Microbiology Study Guide: DNA, Viruses, and Microbial Growth Control

Chp. 11: Genes and Genetic Processes

DNA Replication

DNA replication is the process by which a cell copies its DNA before cell division. It ensures genetic continuity between generations.

• Key Enzymes: DNA polymerase synthesizes new DNA strands; helicase unwinds the double helix; primase lays down RNA primers.

• Directionality: DNA is synthesized in the 5' to 3' direction.

• Semiconservative: Each new DNA molecule contains one old and one new strand.

• Example: Escherichia coli replicates its genome in about 40 minutes.

Transcription

Transcription is the synthesis of RNA from a DNA template. It is the first step in gene expression.

• RNA polymerase: Enzyme that synthesizes RNA.

• Promoter: DNA sequence where transcription begins.

• Product: Messenger RNA (mRNA), transfer RNA (tRNA), or ribosomal RNA (rRNA).

• Example: The lac operon is transcribed when lactose is present.

Enhancer and Silencer

Enhancers and silencers are DNA elements that regulate gene expression by increasing or decreasing transcription.

• Enhancer: Increases transcription when bound by activator proteins.

• Silencer: Decreases transcription when bound by repressor proteins.

Translation

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

• Key Steps: Initiation, elongation, termination.

• Codons: Three-nucleotide sequences in mRNA specify amino acids.

• Example: AUG is the start codon for methionine.

Mutations for DNA, RNA, and Proteins

Mutations are changes in the genetic material that can affect DNA, RNA, and protein function.

• Types: Point mutations, insertions, deletions.

• Effects: Silent, missense, nonsense, frameshift.

• Example: Sickle cell anemia is caused by a missense mutation.

UV-light and X-rays

UV-light and X-rays are mutagens that cause DNA damage.

• UV-light: Causes thymine dimers, leading to mutations.

• X-rays: Cause double-strand breaks in DNA.

Conjugation

Conjugation is a form of horizontal gene transfer in bacteria, involving direct cell-to-cell contact.

• F plasmid: Carries genes for conjugation.

• Example: Transfer of antibiotic resistance genes.

Trp Operon

The trp operon is a repressible operon involved in tryptophan biosynthesis in bacteria.

• Regulation: Repressed when tryptophan is abundant.

• Example: Escherichia coli trp operon.

Lac Operon

The lac operon is an inducible operon controlling lactose metabolism in bacteria.

• Induction: Activated when lactose is present and glucose is absent.

• Regulation: Controlled by repressor and CAP-cAMP complex.

CAP + cAMP

CAP (catabolite activator protein) and cAMP (cyclic AMP) regulate the lac operon.

• CAP-cAMP complex: Binds to promoter, enhances transcription when glucose is low.

Chp. 6: Viruses

Bacteriophage Structure and Infection

Bacteriophages are viruses that infect bacteria. Their structure includes a head, tail, and tail fibers.

• Virulent phage: Causes lytic infection, destroying host cell.

• Temperate phage: Can enter lysogenic cycle, integrating into host genome.

Transduction

Transduction is the transfer of bacterial genes by bacteriophages.

• Generalized transduction: Any gene can be transferred.

• Specialized transduction: Only specific genes near prophage are transferred.

• Importance: Contributes to genetic diversity.

Viral Structure and Classification

Viruses are classified by genome type, envelope status, and clinical features.

• Genome: dsDNA, ssDNA, ssRNA (+ or -).

• Envelope: Enveloped or non-enveloped.

• Shape: Helical, icosahedral, complex.

• Example: Ebola virus is an enveloped, negative-sense ssRNA virus.

Viral Reproduction

Viruses reproduce by infecting host cells and using their machinery.

• Lytic cycle: Virus replicates and lyses host cell.

• Latent cycle: Virus integrates into host genome, remains dormant.

Retrovirus Infection (HIV)

Retroviruses use reverse transcriptase to convert RNA into DNA, which integrates into the host genome.

• Example: HIV infects CD4+ T cells.

• Mechanism: Reverse transcription, integration, transcription, translation, assembly.

Chronic, Acute, and Latent Viral Infection

Viral infections can be classified by their duration and persistence.

• Acute: Rapid onset, short duration (e.g., influenza).

• Chronic: Long-lasting, continuous virus production (e.g., hepatitis B).

• Latent: Virus remains dormant, reactivates later (e.g., herpes simplex).

Viral Isolation and Cytopathic Effects

Viruses are isolated using filters with proper pore size; cytopathic effects are visible changes in host cells due to infection.

• Hemagglutination Assay: Detects viruses that agglutinate red blood cells.

• RT-PCR vs. PCR: RT-PCR detects RNA viruses; PCR detects DNA viruses.

• Enzyme Immunoassay: Detects viral antigens or antibodies.

Prions and Diseases

Prions are infectious proteins causing neurodegenerative diseases.

• Creutzfeldt-Jakob Disease: Human prion disease.

• Mad Cow Disease: Bovine spongiform encephalopathy.

COVID-19

COVID-19 is caused by SARS-CoV-2, an enveloped, positive-sense ssRNA virus.

• Transmission: Respiratory droplets.

• Symptoms: Fever, cough, shortness of breath.

• Diagnosis: RT-PCR, antigen tests.

Chp. 13: Microbial Growth Control

BSL 1-4 Classes

Biosafety levels (BSL) classify laboratory safety based on organism risk.

BSL	Description
1	Minimal risk, basic precautions
2	Moderate risk, PPE required
3	High risk, controlled access, negative pressure
4	Extreme risk, full-body suits, specialized facilities

Terminology

• Sterilization: Complete removal of all microbes.

• Disinfection: Removal of pathogens, not all microbes.

• Antisepsis: Removal of microbes from living tissue.

Clostridium botulinum

Clostridium botulinum is a spore-forming bacterium causing botulism.

• Produces: Botulinum toxin, a neurotoxin.

Levels of Sterilization

• High-level: Kills all microbes, including spores.

• Intermediate-level: Kills most pathogens, not spores.

• Low-level: Kills some pathogens.

DRT and TDT

DRT (Decimal Reduction Time) and TDT (Thermal Death Time) measure microbial death by heat.

• DRT: Time to reduce population by 90% at a given temperature.

• TDT: Time to kill all microbes at a given temperature.

• Formula:

$D = \frac{t}{\log N_0 - \log N}$

Autoclave and Pasteurization

Autoclaves use steam under pressure to sterilize; pasteurization uses mild heat to reduce pathogens.

• Autoclave: 121°C, 15 psi, 15-20 min.

• Pasteurization: 63°C for 30 min (batch), 72°C for 15 sec (flash).

Refrigeration, Freezing, Desiccation, and Salt

Physical methods control microbial growth by altering environmental conditions.

• Refrigeration: Slows growth.

• Freezing: Stops growth, may kill some microbes.

• Desiccation: Removes water, inhibits growth.

• Salt: Creates hypertonic environment, causes plasmolysis.

Radiation

UV and gamma radiation are used for sterilization.

• UV: Damages DNA, used for surfaces.

• Gamma: Penetrates, used for medical equipment.

HEPA and Membrane Filtration

Filters remove microbes from air and liquids.

• HEPA: Removes particles >0.3 µm from air.

• Membrane filtration: Removes microbes from liquids.

Chemical Agents

• Phenols: Disrupt cell membranes; structure is aromatic ring with hydroxyl group.

• Triclosan: Antimicrobial, banned by FDA.

• Betadine: Iodine-based antiseptic.

• Alcohols: Denature proteins, dissolve membranes.

• Soaps: Remove microbes by mechanical action.

• Quats: Quaternary ammonium compounds, disrupt membranes.

• Hydrogen peroxide: Oxidizes cellular components.

Testing Methods

• Disk diffusion: Tests antimicrobial effectiveness.

• In use test: Tests disinfectant effectiveness in real conditions.

CRE (Carbapenem-resistant Enterobacteriaceae)

CRE are multidrug-resistant bacteria affecting hospital patients.

• Risk: Difficult to treat, high mortality.

Possible Essay Topics

• DNA Replication

• Lac Operon

• Trp Operon

• HIV Viral Life Cycle

• Transcription/Translation

Note: Be prepared to transcribe and translate a DNA sequence.