Microbial Genetics

Introduction to 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.

The 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). The structure of DNA allows for the storage and transmission of genetic information.

• DNA contains the bases adenine (A), thymine (T), guanine (G), and cytosine (C).

• RNA contains uracil (U) instead of thymine.

• Base pairing: A pairs with T (or U in RNA), and G pairs with C.

The Structure of Prokaryotic Genomes

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

• Types of plasmids: Fertility plasmids, resistance plasmids, bacteriocin plasmids, and virulence plasmids.

The Structure of Eukaryotic Genomes

Eukaryotic cells usually have multiple, linear chromosomes sequestered within a nucleus and are often diploid (two chromosome copies). Eukaryotes also possess extranuclear DNA in mitochondria and chloroplasts, which resemble prokaryotic chromosomes and code for a small fraction of cellular proteins.

DNA Replication

DNA replication is the process by which a cell duplicates its DNA, ensuring genetic information is passed to daughter cells. Replication is semiconservative: each new DNA molecule consists of one original and one newly synthesized strand.

• Replication requires triphosphate deoxyribonucleotides for both monomers and energy.

• In bacteria, replication begins at the origin and proceeds bidirectionally.

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

• The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously in Okazaki fragments.

Other features include the removal of supercoils by gyrases and topoisomerases, and methylation of DNA for gene regulation, replication initiation, protection, and repair.

In eukaryotes, replication involves multiple DNA polymerases, thousands of origins, and shorter Okazaki fragments.

Gene Function

Genotype and Phenotype

The genotype is the set of genes in the genome, while the phenotype refers to the physical and functional traits expressed by the organism.

The Central Dogma: Transcription and Translation

Genetic information flows from DNA to RNA (transcription) and from RNA to protein (translation). This is known as the central dogma of genetics.

• Transcription: DNA is used as a template to synthesize RNA.

• Translation: Ribosomes use mRNA to synthesize polypeptides.

Transcription in Prokaryotes and Eukaryotes

Transcription involves three main steps: initiation, elongation, and termination. In prokaryotes, it occurs in the nucleoid; in eukaryotes, it occurs in the nucleus, mitochondria, and chloroplasts. Eukaryotic mRNA undergoes additional processing: capping, polyadenylation, and splicing.

Translation: Synthesis of Polypeptides

Translation is the process by which ribosomes synthesize polypeptides using the genetic code carried by mRNA. Key participants include mRNA, tRNA, and ribosomes. Translation occurs in three stages: initiation, elongation, and termination, requiring protein factors and energy (GTP).

In eukaryotes, translation initiation involves the 5′ guanine cap, and the first amino acid is methionine (not f-methionine as in prokaryotes).

Regulation of Genetic Expression

Gene Regulation in Prokaryotes

Most genes are expressed continuously, but some are regulated to conserve energy. Regulation often occurs at the transcriptional level, frequently through operons—clusters of genes under the control of a single promoter and operator.

• Inducible operons (e.g., lac operon): Activated by inducers, regulate catabolic pathways.

• Repressible operons (e.g., trp operon): Deactivated by repressors, regulate anabolic pathways.

Regulatory RNAs (e.g., microRNAs, siRNAs, riboswitches) can also control translation by binding to mRNA and affecting its stability or translation efficiency.

Mutations of Genes

Types and Effects of Mutations

A mutation is a change in the nucleotide sequence of a genome. Most mutations are deleterious, but some may confer advantages. Types include:

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

• Gross mutations: Involve larger changes (inversions, duplications, transpositions).

Mutagens and DNA Repair

Mutagens such as radiation (ionizing, nonionizing) and chemicals (nucleotide analogs, nucleotide-altering chemicals, frameshift mutagens) increase mutation rates. Cells possess several DNA repair mechanisms: direct repair, single-strand repair, and error-prone repair (last resort, may introduce mutations).

Identifying Mutants, Mutagens, and Carcinogens

Mutants are cells with uncorrected mutations. Methods to identify mutants include positive selection, negative (indirect) selection, and the Ames test (for mutagenicity and carcinogenicity).

Genetic Recombination and Transfer

Genetic Recombination

Genetic recombination involves the exchange of nucleotide sequences between homologous DNA molecules, resulting in recombinants with new genetic combinations.

Horizontal Gene Transfer in Prokaryotes

Horizontal gene transfer allows prokaryotes to acquire genetic material from other cells, contributing to genetic diversity. Main mechanisms include:

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

• Transduction: Transfer of DNA via bacteriophages (generalized or specialized).

• Conjugation: Direct transfer of DNA through cell-to-cell contact, often involving plasmids.

Transposons and Transposition

Transposons are DNA segments that can move from one location to another within a genome, causing mutations and genetic rearrangements. They may be simple (insertion sequences) or complex (carrying additional genes).

Additional info: This guide covers the core concepts of microbial genetics, including genome structure, gene expression, mutation, and genetic exchange, as relevant to college-level microbiology.