Microbio exam 3

• What are the planar molecules that fill gaps between hydrocarbon chains in eukaryotes and bacteria?

  Eukaryotes: cholesterol (ergosterol), bacteria: hopanoids
• What do some extremophile Archaea have instead of bilayers?

  tetraether monolayers
• How does transportation across the cell membrane work?

  1. cell membrane is semipermeable barrier, 2. selective transport is essential for survival - small uncharged molecule (O2 and CO2) easily permeate membrane by diffusion, water diffuses slowly across membrane by osmosis (through channels too), charged/strongly polar molecules can't diffuse across cell membranes (ions, proteins, sugars)
• What are membrane proteins and their functions?

  1. Hydrophilic and hydrophobic regions lock protein in membrane, 2. functions: a. transport (ions, sugars, other nutrients and nutrient import, waste product export, secretion of toxins, secretion of proteins/other components of outer layers of cell envelope), b. secretion (toxins, waste products), c. cell signaling (regulation of import/export, energy generation, adhesion, sensing environment)
• What are specific protein transporters/channels that polar/charged molecules require?

  1. passive transport: molecules move along (or down) their concentration gradient, 2. active transport: molecules move against (or up) their concentration gradient (requires energy)
• What is coupled transport?


  Uses energy of one molecule moving down its concentration gradient to move another molecule up its concentration gradient
• What are ABC transporters?

  1. powered by energy released from ATP hydrolysis (ATP->ADP + P), 2. ABC = ATP-Binding Cassette, 3. Huge family of proteins includes nutrient uptake transporters and drug efflux pumps
• What happens in group translocation?

  Imported molecules are covalently modified to prevent export: phosphorylation of glucose changes its chemical structure such that it can't be exported by glucose transporter
• What is the cell wall?

  1. It's a single molecule, 2. confers: shape and rigidity, 3. allows cells to tolerate turgor pressure (Bacteria can tolerate very high and low osmolarity, pure water which would cause animal cells to lyse/burst)
• What are bacterial cell walls made of?

  peptidoglycan - consists of long polymers of disaccharides bound to short peptides, and peptides form cross-bridges (cross-links) connecting parallel glycan strands
• Why is peptidoglycan unique to bacteria?

  enzymes responsible for its biosynthesis are excellent targets for antibiotics, penicillin and vancomycin both inhibit peptide cross-linking
• What are beta-lactams?


  large group/class of antibiotics, Penicillin, and block peptidoglycan cross-linking
• What do most bacteria have outside of PG?

  additional cell envelope layers - 1. Protein S-layers, 2. capsules (carbohydrates, often block phagocytosis), 3. outer membrane
• What do gram-positive vs gram-negative bacteria have?


  Gram-Pos: some species have glycosyl chains and S-layer, >3 layers of PG, Gram-Neg: only gram-negative has outer membrane, 1-3 layers of PG
• What is the mechanisms for gram staining?

  1. Crystal violet is added. 2. iodine complexes with crystal violet 3. decolorizer releases loosely trapped stain
• What does the gram-negative cell envelope contain?

  1. LPS - lipopolysaccharide in outer leaflet of outer membrane, AKA endotoxin, strongly recognized by human immune system, 2. Periplasm
• What is the outer membrane permeability?

  1. porins are proteins that form channels to allow small molecules to freely enter the periplasm, most proteins are too large to pass through porins, gram-neg bacteria adjust porin channel sizes depending on environmental conditions
• What does the gram-positive cell membrane contain>

  1. Glycosyl chains and S-layers - depends on species, no true periplasm
• Examples of gram-positive species?

  Bacillus subtilis, Bacillus anthracis, Staphylococcus aureus, streptopcoccus spp, clostridium difficile
• Examples of gram-negative species?

  Escherichia coli, pseudomonal aeruginosa, Vibrio cholerae, salmonella spp, cyanobacteria, helicobacter pylori
• What species is neither gram-pos or gram-neg?

  Mycobacterium tuberculosis
• What is the bacterial cytoskeleton?

  1. distinct from eukaryotic cytoskeleton, 2. no vesicle transport, 3. regulate cell size and shape, coordinate cell division
• How does bacterial cell adhesion and motility work?

  Chemotaxis: directed movement toward a higher concentration of a chemical, Pili: protein filaments that can be extended and contracted, Flagella: rotating protein structures (same word used for whip-like structures in eukaryotes) - allow cells to run and tumble based on direction of rotation
• What is rotary flagella?


  1. many bacteria swim by means of rotary flagella, 2. each flagellum is rotated by a motor driven by the proton motive force, 3. flagella rotate either clockwise or counterclockwise relative to the cell, 4. swimming motility run (CCW rotation moves cell toward attractant) and tumble (CW rotation stops forward motion, so cell tumbles and charges direction)
• Why are rotary flagella often lost in lab strains?

  1. growth in a homogenous, nutrient-rich environment: there's nowhere better to go, 2. making flagella takes energy
• How does DNA storage and organization work?

  eukaryotic cells: nucleus delimited by a nuclear membrane, prokaryotic cells: nucleoid region in cytoplasm
• What is the genome size of bacteria vs multi-cellular eukaryotic organisms?

  Bacteria ~5k genes, Mammals ~ 20k genes
• What is the organization of a genome?

  1. Chromosome shape: prokaryotes: circular, eukaryotes: linear, 2. plasmids: small, circular DNAs separate from chromosomes: common in prokaryotes, in some unicellular eukaryotes, 3. Noncoding DNA (non encoding proteins), typically >90% of multicellular eukaryotic genomes, ~30% of microbial eukaryotic genomes, <20% of prokaryotic genomes
• Why are microbial genomes so compact?

  Smaller genomes can be replicated faster, selection for rapid growth/replication
• Why do genomes of multicellular ("higher") eukaryotes have so much non-coding DNA?

  Some non-encoding DNA has regulatory functions, different versions (isoforms) of proteins may be made
• How does Bacterial DNA replication work?

  1. replication in bacteria begins at the origin, 2. replication bubble forms - two replication forks move in opposite directions around chromosome, 3. replication ends at termination sites located opposite to the origin, 4. eukaryotes have multiple origins and special mechanisms for replicating the ends of their linear chromosomes
• How does coordination of DNA replication with cell growth and division work?

  Bacterial DNA replication is coordinated with cell wall expansion and septation, origins move toward poles as replication progresses
• How does septation complete cell division work?

  replication of termination site triggers septum formation, new cell wall must be synthesized to allow separation of daughter cells
• What can origins do before the first round of replication is complete?

  re-fire
• How do plasmids replicate separately?

  plasmids are much smaller than chromosomes, found in archaea, bacteria, and some eukaryotic microbes, usally circular
• Why does DNA replication create opportunities for mutations to arise?

  1. every time genome is replicated, mistakes occur (fitness depends on context/environment), 2. some escape correction and become mutations, 3. mutations can cause - drug resistance, other useful phenotypes, deleterious phenotypes
• What is vertical vs horizontal transmission?

  Vertical transmission: DNA passed from mother to daughter cells is vertical transmission of genetic info

  Horizontal gene transfer: bacteria can acquire new DNA from phages, the environment, and each other
• What are the types of the horizontal gene transfer?

  1. conjugation: bacterial sex, direct transfer of DNA (plasmid or entire chromosome) from one cell to another, 2. transduction: viral transmission of DNA from one cell to another, 3. transformation: uptake of free DNA from environment
• What is transformation?


  1. free DNA is imported by protein transporters, 2. competence proteins are required, 3. only some species can do it, 4. DNA used for: nutrition, DNA repair, source of genetic variation (new genes, new alleles (versions of genes))
• What is transformation in the lab look like?

  1. induce competence by chemicals or electricity (no competence proteins required), 2. make mutations, introduce new genes, assemble DNA from diff sources together (recombinant DNA tech)