Lecture Exam 2 – Lim Cabrillo Microbiology Bio 6 – Flashcards
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| factors influencing enzyme activity (5) |
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| -temperature -pH -substrate concentration -competitive inhibitors -non-competitive inhibitors |
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| temperature affects enzyme activity by |
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| increasing activity with increased temp to an optimum temp |
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| pH affects enzyme activity by |
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| increased activity at optimum pH |
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| substrate concentration affects enzyme activity by |
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| increased activity as substrate increases, til saturation |
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| competitive inhibitor affects enzyme activity by |
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| binding to active site to physically block enzyme binding |
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| non-competitive inbhibitor affects enzyme activity by |
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| binding to allosteric site to change shape of enzyme so active site is no longer available for substrate to bind |
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| allosteric site |
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| site separate from enzyme binding site that when non-competitive inhibitor binds, changes shape of enzyme so active site is no longer available for substrate to bind |
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| apoenzyme |
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| main part of enzyme; protein; inactive without co-factor |
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| co-factor |
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| -activator -non protein portion of enzyme reaction - vitamin or mineral |
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| haloenzyme |
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| active enzyme with cofactor intact |
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| feedback inhibition |
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| end product for a pathway is also the inhibitor for the 1st enzyme in that pathway so that when product reaches necessary levels, pathway shuts down -AKA negative feedback |
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| general requirements for microbial metabolism (3) |
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| -electron donor -electron carrier -electron acceptor |
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| aerobic respiration |
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| -most ATP production (38 total ATP for prokaryote) -includes glycolysis, Krebs cycle AND electron transport chain -O2 is final electron acceptor |
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| Glycolysis |
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| -glucose is oxidized - splits from a 6C chain to two 3C chains (pyruvic acid) -oxidation of glucose releases energy -net 2 ATP produced (no O2 involved) -NAD+ is reduced to NADH -occurs in cytoplasm -anaerobic |
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| electron donor |
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| fuel source |
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| electron carrier |
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| transports high energy e- -organic molecules |
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| electron acceptor |
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| accept low energy e- after most of energy is used up |
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| glycolysis starts with |
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| 1 glucose (donor) 2 NAD+ (carrier) 2 ATP (energy input) 4 ADP (to become ATP) 2 Phosphate |
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| glycolysis ends with |
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| 2 pyruvic acid 2 NADH (carrier) 2 net ATP |
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| Krebs cycle starts with |
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| 2 AcetylCoA 6 NAD+ 2 FAD 2 ADP 2 Phosphate |
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| Krebs cycle ends with |
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| 6 NADH 2 FADH2 2 ATP 4 CO2 (waste) |
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| krebs cycle in prokaryotes |
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| occurs in cytoplasm -does not directly require O2, but is considered aerobic -produces 2 ATP |
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| Electron transport chain in prokaryote |
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| occurs in cell membrane -aerobic because O2 is final electron acceptor -e- move along proteins in cell membrane causing H Produces 34 ATP |
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| ATP Synthase |
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| creates ATP when H+ flows back into cell from higher gradient outside cell through oxidative phosphorylation |
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| prokaryotic ATP yield from 1 glucose |
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| 38 ATP |
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| anaerobic respiration |
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| final electron acceptor is NOT O2 electron donor can be organic or inorganic electron carriers are NAD, FAD, FMN ATP production is variable |
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| Fermentation |
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| e- donor is organic molecule e- carrier can be NAD, FAD, FMN e- acceptor is organic (pyruvic acid) - as in glycolysis ATP production is low |
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| if O2 availability is low, many organisms use what for ATP production? |
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| both aerobic respiration and fermentation |
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| pyruvic acid is a substrate for |
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| fermentation Krebs cycle |
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| substrate level phosphorylation |
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| phosphate added to ADP to produce ATP |
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| oxidative phosphorylation |
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| electrons pass through electron transport chain and ATP is formed through proton pump/ATP synthase |
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| energy ranking |
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| glucose pyruvate acetylCoA NADH FADH2 ATP |
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| final electron acceptor |
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| gets rid of low energy e- |
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| common fermentation products |
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| lactic acid ethanol |
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| NADH produces how many ATp |
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| 3 |
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| FADH2 produces how many ATP |
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| 2 |
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| chemiosmosis |
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| electron transport chain and oxidative phosphorylation |
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| binary fission |
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| -DNA is replicated (duplicated) -cell wall and cell membrane begin to constrict (to create a septum which divides DNA into two parts) -cell walls close and cells separate -parent cell becomes two daughter cells |
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| bacterial growth is |
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| exponential |
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| Generation time is |
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| the amount of time it takes a population to double |
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| phases of bacterial growth |
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| -lag phase -log phase -stationary phase -death phase |
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| lag phase |
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| growth is not measureable because the numbers are still too small |
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| log phase |
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| bacterial growth is exponential and measureable bacteria are most metabolically active |
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| stationary phase |
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| cell death is equal to cell growth nutrients and waste products are limiting factors |
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| death phase |
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| cell death is exponential and greater than cell growth |
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| single colony |
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| a discrete colony on a growth plate - all cells in colony are clones |
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| determine number of viable bacteria |
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| -only count living cells "viable cell count) -requires that you can separate cells to get accurate count -types -plate count AND filtration |
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| measuring cell count of both viable and dead cells |
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| -direct count -turbidity (specrophotometer) |
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| direct count |
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| count cells under microscope -allows us to see live VS dead cells |
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| plate count |
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| -stationary phase culture - see how many colonies grow -dilute broth culture (serial dilution) so that you no longer get confluent growth and can count individual colonies -when growing cells on a plate, must use a known volume of broth so that you can calculate now many bacteria are in the original volume |
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| serial dilution |
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| -allows for minimal broth to be used to dilute significantly rather than needing liters and liters of solution |
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| spread plate method |
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| -use known volume from dilution (usually 0.1 ml) -use sterile glass rod to spread liquid on top of sterile media plate |
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| pour plate method |
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| -use known volume from dilution (usually 0.1 ml) -mix dilution with warm agar -pour agar into plate -can make bacteria harder to see since they're embedded in agar |
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| filtration count method |
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| -bacteria get trapped on filter -lay membrane on petrie dish to grow -coliform bacteria turn red with indicator (shows fecal bacteria) |
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| turbidity count method |
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| use spectrophotometer to measure how much light gets through -when calibrated through other counting methods, you can use scale of light to see how many cells are present (both alive and dead) |
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| physical conditions that affect bacterial growth |
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| temperature pH oxygen availability osmotic pressure moisture |
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| acidophile |
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| bacteria grow in pH under 5.4 |
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| neutrophile |
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| bacteria grow in pH 5.4-8.5 |
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| alkalinophile |
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| bacteria grow in pH over 8.5 |
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| psychrophile |
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| -10 to 20 C; optimum 10 C |
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| psychrotroph |
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| 0 to 30 C; optimum 20 C |
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| mesophile |
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| 10 to 50 C; optimum 40 C |
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| thermophile |
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| 40 to 70 C; optimum 60 C |
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| extreme thermophile |
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| 70 to 110 C; optimum 95 C |
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| bacteriacidal |
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| kills bacteria |
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| bacteriastatic |
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| slows growth of bacteria dramatically, but does not kill them |
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| bacterial growth produces by-products that are |
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| acidic -can kill bacteria - this is why we use a buffer in growth plates |
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| osmotic pressure |
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| produces plasmolysis (cell membrane shrinks away from cell wall when water leaves cell in hypertonic solution) |
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| halophile |
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| loves hypertonicity |
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| facultative halophile |
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| range: 0.85% to 15% -can grow with hypertonicity) |
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| obligate halophile |
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| range: must have over 3% |
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| extreme halophile |
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| range: must be over 15% up to 20% |
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| halotolerant |
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| can grow up to 5% but not well |
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| non-halophile |
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| grows most abundantly at 0.85% |
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| osmotic pressure order of organism tolerance |
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| non-halophile halotolerant facultative halophile obligate halophile extreme halophile |
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| order of organism tolerance (temperatiures) |
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| psychrophile psychrotroph mesophile thermophile extreme thermophile |
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| which osmotic pressure is closest to the average biological cell? |
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| 0.85% |
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| Obligate aerobe |
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| needs O2 to survive -only on top of tube |
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| Obligate anaerobe |
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| needs no O2 to survive -only on bottom of tube |
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| Facultative anaerobe |
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| prefers O2, but can adapt to grow without it -grows anywhere, better on top |
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| microaerophile |
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| loves a LITTLE O2 -grows in a band about 1/3 way down the tube |
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| Aerotolerant anaerobes |
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| prefers no O2, but can tolerate growth with O2 -grows anywhere, but better on bottom |
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| to control food spoilage |
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| -heat food to kill microbes (canning) -refridgerate food -create hypertonic environment with salt or sugar -limit air exposure -use acid to limit microbe growth |
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| capnophile |
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| -anaerobic -requires CO2 (found in gut and respiratory tract) |
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| create anaerobic environment in a lab by |
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| sealing a jar and using a gas pack or candle -burns off O2 and replaces it with CO2 |
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| chemical requirements for bacterial growth |
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| -carbon, nitrogen, sulfur, phosphorus -trace elements and vitamins needed as cofactors |
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| unstable O2 |
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| damages cell structures |
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| carbon in cell growth |
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| carbohydrates and proteins |
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| nitrogen in cell growth |
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| nucleic acids, proteins |
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| sulfur in cell growth |
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| proteins (disulfide bonds) |
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| phosphate in cell growth |
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| phospholipids (cell membranes); nucleic acids; ATP |
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| complex media |
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| -details of whats in it are not precise - but there are nutrients -TSA (tryptic soy agar) -BHI (beef heart infusion) |
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| chemically defined media |
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| nutrients are added in a precise way so you know exactly what nutrients the bacteria are getting -Mueller-Hinton |
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| NaCl in cell growth |
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| osmotic balance (isotonic, hypertonic) |
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| buffer in cell growth |
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| -conjugate acid and base -buffers acid waste product that bacteria creates as it grows so that it can keep growing and not poison itself with the acid |
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| agar in media |
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| makes it solid |
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| enriched media |
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| has nutrients added so that cells that have little growth otherwise will grow more abundantly |
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| Glucose in media |
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| provides energy |
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| NH4PO4 (ammonium phosphate) |
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| provides nitrogen (nucleic acids and proteins) and phosphate (phospholipids, nucleic acids and ATP) |
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| MgSO4 (magnesium sulfate) |
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| sulfur (amino acids) |
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| KH2PO4 and K2HPO4 (potassium phosphate salts) |
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| buffer (balance out acid waste from bacterial growth) |
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| selective media |
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| limits growth to a particular type of organism -ex: Mannitol Salts Agar |
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| differential media |
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| has indicator that turns the agar OR bacteria different colors (based on pH) |
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| sterilization |
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| killing or removing all living organisms, including spores |
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| disinfection |
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| reducing number of harmful microbes to safe levels |
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| sanitization |
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| reducing number of harmful microbes to safe levels (less than disinfection) |
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| disinfectant |
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| product used to reduce number of harmful microbes to safe levels (on inanimate objects) |
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| antiseptic |
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| product used to reduce number of harmful microbes to safe levels (on living tissue) |
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| degerming |
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| removal but not necessarily killing microbes (on living tissue) |
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| asepsis |
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| absence of unwanted contamination |
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| sepsis |
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| bacterial contamination |
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| efficiency of antimicrobial agents depends on (5) |
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| -# of microbes initially present -time of exposure to antimicrobial -temperature -organic matter (fat) blocks disinfectants -biofilms |
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| physical methods of controling microbial growth (8) |
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| -moist heat -dry heat -pasteurization -filtration -low temperatures -dessication -osmotic pressure -radiation |
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| moist heat |
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| -boiling -autoclave needs enough time for heat to penetrate entire object |
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| dry heat |
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| -energy intensive -burns away living material -good for glass/metal |
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| pasteurization |
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| -raise temp high enough to kill bacteria without changing taste of food |
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| filtering |
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| -filter traps microbes -0.2 to 0.4 micrometers -use with liquids that are heat unstable |
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| low temperature |
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| -bacteriostatic, NOT bacteriocidal -fridge = 4C -freezer = -20C -ice crystals can damage cells, but not reliably kill |
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| dessication |
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| drying -bacteriostatic NOT bacteriocidal |
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| lyophilization |
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| freeze-drying -can be used to preserve yeast or probiotics |
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| osmotic pressure |
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| -high salt or sugar -molds and yeasts are more resistant than bacteria -used for food |
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| ionizing radiation |
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| -gamma rays or electrons -mutates bacteria by breaking chemical bonds in DNA -water is ionized to form free radicals |
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| non-ionizing radiation |
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| -UV radiation -germicidal lights -mutates DNA - Thymine dimers |
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| chemical control of microbes that target proteins (6) |
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| -acids/bases -oxidizing agents -halogens - chlorine (oxidize) -heavy metals -alkylating agents (donate methyl group) -formaldehyde (cross link protein) |
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| chemical control of microbes that target cell membranes (2) |
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| -surfactants (break lipid bilayer) -detergents (wash away microbes) |
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| physical methods that sterilize (3) |
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| -filtration -moist heat -radiation |
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| phenol |
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| 1st disinfectant - dentaures protein |
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| phenolics |
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| -disrupt plasma membrane -denature proteins/inactivate enzymes |
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| halogens |
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| chlorine -alters amino acids chains and fatty acid chains |
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| alcohol |
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| -denatures protein -disrupts lipid bilayer -does not kill endospores |
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| heavy metals |
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| -denatures protein |
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| aldehydes |
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| cross link protein w covalent bonds |
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| gaseous chemosterilizers |
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| denatures protein |
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| oxidizing agents |
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| denatures protein by breaking disulfide bonds |
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| genetics |
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| science of heredity -study of genes, how they carry information, how they're replicated and how they're expressed |
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| phenotype |
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| physical characteristics of an organism |
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| genotype |
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| genetic information (DNA that determines amino acid sequence) |
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| basic structure of DNA |
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| -sugar phosphate backbone -sugar (deoxyribose) is 5-sided ring -nitrogenous bases (ACGT) |
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| chromosomes |
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| contain DNA that carry information -is supercoiled within cell -bacteria have single circular chromosome |
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| gene |
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| segment of DNA that codes for a specific protein -order of nucleotides in DNA determines order of amino acids in protein |
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| genetic code |
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| sequence of nucleotides and set of rules about how the nucleotides are converted to proteins |
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| replication |
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| DNA to DNA -occurs before cells can divide so that each daughter cell has DNA -hydrogen bonds unzip; DNA polymerase reads single DNA strand and matches base paired nucleotides - hydrogen bonds these to original DNA strand; DNA polymerase creates covalent bonds between nucleotides creating Okazaki fragments; as DNA polymerase moves on to next nucleotide, the DNA ligase joins Okasaki fragments -DNA strands formed are antiparallel (5' and 3' ends are opposite each other) -old strand is read 3' to 5'; new strand grows 5' to 3' -leading strand is copied continuously because it grows in the right direction; lagging strand is copied in fragments opposite the direction that it unzips (Okasaki fragments) which then get joined through DNA ligase |
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| transcription |
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| DNA to RNA -DNA strands separate; RNA polymerase begins at promoter (intitiation site/instructions); RNA polymerase pulls appropriate RNA nucleotides to hydrogen bond with DNA nucleotides and then covalently bonds them together; RNA peels away so DNA base pairs can link up again; termination happens at terminator codon |
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| translation |
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| RNA to protein (protein synthesis) -ribosome sits down on mRNA; two codons within ribosome (in P site and A site); tRNA bind to each codon; ribosime forms peptide bonds between the amino acids linked to each tRNA; first tRNA is released and ribosome moves to next codon; repeat; stop at stop codon - DNA and mRNA separate |
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| DNA base pairing |
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| A pairs with T C pairs with G |
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| DNA to RNA base pairing |
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| A(DNA) pairs with U(RNA) T(DNA) pairs with A(RNA) C pairs with G |
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| how are base pairs held together |
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| hydrogen bonds |
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| semiconservative replication |
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| new double stranded DNA has one old and one new strand of DNA |
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| Okasaki fragment |
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| segment of DNA on lagging strand of DNA in replication - joined later by DNA ligase |
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| codon |
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| set of 3 nucleotides that code for a specific amino acid |
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| 3' end |
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| OH group end -this is the end where nucleotides can be added |
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| 5' end |
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| phosphate end |
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| antiparallel strands of DNA |
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| two strands are complimentary based paired in opposite directions |
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| leading strand in DNA replication |
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| DNA is copied continuously reading from 3' end towards 5' end (copy is growing 5' to 3') |
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| lagging strand in DNA replication |
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| must be copied opposite from direction that DNA is unzipping -DNA polymerase is copied in segments (called Okasaki fragments) -DNA ligase connects fragments |
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| DNA polymerase |
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| adds new bases to chain |
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| DNA ligase |
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| links Okasaki fragments on lagging strand |
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| RNA polymerase |
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| sets down primer before DNA polymerase can begin copying; on lagging strand this must happen before EACH Okasaki fragment |
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| central dogma (flow of genetic information) (3) |
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| -recombination - genetic information can be transferred between cells of same generation -expression - genetic infortmation is used to produce proteins -replication - genetic information is duplicated and cells split from parent to daughter |
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| AUG |
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| start codon codes for Methionine |
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| 3 types of RNA |
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| mRNA (messenger) tRNA (transfer) rRNA (ribosomal) |
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| mRNA |
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| codes for protein |
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| tRNA |
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| carries amino acids to ribosome connects amino acid to codon stem and loop structure - stem=short stretches of base pairing within tRNA; loop=short stretches of nucleotides that are not paired has anticodon - complimentary 3 nucleotide sequence that matching with codon |
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| anticodon |
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| complimentary 3 nucleotide sequence that matching with codon |
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| rRNA |
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| structural part of ribosome |
