Micro final

• FeS based metabolism may be remanent of early form of chemiosmosis
• Photosynthesis evolved from early life
• Stromatolites


  Layered rocks formed by incorporation of mineral sediments into microbial mat
• RNA world

  Life may have begun in an RNA world where RNA can: Backbone of essential molecules, Bind small molecules, Catalyze some biochemical reactions, Be template for own synthesis, Catalyze protein synthesis
• Modern classification uses nucleotide sequence of small subunit ribosomal RNAs (SSU rRNAs) to classify organisms into Bacteria, Archaea, Eucarya
• Archaea and Eucarya are closest related
• Prokaryotic cells


  Lack a true membrane delimited nucleus, No organelles, No nucleus
• Eukaryotic cells


  Have membrane enclosed nucleus, More complex morphologically, Usually larger than prokaryotic
• Taxonomic ranks

  • Domain, Phylum, Class, Order, Family, Genus, Species
• Characteristics among domains

  • Membrane bound nucleus (Absent in Bacteria and Archaea, Present in Eukaryotes), Cell wall (Murein with Muramic Acid in Bacteria, No Muramic Acid in Archaea and Eukaryotes), Membrane lipid (Ester linked, straight chain fatty acids in Bacteria and Eukaryotes, Ester linked, branched aliphatic chains in Archaea), DNA dependent RNA polymerase (1 with 6 subunits in Bacteria, 1 with 8-12 subunits in Archaea, 3 with 12-14 subunits in Eukaryotes)
• Sequence alignment

  Sequence requires homology (inheritance from common ancestors), Sequence similarity is % of nucleotides shared between sequences, Orthologs have same function and originate from a single ancestral gene, Paralogs evolved to have different functions resulting from gene duplication, Phylogenic analyses estimate evolutionary changes from number of sequence differences across a set of homologous nucleotides, Sequence alignment adds gaps to establish positional homology
• Phylogenic trees


  Node shows where ancestor diverged into two lineages, Branch length represents number of changes that have occurred, Limitations: Bootstrapping can deal with uncertainty, Homoplasy (Convergent Evolution) where similar sequence positions result from recurrent mutation instead of inheritance
• Prokaryotic cell shapes

  • Coccus: Spherical, Bacillus: Rod or cylinder shaped, Coccobacillus: Short round rod, Vibrio: Curved rod, Spirillum: More rigid spiral shape, Spirochete: More flexible spiral shape, Mycelium: Network of long multicellular filaments, Pleomorphic: Organisms that are variable in shape
• Prokaryotic cell division patterns

  • Diplococci: Pairs, Streptococci: Chains, Packets: Division along 2 or 3 perpendicular planes, Clusters: Division along several random planes
• Prokaryotic cell membranes


  Plasma membrane encompasses the cytoplasm, Some prokaryotes also have internal membrane systems
• Plasma membrane

  Lipid bilayer in which proteins float, Separation of cell from its environment, Selectively permeable barrier, Location of crucial metabolic processes like energy generation and cell wall biosynthesis, Detection and response to molecules in the environment (membrane receptors)
• Membrane phospholipids

  Amphipathic/Amphiphilic: Both philic and phobic, Polar Head: Interact with water, hydrophilic, Nonpolar Tail: Insoluble in water, hydrophobic
• Membrane proteins

  • Peripheral Proteins: Loosely associated with the membrane and relatively easily removed, Integral Proteins: Embedded within the membrane and not easily removed
• Bacterial membranes

  Differ from eukaryotes by lacking sterols, Contain hopanoids (five ring-sterol like) that fulfill the same function as sterols in making membranes more fluid
• Archaeal membranes

  Composed of unique lipids that are branched-chain, not straight chain, Connected to glycerol by ether linkage, not ester linkage, Monolayer structure instead of bilayer
• Prokaryotic cytoskeleton

  FtsZ: Functional equivalent of eukaryotic tubulin, Required for cell division, Localizes to the center, Makes circular filament, Scaffolding for other cell division proteins, MreB: Functional equivalent of eukaryotic actin, Helix under the plasma membrane, Archaea lack this molecule, Crescentin: Intermediate filament-like protein essential for cell curvature
• Cytoplasmic matrix

  Aqueous substance in which nucleoid, ribosomes and inclusion bodies are suspended
• Organic inclusion bodies


  • Glycogen: Polymer of glucose units, Poly-B-hydroxybutyrate: Polymers of B-hydroxybutyrate used to produce biodegradable plastics, Cyanophycin Granules: Large polypeptides containing about equal quantities of arginine and aspartic acid, Carboxysomes: Contain the enzyme ribulose-1,5-bisphosphate carboxylase (Rubisco) used for CO2 fixation, Gas Vacuoles: Found in cyanobacteria and some other aquatic procaryotes, Provide buoyancy, Aggregates of hollow cylindrical structures called gas vesicles
• Inorganic inclusion bodies


  • Magnetosomes: Particles of iron oxide or iron sulfate placed in an organelle called the magnetosome, Aligned using cytoskeletal components, Used for magnetic sensing of earth to orient bacteria
• Archaea cell walls

  Have a wide variety of cell wall types, None contain peptidoglycan, Some contain pseudopeptidoglycan
• Bacteria lacking cell wall

  Mycoplasma: Bacterium causes mild pneumonia, Antimicrobial directed towards cell wall is ineffective, Sterols in membrane account for strength of membrane
• Gram stain

  Crystal Violet: Primary stain that stains the cell, Gram's Iodine: Mordant that holds primary dye onto cell, Alcohol: Decolorizer that removes primary dye from gram negative cell, Safranin: Counter or secondary stain that recolors cells that lose stain through decolorization
• Gram-positive bacteria

  Retain crystal violet-iodine complex of gram stain, Cell walls consist of a single 20-80nm thick peptidoglycan (murein) layer outside of plasma membrane
• Gram-negative bacteria

  Lose crystal violet-iodine complex, Cell walls are more complex with a 2-7nm peptidoglycan layer covered by a 7-8nm thick outer membrane
• Cell envelope

  Structure from plasma membrane outwards including plasma membrane, outer membrane (when present), cell wall, periplasmic space, capsules and other structures exterior to the cell wall
• Periplasmic space

  In gram positive bacteria: the space between the plasma membrane and cell wall, In gram negative bacteria: the space between the plasma membrane and the outer membrane, Made of periplasm that differs between gram positive and gram negative bacteria
• Peptidoglycan (PTG)

  Also known as murein, Mesh like polymer composed of N-acetyl glucosamine, N-acetylmuramic acid, and several different amino acids including "nonstandard" D-amino acids, Chains of linked peptidoglycan subunits that are cross linked to provide strength and rigidity
• Gram negative cell envelope

  Consist of a thin layer of peptidoglycan surrounded by an outer membrane composed of lipids, lipoproteins, and lipopolysaccharide (LPS), NO teichoic acids, More complex than gram positive cell envelope, Periplasmic space may constitute 20-40% of cell volume and contains many enzymes, Outer membrane lies outside the thin peptidoglycan layer, Braun's lipoproteins connect the outer membrane to the peptidoglycan layer, Lipopolysaccharides are present instead of phospholipids in the outer leaflet of the outer membrane
• Lipopolysaccharides (LPS)

  Consist of three parts: Lipid A, Core polysaccharides, O side chain (O antigen), Provide protection from host defenses, Contribute to negative charge on cell surface, Help stabilize outer membrane structure, Can act as an exotoxin
• Layers outside the cell wall

  • Capsules: Well organized and not easily removed, Slime layers: Similar to capsules except diffuse, unorganized and easily removed, S-layers: Regularly structured layers of protein or glycoprotein
• Functions of capsules, slime layers, and S-layers

  Protection from host defenses, Protection from harsh environmental conditions, Attachment to surfaces
• Flagella

  Have three basic parts: Filament that extends to exterior made of flagellin proteins, Hook that connects filament to cell, Basal Body that anchors flagellum into cell wall, Bacteria use flagella for motility through sensing chemicals (chemotaxis) where nutrients act as attractants and toxins act as repellents, Flagella rotation responsible for run and tumble movement of bacteria
• Pili


  Considerably shorter and thinner than flagella, Similar in structure with protein subunits, Functions include attachment (fimbriae), movement, and conjugation (mechanism of DNA transfer)
• Macroelements required by microorganisms


  • C, O, H, N, S, P, K, Ca, Mg, Fe
• Microelements required by microorganisms


  • Mn, Zn, Co, Mo, Ni, Cu