Vocab

• fermentation


  biooxidative process not requiring oxygen in which electrons stripped by glucose are accepted by one or more organic substrates
• respiration


  requires an external electron acceptor for substrate oxidation; glycolysis, krebs, then ETC (oxidative phosphorylation)
• carbohydrate fermentation


  hydrolysis of disaccharides prior to the fermentation reaction
• catalysts


  biological enzymes, typically end in -ase (b-galactosidase, sucrase)
• lactose fermentation


  uses beta galactosidase enzyme and results in galactose and glucose
• sucrose fermentation


  uses sucrase enzyme and results in fructose and glucose
• PRB tubes


  used to determine if a bacterium can ferment a particular carb; has durham tube for gas collection, phenol red broth with peptones and carbohydrate to be added, and phenol red pH indicator (yellow +, red or pink -)
• indole test


  tryptophan can be broken down by enzyme tryptophanase, which produces indole, pyruvic acid, and ammonia; indole accumulates in medium and kovac's reagent turns indole layer red (SIM DEEP)
• methyl red test


  mixed-acid fermentation produces large amounts of acid, MR-VP medium has glucose, peptones and a phosphate buffer the bacteria must overcome to turn the medium red +, or not, yellow -
• VP test


  bacteria can ferment glucose and convert the acid products to acetoin, barritt's reagent (VP-A AND VP-B) are added to MR-VP medium to produce wine color for + (72 hrs incub.)
• citrate utilization test


  tests if citrate can be used as a sole carbon source, simmons citrate agar consists of citrate, salts, and bromthymol blue as a pH indicator (selective and differential medium); blue and growth is +, green and no growth is -
• litmus milk


  differential medium with lactose, casein, and azolitmin as a pH and redox indicator (blue = basic, pink = acidic)
• litmus milk reactions


  lactose fermentation (acid curd or fissures), litmus reduction, casein coagulation, or casein hydrolysis (alkaline rxn if partial, proteolysis if full degradation of casein)
• sterilization


  complete elimination of vegetative bacterial cells through irradiation, heat, high pressure, filtration, or chemicals
• ionizing radiation


  x-rays and gamma rays affect cell metabolism and physiology but not nucleic acids
• filtration


  uses filter with .2 um pore size to trap normal bacteria
• steam sterilization


  autoclave with steam under pressure, 121C @ 15 psig for 15 minutes
• dry heat


  temps of 180C and long times (3hrs+)
• non-ionizing radiation


  solar UV radiation
• UV-A (320-400 nm)


  95% of solar radiation, harmless
• UV-B (290-320 nm)


  absorbed by nucleic acids and forms pyridimine dimers to thymine; distorts DNA and stops replication
• UV-C (200-280 nm)


  absorbed by all cellular constituents, lethal; stopped by ozone and oxygen
• light repair


  photolyases bind to pyridimine dimers, split dimer, and restore native pyridimines with energy of light (not present in humans)
• dark repair


  endonucleases excise damaged DNA and create a gap for DNA polymerase and ligase to repair
• decimal reduction time


  amount of time it takes a particular chemical at a certain concentration to kill 90 % of bacteria on a surface; to kill 100% use (DRT)(n+1) where n = degree of exponent from bacterial concentration
• kirby-bauer test


  disc diffusion method used to test antibiotic effectiveness against micros; uses mueller-hinton agar with casein, beef extract, agar, and starch for diffusion
• transformation


  transfer of genetic material from one bacterium to another whereby one cell takes up naked DNA from the environment; can be natural (Streptococcus and Bacillus are naturally competent), or artificial
• artificial transformation


  naturally incompetent bacteria can be made competent by manipulating cell membrane permeability through electroporation and ice-cold CaCl2 + heat
• plasmid cloning vectors


  genetically engineered plasmids used for transformation experiments in lab settings; contains an antibiotic resistance gene and a region to insert DNA fragments
• pGLO plasmid


  contains GFP, araC gene which regulates the expression of GFP depending on the presence of arabinose, and beta-lactamase antibiotic resistance
• virus


  obligate intracellular parasite (cannot replicate outside of host); genetic info can be dsDNA, ssDNA, dsRNA, or ssRNA
• viral replication


  attachment, penetration, synthesis, assembly, and release; lytic or lysogenic pathway
• titer


  concentration of virus particles in pfu/mL; (# of plaque)/(vol of virus in mL)(total dilution factor)
• polymorphism


  site of variation in DNA (1 in every 100), alters the length of DNA fragments cut by enzymes
• human genome


  3 million base pairs long, can't be used for fingerprinting because the restriction pattern can't be seen due to smearing
• gel electrophoresis


  DNA carries a negative charge, so fragments move toward positive anode when running electricity through the gel; requires a power supply, agarose gel, TAE buffer (conducts charge), and ethidium bromide (makes it glow)
• loading dye


  charged and shows when to stop applying current because DNA can run off gel, not necessary; contains bromophenol blue and glycerol
• denaturation


  dsDNA template is converted to ssDNA by heating to 94C
• annealing


  specific pair of primers binds to complementary DNA sequences on the ssDNA template between 50-65C (sense primer binds to 3' end of bottom strand, antisense primer binds to 3' of top strand)
• elongation


  DNA polymerase synthesizes a complementary DNA strand for each ssDNA template at 68-72C