Microbial Genetics and Molecular Biology ~ Chp 8

I. Genetics

A. Structure and Function of DNA

Deoxyribonucleic acid (DNA) is the hereditary material in most organisms, encoding genetic information essential for cellular function and inheritance. Its structure and replication are foundational concepts in microbiology.

• DNA Structure: DNA is a double-stranded (DS), anti-parallel molecule. The two strands are held together by base pairing rules: adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).

• Nucleotide Composition: Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (A, T, G, or C).

• ATP as a Precursor: ATP (adenosine triphosphate) is not only the cell's energy molecule but also the precursor monomer for DNA synthesis (specifically, dATP).

• Transcription: DNA instructions are transcribed into RNA, which is then used for protein synthesis.

B. Structure and Function of RNA

Ribonucleic acid (RNA) is typically single-stranded (SS) and plays several roles in gene expression and protein synthesis. RNA uses uracil (U) instead of thymine (T) and follows base pairing rules: A-U, G-C.

• Types of RNA: There are three main classes of RNA, each with a distinct function in protein synthesis:

Type	Function
mRNA	Messenger RNA; carries genetic information from DNA to the ribosome, directing the sequence of amino acids in a polypeptide chain.
tRNA	Transfer RNA; brings specific amino acids to the ribosome according to the mRNA codon sequence.
rRNA	Ribosomal RNA; forms the core of the ribosome's structure and catalyzes peptide bond formation.

C. Replication (DNA)

DNA replication is the process by which a cell duplicates its DNA, ensuring genetic continuity during cell division. The process is semi-conservative, meaning each new DNA molecule contains one original and one new strand.

• Initiation: DNA polymerase binds to a short RNA primer and begins synthesis of a new DNA strand, anti-parallel and complementary to the template strand.

• Elongation: DNA polymerase extends the new strand in the 5' to 3' direction.

• Primer Replacement: RNA primers are replaced with DNA nucleotides.

• Ligase Activity: DNA ligase seals adjacent DNA fragments, completing the strand.

• Proofreading: DNA polymerase has high fidelity but occasional errors (mutations) can occur.

D. Transcription

Transcription is the synthesis of RNA from a DNA template. The process is complementary and anti-parallel, occurring in the 5' to 3' direction.

• Initiation: RNA polymerase binds to the start of a gene.

• Elongation: RNA polymerase synthesizes a single-stranded RNA molecule complementary to the DNA template.

• Termination: Synthesis ends at a termination signal.

E. Translation

Translation is the process by which ribosomes synthesize proteins using mRNA as a template. It involves decoding the mRNA sequence into a polypeptide chain.

• Initiation: The ribosome binds mRNA and begins synthesis at the start codon (AUG, which codes for methionine).

• Elongation: tRNA molecules bring amino acids to the ribosome, matching their anti-codon to the mRNA codon. Peptide bonds form between amino acids.

• Translocation: The ribosome shifts three nucleotides (one codon) along the mRNA, continuing the process.

• Termination: When a stop codon is reached, the polypeptide chain is released.

Step	Description
Initiation	Ribosome assembles at the start codon (AUG) on mRNA.
Elongation	tRNAs bring amino acids; peptide bonds form between them.
Translocation	Ribosome moves along mRNA, reading codons sequentially.
Termination	Stop codon signals end of translation; polypeptide is released.

F. Gene Regulation (lac operon)

Gene regulation ensures that genes are expressed only when needed, optimizing cellular resources. The lac operon is a classic example of gene regulation in bacteria.

• Constitutive Genes: Some genes are always on.

• Inducible Genes: Genes not needed are turned off; they are activated only when required (e.g., in the presence of lactose).

• Control Mechanisms: Repression and activation can occur simultaneously to fine-tune gene expression.

G. Mutation

Mutations are changes in the DNA sequence that can affect gene function and phenotype. They are a source of genetic variation and can have various outcomes.

• Types of Mutations:

  • Spontaneous: Errors in DNA replication, uncorrected.

  • Chemical: DNA damage repaired with errors.

  • Radiation: DNA damage repaired with errors.

• Outcomes of Mutation:

  • Silent: No change in amino acid due to redundancy in the genetic code.

  • Neutral: New amino acid is produced but does not affect protein function.

  • Harmful: Protein function is lost or deleterious effects occur.

  • Beneficial: Rare but can confer advantages; more likely to persist in populations.

Type	Description
Silent	Mutation does not change the amino acid sequence.
Neutral	Mutation changes amino acid but does not affect function.
Harmful	Mutation impairs protein function.
Beneficial	Mutation improves organism's fitness.

II. Microbial Genetics

A. Plasmid

Plasmids are small, circular, autonomously replicating DNA molecules found in bacteria. They play a crucial role in horizontal gene transfer and can carry genes for antibiotic resistance, virulence, and other traits.

• Plasmids can be easily transmitted between cells, accelerating the development of new genetic types in a population.

B. Mechanisms for Taking on New Genetic Information

Bacteria can acquire new genetic material through several mechanisms, leading to genetic diversity and adaptation.

1. Transformation

Transformation is the uptake of naked DNA from the environment by a bacterial cell. This process can result in the acquisition of new traits, such as antibiotic resistance or virulence.

• Example: Streptococcus pneumoniae can acquire a capsule gene via transformation, making it virulent.

• Transformation is relatively rare and inefficient but can be selected for in laboratory experiments.

2. Conjugation

Conjugation is the transfer of DNA from one cell to another via direct contact, often mediated by a pilus. The F (fertility) system in E. coli is a well-studied example.

• F+ cells: Possess the F plasmid and can transfer it to F- cells.

• Hfr cells: Have the F plasmid integrated into the chromosome, allowing transfer of chromosomal genes.

• Conjugation is a major mechanism for spreading antibiotic resistance.

Type	Description
F+ cell	Transfers F plasmid only; recipient becomes F+.
Hfr cell	Transfers chromosomal DNA and some F DNA; recipient rarely becomes F+.

3. Transduction

Transduction is the transfer of DNA from one cell to another via a virus (bacteriophage). It is an important mechanism for gene transfer in bacteria.

• Generalized Transduction: Any gene from the donor can be transferred; occurs when a phage accidentally packages host DNA.

• Specialized Transduction: Only specific genes near the phage insertion site are transferred; occurs with temperate phages.

Type	Description
Generalized	Any host gene can be transferred; random packaging of host DNA.
Specialized	Only genes near the phage insertion site are transferred.

Similarities: Both mechanisms describe viral transfer of cellular DNA from one cell to another.

Differences:

• Generalized: Any DNA from the previous host is as likely as any other to be transferred to the next host.

• Specialized: DNA transferred is restricted to only those genes near the viral insertion site.

Resistance Factors: Plasmids and episomes may carry genes for resistance to antibiotics and toxic materials, facilitating the spread of resistance in microbial populations.

Additional info: Transduction and conjugation are important tools in genetic engineering and biotechnology, allowing scientists to manipulate bacterial genomes for research and industrial applications.