Chapter Seven: Microbial Genetics

Microbial Genetics: Structure and Replication of Genomes

Genetics and Genomes

Genetics is the study of inheritance and inheritable traits as expressed in an organism’s genetic material. The genome is the entire genetic complement of an organism, including its genes and nucleotide sequences.

• Genetics: Focuses on how traits are passed from one generation to the next.

• Genome: All the DNA (or RNA in some viruses) present in a cell or organism.

Structure of Nucleic Acids

Nucleic acids are polymers of nucleotides, each consisting of a phosphate group, a pentose sugar, and a nitrogenous base. The length of DNA is expressed in base pairs (bp).

• Nucleotide: The basic building block of nucleic acids.

• Base Pairing: In DNA, adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).

Prokaryotic Genomes

Prokaryotic genomes are typically composed of a single, circular chromosome located in the nucleoid. Prokaryotic cells are haploid, meaning they have a single chromosome copy. In addition to chromosomes, prokaryotes often contain plasmids—small, circular DNA molecules that replicate independently and can confer survival advantages.

• Chromosome: Main DNA molecule containing essential genes.

• Plasmids: Non-essential DNA elements that may carry genes for antibiotic resistance, virulence, or metabolism.

Note: Plasmids are 1% to 20% the size of a chromosome.

Eukaryotic Genomes

Eukaryotic genomes are more complex, typically consisting of multiple linear chromosomes located within the nucleus. Eukaryotic cells are often diploid (two chromosome copies). DNA is tightly packaged with histone proteins into chromatin and further into chromosomes. Eukaryotes also have extranuclear DNA in mitochondria and chloroplasts, which resemble prokaryotic chromosomes.

• Nuclear Chromosomes: Linear, multiple, and sequestered within the nucleus.

• Extranuclear DNA: Found in mitochondria and chloroplasts; codes for a small fraction of cellular proteins.

Comparison of Microbial Genomes

The following table summarizes key differences among bacterial, archaeal, and eukaryotic genomes:

	Bacteria	Archaea	Eukarya
Number of Chromosomes	Single (haploid) copies of one or more	One (haploid)	Two or more, typically diploid
Plasmids Present?	In some cells; frequently more than one per cell	In some cells	In some fungi, algae, and protozoa
Type of Nucleic Acid	Circular or linear dsDNA	Circular dsDNA	Linear dsDNA in nucleus and chloroplasts; circular dsDNA in mitochondria and plasmids
Location of DNA	In nucleoid of cytoplasm and in plasmids	In nucleoid of cytoplasm and in plasmids	In nucleus and in mitochondria, chloroplasts, and plasmids in cytosol
Histones Present?	No, though chromosome is associated with a small amount of nonhistone protein	Yes	Yes, in nuclear chromosomes; not in extranuclear chromosomes

DNA Replication

Semiconservative Replication

DNA replication is semiconservative, meaning each new DNA molecule consists of one original (parental) strand and one newly synthesized (daughter) strand. The process relies on the complementary base pairing of nucleotides.

• Key Enzymes: DNA helicase, DNA polymerase, primase, ligase, gyrase, and topoisomerase.

• Directionality: DNA polymerase synthesizes new DNA only in the 5′ to 3′ direction.

DNA Replication in Prokaryotes

Replication begins at a single origin and proceeds bidirectionally. The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously in Okazaki fragments. DNA ligase joins these fragments.

• Leading Strand: Synthesized continuously toward the replication fork.

• Lagging Strand: Synthesized discontinuously away from the fork in short Okazaki fragments.

• Primase: Synthesizes RNA primers to provide a 3′ end for DNA polymerase.

• DNA Ligase: Seals gaps between Okazaki fragments.

DNA Replication in Eukaryotes

Eukaryotic DNA replication is similar to that in prokaryotes but involves multiple origins of replication, four types of DNA polymerases, and shorter Okazaki fragments. Plant and animal cells methylate only cytosine bases, and no gyrases are present.

Gene Function: From Genotype to Phenotype

Genotype vs. Phenotype

The genotype is the set of genes in the genome, while the phenotype refers to the physical features and functional traits of the organism. The flow of genetic information follows the central dogma: DNA is transcribed into RNA, which is then translated into polypeptides (proteins).

Transcription: Synthesis of RNA

Transcription is the process by which information in DNA is copied into RNA. In prokaryotes, this occurs in the nucleoid; in eukaryotes, it occurs in the nucleus, mitochondria, and chloroplasts. There are three main steps: initiation, elongation, and termination.

• Types of RNA: mRNA, rRNA, tRNA, RNA primers, regulatory RNA, ribozymes.

• Initiation: RNA polymerase binds to the promoter region.

• Elongation: RNA polymerase synthesizes RNA in the 5′ to 3′ direction.

• Termination: Transcription ends when RNA polymerase reaches a terminator sequence.

Transcriptional Differences in Eukaryotes

In eukaryotes, transcription involves three types of nuclear RNA polymerases and numerous transcription factors. mRNA is processed before translation through capping, polyadenylation, and splicing to remove introns.

Translation: Protein Synthesis

Translation is the process by which ribosomes use the genetic information in mRNA to synthesize polypeptides. The process involves mRNA, tRNA, and ribosomes, and occurs in three stages: initiation, elongation, and termination.

• Genetic Code: Triplet codons in mRNA specify amino acids.

• tRNA: Brings amino acids to the ribosome and matches them to the mRNA codon via its anticodon.

• Ribosomes: Facilitate the binding of tRNA and catalyze peptide bond formation.

Regulation of Genetic Expression

Not all genes are expressed at all times. Regulation allows cells to conserve energy by expressing genes only when needed. Regulation can occur at the level of transcription or translation.

• Operon: A group of genes regulated together and transcribed into a single mRNA molecule. The operon's "on" or "off" switch allows cells to respond to environmental changes.

• Inducible Operons: Activated by inducers (e.g., lactose operon for lactose catabolism).

• Repressible Operons: Transcribed continually until deactivated by repressors (e.g., tryptophan operon for tryptophan synthesis).

Mutation of Genes

A mutation is a change in the nucleotide base sequence of a genome. Mutations are rare and usually deleterious, but occasionally they can improve an organism's survival.

• Point Mutations: Affect a single base pair (substitutions, insertions, deletions).

• Frameshift Mutations: Insertions or deletions that shift the reading frame.

• Gross Mutations: Include inversions, duplications, and transpositions.

• Mutagens: Physical or chemical agents that increase mutation rates (e.g., radiation, nucleotide analogs).

Horizontal Gene Transfer in Prokaryotes

Horizontal gene transfer is the movement of genetic material between organisms other than by descent. It is a major source of genetic diversity in prokaryotes.

• Transformation: Uptake of naked DNA from the environment by competent cells.

• Transduction: Transfer of DNA by bacteriophages (not detailed in the provided content).

• Conjugation: Transfer of DNA through direct cell-to-cell contact, often involving plasmids.

Example: The transformation of Streptococcus pneumoniae provided conclusive proof that DNA is the genetic material.

Additional info: Transduction and other mechanisms of horizontal gene transfer are also important in microbial evolution but were not detailed in the provided content.