Comprehensive Study Guide: Key Topics in Microbiology

Antimicrobial Drugs and Persistence

Antibiotics: Definition and Mechanisms

Antibiotics are chemical substances produced by microorganisms that inhibit or kill other microbes. They are crucial in treating bacterial infections and are classified based on their origin and mechanism of action.

• Definition: Antibiotics are natural or synthetic compounds that target specific bacterial processes.

• Target: Antibiotics may target cell wall synthesis, protein synthesis, nucleic acid synthesis, or metabolic pathways.

• Example: β-lactam antibiotics (e.g., penicillins) inhibit cell wall synthesis by targeting peptidoglycan cross-linking.

Antibiotic Biosynthesis

• Source: Many antibiotics are produced by bacteria (e.g., Streptomyces) and fungi (e.g., Penicillium).

• Biosynthetic Pathways: Eukaryotes (fungi) and target cell wall biosynthesis differently than prokaryotes.

Bacterial Strategies for Antibiotic Resistance

• Persistence: Bacteria may survive antibiotic treatment by entering a dormant state or by expressing resistance genes.

• Mechanisms: Enzymatic degradation, efflux pumps, target modification.

Metabolic Regulation

Constitutive vs. Regulated Genes

Gene expression in bacteria can be constitutive (always on) or regulated (turned on/off in response to environmental signals).

• Constitutive Genes: Expressed continuously, often encode essential functions.

• Regulated Genes: Expression varies depending on cellular needs.

DNA Binding Proteins

• Function: Bind to specific DNA sequences to regulate transcription.

• Types: Repressors (inhibit transcription), activators (promote transcription).

Negative and Positive Regulation

• Negative Regulation: Repressor proteins bind to operators to block transcription.

• Positive Regulation: Activator proteins enhance transcription by facilitating RNA polymerase binding.

• Induction: Genes are turned on in response to specific signals (e.g., presence of lactose induces lac operon).

• Repression: Genes are turned off when not needed (e.g., tryptophan represses trp operon).

Quorum Sensing

• Definition: Cell-to-cell communication mechanism that enables bacteria to coordinate gene expression based on population density.

• Role: Regulates processes such as biofilm formation, virulence, and sporulation.

Viruses and Their Replication

General Structure of Viruses

Viruses are acellular entities composed of genetic material (DNA or RNA) enclosed in a protein coat (capsid), sometimes with a lipid envelope.

• Capsid: Protein shell protecting viral genome.

• Envelope: Lipid membrane derived from host cell.

• Attachment: Viruses attach to host cells via specific receptors.

Viral Life Cycles

• Lytic Cycle: Virus replicates and lyses host cell.

• Lysogenic Cycle: Viral genome integrates into host DNA and replicates passively.

• Bacteriophage T4: Example of a lytic bacteriophage infecting E. coli.

Differences Between Prokaryotic and Animal Viruses

• Entry Mechanisms: Animal viruses often enter via endocytosis; bacteriophages inject DNA.

• Host Range: Determined by viral attachment proteins and host cell receptors.

Bacterial Genetics

Genotype vs. Phenotype

Genotype refers to the genetic makeup of an organism, while phenotype is the observable characteristics resulting from gene expression.

• Genotype: DNA sequence of genes.

• Phenotype: Physical traits, metabolic capabilities.

Genetic Exchange in Bacteria

Transformation, Transduction, and Conjugation

• Transformation: Uptake of free DNA from environment.

• Transduction: Transfer of DNA via bacteriophages.

• Conjugation: Direct transfer of DNA between bacteria via pilus.

CRISPR System

• Definition: Prokaryotic immune system using spacer RNAs and Cas proteins to target foreign DNA.

• Application: Gene editing in biotechnology.

Survival Agents: Viroids and Prions

Viroids

• Definition: Small, circular RNA molecules that infect plants.

• Composition: RNA only, no protein coat.

Prions

• Definition: Infectious proteins causing neurodegenerative diseases.

• Mutation: Prions arise from misfolded normal proteins.

Genetic Engineering and Biotechnology

PCR (Polymerase Chain Reaction)

• Definition: Technique to amplify specific DNA sequences.

• Applications: Diagnostics, cloning, forensics.

• Equation: $N = N_0 imes 2^n$ (where $N$ is final DNA copies, $N_0$ is initial, $n$ is cycles)

Molecular Cloning

• Selectable Marker: Gene conferring resistance to antibiotics, used to identify successful clones.

• Vectors: Plasmids, cosmids, and BACs used to carry foreign DNA.

• Recombinant DNA: DNA molecules formed by laboratory methods to bring together genetic material from multiple sources.

Phototrophy

Photosynthesis in Microorganisms

• Definition: Conversion of light energy into chemical energy by microorganisms.

• Photosystems: Protein complexes containing pigments (chlorophyll, bacteriochlorophyll, carotenoids).

• ATP Generation: $ADP + P_i \rightarrow ATP$

Phototrophic Bacteria

• Groups: Cyanobacteria, purple bacteria, green bacteria.

• Role: Oxygenic and anoxygenic photosynthesis.

Anaerobic Respiration, Acetogenesis, and Methanogenesis

Anaerobic Respiration

• Definition: Respiration using electron acceptors other than oxygen (e.g., nitrate, sulfate).

• Assimilative vs. Dissimilative Reduction: Assimilative reduction incorporates compounds into biomass; dissimilative reduction uses them for energy.

Methanogenesis

• Definition: Biological production of methane by archaea.

• Electron Donors: H2, acetate.

• Equation: $CO_2 + 4H_2 \rightarrow CH_4 + 2H_2O$

Fermentation

Fermentation Pathways

• Definition: Metabolic process converting sugar to acids, gases, or alcohol in absence of oxygen.

• ATP Generation: Substrate-level phosphorylation.

• Products: Ethanol, lactic acid, CO2.

Heterolactic vs. Homolactic Fermentation

• Homolactic: Produces lactic acid only.

• Heterolactic: Produces lactic acid, ethanol, and CO2.

Microbiology of the Built Environment

Microorganisms in Contaminated Environments

• Remediation: Microbes break down pollutants in soil and water.

• Key Enzymes: Oxygenases, reductases.

Wastewater Treatment

• Primary Treatment: Removal of solids.

• Secondary Treatment: Biological degradation of organic matter.

• BOD (Biochemical Oxygen Demand): Measure of organic pollution.

Microbial Symbioses

Types of Symbiosis

• Mutualism: Both partners benefit.

• Parasitism: One benefits, one is harmed.

• Commensalism: One benefits, other is unaffected.

Examples of Symbiosis

• Termite Symbionts: Microbes in termite gut digest cellulose.

• Bobtail Squid and Aliivibrio fischeri: Bacteria provide bioluminescence; squid offers nutrients and habitat.

• The Rumen: Chamber in ruminant animals hosting bacteria that ferment plant material.

Table: Types of Bacterial Symbiosis

Type	Definition	Example
Mutualism	Both organisms benefit	Termite gut bacteria
Parasitism	One benefits, one harmed	Pathogenic bacteria
Commensalism	One benefits, other unaffected	Skin microbiota

Additional info: Some explanations and examples have been expanded for clarity and completeness.