Micro Test – Flashcards with Answers
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| Transcription initiation requirements |
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| **** RNA polymerase, promoter, Sigma factor**** |
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| PCR things needed |
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| 1. template DNA 2. DNA polymerase (Taq) 3. dNTPs 4. Primers |
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| Okazaki fragments |
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| 1000-2000 bp long |
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| H bonds between A and T |
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| 2 |
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| Promoter |
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| 2 consensus sequences -35 (TTGACA)- titty gaca -10 (TATAAT)- TATA box (Pribnow box) |
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| H bonds between C and G |
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| 3 |
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| Initiation complex |
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| 30S + 50S subunits + mRNA + fMet-tRNA |
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| DNA synthesizes in |
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| 5' to 3' direction |
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| CO2 requirements |
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| 5-10% required by many clinical isolates |
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| Doubling time |
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| AKA generation time E Coli TAKES 20 minutes **** Humans = 1 day |
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| RNA polymerase |
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| AKA primase creates free 3' OH |
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| Metabolic energy stored as |
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| ATP, GTP, CTP TTP |
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| Modification after translation |
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| Adds stuff to protein + lipids- lipoprotein + sugars- glycoproteins |
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| Peptide formation |
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| Aminoacyl tRNA arrives @ A site Transpeptidation Translocation- empty tRNA exits E site, tRNA w/ growing chain moves A to P site, new tRNA comes to A site |
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| Biofilms |
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| Bacteria sit down on surface, communicate, secrete film which is usually antibiotic resistant |
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| Anabolism |
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| Biosynthesis of molecules |
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| Elements required for life- macronutrients |
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| CNHOSP (components of cell) also K, Fe, Ca, Mg |
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| Obligate anaerobe |
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| Can't have oxygen |
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| Steps of binary fission |
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| Cell elongates, DNA replicates, Septum forms, cell divides NO MITOSIS OR MEIOSIS |
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| PCR applications |
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| Crime scene Paternal testing Protein expression Disease diagnosis |
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| DNA pol I and DNA ligase |
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| DNA pol I- replaces RNA nucleotides w/ DNA DNA ligase- glues together, makes nucleotides continued strands, finishes final bonds |
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| Anaerobe |
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| Doesn't need oxygen |
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| Heterotroph |
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| Don't make own energy Most bacteria are this Eat organic compounds (carbs, lipids, proteins) |
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| Accuracy of replication |
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| E coli 1 in a million per gene, per generation |
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| Speed of replication |
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| E coli doubles in 20 minutes (750-1000 bp/sec) |
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| Ribosome binding sites for tRNAs |
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| E site- exit P site- peptidyl, donor site A site- aminoacyl, acceptor |
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| Compound is oxidized |
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| Energy released |
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| Selective media |
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| Ex: MacConkey's agar (even though it's differentiation too) Inhibits growth of UNDESIRED organisms |
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| Differentiation media |
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| Ex: blood agar (hemolytic vs. other) many organisms will grow differentiates between 2 types of bacteria |
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| Cost of biosynthesis |
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| Expensive. COSTS ATP DNA (60 k per sec) RNA (75 k per sec) Proteins (2,120,000 per sec) |
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| Plasmids uses as tools |
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| Expressing proteins Knockouts Fluorescent reporters |
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| Most desired nutrient by bacteria |
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| Fe, IRON most pathogens really want it |
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| Electron Transport Chain |
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| Final e- acceptors are inorganic compounds ***(O2, NO3, SO4) NADH and FADH2 take electrons to chain electrons flow form carriers w/ negative reduction potentials to ones with more positive |
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| Fermentation |
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| Final e- acceptors are organic molecules Buildup of NADH pyruvate and NADH available implies anaerobic catabolism |
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| Nitrogen acquisition |
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| From organic compounds From NO3- From NH4+ SOME can use nitrogen fixation (from N2) |
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| Limited nutrient Adaptation strategies |
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| Go where nutrients are (habitat selection) Adhere to surface, form biofilm |
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| Mesophile |
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| Grows 20-45 degrees C Most pathogens |
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| PCR steps |
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| Heat denaturation (94-96 C) Annealing (55-65 C) Elongation (68-72 C) REPEAT |
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| Histidine auxotroph |
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| Histidine is an amino acid, must be given histidine to live, can't synthesize it |
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| Shine-Dalgarno sequence |
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| In the RBS, where ribosome binds to mRNA, 8 base pairs upstream from start codon |
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| Barophilic |
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| LOVES to grow at high pressures (up to 590 atm) |
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| Psychrophile |
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| Likes to grow under 15 degrees C |
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| Reducing power stored as |
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| NADH, FADH2 |
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| Aerobe |
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| Needs oxygen |
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| Heterotrophs |
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| Obtain from preformed organic compounds often get H, N, O from same organic compounds |
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| Enrichment media |
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| Promotes growth of desired organisms Almost ALWAYS DEFINED media |
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| Water availability (AsubW) |
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| Pure water =1 Saturated salt water= .75 Dried fruit= .5 Most organisms need above .98 |
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| RNA holoenzyme |
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| RNA polymerase + sigma factor all together unwinds DNA, Elongation can begin |
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| Negative control |
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| Repressor protein inhibits transcription (binds downstream) |
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| Agar |
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| Seaweed extract melts at 100 degrees C, solidifies at 44 degrees C |
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| Use of micronutrients |
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| Serve as cofactors for many enzymes Usually plentiful, supplied in lab from glassware contamination |
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| Point mutations |
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| Silent- results in same amino acid produced Missense mutation- results in altered base pair, different amino acid Nonsense mutation- doneski, results in stop codon |
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| Salt level toleration |
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| Staph. aureus is a good example (salt on skin) Usually salt plasmolyzes cells in hypertonic solutions (water leaves cell) |
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| After mRNA is made |
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| TRANSLATION begins |
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| Plasmids hold these informations |
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| Transmittance Virulence Antibiotic resistance Xenobiotic degradation (eating something not usually eaten) |
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| Termination |
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| Two ways ter sites- Tus proteins bind to here, hold replication bubble until other side reaches it Two replication forks- topoisomerase clips one strand into 2 |
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| Activator protein |
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| Type of positive control in which protein promotes transcription initiation |
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| Can translation begin before transcription is complete? |
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| YES |
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| Autotrophs |
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| acquire carbon from CO2 |
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| Frame shift mutations |
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| addition/removal of base, always deleterious |
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| DNA polymerase |
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| adds nucleotides E Coli has 5 polymerases (i-v), only iii and i are important |
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| when sigma factor falls off |
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| after elongation starts, sigma factor is recycled |
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| Chemoautotroph |
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| aka lithotrophs reduce simple chemical compounds H2S, CH4, NH4+ |
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| Metabolism |
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| all chemical reactions within organisms |
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| Constitutive expression |
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| always, like an alarm clock |
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| Oxidative phosphorylation |
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| another way to make ATP AKA chemiosmosis Associated with Elec. Trans. Chain e- transport pumps protons out of cell, uses proton gradient to make ATP |
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| Reversion |
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| back mutation, reverses 1st mutation |
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| Lipid pathway |
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| beta oxidation |
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| Induced mutation |
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| by a mutagen |
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| Barotolerant |
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| can grow under high pressure |
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| Krebs Cycle |
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| central aspect of metabolism in some bacteria Produces NADH, FADH, ATP, CO2 |
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| Metabolism |
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| chemical reactions occurring within |
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| SEC pathway |
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| common pathway for proteins to exit cell |
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| Barbara McClintock |
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| discovered transposons in Indian corn in 1940s Won Nobel prize in 1983 |
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| Facultative anaerobe |
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| either way, doesn't give a damn with or without air |
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| Compound reduced |
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| energy required |
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| Substrate level phosphorylation |
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| enzymatic reaction coupled directly to ATP production, seen in glycolysis |
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| Covalent modification |
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| enzymes can have chemical groups added, can turn enzyme on or off, removed when conditions change |
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| Spontaneous mutation |
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| error in replication, very low 1 in a million per gene |
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| Mutagenic determination |
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| experiment w/ bacteria, know mutation rate |
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| Plasmids |
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| extrachromosomal DNA Less than 30 genes Found in yeast, rarely in others Small and circular (1/1000 size of chromosome) May replicate using DNA pol like chromosome |
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| Pentose Phosphate Pathway |
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| generates ribose, NADPH for biosynthesis, Erythrose-4-P |
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| Glycolysis |
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| glucose (6C's) + 2ADP + 2 Pi + 2NAD+ ---- 2 pyruvate +2NADH + 2 ATP |
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| 3 Glucose pathways |
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| glycolysis, entner doudoroff, pentose phosphate |
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| Operon |
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| group of genes put together because they're used around the same time (TRANSCRIBED FROM SINGLE PROMOTER) |
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| Thermophiles |
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| grow above 45 degrees celsius |
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| Exponential (log) phase- phase of growth curve |
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| growing exponentially food and space good, doing great |
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| Acidophile |
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| grows in pH 0-5.5 ACIDIC |
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| Neutrophile |
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| grows in pH 5.5-8 HUMAN PATHOGENS |
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| Alkalophile |
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| grows in pH 8-11.5 BASIC |
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| DNA methylation |
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| happens after replication Old DNA methylated, new DNA hasn't, recognizes incorrect base pairs |
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| Sigma factor |
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| helps RNA polymerase see and find promoter, pushes along |
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| PCR |
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| in vitro replication of target DNA Single DNA molecule amplified Heating, cooling, heating |
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| 3 steps of replication |
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| initiation, elongation, termination (replication, transcription, translation) |
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| Siderophores |
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| iron boomerang, cell sends it out to environment, grabs iron, comes back |
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| 3' OH |
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| is created by RNA polymerase, starts the job, gives polymerase something to grab |
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| Elements required for life- micronutrients |
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| just need very small amounts of Mn, Fn, Cu |
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| Gyrase and Topoisomerases |
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| keeps DNA from getting twisted, uncoils DNA before helicase comes through |
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| Two component phosphorelay system |
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| link events outside to inside (temperature or oxygen level) Two components- Sensor- puts phosphoric group on RESPONSE-REGULATOR- which causes gene regulation, repression |
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| Motility mutation |
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| loss of flagella, loss of function of flagella |
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| Endonucleases |
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| made from bacteria, cuts DNA into chunks, used to destroy viral DNA that invades, won't chop up methylated DNA |
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| Entner-Douderoff Pathway |
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| many aerobic bacteria undergo replaces first phase of glycolysis |
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| Catabolism |
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| metabolic breakdown |
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| AUG codon |
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| methionine normally 1st amino acid in EVERY bacterial protein- N-formylmethionine (fMET) Goes back to normal after 1st AUG |
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| What do bacteria do with energy |
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| motility, membrane transport, biosynthesis (anabolism) |
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| Transpeptidation |
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| moves growing chain catalyzed by peptidyl transferase Occurs between P and A sites |
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| Positive mutations |
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| new compounds can be produced, engineer avirulent organisms for vaccines |
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| Complex |
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| not chemically defined made from plant or animal name Digest- clue Used just to get shit to grow in lab |
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| DNA III needs 3 things |
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| nucleotides, template, needs 3' OH to grab onto |
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| General purpose media |
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| nutrient agar, nutrient broth used for general growth many organisms will grow on it |
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| Dormancy |
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| nutrients limited spore formation in bacteria ultramicrobacteria-small forms of larger bacteria that are dormant, remain viable for years |
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| Stationary phase |
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| nutrients ran out growth rate=death rate |
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| Auxotroph |
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| nutritional mutant that requires an additional growth factor PARENT of auxotroph = PROTOTROPH |
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| Continuous culture |
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| one essential nutrient limiting fresh medium added as waste removed mimics nature, used in food and industrial microbiology |
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| Growth in nature |
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| organisms usually stressed viable, non culturable less than 1 percent or organisms can be cultured |
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| oriC |
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| origin of initiation A/T rich (has 2 H bonds, easier to separate) Region with consensus sequences DnaA binds oriC Energy melts bonds here, ATP-> ADP |
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| Negative mutations |
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| pathogens develop, antibiotic resistance spreads |
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| Microaerophilic |
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| picky, needs just enough air to be happy |
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| Media |
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| plural (like bacteria, bacterium) |
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| Polymer uptake |
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| polymers often insoluble, must be solubilized to take in, secrete enzymes, break down, bring monomers in Cellulose--cellobiose---glucose |
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| Protein pathway |
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| proteolysis |
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| Flaggelar motility |
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| proton motive force Proton into the cell drives turbine in flagellar basal body, ROTATION |
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| Defined media |
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| pure chemicals, known concentrations nutritional studies |
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| Plasmid joining to chromosome |
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| random event, rarely occurs |
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| Global regulation |
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| regulation in large # of genes can involve sigma factors involves quorum sensing (pop. density, talking with chemicals) |
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| Positive control |
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| regulatory protein promotes transcription initiation |
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| RNA polymerase |
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| requires glasses, synthesizes RNA, has 5 subunits |
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| Transposons |
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| segments of DNA that move around to different positions in the genome of a single cell Cause mutations, increase amount of DNA in genome |
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| Regulatory proteins |
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| sense environmental change, change 3d conformation to not fit in regulatory region |
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| Helicase |
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| separates, unwinds starting at the origin |
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| Medium |
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| singular! |
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| Light requirements |
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| some photosynthetic organisms (cyanobacteria) |
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| Death phase |
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| some still dividing death rate > growth rate |
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| Reproduction |
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| spore formation in molds |
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| Phase of growth curve- Lag phase |
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| starting out, not shit happening waking up and getting ready |
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| Termination of translation |
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| stops at nonsense codon (UAA, UAG, UGA) Final bond made, peptide released, ribosomes dissociate from mRNA |
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| Strong vs weak promoter |
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| strong has good spacing in promoter, weak doesn't |
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| Ames test*** |
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| tests for chemical carcinogen, quickly determines mutagenecity, observes reversion rate, uses need for histidine in media, observes growth |
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| Attenuation |
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| transcriptional control based on DNA sequence/folding Coupled to translation (trp operon) |
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| Allosteric regulation |
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| type of translational control (post transcriptional) end product ends biosynthesis by binding to allosteric site and tells slow down |
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| Photoautotrophs |
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| use light to make energy |
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| genes closest to oriC |
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| used all of the time, 2 copies to start with, often ribosomal |
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| ATP synthase |
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| water wheel motor used in oxidative phosphorylation to crank ADP into ATP |
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| Replication Bubble |
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| what forms after oriC is split open |
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| Conjugation |
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| when 2 bacteria connect w/ sex pilus and transfer plasmid shit |
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| Inducible expression |
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| when advantageous |
