Bacteriophage Biology Quiz

Learning Objectives

• Learning objectives are provided for the final General Microbiology exam at the University of Ottawa.
• Mastering these objectives will help in answering applied questions.
• Synthesis and contextualization of knowledge are essential.

Bacteria

• Cell Morphologies and Arrangements:
  • Bacteria exhibit various shapes (cocci, bacilli, spirochetes).
  • Cell arrangements include diplococci, tetrads, streptococci, staphylococci, and streptobacilli.
• Bacterial Cell Structures:
  • A typical bacterial cell contains a cell membrane, chromosomal DNA (nucleoid), plasmids, ribosomes, and a cell wall.
  • Some prokaryotic cells possess flagella, pili, fimbriae, and capsules.
• Cell Walls:
  • The cell wall provides shape, rigidity, and protection against osmotic pressure.
  • Cell walls consist of peptidoglycan.
  • Gram-positive, gram-negative, and acid-fast bacteria have different cell wall structures.
• Cytoplasmic Membrane:
  • Separates intracellular from extracellular environments.
  • Contains proteins for transport, energy production (respiration), sensing, and secretion.
  • Composed of a lipid bilayer with integral and peripheral proteins.
• Cytoplasm:
  • Contains DNA (nucleoid), RNA, proteins, and ribosomes.
  • Includes other structures like inclusion bodies, magnetosomes, and cytoskeleton.
  • Nucleoid is the region where the chromosomonal DNA is concentrated.
  • Plasmids are extra-chromosomal DNA which carries non-essential genetic information.
• Endospores:
  • Specialized structures of some bacteria for survival under harsh conditions.
  • Complex structures; resistant to desiccation, heat, radiation, and chemicals.
• DNA:
  • Contains dipicolinic acid (DPA) and is enriched in Ca2+.
• Fimbriae and Pili:
• • Fimbriae are used for attachment
• • Pili are used for exchange of genetic material
• Flagella:
• • Used for cell motility
• Thylakoids and Carboxysomes:
  • Unique to photosynthetic bacteria.
  • Thylakoids are extensively folded intracellular membranes.
  • Carboxysomes are polyhedral bodies that contain the enzyme rubisco for CO2 fixation.
  • Gas vesicles are protein-bound gas-filled structures that help with buoyancy.
  • Holds transport proteins in place, creates a proton motive force, and transports polar/ charged molecules.
• Archaea:
  • Archaea are a domain of life distinct from bacteria and eukaryotes.
  • Different physical/chemical structure/function in comparison to bacteria and eukaryotes.
  • Cell walls lack peptidoglycans.
  • Unique lipids with ether linkages.
  • Many differences in their genetic and genomic structure
• • Structures:
    • Pseudo-murein, S-layer, and hami

Viruses

• General structure and composition:
  • All viruses have a genome (DNA or RNA) enclosed in a protein coat (capsid).
  • Some viruses have an additional envelope derived from the host cell membrane.
• Genomes:
  • May be DNA or RNA, linear or circular, single-stranded or double-stranded.
• Viral Replication (life cycles):
• Lytic:
  • Virus replicates rapidly, lyses the host cell to release new viruses.
• Lysogenic:
  • Viral genome integrates into host cell's DNA and can remain dormant.
  • Virus can transition to lytic cycle under certain conditions.
• Viral Entry:
  • Virus must attach to specific receptors on the host cell.
• • Virulent viruses enter host cells while temperate viruses can insert their genome into the host's genome
• Viral Replication:
• Host genome (metabolism) is rechanneled to produce viral components.
• Viral mRNA takes over host cell's machinery to make new virus.
• Viral Assembly and Release:
  • New viral particles assemble.
  • Virus progeny leaves host cell by budding or cell lysis.

Microbial Metabolism

• Catabolism and Anabolism:
  • Catabolism is the breakdown of complex molecules into simpler ones to release energy.
  • Anabolism is the building up of complex molecules from simpler ones using energy released from catabolism.
• Energy Carriers:
  • ATP, NADH, FADH2, PEP are crucial in energy transfer.
• Chemotrophs and Phototrophs:
  • Chemotrophs obtain energy from chemical reactions.
  • Phototrophs obtain energy from light.
• Organotrophs and Lithotrophs:
  • Organotrophs use organic compounds as an electron source.
  • Lithotrophs use inorganic compounds as an electron source.
• Autotrophs and Heterotrophs:
  • Autotrophs make their own organic compounds from inorganic sources (CO2).
  • Heterotrophs obtain organic compounds from other organisms.

Microbial Growth

• Growth Phases:
  • Lag phase, log phase, stationary phase, death phase.
• Environmental Factors:
  • Temperature, pH, osmotic pressure, and oxygen requirement influence growth.
• Microbial Biofilms:
  • Surface-attached communities of microorganisms producing an extracellular matrix.
  • Provide protection and enhanced persistence

Microbial Genetics and Genomics

• Sexual and Asexual Reproduction:
  • Asexual reproduction creates genetically identical copies.
  • Sexual reproduction leads to genetic variation through recombination.
• Horizontal Gene Transfer:
  • Transformation, transduction, and conjugation.
  • Transfer of genes between bacteria, often by plasmids
• Operons:
  • Cluster of genes transcribed together; important in metabolic pathways.
• Regulation:
  • Activator and repressor proteins and two-component systems control gene expression in response to environmental cues.
  • Sigma factors are major players in the regulation by choosing what genes are transcribed
• Global Control Systems (regulons): Coordinate gene expression in response to a wider array of conditions.
• Chromosomal Islands: Code for non-essential genes associated with virulence, antibiotic resistance, or metabolic capabilities.

Microbial Symbiosis with Humans

• Diversity and Dynamics of Microbial Populations:
  • The human microbiome (many species, some are commensals (harmless for the host)).
  • The microbial composition is affected by factors like diet, medications, and age
• Dysbiosis:
  • An imbalance in the gut microbiota leading to illness,
• Role of Commensal Microbiota: -Essential for nutrient digestion, vitamin synthesis and immune system training
• Impact of microbiota on disease:
  • Links between gut microbiota and diseases such as inflammatory bowel disease (IBD)
• Mechanisms of microbial colonization:
  • Adherence, biofilm formation, and immune barriers play a role
• Microbiota and human health and diseases:
  • Impact of a healthy, balanced microbiota on maintaining wellness

Host-Pathogen Responses

• Virulence Factors
  • Microbial products that facilitate colonization, invasion, and damage to host tissues or systems.
• Mechanisms of Pathogenesis
  • Virulence factors are mechanisms used by pathogens to cause infections or diseases
• Cellular and Systemic Mechanisms of Action:
  • Microbial toxins (endogenous or exogenous), and their impact on cellular structures or signalling pathways.
• Secretion Systems (particularly T3SS):
  • Special pathways that bacteria use to transport effector proteins into host cells.
• Effectors:
  • Proteins secreted by a pathogen that interfere with host cellular processes.