., haploid) chromosome.
The bacterial chromosome contains all genes essential for viability and exists as a double-stranded, closed circular, naked (i.e., not enclosed within a membrane) macromolecule. The molecule is extensively folded and twisted (i.e., supercoiled) so that it may be accommodated within the confines of the bacterial cell. The fact that the linearized, unsupercoiled chromosome of the bacterium Escherichia coli is about 1300 |im in length but fits within a 1 \tm x 3 |im cell attests to the extreme compactness that the bacterial chromosome must achieve. For genes within the compacted chromosome to be expressed and replicated, unwinding or relaxation of the molecule is essential.
In contrast to the bacterial chromosome, the chromosomes of parasites and fungi number greater than one per cell, are linear, and are housed within a membrane structure known as the nucleus. This difference is a major criterion for classifying bacteria as prokaryotic organisms, while classifying fungi and parasites as eukaryotes. The genome of viruses may be referred to as a chromosome, but the DNA (or RNA) is contained within a protein coat rather than within a cell.
Although the bacterial chromosome represents the majority of the genome, not all genes within a given cell are confined to the chromosome. Many genes are also located on plasmids and transposable elements. Both of these are able to replicate and encode information for the production of various cellular products. Although considered part of the bacterial genome, they are not as stable as the chromosome and may be lost during cellular replication, often without severe detrimental effects on the cell.
Plasmids exist as "miniature'' chromosomes in being double-stranded, closed, circular structures with size ranges from 1 to 2 kilobases up to 1 megabase or more. The number of plasmids per bacterial cell varies extensively, and each plasmid is composed of several genes. Some genes encode products that mediate plasmid replication and transfer between bacterial cells, whereas others encode products that provide a survival edge such as determinants of antimicrobial
Deoxyribose 3' sugar
Deoxyribose 3' sugar
Base-pair Base v \l
Figure 2-2 A, Molecular structure of DNA showing nucleotide structure, phosphodiester bond connecting nucleotides, and complementary pairing of bases (A, adenine; T, thymine; G, guanine; C, cytosine) between antiparallel nucleic acid strands. B, 5' and 3' antiparallel polarity and helical ("twisted ladder") configuration of DNA.
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