Comparative Genomics and Endosymbiotic Theory
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Questions and Answers

What percentage of genetic material do Eukarya share with Archaea, primarily related to information processing?

  • 10% (correct)
  • 20%
  • 30%
  • 5%

    • Which of the following best describes the pan-genome?

  • The complete set of shared genes in all strains of a species
  • The genes that are unique to specific strains within a species
  • The common genes involved in basic metabolic processes
  • All of the genes present in the strains of a species (correct)

    • What is the main function of the genes shared with bacteria by Eukarya?

  • Metabolic functions such as glycolysis (correct)
  • Protein synthesis
  • Information processing
  • Cellular respiration

    • According to the endosymbiotic theory, how did mitochondria originate?

    <p>From the engulfment of a cell capable of aerobic respiration</p> Signup and view all the answers

    Which component of a genome includes genes that are not shared by all strains of a species?

    <p>Flexible genome</p> Signup and view all the answers

    What are exotoxins primarily characterized by?

    <p>Being secreted proteins that are highly toxic and lethal</p> Signup and view all the answers

    Which immune system component is primarily responsible for rapid defense against a broad range of pathogens?

    <p>Innate immunity</p> Signup and view all the answers

    What role do M cells in the gastrointestinal tract serve in relation to the lymphatic system?

    <p>They capture pathogens crossing mucous membranes</p> Signup and view all the answers

    How do neutrophils function in the immune response?

    <p>They primarily function as phagocytes</p> Signup and view all the answers

    What is the main function of defensins in the immune system?

    <p>To act as antimicrobial peptides</p> Signup and view all the answers

    What distinguishes adaptive immunity from innate immunity?

    <p>Adaptive immunity targets specific pathogens</p> Signup and view all the answers

    What process do macrophages participate in after they encounter pathogens?

    <p>They promote inflammation and cytokine secretion</p> Signup and view all the answers

    What is the primary role of the lymphatic system?

    <p>To filter pathogens and facilitate immune responses</p> Signup and view all the answers

    What characteristic is associated with endotoxins?

    <p>They are found in the outer membrane of gram-negative bacteria</p> Signup and view all the answers

    Which cells are primarily involved in presenting antigens to T cells?

    <p>Dendritic cells</p> Signup and view all the answers

    What is the role of perforins in the immune response?

    <p>To form pores in the cell membrane of infected cells</p> Signup and view all the answers

    Which type of immunity results from the direct interaction of antibodies with an antigen?

    <p>Humoral immunity</p> Signup and view all the answers

    What molecules are typically considered not immunogenic due to their flexibility?

    <p>Nucleic acids and lipids</p> Signup and view all the answers

    In the context of immunity, what distinguishes active immunity from passive immunity?

    <p>Active immunity results from infection or vaccination, while passive is acquired from another source</p> Signup and view all the answers

    What is the primary function of a memory cell in the immune response?

    <p>To rapidly convert to plasma cells upon re-exposure to the same antigen</p> Signup and view all the answers

    How do interferons contribute to the defense against viral infections?

    <p>By stimulating uninfected cells to produce antiviral proteins</p> Signup and view all the answers

    What is the role of antibodies in the complement system?

    <p>They facilitate the killing of pathogens bound to them</p> Signup and view all the answers

    What distinguishes T cell-dependent antigens from T cell-independent antigens?

    <p>T cell-dependent antigens require T cell help for B cell activation</p> Signup and view all the answers

    Which type of protein is produced by B cells in response to an antigen?

    <p>Antibodies</p> Signup and view all the answers

    What happens during the primary immune response?

    <p>B cells multiply and differentiate into plasma and memory cells</p> Signup and view all the answers

    What best describes the relationship of obligate mutualists?

    <p>They can only survive together and are found in all hosts.</p> Signup and view all the answers

    Which of the following is a criterion to determine if two bacterial strains are the same species?

    <p>They have 97%+ similarity in their 16S rRNA sequences.</p> Signup and view all the answers

    What is indicated by the length of branches in a phylogenetic tree?

    <p>The relatedness of the organisms.</p> Signup and view all the answers

    Which term refers to a prolonged association between different species that can vary in its effects?

    <p>Symbiosis</p> Signup and view all the answers

    What defines a strain in microbiology?

    <p>A population descended from a single organism.</p> Signup and view all the answers

    Why is the gut microbiome considered to be in a delicate state of equilibrium?

    <p>It is subject to constant changes and can easily be disrupted.</p> Signup and view all the answers

    What is the role of rhizobia in symbiotic relationships with legumes?

    <p>They fix nitrogen for the plants.</p> Signup and view all the answers

    In the classification of a bacterial name, which of the following is correct?

    <p>Genus + species + strain</p> Signup and view all the answers

    What correctly characterizes the human microbiome?

    <p>It includes all microbes found in and on the human body.</p> Signup and view all the answers

    What process is correctly described as the growth of a pathogen on or in a host?

    <p>Infection</p> Signup and view all the answers

    What is true about ectomycorrhizal fungi?

    <p>They are mostly found on forest trees and colonize roots.</p> Signup and view all the answers

    Which of the following mechanisms helps to minimize microbial growth in the oral cavity?

    <p>Continuous mechanical flushing from salivation</p> Signup and view all the answers

    Study Notes

    Comparative Genomics

    • Shared Genes: Bacteria and Eukarya share 20% of genes, primarily for metabolic functions (like glycolysis). Archaea and Eukarya share 10% of genes, mostly for information processing (DNA replication).
    • Unique Genes: 70% of eukaryotic genes are unique to Eukarya.
    • Core Genome: All strains of a species share these genes.
    • Flexible Genome: Genes not shared by all strains.
    • Pan-Genome: All genes present in strains of a species.
    • Applications: This approach can analyze both closely related and highly divergent organisms.

    Endosymbiotic Theory

    • Origin of Eukaryotic Cells: Eukaryotic cells arose from one prokaryotic cell engulfing another.
    • Mitochondria: Derived from aerobic respiration-capable cells.
    • Chloroplasts: Derived from oxygenic photosynthesis-capable cells.
    • Evidence: Both mitochondria and chloroplasts possess outer and inner membranes, bacterial-like ribosomes, and circular chromosomes.

    Serial Endosymbiosis

    • Sequential Engulfment: Archaeal cells sequentially engulfed other cells to form mitochondria and chloroplasts.

    Symbiogenesis

    • Symbiosis First: Archaeal cells formed a symbiotic relationship with the ancestor of mitochondria before developing a nucleus.

    LUCA (Last Universal Common Ancestor)

    • The hypothesized ancestor of all living organisms.

    Microbial Systematics

    • Phylogeny: Evolutionary history of organisms, inferred from genetic relatedness.
    • Phylogenetic Tree: Diagram displaying evolutionary relationships; branch length signifies relatedness.
    • Classification: Grouping organisms into taxa.
    • Nomenclature: Naming groups of organisms systematically.
    • Molecular Clocks: Using molecules to track the timing of lineages branching apart. It requires similar function in the different organisms in order to work properly.

    Species Definitions (Prokaryotes & Higher Organisms)

    • Higher Organisms: A species is a group of interbreeding organisms reproductively isolated from other groups.
    • Prokaryotes: A species is a collection of strains with shared stable phenotypic and genotypic traits, descended from a common ancestor.

    Strain Criteria (Prokaryotes)

    • 16S rRNA sequence similarity: 97%+ similarity indicates same species.
    • DNA hybridization: >70% genomic sequence hybridization suggests same species.
    • Average nucleotide identity (ANI): >95% similarity in orthologous genes implies same species.

    Bacterial Names

    • Consist of genus + species + strain

    Taxon

    • A set of microbes that share a predefined level of similarity.

    Candidatus

    • A new species described from genetic data but with no cultured strains. Must be documented and strains kept in culture collections, and the designated strain is the type strain of the species.

    Microbial Ecology

    • Population: Assemblage of similar organisms in a specific location.
    • Community: Assemblage of populations in a specific location.
    • Symbiosis: Prolonged, intimate association of different species.
    • Commensalism: One organism benefits, the other is unaffected.
    • Mutualism: Both species benefit.
    • Parasitism: One species benefits at the expense of another.
    • Obligate mutualists: Depend on each other for survival. (Ex. Rhizobium and legumes)

    Rhizobia

    • Bacteria that form nitrogen-fixing symbioses with plants.

    Ectomycorrhizal

    • Fungi that colonize within roots of principally forest trees.

    Microbe-Insect Relationships

    • Many insects have obligate mutualistic relationships with bacteria (vertical transmission). Some can also have relationships that are obligate based on whether it is the microbe being beneficial or not to the host (horizontal transmission).
    • Primary symbionts: Mutualism is obligate for both.
    • Secondary symbionts: Mutualism is obligate only for the microbe.

    Human Microbiome

    • All microbes in and on the human body.
    • Primarily housed in areas outside the epidermal layers in a healthy host (not organs, etc)

    Human GI Tract Microbiome

    • Digestion and Nutrients: Site for food digestion and nutrient absorption.
    • Mucous Membranes: Lined with mucous membranes.
    • Mucin: Glycoprotein layer that inhibits microbial attachment.
    • pH Variation: Stomach (very acidic), small intestine (transitional, increases to ~7), large intestine (relatively less acidic).
    • Pathogen Colonization: Antibiotics can disrupt the balance, allowing pathogens to emerge. Fecal transplants can help restore normal microflora.
    • Clostridium difficile: A gut pathogen typically kept in check by normal gut microbiome

    Human Oral Cavity Microbiome

    • Mucous Membranes: Lined with a mucous membrane.
    • Defense Mechanisms: Saliva with antibacterial enzymes, mechanical flushing, and epithelial cell turnover.
    • Dental Plaque: Multispecies biofilm on teeth. Fluoride strengthens calcium phosphate to prevent decalcification.

    Human Skin Microbiome

    • Acidic Environment: Acidic pH (4-6) due to fatty acids in sweat. Higher microbial density in moister regions.
    • Sebum: Sebum further contributes to the acidity of the skin surface from secreted oil.

    Pathogen, Infection, and Disease

    • Pathogen: Microorganism causing disease.
    • Infection: Pathogen growth in or on a host.
    • Disease: Host tissue damage due to a pathogen.
    • Infection Process: Adherence, invasion, spread.
    • Virulence Factors: Traits contributing to pathogenicity.
    • Exotoxins: Secreted proteins. Highly toxic and lethal.
    • Endotoxins: Outer membrane lipids from Gram-negative bacteria; released upon lysis. Moderately toxic.

    Immunology

    • Innate Immunity: Broad-spectrum, rapid (hours). Phagocytes are major player.
    • Adaptive Immunity: Specific, slow (days). Lymphocytes are major players.

    Competitive Exclusion

    • Microbiome's ability to outcompete invaders.

    Physical and Chemical Barriers

    • Physical Barriers: Skin tight junctions, mucociliary escalator, blood-brain barrier
    • Chemical Barriers: Stomach acidity, skin secretions, defensins
    • Physical and chemical barriers are essential for inhibiting infections.

    Lymphatic System

    • Lymph: Fluid-like blood, without red blood cells.
    • Primary Organs: Thymus and bone marrow— sites where cells responsible for antibody production.
    • Secondary Organs: Spleen, lymph nodes, MALT— filter and monitor for pathogens.
    • MALT (Mucosa-Associated Lymphoid Tissue): Specialized for pathogens traversing mucous membranes, like M cells of the GI tract.
    • Lymph Nodes: Filter lymph, promote interactions between immune cells and pathogens.

    Immune System Cells

    • Erythrocytes: Red blood cells— oxygen transport.
    • Leukocytes: White blood cells— immune response.
    • Plasma: Fluid component of blood, without clotting proteins.
    • Serum: Plasma minus clotting proteins.
    • Monocytes: Circulate in blood, differentiate into macrophages (phagocytes) and dendritic cells (antigen-presenting cells).
    • Phagocytes: Ingest and destroy pathogens (Ex. neutrophils, macrophages, dendritic cells)
    • Neutrophils: Major circulating phagocytes.
    • Eosinophils: Minor phagocytes.
    • Basophils and mast cells: Involved in inflammatory response, not phagocytic.

    Phagocytosis

    • Pathogen uptake and destruction.
    • Inflammation, fever, cell death (by NK cells), interferon production are part of the process.
    • Pathogens can avoid phagocytosis via various mechanisms like carotenoid production, capsules that are impenetrable, and leukocidins.

    Pathogen Recognition

    • PAMPs (Pathogen-Associated Molecular Patterns): Surface molecules on pathogens.
    • PRRs (Pattern Recognition Receptors): On phagocytes, recognize PAMPs.

    MHC-1 & Cellular Immunity Mechanisms

    • MHC-1 (Major Histocompatibility Complex 1): Surface proteins on all nucleated cells.
    • Virus-infected cells: Often repress MHC-1 genes.
    • Cancer cells: Often do not express MHC-1.
    • Natural Killer (NK) cells: Recognize and destroy cells lacking MHC-1 (virus-infected or cancer).
    • Cytotoxic T cells or T-killer cells use perforin to lyse a cell and granzymes to destroy its contents.

    Interferons

    • Cytokines: Small soluble proteins affecting cell behavior.
    • Viral Inhibition: Stimulate uninfected cells to produce antiviral proteins.

    Adaptive Immunity

    • Humoral: Antibody-mediated immunity (B cells).
    • Cell-mediated: T cell-mediated immunity (T cells).

    Antibodies

    • B cell receptors (BCRs): Membrane-bound antibodies on B cells.
    • T cell receptors (TCRs): Cell surface proteins on T cells bind to antigens.
    • Serum: Blood plasma minus clotting proteins.
    • Antiserum: Serum with specific antibodies.
    • Cross-reactions: Antibodies binding to similar antigens.

    Active vs. Passive Immunity

    • Active: Long-lived immunity.
    • Passive: Short-lived immunity (e.g., from mother to child).

    Antibody Functions

    • Neutralize toxins
    • Block virus binding
    • Mark pathogens for destruction by phagocytes or complement
    • Complement: Proteins marking pathogens for destruction.

    Antigens

    • Substances triggering an immune response.
    • Epitopes: Specific regions of an antigen recognized by immune system.

    B Cell Activation

    • B cell activation and antibody production to specific antigens depends on whether the antigen is T dependent or independent

    T-Dependent vs. T-Independent Antigens

    • T-dependent: Require T cell activation. Not easily recognized by a B-cell.
    • T-independent: Activate B cells directly, often multivalent Antigens.

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    Description

    This quiz explores the concepts of comparative genomics, focusing on gene sharing among bacteria, archaea, and eukarya, as well as the endosymbiotic theory which explains the origin of eukaryotic cells. Understand the core and flexible genomes, pan-genomes, and the evidence supporting the evolution of mitochondria and chloroplasts. Test your knowledge on these foundational biological principles.

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