Microbial Genetics: DNA, RNA, Replication, Mutation, and Gene Transfer

A. Structure and Function of DNA

Overview of DNA Structure

Deoxyribonucleic acid (DNA) is the hereditary material in most organisms, including bacteria. Its structure and function are central to understanding microbial genetics.

• Double-stranded (DS): DNA consists of two strands arranged in an anti-parallel fashion.

• Base pairing rules: Adenine (A) pairs with Thymine (T), and Guanine (G) pairs with Cytosine (C).

• Nucleotides: The building blocks of DNA, each composed of a phosphate group, deoxyribose sugar, and a nitrogenous base.

• ATP: Adenosine triphosphate is the energy molecule important in DNA synthesis; GTP is the precursor for RNA synthesis.

• Genetic instructions: DNA encodes instructions for cellular function and is transcribed into RNA.

B. Structure and Function of RNA

Overview of RNA Structure

Ribonucleic acid (RNA) is typically single-stranded and plays several roles in gene expression.

• Single-stranded (SS): RNA is usually single-stranded.

• Base pairing rules: Adenine (A) pairs with Uracil (U), and Guanine (G) pairs with Cytosine (C).

Classes of RNA and Their Functions

Type	Function
mRNA (messenger RNA)	Conveys genetic information from DNA to the ribosome, specifying the amino acid sequence of the polypeptide.
tRNA (transfer RNA)	Transfers specific amino acids to the ribosome during protein synthesis, matching each amino acid to its corresponding codon on the mRNA.
rRNA (ribosomal RNA)	Forms the core of the ribosome's structure and catalyzes protein synthesis.

C. Replication (DNA)

DNA Replication Process

DNA replication is the process by which a cell duplicates its DNA before cell division. It is highly accurate and involves several key enzymes.

• Unwinding proteins: Break hydrogen bonds between DNA strands, separating them.

• RNA polymerase (primase): Synthesizes a short RNA primer to initiate DNA synthesis.

• DNA polymerase: Extends the new DNA strand by adding nucleotides complementary to the template strand. It also removes RNA primers and replaces them with DNA.

• DNA ligase: Joins Okazaki fragments on the lagging strand, completing the DNA molecule.

Key features: Replication is semi-conservative, meaning each new DNA molecule contains one old and one new strand. Mistakes can occur, leading to mutations.

D. Transcription

RNA Synthesis

Transcription is the process by which RNA is synthesized from a DNA template. RNA polymerase synthesizes a single-stranded RNA molecule complementary to one DNA strand.

• Synthesis is complementary and anti-parallel to the DNA template.

• RNA is synthesized in the 5' to 3' direction.

E. Translation

Protein Synthesis

Translation is the process by which ribosomes synthesize proteins using mRNA as a template.

• The ribosome binds mRNA and synthesizes a polypeptide chain according to the mRNA's codons.

• Translation begins at the start codon (AUG) and proceeds codon by codon.

• tRNA molecules bring specific amino acids to the ribosome, matching their anticodon to the mRNA codon.

• Peptide bonds form between amino acids, elongating the polypeptide chain.

• Translation ends at a stop codon, releasing the completed protein.

Example: The codon AUG codes for methionine and serves as the start signal for translation.

F. Gene Regulation (Lac Operon)

Regulation of Gene Expression

Gene regulation ensures that genes are expressed only when needed. The lac operon is a classic example in bacteria.

• Some genes are always on (constitutive), while others are regulated.

• Natural selection optimizes gene expression, ensuring that unnecessary genes are not expressed.

• The lac operon is induced only in the presence of lactose.

G. Mutation

Types and Outcomes of Mutations

Mutations are changes in the DNA sequence that can arise spontaneously or due to external factors.

• Types:

  • Spontaneous errors during DNA replication

  • Chemical damage to DNA

  • Radiation-induced DNA damage

• Outcomes:

  • Silent mutations: No change in protein function (e.g., codon change does not alter amino acid).

  • Harmful mutations: Result in loss of function or deleterious effects.

  • Beneficial mutations: Provide an advantage and may be selected for in evolution.

Example: A mutation from UUU to UUC in mRNA does not change the encoded amino acid (phenylalanine), so it is silent.

II. Microbial Genetics

A. Plasmids

Plasmids are small, circular, autonomously replicating DNA molecules found in bacteria. They often carry genes for antibiotic resistance and can be transferred between cells.

• Plasmids facilitate the spread of genetic traits within bacterial populations.

B. Mechanisms for Taking on New Genetic Information

Bacteria can acquire new genetic material through several mechanisms, increasing genetic diversity and adaptability.

• Transformation: Uptake of free DNA from the environment by a competent cell.

• Conjugation: Direct transfer of DNA from one cell to another via cell-to-cell contact, often involving plasmids.

• Transduction: Transfer of DNA from one cell to another by a virus (bacteriophage).

Transformation

Transformation involves the uptake of naked DNA from the environment. It is relatively rare and inefficient but important for genetic engineering.

• Example: Streptococcus pneumoniae can acquire capsule-producing genes via transformation, increasing virulence.

Conjugation

Conjugation requires direct cell-to-cell contact and is mediated by plasmids (e.g., F plasmid in E. coli).

Feature	F+ Cell	F- Cell
Ability to transfer DNA	Can transfer DNA	Cannot transfer DNA
Presence of F plasmid	Has F plasmid	No F plasmid

• High frequency recombination (Hfr) cells can transfer chromosomal DNA as well as plasmid DNA.

• Conjugation is a major mechanism for spreading antibiotic resistance genes.

Transduction

Transduction is the transfer of bacterial DNA by a bacteriophage (virus).

• Generalized transduction: Any bacterial gene can be transferred; occurs during lytic infection.

• Specialized transduction: Only genes near the viral insertion site are transferred; occurs during lysogenic infection.

Type	Description
Generalized	Any DNA from previous host can be transferred to next host; not limited to specific genes.
Specialized	Only DNA near the viral insertion site is transferred; limited to specific genes.

• Transduction can be used in genetic engineering to transfer specific genes between organisms.

Additional info: The notes infer the importance of these mechanisms in the spread of antibiotic resistance and genetic diversity among bacteria. The lac operon is a model for gene regulation, and mutations drive evolution and adaptation in microbial populations.