Micro 201 - exam 2 learning objectives/study guide

• describe the major steps of binary fission

  1. cell elongation:increase in cell size due to accumulation of cellular structures (anabolism)2. septum formation:partition that forms between dividing cells (causes one pole in the cell to be older than the other)3. completion of septum; formation of cell walls; cell separationgeneration:one cell divides into 2, 2^#
• interpret cellular physiology from a growth curve (lag, exponential, stationary, decline)


  growth curve: measurements of a microbial population over time, types of measurements - # cells, # viable cells, turbidity

  lag: cells acclimate to new growth conditions exponential: cells replicate at regular intervals stationary: a nutrient is depleted ( or waste product accumulated)decline: viability of cells decreases (potential lysis)
• compare and contrast methods to measure microbial growth

  spread-plate method: sample spread evenly over agar and colonies form CFU=colony forming unit; each colony represents the structure resulting from the growth an individual cell turbidity: shows growth, more turbid means more growth serial dilutions: sample diluted until there is just enough colonies, not too much and not loo little (10^ 3 maybe ??)
• compare and contrast molecular changes that promote microbial growth at different temperatures

  adaptions to cold- proteins exhibit more a-helices and less B-sheets--> increases flexibility of enzyme- cytoplasmic membrane contains lipids with more unsaturated fatty acids--> increases fluidity

  adaptations to warm/hot- acidic/basic amino acids --> ionic bonds- hydrophobic amino acids --> hydrophobic centers--> promotes stability at high temps-cytoplasmic membranes contain lipids with more saturated fatty acids--> stronger hydrophobic region and higher melting point
• compare and contrast the enzymes that neutralize oxidative stress

  catalase:H2O2 + H2O2 --> 2 H2O + O2 peroxidase:H2O2 + NADH + H+ --> 2 H20 + NAD+ superoxide dismutase:O2- + O2- + 2H+ --> H2O2 + O2

  - high reduction potentials = excellent oxidizing agents
• -cidal chemical agents

  kill viable bactera/cells
• -static chemical agents


  stops growth

  - if removed growth occurs again
• -lytic chemical agents

  kills through cell lysis
• describe how two-component systems enable cells to respond to environmental signals

  1. sensor detects signal

  - histidine is phosphorylated

  2. sensor phosphorylates RR

  - aspartate is phosphorylated

  3. RR function is altered

  - cellular response

  4. sensor can dephosphorylate
• describe how quorum sensing coordinates cellular processes across a population

  - AHL reaches activator protein

  - activator protein promotes transcription of AHL synthase

  - more AHL produced

  - amplifies quorum sensing effects
• compare and contrast gene regulation by sRNAs and riboswitches

  · sRNA

  o translation inhibition/stimulation: if the ribosomal binding site is free, then transcription can occur

  o RNA degradation/ protection: small RNAs bind mRNAs in a manner that promotes mRNA degradation, while in others small RNA:mRNA base-pairing prevents ribonuclease-mediated degradation

  · Riboswitches

  o If a metabolite is bound to the aptamer region, then transcription cannot occur
• describe the molecular mechanisms underlying chromosome replication, cell division, and peptidoglycan synthesis in the bacterial cell cycle

  · DNAA-ATP binds to the Oric. Then RNA polymerase is recruited, and replication begins

  · As cell division proceeds, the FTZs ring gets smaller

  · Peptidoglycan requires autolysin to break bonds and transpeptidation for cross linking
• describe how biofilm formation depends in a second messenger

  second messenger:intracellular signaling molecule- relies on c-di-GMP to promote the biofilm cell cycle
• describe the major events of the virus replication cycle

  1. attachment

  2. penetration of viral nucleic acid

  3. synthesis of viral nucleic acid and protein

  4. assembly and packaging of new viruses

  5. cell lysis and release of new virions
• determine the abundance of a virus within a sample

  plaque assay

  - cell/phage mixture is poured onto a solidified nutrient agar plate

  - the mixture is left to solidify

  - incubation allows for bacterial growth and phage replication
• describe how the CRISPR system immunizes bacteria to viral infection

  Cas protein- processes transcript into crRNA- binds viral DNA- endonuclease activity cleaves duplex--> interferes with viral replicationPAM (protospacer adjacent motif)- recognized by Cas protein- endonuclease activity releases protospacer- insertion into CRISPR region--> immunization--> specific editing of chromosome
• genotype


  nucleotide sequence of the genome
• phenotype


  observable property
• state the mechanisms by which DNA can be introduced into cells

  horizontal gene transfer:genetic info acquired from another cell- through transformation, transduction, or conjugation
• state the potential fates of DNA that has entered the cell

  - degrade by host cell defenses (catabolism)

  - replicate independent of chromosome (plasmid)

  - incorporation into chromosome (homologous recombination)
• describe how homologous recombination results in genetic exchange

  - donor DNA yields a single strand

  - donor must exhibit sequence homology with recipient

  - RecA mediates interaction between ssDNA and recipient DNA

  
  

  1. endonuclease nicks DNA

  2. binding of SSB protein

  3. strand invasion by RecA protein

  4. development of cross-strand exchange

  5. 180 rotation of heteroduplex DNA

  6. resolution at sites

  7. creates splices and patches

  
• compare and contrast transformation among different bacteria

  transformation:free DNA is incorporated into the genome of a recipient cellnatural transformation:some species can naturally take up DNA- competent cells readily bind DNA- single DNA strand undergoes homologous recombination
• describe how polymerase chain reaction amplifies target DNA

  · PCR: method to amplify specific region of DNA

  · Denaturation of the template strand

  · Annealing of primers to each original strand for new strand synthesis

  · Extension of new DNA strands from the primers
• describe how gel electrophoresis separates nucleic acids by molecular weight

  the lighter acids/molecules move further down the gel

  - so the lines at the bottom are less bp
• describe the major steps of molecular cloning

  molecular cloning:move target DNA into plasmid tool1. cut DNA with restriction enzyme2. add vector cut with same restriction enzyme3. add ligase to form recombinant molecules4. introduce recombinant vector into a host
• describe how restriction endonucleases generate double-stranded breaks

  restriction endonuclease:enzymes that cleave double-stranded DNA- recognize 6-bp palindrome- only matching ends can be ligated- 100's of restriction enzymes
• obligate aerobe


  use normal atmospheric O2 (21%)

  - necessary for growth
• facultative aerobe


  can grow in O2 but anaerobic metabolism(s) possible
• microaerophilic aerobe


  can grow in O2only if <21%
• aerotolerant anaerobe


  anaerobic metabolism(s) and insensitive to O2
• obligate anaerobe


  O2 is lethal to microbe
• bacteriostatic agent


  inhibits growth of bacteria

  - if agent removed growth will occur again
• bactericidal agent

  kills bacteria

  - total cell count remains same, viable cell count decreases
• bacteriolytic agent

  kill by lysis

  - total and viable cell counts decrease
• transcription factors

  DNA-binding proteins that affect gene expression
• operator


  genetic element that is recognized by DNA-binding proteins

  - sequence and spacing matters
• repression


  enzyme activity decreases when specific compound is presented
• co-repressor function


  - binds to repressor

  - change in repressor's tertiary structure

  - repressor binds to operator

  - transcription blocked
• induction


  enzyme activity increases when specific compound is present
• inducer function

  - binds to repressor

  - change in repressors tertiary structure

  - repressor no longer binds to operator

  - transcription occurs