Microbial Genetics: Structure, Function, and Regulation

Microbial Genetics

Genome, Genes, Genotype, and Phenotype

The genome is the complete set of genetic material in an organism, including chromosomes and plasmids. A gene is a segment of DNA that encodes a functional product, usually a protein. The genotype refers to the genetic makeup of an organism, while the phenotype is the observable characteristics resulting from gene expression.

• Genome: All genetic material (chromosomes, plasmids, organelle DNA)

• Gene: DNA segment coding for a product

• Genotype: DNA sequence of an organism

• Phenotype: Physical and biochemical traits

Structure of Prokaryotic Genomes

Prokaryotic cells are typically haploid, possessing a single, circular chromosome located in the nucleoid. Chromosomes are looped, folded, and supercoiled to fit within the cell. Plasmids are small, circular DNA molecules that replicate independently and often carry useful traits such as antibiotic resistance.

• Chromosome: Circular, supercoiled DNA

• Plasmid: Small, circular DNA, not essential for survival

Locations and Forms of Genome in Cells and Viruses

The genome can be found in different locations depending on the organism. In eukaryotes, it is mainly in chromosomes, but also in mitochondria and chloroplasts. In bacteria, it is in the chromosome and plasmids. Viruses may have DNA or RNA genomes.

• Eukaryotes: Chromosomes, mitochondria, chloroplasts

• Bacteria: Chromosome, plasmids

• Viruses: DNA or RNA

DNA Structure and Base Pairing

DNA is composed of nucleotides, each containing a phosphate group, deoxyribose sugar, and a nitrogenous base. The backbone is formed by sugar-phosphate linkages. Base pairing occurs via hydrogen bonds: Adenine (A) pairs with Thymine (T), and Guanine (G) pairs with Cytosine (C).

• Nucleotide: Phosphate, deoxyribose, nitrogenous base

• Base pairs: A-T, G-C

• Antiparallel strands: Strands run in opposite directions

The Flow of Genetic Information: Central Dogma

Genetic information flows from DNA to RNA to protein. DNA replication duplicates the DNA. Transcription copies DNA into RNA. Translation interprets RNA to synthesize proteins.

• Replication: DNA → DNA

• Transcription: DNA → RNA

• Translation: RNA → Protein

Bacterial DNA Replication

Bacterial chromosome replication is semiconservative and bidirectional. At completion, two identical daughter chromosomes are produced. Key enzymes include DNA polymerase, helicase, primase, and topoisomerase. Replication is highly accurate.

• Semiconservative: Each new DNA has one old and one new strand

• Bidirectional: Replication proceeds in both directions

• Topoisomerase: Separates completed chromosomes

Relationship Among DNA, RNA, and Proteins

DNA encodes genes, which are transcribed into RNA. RNA is translated into proteins, which perform cellular functions. This process is known as the central dogma of molecular biology.

• DNA: Genetic blueprint

• RNA: Messenger and functional molecules

• Protein: Functional products

Transcription and Translation: Prokaryotes vs. Eukaryotes

In prokaryotes, transcription and translation occur simultaneously in the cytoplasm. In eukaryotes, transcription occurs in the nucleus, and translation in the cytoplasm. Eukaryotic genes contain introns (noncoding regions) that are spliced out.

• Prokaryotes: Simultaneous transcription and translation

• Eukaryotes: Transcription in nucleus, translation in cytoplasm; introns and exons

Genetic Recombination and Horizontal Gene Transfer

Genetic recombination involves the exchange of DNA between organisms, resulting in new gene combinations. Horizontal gene transfer allows bacteria to acquire genes from other cells, not just from parent organisms. Three main mechanisms are transformation, conjugation, and transduction.

• Transformation: Uptake of naked DNA

• Conjugation: DNA transfer via pilus between cells

• Transduction: DNA transfer via bacteriophage

Mechanisms of Horizontal Gene Transfer

Transformation

Transformation is the uptake of free DNA from the environment by a competent recipient cell. No direct contact is required.

Conjugation

Conjugation requires direct contact between donor and recipient cells via a pilus. The F plasmid encodes the pilus.

Transduction

Transduction involves the transfer of DNA from one bacterium to another via a bacteriophage. The phage injects DNA, which may integrate into the bacterial chromosome (lysogenic cycle) or cause cell lysis (lytic cycle).

Types of Horizontal Gene Transfer in Bacteria

Mode	Factors Involved	Direct/Indirect	Genes Commonly Transferred
Conjugation	Donor cell with pilus, F plasmid	Direct	Drug resistance, toxin production, enzymes
Transformation	Free donor DNA, competent recipient	Indirect	Polysaccharide capsule
Transduction	Bacteriophage, lysed donor cell	Indirect	Toxins, drug resistance

Mutations: Types and Effects

A mutation is a change in the nucleotide sequence of the genome. Mutations can be spontaneous or induced by mutagens. They may be deleterious, neutral, or beneficial.

• Base substitution (point mutation): Single base change

• Silent mutation: No change in protein

• Missense mutation: Amino acid substitution

• Nonsense mutation: Premature stop codon

• Frameshift mutation: Insertion/deletion shifts reading frame

Identification of Mutants in the Laboratory

Bacteria are ideal for studying mutations due to rapid division and haploid genomes. Mutants can be identified by positive or negative selection.

• Positive selection: Mutant cells survive (e.g., drug resistance)

• Negative selection: Mutant cells die (e.g., loss of function)

Regulation of Bacterial Gene Expression

Gene expression can be constitutive (always on) or regulated (turned on/off as needed). Regulation occurs via repression (turning off) or induction (turning on).

• Constitutive genes: Always expressed (e.g., ribosomal proteins)

• Regulated genes: Expressed in response to environmental signals

• Repression: Inhibits gene expression

• Induction: Stimulates gene expression

The Lactose Operon: Inducible Operon Model

The lac operon is an example of an inducible operon. It contains genes for lactose metabolism, which are expressed only when lactose is present. The operon includes structural genes (lacZ, lacY, lacA), a promoter, operator, and regulatory gene (lacI).

• Inducer: Lactose or IPTG

• Repressor: Protein encoded by lacI

The Tryptophan Operon: Repressible Operon Model

The trp operon is a repressible operon. It contains genes for tryptophan synthesis, which are repressed when tryptophan is abundant.

• Structural genes: trpE, trpD, trpC, trpB, trpA

• Repressor: Activated by tryptophan

Summary Table: Types of Mutations

Type	Description	Effect
Silent	Codon codes for same amino acid	No change in protein
Missense	Codon codes for different amino acid	Altered protein function
Nonsense	Codon becomes stop codon	Truncated protein
Frameshift	Insertion/deletion shifts reading frame	Major disruption of protein

Concept Checks

• DNA replication produces two brand-new daughter strands: True

• Transduction involves transfer of bacterial DNA through a bacteriophage.

• Frameshift mutations have the most devastating effect on a cell.