CH 7

Microbial Genetics and Gene Regulation

Genome Structure and DNA Organization

The genetic material of bacteria is organized in specific ways that differ from eukaryotes. Understanding these differences is fundamental to microbiology.

• Bacterial Genome: Typically consists of a single, circular, double-stranded DNA molecule. It is haploid, meaning only one copy of each gene is present. The chromosome is not enclosed in a nucleus but is located in a region called the nucleoid.

• Structure of DNA: DNA is a double helix composed of two antiparallel strands. Each strand is made of nucleotides, which include a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, or guanine). Complementary base pairing occurs (A-T, C-G), stabilized by hydrogen bonds.

• Comparison: DNA vs. RNA: DNA contains deoxyribose sugar and thymine, is double-stranded, and is more stable. RNA contains ribose sugar, uracil instead of thymine, is usually single-stranded, and is less stable.

DNA Replication

DNA replication is the process by which a cell duplicates its DNA before cell division. Bacteria use a semi-conservative mechanism, ensuring genetic continuity.

• Semi-Conservative Replication: Each new DNA molecule consists of one parental and one newly synthesized strand. Existing DNA strands serve as templates for new synthesis.

• Prokaryotic vs. Eukaryotic Replication: Prokaryotes typically have a single origin of replication and replicate faster due to their smaller genome size. Eukaryotes have multiple origins and more complex regulation.

Plasmids

Plasmids are small, circular, double-stranded DNA molecules found in bacteria, separate from the chromosomal DNA.

• Function: Plasmids are not essential for normal metabolism, growth, or reproduction but often carry genes that confer advantages, such as antibiotic resistance.

• Replication: Plasmids replicate independently of the bacterial chromosome.

DNA Methylation

Methylation of DNA in bacteria plays several roles in cellular processes.

• Genetic Expression Control: Methylation can regulate gene expression by affecting the binding of transcription factors.

• Initiation of DNA Replication: Methylation marks the origin of replication and helps distinguish old and new DNA strands.

• Protection: Methylation protects bacterial DNA from restriction enzymes that degrade foreign DNA, such as that from viruses.

Genotype and Phenotype

The genotype is the genetic makeup of an organism, while the phenotype is the observable characteristics resulting from gene expression.

• Relationship: The genotype determines the potential phenotype, but environmental factors and gene regulation also play roles.

Gene Expression and Protein Synthesis

Gene expression involves transcription and translation, leading to protein synthesis.

• Transcription: The process by which RNA is synthesized from a DNA template. Involves DNA, RNA polymerase, and promoter regions.

• Translation: The process by which proteins are synthesized from mRNA templates.

• Promoters: DNA sequences where RNA polymerase binds to initiate transcription. Their strength and regulation affect gene expression levels.

Operon Regulation

Operons are clusters of genes under the control of a single promoter, common in prokaryotes.

• Repressible vs. Inducible Operons: Repressible operons (e.g., trp operon) are usually on and can be turned off, while inducible operons (e.g., lac operon) are usually off and can be turned on.

• trp Operon Regulation: The trp operon is regulated by a repressor protein that binds to the operator in the presence of tryptophan (co-repressor), blocking transcription.

Mutations and DNA Repair

Mutations are changes in the DNA sequence. They can occur spontaneously or be induced by external factors.

• Spontaneous Mutations: Occur naturally during DNA replication.

• Induced Mutations: Caused by mutagens such as UV light or chemical agents (e.g., nucleotide analogs).

• DNA Repair Mechanisms: Bacteria have several repair systems, including direct repair, excision repair, and SOS response, to correct mutations and damage (e.g., from UV-induced thymine dimers).

Genetic Exchange in Bacteria

Bacteria can exchange genetic material through several mechanisms, contributing to genetic diversity.

• Transformation: Uptake of free DNA from the environment. Competency refers to the ability of a cell to take up DNA.

• Transduction: Transfer of DNA via bacteriophages. Can be generalized (any gene transferred) or specialized (specific genes transferred).

• Conjugation: Direct transfer of DNA between bacteria via cell-to-cell contact, often involving plasmids such as the F plasmid.

• F Plasmid Spread: The F (fertility) plasmid enables the formation of a pilus for DNA transfer during conjugation, spreading genetic traits within a population.

Table: Comparison of Genetic Exchange Mechanisms

Mechanism	DNA Source	Requirement	Example
Transformation	Free DNA from environment	Competent cells	Streptococcus pneumoniae
Transduction	Bacteriophage-mediated	Phage infection	Generalized or specialized
Conjugation	Plasmid or chromosomal DNA	Cell-to-cell contact, F plasmid	Escherichia coli F+ x F-

Key Equations

• Central Dogma of Molecular Biology:

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

• Mutation Rate:

$\text{Mutation Rate} = \frac{\text{Number of mutations}}{\text{Total number of cells or generations}}$

Additional info:

• Some explanations and examples have been expanded for clarity and completeness.

• Table entries and definitions are inferred from standard microbiology knowledge.