MCB3020 Midterm Study Guide: Core Concepts in Microbiology

Ch. 1: The Microbial World

Beneficial and Harmful Roles of Microbes

• Beneficial roles: Microbes are essential for nutrient cycling (e.g., nitrogen fixation), food production (e.g., fermentation), and biotechnology (e.g., antibiotics, recombinant proteins).

• Harmful roles: Some microbes cause diseases in humans, animals, and plants, and can spoil food or contaminate water.

• Example: Lactobacillus in yogurt production (beneficial); Salmonella causing foodborne illness (harmful).

Cell Size and Its Advantages

• Small cell size increases the surface area-to-volume ratio, enhancing nutrient uptake and waste elimination.

• Allows for faster growth rates and adaptation to environmental changes.

Microscopy Types and Applications

• Light microscopy: Used for observing live cells, cell shape, and arrangement.

• Electron microscopy (TEM, SEM): Provides high-resolution images of cell ultrastructure.

• Fluorescence microscopy: Used to visualize specific structures using fluorescent dyes or proteins.

Bacterial Morphologies and Arrangements

• Shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral), vibrio (comma-shaped).

• Arrangements: Chains (strepto-), clusters (staphylo-), pairs (diplo-).

Ch. 2: Microbial Cell Structure and Function

Prokaryotic vs. Eukaryotic Microbes

• Prokaryotes: Lack a nucleus and membrane-bound organelles; include Bacteria and Archaea.

• Eukaryotes: Have a nucleus and organelles; include fungi, protozoa, algae.

Gram-Positive vs. Gram-Negative Bacteria

• Gram-positive: Thick peptidoglycan layer, teichoic acids, no outer membrane.

• Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS).

• Gram stain: Differential staining technique to distinguish between Gram+ (purple) and Gram– (pink) bacteria.

Archaeal Cell Envelope

• Archaea lack peptidoglycan; may have pseudopeptidoglycan or S-layers.

• Membrane lipids are ether-linked (not ester-linked as in bacteria).

Cytoplasmic Membrane Structure and Function

• Phospholipid bilayer with embedded proteins; selectively permeable barrier.

• Functions in transport, energy generation, and cell signaling.

Motility Structures

• Prokaryotes: Flagella (rotary motion), pili (twitching), gliding.

• Eukaryotes: Flagella and cilia (whip-like motion).

Endospore Formation

• Endospores are dormant, resistant structures formed by some bacteria (e.g., Bacillus, Clostridium).

• Enable survival in harsh conditions (heat, desiccation, chemicals).

Flagella: Prokaryotic vs. Eukaryotic

• Prokaryotic flagella: Composed of flagellin, rotate like a propeller.

• Eukaryotic flagella: Composed of microtubules, move in a whip-like fashion.

Endosymbiotic Theory

• Mitochondria and chloroplasts originated from free-living bacteria engulfed by ancestral eukaryotic cells.

• Supported by similarities in DNA, ribosomes, and double membranes.

Ch. 3: Microbial Metabolism

Redox Tower and Electron Transport Chain (ETC)

• The redox tower ranks redox couples by their reduction potential (E').

• Electron carriers in the ETC are arranged from most negative to most positive E', facilitating electron flow and energy release.

Oxidation and Reduction

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Redox reactions drive energy generation in cells.

Major Metabolic Pathways

• Glycolysis, TCA cycle, fermentation, respiration.

• ATP generated by substrate-level phosphorylation, oxidative phosphorylation, or photophosphorylation.

• Reducing power (NADH, FADH2) produced in catabolic pathways.

Redox Balance in Fermentation vs. Respiration

• Fermentation: Organic molecules serve as both electron donors and acceptors; redox balance achieved by regenerating NAD+.

• Respiration: External electron acceptors (e.g., O2) used; more efficient ATP production.

Proton Motive Force (PMF)

• Generated by ETC pumping protons across membrane, creating electrochemical gradient.

• Used for ATP synthesis, transport, and motility.

ATP Generation Mechanisms

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

• Oxidative phosphorylation: ATP synthase uses PMF.

• Photophosphorylation: Light-driven ATP synthesis in phototrophs.

Microbial Trophic Types

• Phototrophs: Use light as energy source.

• Chemoorganotrophs: Oxidize organic compounds.

• Chemolithotrophs: Oxidize inorganic compounds.

CO2 and N2 Fixation

• CO2 fixation: Conversion of CO2 to organic carbon (e.g., Calvin cycle).

• N2 fixation: Reduction of atmospheric N2 to NH3 by nitrogenase.

Ch. 4: Microbial Growth and Its Control

Measuring Microbial Growth

• Direct counts: Microscopy or flow cytometry; fast but cannot distinguish live/dead cells.

• Viable counts: Plate counts; only live cells counted, but may underestimate total numbers.

• Turbidity: Spectrophotometry; rapid, but indirect and affected by cell size/shape.

Complex vs. Defined Media

• Complex media: Contains unknown components (e.g., yeast extract); supports diverse growth.

• Defined media: All components known; used for specific metabolic studies.

Biofilm Formation

• Steps: Attachment, microcolony formation, maturation, dispersal.

• Biofilms protect microbes from antibiotics and immune responses; cause persistent infections and industrial fouling.

Exponential Growth Consequences

• Rapid population increase; resource depletion and waste accumulation can limit growth.

Batch vs. Continuous Culture

• Batch culture: Closed system; nutrients deplete, waste accumulates.

• Continuous culture: Open system (e.g., chemostat); steady-state growth maintained.

Environmental Effects and Classification

• Temperature: Psychrophiles, mesophiles, thermophiles, hyperthermophiles.

• pH: Acidophiles, neutrophiles, alkaliphiles.

• Salinity: Halophiles, halotolerant organisms.

• Oxygen: Obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles, aerotolerant anaerobes.

Ch. 5: Viruses and Their Multiplication

Obligate Intracellular Parasitism

• Viruses require host cells for replication; lack metabolic machinery for independent life.

Virion Structure

• Naked virus: Nucleic acid + capsid (protein coat).

• Enveloped virus: Nucleic acid, capsid, and lipid envelope derived from host membrane.

Viral Genomes

• DNA or RNA; single-stranded (ss) or double-stranded (ds); linear or circular.

Measuring Virus Quantity

• Plaque assay: Quantifies infectious virus particles; analogous to bacterial colony counts.

T4 Phage Replication Cycle

• Steps: Attachment, penetration, synthesis, assembly, release.

Lytic vs. Temperate Phages

• Lytic (virulent): Immediately lyse host cell.

• Temperate: Can integrate into host genome (prophage) and enter lysogenic cycle.

Lytic vs. Lysogenic Cycles

• Lytic: Phage replicates and lyses cell.

• Lysogenic: Phage DNA integrates into host genome; can later enter lytic cycle.

T4 Bacteriophage Structure

• Complex head-tail structure; icosahedral head, contractile tail, tail fibers.

Coronavirus Virion and SARS-CoV-2

• Enveloped, positive-sense ssRNA genome, spike proteins.

• ACE2 and TMPRSS2 are host proteins facilitating viral entry.

• Lifecycle: Attachment, entry, translation/replication, assembly, release.

• Testing: PCR, antigen, antibody tests.

• Vaccines: mRNA, viral vector, inactivated virus types.

Ch. 6: Molecular Information Flow and Protein Processing

Central Dogma of Molecular Biology

• Information flows from DNA → RNA → Protein.

• Processes: Replication, transcription, translation.

Proteins in Bacterial DNA Replication

• Origin binding protein: Recognizes replication origin.

• Gyrase, topoisomerase IV: Relieve supercoiling.

• Helicase: Unwinds DNA.

• Single-strand binding proteins: Stabilize unwound DNA.

• Primase: Synthesizes RNA primers.

• DNA polymerase III: Main DNA synthesizing enzyme.

• DNA polymerase I: Removes primers, fills gaps.

• Tau: Coordinates polymerase activity.

• Ligase: Seals nicks in DNA.

• Tus protein: Terminates replication.

Replication Initiation and Termination

• Initiation at oriC; termination at ter sites (Tus protein binds).

Continuous vs. Discontinuous Replication

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized discontinuously as Okazaki fragments.

Transcription in Bacteria

• Initiation: RNA polymerase binds promoter.

• Termination: Rho-dependent or intrinsic (hairpin) mechanisms.

• RNA polymerase catalyzes transcription.

Plasmids vs. Chromosomes

• Plasmids: Small, circular, extrachromosomal DNA; replicate independently.

• Chromosome: Main genetic material; essential genes.

Eukaryotic mRNA Processing

• 5' capping, 3' polyadenylation, splicing (removal of introns).

Classes of RNA in Protein Synthesis

• mRNA: Messenger RNA; encodes proteins.

• tRNA: Transfer RNA; brings amino acids to ribosome.

• rRNA: Ribosomal RNA; structural and catalytic component of ribosomes.

tRNA Structure

• Cloverleaf structure; anticodon loop, acceptor stem for amino acid attachment.

Translation Steps in Bacteria

• Initiation: Ribosome assembly on mRNA.

• Elongation: Addition of amino acids.

• Termination: Release of completed polypeptide.

Coupled Transcription and Translation

• Prokaryotes: Both processes occur simultaneously in cytoplasm.

• Eukaryotes: Separated by nuclear envelope.

Chaperone Proteins

• Assist in proper folding of proteins; prevent aggregation.

Sec and Tat Systems

• Sec: Translocates unfolded proteins across membrane.

• Tat: Translocates folded proteins.

Protein Secretion Systems in Gram-Negative Bacteria

• Types I, II, III, IV, V, VI; differ in structure and function.

• One-step (e.g., Type I, III, IV) vs. two-step (e.g., Type II, V) translocases.

• Some systems transport proteins outside cell; others inject into host cells.

Ch. 7: Microbial Regulatory Systems

Negative vs. Positive Control of Transcription

• Negative control: Repressor proteins inhibit transcription.

• Positive control: Activator proteins enhance transcription.

Operon Regulation (lac, mal, arg)

• lac operon: Inducible; controlled by repressor (LacI) and activator (CRP-cAMP); involved in lactose metabolism.

• mal operon: Inducible; activated by maltose and MalT protein.

• arg operon: Repressible; repressed by arginine (corepressor) and ArgR repressor.

Catabolite Repression and Diauxic Growth

• Catabolite repression: Presence of preferred carbon source (e.g., glucose) inhibits other pathways.

• CRP (cAMP receptor protein) and cAMP regulate lac operon expression.

• Diauxic growth: Sequential use of sugars.

Quorum Sensing

• Cell-density dependent regulation using signaling molecules (autoinducers).

• A. fischeri: Controls bioluminescence.

• Pathogens (e.g., E. coli, S. aureus): Regulate virulence factors.

Ch. 9: Genetics of Bacteria and Archaea

Selectable vs. Non-Selectable Mutants

• Selectable: Confer growth advantage under certain conditions (e.g., antibiotic resistance).

• Non-selectable: No obvious advantage; require screening.

Auxotrophs and Screening

• Auxotroph: Mutant unable to synthesize a required nutrient.

• Detected by replica plating.

Horizontal Gene Transfer Mechanisms

• Transformation: Uptake of free DNA.

• Transduction: DNA transfer by bacteriophages.

• Conjugation: Direct transfer via cell-to-cell contact.

Point Mutations and Effects

• Silent: No amino acid change.

• Missense: Amino acid change.

• Nonsense: Introduces stop codon.

• Degeneracy of genetic code can buffer effects.

Frameshift Mutations

• Caused by insertions/deletions; shift reading frame, often resulting in nonfunctional proteins.

SOS Response

• Induced by DNA damage; RecA and LexA proteins involved.

• RecA promotes repair; LexA represses SOS genes until cleaved.

Homologous Recombination

• Exchange of genetic material between similar sequences; involves RecA protein.

Transposable Elements

• DNA sequences that move within genome.

• Conservative: Element excised and inserted elsewhere.

• Replicative: Copy inserted elsewhere; original remains.

CRISPR in Bacteria

• Adaptive immune system; provides resistance to foreign DNA (e.g., phages).

Bacterial Defense Mechanisms Against Viruses

• Restriction-modification systems, CRISPR, abortive infection systems.