Microbiology Study Guide: DNA Structure, Replication, Mutation, and Gene Transfer

Structure and Function of Bacterial Cells

Chromosome Organization

Bacterial cells typically possess a single, circular chromosome located in the nucleoid region of the cell. This chromosome is haploid, meaning only one copy is present per cell.

• Nucleoid: Region where the bacterial chromosome is found.

• Haploid: Only one set of genetic material.

Structure of DNA Molecule

Components and Base Pairing

DNA is a double-stranded helical molecule composed of nucleotides. Each nucleotide consists of a phosphate group, a deoxyribose sugar, and a nitrogenous base.

• Nucleotides: Building blocks of DNA; each contains a phosphate, deoxyribose sugar, and nitrogenous base.

• Sugar-phosphate backbone: Alternating deoxyribose sugars and phosphate groups form the structural framework of DNA.

• Hydrogen bonds: Hold complementary base pairs together.

• Complementary base pairing: Adenine (A) pairs with Thymine (T); Cytosine (C) pairs with Guanine (G).

Example: In a DNA strand, if the sequence is 5'-ATCG-3', the complementary strand will be 3'-TAGC-5'.

Comparison of DNA and RNA Structure

Key Differences

DNA and RNA differ in their structure, stability, and function.

• DNA: Double-stranded, contains deoxyribose sugar, bases are A, T, C, G.

• RNA: Single-stranded, contains ribose sugar, bases are A, U, C, G (Uracil replaces Thymine).

• RNA is less stable than DNA due to the presence of the 2' hydroxyl group in ribose.

Example: Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis.

DNA Replication

Semi-Conservative Replication

DNA replication is semi-conservative, meaning each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.

• Process: The double helix "unzips"; each strand serves as a template for a new strand.

• Importance: Ensures genetic consistency and reduces mutation rates.

Equation:

$\text{Parental DNA} \rightarrow \text{Template for new strand}$

Steps in Prokaryotic DNA Replication

• Initiation: Topoisomerase binds to origin, relieves supercoiling.

• Helicase unwinds the double helix.

• Single-strand binding proteins stabilize unwound DNA.

• Primase synthesizes RNA primers.

• DNA polymerase III adds nucleotides to the 3' end.

• DNA polymerase I replaces RNA primers with DNA.

• DNA ligase joins Okazaki fragments on the lagging strand.

Differences in Eukaryotes: Multiple origins of replication, linear chromosomes, different polymerases, shorter Okazaki fragments.

Plasmids

Structure and Function

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

• Carry extra genetic information, often including antibiotic resistance genes.

• Can replicate independently of the chromosome.

Methylation of Bacterial DNA

Roles in Cellular Processes

Methylation of DNA in bacteria serves several functions:

• Controls gene expression.

• Initiates DNA replication.

• Protects against viral infection.

• Repairs DNA.

Genotype and Phenotype

Definitions

Genotype: The genetic makeup of an organism.

Phenotype: Observable characteristics resulting from genotype and environment.

• Genotype determines phenotype.

Gene Expression: Transcription and Translation

Processes

Gene expression involves transcription (DNA to RNA) and translation (RNA to protein).

• Transcription: DNA is transcribed into RNA by RNA polymerase.

• Translation: RNA is translated into protein at the ribosome.

Central Dogma:

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

Transcription Steps

• Initiation: RNA polymerase binds to promoter sequence.

• Elongation: RNA polymerase synthesizes RNA strand using DNA template.

• Termination: RNA polymerase releases the completed RNA transcript.

Key Terms

• Promoter: DNA sequence where RNA polymerase binds.

• RNA polymerase: Enzyme that synthesizes RNA.

• Template: DNA strand used for RNA synthesis.

Transcriptional Control: Promoters and Operons

Promoters

Promoters are DNA sequences that signal RNA polymerase to start transcription.

Operons

Operons are clusters of genes under control of a single promoter, allowing coordinated regulation.

• Inducible operons: Usually inactive, can be turned on by inducers (e.g., lac operon).

• Repressible operons: Usually active, can be turned off by repressors (e.g., trp operon).

Regulation of Operons

• Lac operon: Inducible; repressor binds operator to block transcription. Inducer (allolactose) binds repressor, releasing it and allowing transcription.

• Trp operon: Repressible; repressor binds operator when co-repressor (tryptophan) is present, blocking transcription.

Mutations

Spontaneous vs. Induced Mutations

• Spontaneous mutations: Occur naturally, due to errors in DNA replication or natural background radiation.

• Induced mutations: Caused by external factors (mutagens) such as chemicals, UV light, or X-rays.

Mutagens and Mutation Rate

• UV radiation: Causes thymine dimers, distorting DNA structure.

• Nucleotide analogs: Mimic normal nucleotides, causing base pairing errors.

DNA Repair Mechanisms

Spontaneous Mutation Repair

• DNA polymerase proofreading: Corrects mismatched bases during replication.

• Mismatch repair: Detects and replaces incorrect bases after replication.

UV-Induced Damage Repair

• Photoreactivation: Enzyme photolyase uses visible light to break thymine dimers.

• Nucleotide excision repair: Removes damaged DNA segments; DNA polymerase fills in correct bases, DNA ligase seals the strand.

Horizontal Gene Transfer in Bacteria

Mechanisms

• Transformation: Uptake of naked DNA from environment.

• Transduction: Transfer of DNA by bacteriophage.

• Conjugation: Direct transfer of DNA via pilus; usually involves plasmid transfer.

Comparison Table: Horizontal Gene Transfer Mechanisms

Mechanism	DNA Source	Contact Required	Key Feature
Transformation	Naked DNA from environment	No	Competent cells required
Transduction	Bacteriophage-mediated	No	Virus transfers DNA
Conjugation	Plasmid or chromosomal DNA	Yes	Pilus formation; cell-to-cell contact

Specialized vs. Generalized Transduction

• Generalized transduction: Any gene, random, lytic cycle.

• Specialized transduction: Specific genes, lysogenic cycle, prophage involvement.

Spread of F Plasmid in Bacterial Populations

Steps in Conjugation

• Step 1: F+ and F- cells (F+ have plasmid, F- do not).

• Step 2: F+ cell forms sex pilus connecting to F- cell.

• Step 3: F plasmid replicates; copy transferred through pilus.

• Step 4: Recipient F- cell becomes F+.

Result: Rapid spread of F plasmid as more cells become F+.

Competency and Transformation

Role of Competency

Only competent cells can undergo transformation. Competency can be natural (some bacteria become competent at certain growth stages) or induced (chemicals/electrical methods in lab).

• Natural competency: Occurs in some bacteria during specific growth phases.

• Induced competency: Achieved in laboratory settings.

Summary: Competency is essential for transformation; without it, bacteria cannot take up and incorporate new genetic material.

Additional info: This guide expands on brief points with academic context, definitions, and examples for clarity and completeness.