Microbiology Exam 2 Study Guide: Genetics, Microbial Diversity, and Molecular Techniques

Nitrogen-Fixing Alphaproteobacteria

Overview and Importance

Nitrogen-fixing bacteria are essential for converting atmospheric nitrogen (N2) into ammonia (NH3), which plants can use for growth. Alphaproteobacteria include several genera that participate in this process, either as free-living organisms or in symbiosis with plants.

• Free-Living Bacteria: Azotobacter, Beijerinckia fix nitrogen independently in the rhizosphere.

• Symbiotic Bacteria: Rhizobium, Bradyrhizobium, Azorhizobium form root nodules on legumes, facilitating nitrogen fixation.

• Cyanobacteria: Anabaena fixes nitrogen in heterocysts, specialized cells providing anaerobic conditions.

Root Nodule Formation Process:

1. Attachment to root hairs

2. Infection thread formation

3. Bacteroid formation (specialized for nitrogen fixation)

4. Nodule development

Example: Bradyrhizobium infects soybean roots, forming nodules and enhancing soil fertility.

Genetic Concepts and Mechanisms

Definition of Gene

A gene is a segment of DNA that codes for a functional product, usually a protein or RNA molecule.

DNA Structure

DNA consists of two antiparallel strands of nucleotides. Each nucleotide contains:

• Deoxyribose (pentose sugar)

• Phosphate group

• Nitrogenous base: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

Base Pairing: A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds).

Mechanisms of Genetic Regulation

Repression

Repression is a genetic control mechanism where a corepressor activates a repressor protein, which then binds to DNA and blocks transcription.

• In a repressible operon, genes are "on" unless the repressor is activated by a corepressor.

• When the corepressor binds the repressor, it becomes active and attaches to the operator region, preventing RNA polymerase from transcribing the genes.

Translation

Translation is the process where mRNA is decoded at the ribosome to build a protein. The operon structure includes:

• Promoter (P): RNA polymerase binding site

• Operator (O): Regulatory switch

• Structural genes: Code for proteins

Catabolite Repression

Catabolite repression is a regulatory mechanism where glucose inhibits transcription of other sugar-metabolizing genes (e.g., lac operon).

• When glucose is present, cAMP levels are low, preventing CAP from activating transcription.

• When glucose is absent, cAMP rises, CAP binds to the promoter, and transcription occurs if lactose is present.

DNA Polymerase

DNA polymerase synthesizes new DNA strands during replication. It requires a primer and adds nucleotides to the 3' end.

• Leading strand: Synthesized continuously (5' to 3')

• Lagging strand: Synthesized in Okazaki fragments, joined by DNA ligase

Induction

Induction is the activation of transcription when an inducer inactivates a repressor, allowing gene expression.

Functions of Key Enzymes

• RNA polymerase: Synthesizes RNA from DNA template

• Transposase: Moves transposons (jumping genes) within the genome

• Restriction enzymes: Cut DNA at specific sequences

• DNA ligase: Joins DNA fragments

• DNA polymerase: Replicates DNA

Inducible Enzyme

An enzyme produced in response to the presence of a substrate is called an inducible enzyme.

Genetic Changes in Bacteria

• Mutation: Change in DNA sequence

• Transformation: Uptake of naked DNA

• Transduction: DNA transfer via bacteriophages

• Conjugation: DNA transfer through direct contact

Molecular Techniques

FISH (Fluorescent In Situ Hybridization)

FISH uses fluorescent DNA probes to detect specific DNA or RNA sequences in cells. It is used in oncology, prenatal testing, genomics, and microbiology.

• Probe preparation: Fluorescently labeled DNA

• Denaturation: Separates DNA strands

• Hybridization: Probe binds to target sequence

• Visualization: Fluorescence microscopy

Advantages: High sensitivity, versatility. Limitations: Targeted, costly.

Microbial Diversity and Classification

Domain Bacteria

• Prokaryotic

• Peptidoglycan cell wall

• Binary fission

• Gram-positive/Gram-negative classification

Domain Archaea

• Prokaryotic

• No peptidoglycan

• Unique membrane lipids

• Extremophiles (methanogens, halophiles, hyperthermophiles)

Proteobacteria

• Gram-negative

• Largest bacterial group

• Includes many pathogens

• Metabolic versatility

Plants

• Multicellular

• Photosynthetic

• Cellulose cell walls

• Alternation of generations

Additional Key Terms and Concepts

Clone

A clone is a genetically identical population derived from one cell.

Mycology

Mycology is the study of fungi. Systemic mycoses are fungal infections affecting internal organs (e.g., histoplasmosis).

Gram-Positive Endospore-Forming Bacteria

• Bacillus

• Clostridium

Similarities Between Archaea & Bacteria

• Prokaryotic

• No nucleus

• Circular DNA

• Ribosomes (70S)

Nucleic Acid Hybridization

Technique using complementary DNA/RNA strands to identify organisms (e.g., DNA probe tests).

Viruses vs. Bacteria

• Viruses: Not cells, require host, DNA or RNA

• Bacteria: Living cells, independent metabolism, DNA only

Culturing Viruses

Viruses must be cultured in living cells (cell culture, embryonated eggs, animals).

Complex Viruses

Complex viruses have unusual structures (e.g., bacteriophages).

Definitions

• Prion: Infectious protein

• Bacteriophage: Virus that infects bacteria

• Retrovirus: RNA virus using reverse transcriptase

• Persistent infection: Virus remains long-term

• Latent infection: Virus dormant (e.g., Herpes simplex)

Virus Families

• Picornavirus: Small RNA viruses (e.g., polio)

• Togavirus: RNA viruses (e.g., rubella)

• Papovavirus: DNA viruses (HPV)

• Herpesvirus: Latent DNA viruses

• Retrovirus: RNA + reverse transcriptase (e.g., HIV)

Viruses with Reverse Transcriptase

Retroviruses (e.g., HIV) contain reverse transcriptase.

Definitions (Reproduction)

• Dioecious: Male & female on separate individuals

• Monoecious: Both sexes in one organism

• Budding: Asexual reproduction by outgrowth

• Fission: Cell splitting into two

Uses of Algae

• Red algae: Food (agar)

• Brown algae: Alginates (thickeners)

• Green algae: Oxygen production

• Diatoms: Filters, abrasives

Transmission of Helminths

• Contaminated food/water

• Skin penetration

• Insect vectors

Gammaproteobacteria

• Escherichia

• Salmonella

• Vibrio

• Pseudomonas

Cyanobacteria

Photosynthetic bacteria (blue-green algae).

Lichens

• Symbiosis: fungus + algae/cyanobacteria

• Indicators of air quality

Kingdom Plants

• Multicellular

• Photosynthetic

• Alternation of generations

Definitions (Fungi Reproduction)

• Karyogamy: Fusion of nuclei

• Plasmogamy: Fusion of cytoplasm

• Meiosis: Reduction division producing haploid cells

• Anamorph: Asexual fungal stage

• Deuteromycota: Fungi without known sexual stage