i/1Microbial Genetics

Genetics and Genomes

The study of microbial genetics focuses on the inheritance and expression of traits encoded in an organism’s genetic material. The genome is the complete set of genetic information, including genes and nucleotide sequences, found within an organism.

• Genetics: The science of inheritance and inheritable traits.

• Genome: All genetic material in an organism, including genes and non-coding sequences.

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 measured in base pairs.

• Nucleotide: Basic unit of nucleic acids; composed of phosphate, sugar, and base.

• Base Pairing: Adenine pairs with Thymine (DNA) or Uracil (RNA); Guanine pairs with Cytosine.

Prokaryotic Genomes

Prokaryotes typically possess a single, circular chromosome located in the nucleoid. They are haploid, meaning they have one chromosome copy. Plasmids are small, independently replicating DNA molecules that can confer survival advantages.

• Chromosome: Main DNA molecule, circular in prokaryotes.

• Plasmids: Non-essential DNA molecules; types include fertility, resistance, bacteriocin, and virulence plasmids.

Eukaryotic Genomes

Eukaryotes have multiple, linear chromosomes sequestered within the nucleus and are often diploid. Extranuclear chromosomes are found in mitochondria and chloroplasts, resembling prokaryotic chromosomes.

• Nuclear Chromosomes: Linear, multiple per cell, located in nucleus.

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

Comparison of Microbial Genomes

The following table summarizes key differences among Bacteria, Archaea, and Eukarya:

DNA Replication

DNA replication is a semiconservative process, meaning each new DNA molecule contains one original and one daughter strand. The complementary structure of DNA strands is key to accurate replication. Triphosphate deoxyribonucleotides provide both monomers and energy for synthesis.

• Semiconservative Replication: Each daughter DNA has one original strand.

• Energy Source: Triphosphate nucleotides.

Mechanism of DNA Replication

Replication begins at the origin. DNA polymerase synthesizes new DNA in the 5′ to 3′ direction. The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously.

• Leading Strand: Continuous synthesis.

• Lagging Strand: Discontinuous synthesis (Okazaki fragments).

Bidirectional Replication and DNA Methylation

Bacterial DNA replication is bidirectional. Enzymes such as gyrases and topoisomerases remove supercoils. DNA methylation plays roles in gene expression, replication initiation, protection against viral infection, and DNA repair.

Differences in Eukaryotic DNA Replication

Eukaryotic DNA replication uses four DNA polymerases, has thousands of origins, and produces shorter Okazaki fragments. Only cytosine bases are methylated in plant and animal cells.

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.

Central Dogma of Genetics

Genetic information flows from DNA to RNA (transcription) and from RNA to polypeptides (translation).

• Transcription: DNA is copied as RNA.

• Translation: Polypeptides are synthesized from RNA.

Transcription: Process and Types of RNA

Transcription occurs in three steps: initiation, elongation, and termination. Six types of RNA are transcribed: RNA primers, mRNA, rRNA, tRNA, regulatory RNA, and ribozymes.

Transcriptional Differences in Eukaryotes

In eukaryotes, transcription occurs in the nucleus, mitochondria, and chloroplasts. mRNA is processed before translation through capping, polyadenylation, and splicing.

Translation and the Genetic Code

Translation is the process by which ribosomes use mRNA sequences to synthesize polypeptides. The genetic code specifies which codons correspond to which amino acids.

Participants in Translation

• Messenger RNA (mRNA): Carries genetic information.

• Transfer RNA (tRNA): Brings amino acids to ribosome.

• Ribosomes: Site of protein synthesis; composed of rRNA and polypeptides.

Stages of Translation

Translation occurs in three stages: initiation, elongation, and termination. Each stage requires protein factors and energy (GTP).

Translation Differences in Eukaryotes

• Initiation begins at the 5′ guanine cap.

• First amino acid is methionine (not f-methionine).

• Ribosomes can synthesize polypeptides into the rough endoplasmic reticulum.

Comparison of Genetic Processes

Regulation of Genetic Expression

Gene expression is regulated to conserve energy. Most genes are always expressed, but others are transcribed and translated only when needed. Regulation typically halts transcription or translation.

Prokaryotic Operons

An operon consists of a promoter, operator, and a series of genes. Operons are controlled by regulatory elements and can be inducible or repressible.

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

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

Roles of Operons in Regulation

RNA Regulation of Translation

• microRNAs (miRNAs): Bind mRNA and inhibit translation.

• Small interfering RNA (siRNA): Binds and inactivates target RNA.

• Riboswitch: RNA molecule that changes shape to regulate translation.

Mutations of Genes

Mutation Types and Effects

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

• Point Mutations: Affect one base pair; include substitutions and frameshift mutations.

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

Mutagens

Mutagens are agents that increase mutation rates, including radiation (ionizing and nonionizing) and chemicals (nucleotide analogs, nucleotide-altering chemicals, frameshift mutagens).

DNA Repair Mechanisms

Cells employ direct repair, single-strand repair, and error-prone repair mechanisms to fix DNA damage. Error-prone repair is a last resort, such as the SOS response in E. coli.

Identifying Mutants, Mutagens, and Carcinogens

• Mutants: Descendants of cells with unrepaired mutations.

• Wild-type: Cells normally found in nature.

• Methods: Positive selection, negative (indirect) selection, Ames test.

Genetic Recombination and Transfer

Genetic Recombination

Exchange of nucleotide sequences between homologous DNA regions produces recombinants—cells with new DNA sequences.

Horizontal Gene Transfer in Prokaryotes

Horizontal gene transfer involves the movement of genetic material between cells, not from parent to offspring. Three mechanisms are transformation, transduction, and conjugation.

• Transformation: Uptake of free DNA by competent cells.

• Transduction: Transfer of DNA via bacteriophage; can be generalized or specialized.

• Conjugation: Transfer of DNA through direct cell-to-cell contact; donor cell remains alive.

Transposons and Transposition

Transposons are DNA segments that move within or between DNA molecules, causing frameshift insertions. Insertion sequences are the simplest transposons, while complex transposons carry additional genes.

Summary

This study guide covers the structure, replication, and expression of microbial genomes, including the mechanisms of gene regulation, mutation, and genetic recombination. Understanding these processes is fundamental to microbiology and the study of microbial diseases.