Chapter 3 Notes: Bacteria and Archaea (McGraw Hill 2022)

Bacteria and Archaea: Comprehensive Notes (Chapter 3)

  • Scope: Bacteria and Archaea overview with emphasis on cellular structures, shapes, envelopes, external appendages, cytoplasm components, endospores, archaea differences, and taxonomic concepts as presented in the 2022 McGraw Hill Fundamentals text.

Structures common to all bacteria

  • All bacterial cells possess:
    • Cytoplasmic membrane
    • Cytoplasm
    • Ribosomes
    • Cytoskeleton
    • One (or a few) chromosome(s)
  • Most bacterial cells possess:
    • Cell wall
    • A surface coating called a glycocalyx
  • Key numerical references:
    • Average bacterial size is about 1 μm1\,\mu m (single cells)
    • Cocci typically have a circumference of about 1 μm1\,\mu m; rods often about 2 μm  long2\,\mu m\;\text{long} and 1 μm  wide1\,\mu m\;\text{wide}
  • Pleomorphism: variations in cell wall structure due to slight genetic or nutritional differences

Structures found in some bacteria (not universal)

  • Flagella, Pili (fimbriae), and Nanowires/Nanotubes
  • Outer membrane (in Gram-negatives and some others)
  • Plasmids
  • Inclusions
  • Endospores
  • Microcompartments
  • Note: Many of these features are also observed in archaea

Basic bacterial cell anatomy (illustrative structure)

  • Cytoplasmic membrane: phospholipid bilayer controlling material flow
  • Cytoplasm: aqueous matrix with macromolecules
  • Ribosomes: sites of protein synthesis
  • Cytoskeleton: contributes to cell shape; potential antibiotic target
  • Chromosome(s): typically a single circular chromosome located in the nucleoid

Bacterial shapes and arrangements

  • Shapes:
    • Coccus (spherical)
    • Bacillus (rod-shaped)
    • Vibrio (gently curved rod)
    • Spirillum (slightly curled or spiral)
    • Spirochete (more flexible spiral with periplasmic flagella)
    • Branching filaments (e.g., Streptomyces)
  • Size references:
    • Cocci: ~ 1 μm1\,\mu m in circumference
    • Rods: ~ 2 μm2\,\mu m long and 1 μm1\,\mu m wide
  • Pleomorphism: variation in shape due to genetic/nutritional differences

Bacterial arrangements (Cocci and Bacilli)

  • Cocci arrangements:
    • Single
    • Diplococci: pairs
    • Tetrads: groups of four
    • Staphylococci/micrococci: irregular clusters
    • Streptococci: chains
    • Sarcina: cubical packets of eight, sixteen, or more
  • Diagrams illustrate division planes:
    • One plane: diplococcus; chains (Streptococcus)
    • Two perpendicular planes: tetrad; sarcina
    • Several planes: irregular clusters; staphylococci/micrococci
  • Bacilli arrangements:
    • Single
    • Diplobacilli: pair
    • Streptobacilli: chain
    • Palisades: chain ends attached by hinge-like region (Corynebacterium)
  • Spirilla and Spirochetes:
    • Spirilla: short chains; rigid
    • Spirochetes: flagella (axial/periplasmic) internal to cell wall

External structures and motility appendages

  • Appendages enable motility (flagella) or attachment (fimbriae, pili) or intercellular channels (nanotubes/nanowires)
  • Flagellum:
    • Primary function: motility
    • Three main parts: Filament, Hook (sheath), Basal body
  • Flagellar arrangements:
    • Polar: attached at one or both ends
    • Monotrichous: single flagellum
    • Lophotrichous: tuft from same site
    • Amphitrichous: flagella at both poles
    • Peritrichous: flagella dispersed over the surface
  • Fine points of flagellar function (Chemotaxis): movement toward/away from chemical stimuli
    • Positive chemotaxis: movement toward favorable chemical stimulus
    • Negative chemotaxis: movement away from repellant
    • Run: flagellum rotates counterclockwise (CCW) for straight movement
    • Tumble: rotation changes direction, reorients cell
  • Periplasmic flagella (axial filaments) in spirochetes:
    • Internal flagellum enclosed between cell wall and cytoplasmic membrane
    • Produces corkscrew-like locomotion
  • Attachment and channels:
    • Fimbriae (fimbria): thin, hair-like; tight adhesion to epithelial cells; assist colonization and infection
    • Pili: used in conjugation; Type IV pili can transfer genetic material, assist attachment, and enable motility
    • Nanotubes/Nanowires: thin extensions used to transfer metabolites or harvest energy (electrons) from environment
  • Conjugation and transfer: fimbriae and pili mediate genetic exchange between bacteria

S layer and glycocalyx

  • S layer: a single layer of protein monolayers; produced in hostile environments; protective and attachment roles
  • Glycocalyx: coating of repeating polysaccharide or glycoprotein units
    • Slime layer: loose, protects against water/nutrient loss
    • Capsule: tightly bound, dense; imparts mucoid appearance to colonies
  • Positioning: S layer and glycocalyx overlay the cell; may be outside the peptidoglycan layer depending on species
  • Encapsulated bacteria: examples of disease association and immune interactions
  • Glycocalyx functions:
    • Capsule formation linked to increased pathogenicity (evading phagocytes)
    • Biofilms: dental plaque; persistence on catheters, IUDs, implants; protection from dislodgement
  • Biofilm formation process:
    • Surface colonization by first cells via glycocalyx
    • Growth into a dense, cohesive microbial mat bound by extracellular deposits
    • Maturation into a complex, multi-species community with enhanced intercellular cooperation

Concept Check (2)

  • Question: Which appendages are used for attachment? (Choose one not used for attachment) A. Slime layer B. Flagellum C. Pilus D. Fimbriae

The cell envelope: two or three layers

  • The cell envelope lies outside the cytoplasm and can include:
    • Cell wall
    • Cytoplasmic membrane
    • Outer membrane (in some bacteria)
  • Gram-positive vs Gram-negative cell envelopes (contrast)
  • Outer membrane contributes an extra barrier in Gram-negative cells; differences influence antimicrobial susceptibility
  • Alcohol-based sanitizers disrupt lipids in the outer membrane, aiding lysis of Gram-negative cells; Gram-positive cells are more affected by other mechanisms due to their thicker peptidoglycan
  • Drugs targeting the envelope may need to cross the outer membrane in Gram-negative bacteria

The cell wall and peptidoglycan

  • Purpose: defines shape; provides structural integrity to resist osmotic lysis
  • Peptidoglycan structure:
    • Repeating glycan chains cross-linked by short peptide fragments
    • Provides a strong but flexible supportive framework
  • Bacterial cell wall thickness differences:
    • Gram-positive cell wall: thick, homogeneous layer of peptidoglycan; approx 20−80 nm20-80\,nm thick; contains teichoic and lipoteichoic acids
    • Gram-negative cell wall: a thin layer of peptidoglycan within an outer membrane; approx 1−3 nm1-3\,nm thick; additional outer membrane contributes to barrier function
  • Teichoic acids and lipoteichoic acids contribute to negative charge on the cell surface and wall maintenance

Peptidoglycan chemistry (highlights)

  • Glycan backbone: alternating residues NN{-acetylglucosamine} (G) and NN{-acetylmuramic acid} (M)</li><li>Peptidecross−links:shortpeptides(tetrapeptides)linkedtoMurNAcresidues</li><li>Cross−linksandinterbridgesstabilizethemesh;penicillinandrelatedantibioticstargettheselinkages</li><li>Importantterminology:<ul><li>G=N−acetylglucosamine</li><li>M=N−acetylmuramicacid</li><li>Tetrapeptide:sequenceofaminoacids(e.g.,L−alanine,D−glutamate,L−lysine,D−alanine)inMurNAcsidechains</li><li>Cross−linksproviderigidity;disruptionleadstolysis</li></ul></li></ul><h4id="grampositivevsgramnegativecellenvelopesvisualcontrasts">Gram−positivevsGram−negativecellenvelopes(visualcontrasts)</h4><ul><li>Gram−positive:<ul><li>Thickpeptidoglycanlayerwithteichoic/lipoteichoicacids</li><li>Nooutermembrane</li></ul></li><li>Gram−negative:<ul><li>Thinpeptidoglycanlayersandwichedbetweencytoplasmicmembraneandoutermembrane</li><li>OutermembranecontainsLPSandporins;periplasmicspaceliesbetweenmembranes</li></ul></li><li>ConsequencesforstainingandantibioticsusceptibilityasdescribedinGramstainprocedure</li></ul><h4id="nontypicalcellwalls">Nontypicalcellwalls</h4><ul><li>Acid−fastbacteria(Mycobacterium,Nocardia):<ul><li>Containpeptidoglycanbutenrichedwithmycolicacids(verylong−chainfattyacids)</li><li>Lipid−richcellwallmakesthemresistanttomanychemicalsanddyes;requireacid−faststaining(e.g.,Ziehl−Neelsen)</li></ul></li><li>Archaea:cellwallschemicallydistinct;lacktruepeptidoglycan<ul><li>Somewallsarepolysaccharide−based;othersareprotein−based;somearchaealackacellwallentirely</li></ul></li><li>Mycoplasmas:cell−wall−deficientbacteria;membranestabilizedbysterols;example:Mycoplasmapneumoniae(causeswalkingpneumonia)</li><li>Lforms:bacteriathatcanlosetheircellwallduringpartoftheirlifecycle;associatedwithpersistentinfectionsandantibioticresistance</li></ul><h4id="thegramnegativeoutermembrane">TheGram−negativeoutermembrane</h4><ul><li>Composition:similartoothermembranesbutincludesspecializedpolysaccharidesandproteins</li><li>Lipopolysaccharide(LPS):signalingmolecules/receptors;endotoxiceffects</li><li>Porinproteins:outermembranechannelsthatregulatepermeabilitytosmallmolecules</li><li>Outermembraneprovidesanadditionalpermeabilitybarrierandcontributestointrinsicresistance</li></ul><h4id="thecytoplasmicmembrane">Thecytoplasmicmembrane</h4><ul><li>Structure:phospholipidbilayerwithembeddedproteins</li><li>Functions:<ul><li>Siteofenergyreactionsandnutrientprocessing</li><li>Synthesisofcellularcomponents</li><li>Regulatestransportofnutrientsandwastes;selectivelypermeableviatransportproteins</li></ul></li></ul><h4id="differencesinenvelopestructureandimplications">Differencesinenvelopestructureandimplications</h4><ul><li>Gram−negativeoutermembraneaddsabarrierthatcancomplicateantibiotictreatment</li><li>Alcohol−basedhandsanitizersdisruptlipidsandmembranes;efficacyvariesbyorganism</li><li>ConceptCheck(3):True/FalseitemaboutoutermembranebarrierandGram−positives</li></ul><h4id="thecytoplasmanditsinclusions">Thecytoplasmanditsinclusions</h4><ul><li>Thecytoplasm:<ul><li>About</li> <li>Peptide cross-links: short peptides (tetrapeptides) linked to MurNAc residues</li> <li>Cross-links and interbridges stabilize the mesh; penicillin and related antibiotics target these linkages</li> <li>Important terminology:<ul> <li>G = N-acetylglucosamine</li> <li>M = N-acetylmuramic acid</li> <li>Tetrapeptide: sequence of amino acids (e.g., L-alanine, D-glutamate, L-lysine, D-alanine) in MurNAc side chains</li> <li>Cross-links provide rigidity; disruption leads to lysis</li></ul></li> </ul> <h4 id="grampositivevsgramnegativecellenvelopesvisualcontrasts">Gram-positive vs Gram-negative cell envelopes (visual contrasts)</h4> <ul> <li>Gram-positive:<ul> <li>Thick peptidoglycan layer with teichoic/lipoteichoic acids</li> <li>No outer membrane</li></ul></li> <li>Gram-negative:<ul> <li>Thin peptidoglycan layer sandwiched between cytoplasmic membrane and outer membrane</li> <li>Outer membrane contains LPS and porins; periplasmic space lies between membranes</li></ul></li> <li>Consequences for staining and antibiotic susceptibility as described in Gram stain procedure</li> </ul> <h4 id="nontypicalcellwalls">Nontypical cell walls</h4> <ul> <li>Acid-fast bacteria (Mycobacterium, Nocardia):<ul> <li>Contain peptidoglycan but enriched with mycolic acids (very long-chain fatty acids)</li> <li>Lipid-rich cell wall makes them resistant to many chemicals and dyes; require acid-fast staining (e.g., Ziehl-Neelsen)</li></ul></li> <li>Archaea: cell walls chemically distinct; lack true peptidoglycan<ul> <li>Some walls are polysaccharide-based; others are protein-based; some archaea lack a cell wall entirely</li></ul></li> <li>Mycoplasmas: cell-wall-deficient bacteria; membrane stabilized by sterols; example: Mycoplasma pneumoniae (causes walking pneumonia)</li> <li>L forms: bacteria that can lose their cell wall during part of their life cycle; associated with persistent infections and antibiotic resistance</li> </ul> <h4 id="thegramnegativeoutermembrane">The Gram-negative outer membrane</h4> <ul> <li>Composition: similar to other membranes but includes specialized polysaccharides and proteins</li> <li>Lipopolysaccharide (LPS): signaling molecules/receptors; endotoxic effects</li> <li>Porin proteins: outer membrane channels that regulate permeability to small molecules</li> <li>Outer membrane provides an additional permeability barrier and contributes to intrinsic resistance</li> </ul> <h4 id="thecytoplasmicmembrane">The cytoplasmic membrane</h4> <ul> <li>Structure: phospholipid bilayer with embedded proteins</li> <li>Functions:<ul> <li>Site of energy reactions and nutrient processing</li> <li>Synthesis of cellular components</li> <li>Regulates transport of nutrients and wastes; selectively permeable via transport proteins</li></ul></li> </ul> <h4 id="differencesinenvelopestructureandimplications">Differences in envelope structure and implications</h4> <ul> <li>Gram-negative outer membrane adds a barrier that can complicate antibiotic treatment</li> <li>Alcohol-based hand sanitizers disrupt lipids and membranes; efficacy varies by organism</li> <li>Concept Check (3): True/False item about outer membrane barrier and Gram-positives</li> </ul> <h4 id="thecytoplasmanditsinclusions">The cytoplasm and its inclusions</h4> <ul> <li>The cytoplasm:<ul> <li>About70\%\text{–}80\%water</li><li>Complexmixtureofsugars,aminoacids,andsalts</li></ul></li><li>Chromosomesandplasmids:<ul><li>Bacterialchromosomelocatedinthenucleoidregion</li><li>Plasmids:small,circular,nonessentialDNAthatconfertraitslikedrugresistanceortoxinproduction</li></ul></li><li>Ribosomes:<ul><li>Proteinsynthesissites;composedofrRNAandprotein</li><li>Subunits:small30Sandlarge50S;togetherforma70Sribosomeinbacteria</li><li>Innotation:water</li> <li>Complex mixture of sugars, amino acids, and salts</li></ul></li> <li>Chromosomes and plasmids:<ul> <li>Bacterial chromosome located in the nucleoid region</li> <li>Plasmids: small, circular, nonessential DNA that confer traits like drug resistance or toxin production</li></ul></li> <li>Ribosomes:<ul> <li>Protein synthesis sites; composed of rRNA and protein</li> <li>Subunits: small 30S and large 50S; together form a 70S ribosome in bacteria</li> <li>In notation:70S = 30S + 50S;archaealribosomeisalso; archaeal ribosome is also70Sbutmorecloselyrelatedtoeukaryotic80S;eukaryoticribosomeis80S</li></ul></li><li>Inclusionsandmicrocompartments:<ul><li>Foodstoragegranules</li><li>Gasvesiclesforbuoyancy</li><li>Ironoxidecrystalsformagneticproperties</li><li>Bacterialmicrocompartments:proteinshellsenclosingenzymesforspecificbiochemicalpathways</li></ul></li><li>Cytoskeleton:protein−basedfilamentsthathelpshapethecell;presentinsomebacteriaandarchaea;potentialantibiotictarget</li></ul><h4id="endosporessporulationandgermination">Endospores:sporulationandgermination</h4><ul><li>Endosporesaredormant,highlyresistantstructuresformedbycertainbacteria(e.g.,Bacillus,Clostridium,Sporosarcina)tosurviveharshconditions</li><li>Sporulationistriggeredbynutrientdepletionandenvironmentalstress;germinationresumesvegetativegrowthwhenconditionsimprove</li><li>Endosporestructurecomponents:<ul><li>Core,cortex,coatlayers,exosporium</li><li>DormantcorecontainsDNAandessentialcomponents;resistanttoheat,desiccation,radiation,chemicals</li></ul></li><li>Medicalsignificanceofendospores:<ul><li>Bacillusanthracis(anthrax)</li><li>Clostridiumtetani(tetanus)</li><li>Clostridiumperfringens(gasgangrene)</li><li>Clostridiumbotulinum(botulism)</li><li>Clostridioidesdifficile(C.diff)</li></ul></li><li>Sporulationprocess(Bacillusspecies)–high−levelsteps:<ul><li>Vegetativecelldepletesnutrients</li><li>Chromosomeduplicationandsegregation</li><li>Divisiontoformasporangiumandforespore</li><li>Sporangiumengulfsforespore</li><li>Endosporecoatformationbeginsaroundforespore</li><li>Cortexandoutercoatlayersdeposited</li><li>Maturationintoamatureendospore</li><li>Endosporereleasedaftersporangiumlysis</li><li>Germination:endosporeswellsandreturnstovegetativecell</li></ul></li></ul><h4id="archaeadistinctivefeatures">Archaea:distinctivefeatures</h4><ul><li>Athirdcelltypeinaseparatesuperkingdom;morecloselyrelatedtoEukaryathantoBacteriainseveralrespects<ul><li>SharesrRNAsequencesnotfoundinbacteria</li><li>ProteinsynthesisandribosomalsubunitstructuresresembleEukarya</li></ul></li><li>Archaeadifferfrombacteriain:<ul><li>UniquerRNAsignatures</li><li>NovelDNApackagingmethods</li><li>Uniquemembranelipidsandcellwallcomponents(notruepeptidoglycan)</li></ul></li><li>Extremophiles:someliveinextremetemperatures,salinities,pH,orsulfur/methaneenvironments</li><li>Somearchaeacolonizethehumanbodyandmaybeimplicatedindiseaseincertaincontexts</li></ul><h4id="comparisonofthethreecellulardomains">Comparisonofthethreecellulardomains</h4><ul><li>Keytablehighlights(conceptual):<ul><li>Chromosomes:Bacteria−single/circular;Archaea−single/circular;Eukarya−multiple/linear</li><li>Ribosomes:Bacteria−70S;Archaea−70S;Eukarya−80S</li><li>Cellwall:Bacteria−peptidoglycan(presentinmost);Archaea−rarelypeptidoglycan;Eukarya−absent(inmostorganisms)</li><li>Cytoplasmicmembranelipids:Bacteria−fattyacidswithesterlinkages;Archaea−branchedhydrocarbonswithetherlinkages;Eukarya−similartobacteria(ester)</li><li>Sterolsinmembrane:Bacteria−generallyabsentorvariable;Archaea−absent;Eukarya−presentinmanymembranes</li><li>Nucleusandmembrane−boundorganelles:Bacteria−No;Archaea−No;Eukarya−Yes</li><li>Flagella:Bacteria−bacterialflagellum;Archaea−archaellum;Eukarya−eukaryoticflagellum</li></ul></li></ul><h4id="bergeysmanualandtaxonomyinbacteriaarchaea">Bergey’sManualandtaxonomyinbacteria/archaea</h4><ul><li>Bergey’sManualofSystematicBacteriology:<ul><li>ComprehensiveviewofrelatednessbasedonrRNAsequencing</li></ul></li><li>Bergey’sManualofDeterminativeBacteriology:<ul><li>Basedonphenotypiccharacteristics(shape,metabolictraits,etc.)usedinclinical/labcontexts</li></ul></li></ul><h4id="taxonomicschemeandmajordivisions">Taxonomicschemeandmajordivisions</h4><ul><li>Fourmajordivisionsbycell−walltype:<ul><li>Gracilicutes:Gram−negativewiththincellwalls</li><li>Firmicutes:Gram−positivewiththick,strongcellwalls</li><li>Tenericutes:lackacellwall;soft</li><li>Mendosicutes:archaeawithunusualcellwalls/nutritionalhabits</li></ul></li></ul><h4id="speciesandsubspeciesconceptsinbacteriaarchaea">Speciesandsubspeciesconceptsinbacteria/archaea</h4><ul><li>Bacterialspecies:acollectionofcellssharingabroadlysimilartraitpattern;typicallyshareatleastbut more closely related to eukaryotic 80S; eukaryotic ribosome is 80S</li></ul></li> <li>Inclusions and microcompartments:<ul> <li>Food storage granules</li> <li>Gas vesicles for buoyancy</li> <li>Iron oxide crystals for magnetic properties</li> <li>Bacterial microcompartments: protein shells enclosing enzymes for specific biochemical pathways</li></ul></li> <li>Cytoskeleton: protein-based filaments that help shape the cell; present in some bacteria and archaea; potential antibiotic target</li> </ul> <h4 id="endosporessporulationandgermination">Endospores: sporulation and germination</h4> <ul> <li>Endospores are dormant, highly resistant structures formed by certain bacteria (e.g., Bacillus, Clostridium, Sporosarcina) to survive harsh conditions</li> <li>Sporulation is triggered by nutrient depletion and environmental stress; germination resumes vegetative growth when conditions improve</li> <li>Endospore structure components:<ul> <li>Core, cortex, coat layers, exosporium</li> <li>Dormant core contains DNA and essential components; resistant to heat, desiccation, radiation, chemicals</li></ul></li> <li>Medical significance of endospores:<ul> <li>Bacillus anthracis (anthrax)</li> <li>Clostridium tetani (tetanus)</li> <li>Clostridium perfringens (gas gangrene)</li> <li>Clostridium botulinum (botulism)</li> <li>Clostridioides difficile (C. diff)</li></ul></li> <li>Sporulation process ( Bacillus species ) – high-level steps:<ul> <li>Vegetative cell depletes nutrients</li> <li>Chromosome duplication and segregation</li> <li>Division to form a sporangium and forespore</li> <li>Sporangium engulfs forespore</li> <li>Endospore coat formation begins around forespore</li> <li>Cortex and outer coat layers deposited</li> <li>Maturation into a mature endospore</li> <li>Endospore released after sporangium lysis</li> <li>Germination: endospore swells and returns to vegetative cell</li></ul></li> </ul> <h4 id="archaeadistinctivefeatures">Archaea: distinctive features</h4> <ul> <li>A third cell type in a separate superkingdom; more closely related to Eukarya than to Bacteria in several respects<ul> <li>Shares rRNA sequences not found in bacteria</li> <li>Protein synthesis and ribosomal subunit structures resemble Eukarya</li></ul></li> <li>Archaea differ from bacteria in:<ul> <li>Unique rRNA signatures</li> <li>Novel DNA packaging methods</li> <li>Unique membrane lipids and cell wall components (no true peptidoglycan)</li></ul></li> <li>Extremophiles: some live in extreme temperatures, salinities, pH, or sulfur/methane environments</li> <li>Some archaea colonize the human body and may be implicated in disease in certain contexts</li> </ul> <h4 id="comparisonofthethreecellulardomains">Comparison of the three cellular domains</h4> <ul> <li>Key table highlights (conceptual):<ul> <li>Chromosomes: Bacteria - single/circular; Archaea - single/circular; Eukarya - multiple/linear</li> <li>Ribosomes: Bacteria - 70S; Archaea - 70S; Eukarya - 80S</li> <li>Cell wall: Bacteria - peptidoglycan (present in most); Archaea - rarely peptidoglycan; Eukarya - absent (in most organisms)</li> <li>Cytoplasmic membrane lipids: Bacteria - fatty acids with ester linkages; Archaea - branched hydrocarbons with ether linkages; Eukarya - similar to bacteria (ester)</li> <li>Sterols in membrane: Bacteria - generally absent or variable; Archaea - absent; Eukarya - present in many membranes</li> <li>Nucleus and membrane-bound organelles: Bacteria - No; Archaea - No; Eukarya - Yes</li> <li>Flagella: Bacteria - bacterial flagellum; Archaea - archaellum; Eukarya - eukaryotic flagellum</li></ul></li> </ul> <h4 id="bergeysmanualandtaxonomyinbacteriaarchaea">Bergey’s Manual and taxonomy in bacteria/archaea</h4> <ul> <li>Bergey’s Manual of Systematic Bacteriology:<ul> <li>Comprehensive view of relatedness based on rRNA sequencing</li></ul></li> <li>Bergey’s Manual of Determinative Bacteriology:<ul> <li>Based on phenotypic characteristics (shape, metabolic traits, etc.) used in clinical/lab contexts</li></ul></li> </ul> <h4 id="taxonomicschemeandmajordivisions">Taxonomic scheme and major divisions</h4> <ul> <li>Four major divisions by cell-wall type:<ul> <li>Gracilicutes: Gram-negative with thin cell walls</li> <li>Firmicutes: Gram-positive with thick, strong cell walls</li> <li>Tenericutes: lack a cell wall; soft</li> <li>Mendosicutes: archaea with unusual cell walls/nutritional habits</li></ul></li> </ul> <h4 id="speciesandsubspeciesconceptsinbacteriaarchaea">Species and subspecies concepts in bacteria/archaea</h4> <ul> <li>Bacterial species: a collection of cells sharing a broadly similar trait pattern; typically share at least95\%oftheirgenesasmatches</li><li>Subspecies/strain/type:bacteriawithinthesamespecieswithdifferingtraits</li><li>Serotype:representativesofaspeciesthatstimulatedistinctantibody(serum)responsesduetouniquesurfacemolecules</li></ul><h4id="conceptcheck4and5exercises">ConceptCheck(4)and(5)exercises</h4><ul><li>(4)Whereisgeneticmaterialfoundinabacterialcell?A.NucleusB.NucleolusC.NucleocapsidD.Nucleoid</li><li>(5)WhichfeatureissharedbyBacteriaandArchaea?A.LinearDNAB.NucleusC.70SribosomesD.Fattyacidswithetherlinkages</li></ul><h4id="textbookreferencesandsupplementaldetails">Textbookreferencesandsupplementaldetails</h4><ul><li>TextAlternativecontent(imagedescriptions)providedforaccessibilityincludes:<ul><li>Structureofabacterialcell:commonpartspresentinallbacteria,plusoptionalpartspresentinsome</li><li>Arrangementandmorphologydiagrams(cocci,bacilli,spirilla,spirochetes)</li><li>Flagellaranatomyandtypesofarrangements</li><li>Gramstainstepsandinterpretation</li><li>Gram−positivevsGram−negativeenvelopediagrams</li><li>Peptidoglycanstructuraldetailsandcross−links</li><li>Outermembranecomponents(LPS,porins)</li><li>Capsule,slimelayer,andbiofilmformation</li><li>Endosporestructureandsporulation/germinationsteps</li><li>Archaea−specificcharacteristicsanddomainrelationships</li></ul></li></ul><h4id="quickreferencetokeynumericalvaluesandterms">Quickreferencetokeynumericalvaluesandterms</h4><ul><li>Averagebacterialsize:of their genes as matches</li> <li>Subspecies/strain/type: bacteria within the same species with differing traits</li> <li>Serotype: representatives of a species that stimulate distinct antibody (serum) responses due to unique surface molecules</li> </ul> <h4 id="conceptcheck4and5exercises">Concept Check (4) and (5) exercises</h4> <ul> <li>(4) Where is genetic material found in a bacterial cell? A. Nucleus B. Nucleolus C. Nucleocapsid D. Nucleoid</li> <li>(5) Which feature is shared by Bacteria and Archaea? A. Linear DNA B. Nucleus C. 70S ribosomes D. Fatty acids with ether linkages</li> </ul> <h4 id="textbookreferencesandsupplementaldetails">Textbook references and supplemental details</h4> <ul> <li>Text Alternative content (image descriptions) provided for accessibility includes:<ul> <li>Structure of a bacterial cell: common parts present in all bacteria, plus optional parts present in some</li> <li>Arrangement and morphology diagrams (cocci, bacilli, spirilla, spirochetes)</li> <li>Flagellar anatomy and types of arrangements</li> <li>Gram stain steps and interpretation</li> <li>Gram-positive vs Gram-negative envelope diagrams</li> <li>Peptidoglycan structural details and cross-links</li> <li>Outer membrane components (LPS, porins)</li> <li>Capsule, slime layer, and biofilm formation</li> <li>Endospore structure and sporulation/germination steps</li> <li>Archaea-specific characteristics and domain relationships</li></ul></li> </ul> <h4 id="quickreferencetokeynumericalvaluesandterms">Quick reference to key numerical values and terms</h4> <ul> <li>Average bacterial size:\sim 1\,\mu m</li><li>Coccicircumference:≈</li> <li>Cocci circumference: ≈1\,\mu m</li><li>Roddimensions:≈</li> <li>Rod dimensions: ≈2\,\mu mlength,length,1\,\mu mwidth</li><li>Ribosomes:width</li> <li>Ribosomes:70S(composedof(composed of30S + 50Ssubunits)</li><li>Gram−positivecellwallthickness:subunits)</li> <li>Gram-positive cell wall thickness:20\,\text{to}\,80\,nm</li><li>Gram−negativecellwallthickness:</li> <li>Gram-negative cell wall thickness:1\,\text{to}\,3\,nm$$ (thin peptidoglycan layer inside outer membrane)
  • Endospore resistance: withstands heat, drying, freezing, radiation, chemicals
  • Four divisions by cell-wall type: Gracilicutes, Firmicutes, Tenericutes, Mendosicutes
  • 95% gene similarity benchmark for bacterial species
  • Tetrapeptide components in peptidoglycan: L-alanine, D-glutamate, L-lysine, D-alanine (plus cross-linking peptides)
End of notes