Term
| Transcription initiation requirements |
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Definition
| **** RNA polymerase, promoter, Sigma factor**** |
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Term
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Definition
1. template DNA
2. DNA polymerase (Taq)
3. dNTPs
4. Primers |
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Definition
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Definition
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Definition
2 consensus sequences
-35 (TTGACA)- titty gaca
-10 (TATAAT)- TATA box (Pribnow box) |
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Definition
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Definition
| 30S + 50S subunits + mRNA + fMet-tRNA |
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Definition
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Definition
| 5-10% required by many clinical isolates |
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Term
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Definition
AKA generation time
E Coli TAKES 20 minutes ****
Humans = 1 day |
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Term
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Definition
AKA primase
creates free 3' OH |
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Term
| Metabolic energy stored as |
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Definition
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Term
| Modification after translation |
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Definition
Adds stuff to protein
+ lipids- lipoprotein
+ sugars- glycoproteins |
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Term
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Definition
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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Definition
| Bacteria sit down on surface, communicate, secrete film which is usually antibiotic resistant |
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Term
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Definition
| Biosynthesis of molecules |
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Term
| Elements required for life- macronutrients |
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Definition
CNHOSP (components of cell)
also K, Fe, Ca, Mg |
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Definition
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Term
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Definition
Cell elongates, DNA replicates, Septum forms, cell divides
NO MITOSIS OR MEIOSIS |
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Term
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Definition
Crime scene
Paternal testing
Protein expression
Disease diagnosis |
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Term
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Definition
DNA pol I- replaces RNA nucleotides w/ DNA
DNA ligase- glues together, makes nucleotides continued strands, finishes final bonds |
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Definition
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Term
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Definition
Don't make own energy
Most bacteria are this
Eat organic compounds (carbs, lipids, proteins) |
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Term
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Definition
| E coli 1 in a million per gene, per generation |
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Term
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Definition
| E coli doubles in 20 minutes (750-1000 bp/sec) |
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Term
| Ribosome binding sites for tRNAs |
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Definition
E site- exit
P site- peptidyl, donor site
A site- aminoacyl, acceptor |
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Term
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Definition
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Term
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Definition
Ex: MacConkey's agar (even though it's differentiation too)
Inhibits growth of UNDESIRED organisms |
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Term
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Definition
Ex: blood agar (hemolytic vs. other)
many organisms will grow
differentiates between 2 types of bacteria |
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Term
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Definition
Expensive.
COSTS ATP
DNA (60 k per sec)
RNA (75 k per sec)
Proteins (2,120,000 per sec) |
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Term
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Definition
Expressing proteins
Knockouts
Fluorescent reporters |
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Term
| Most desired nutrient by bacteria |
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Definition
Fe, IRON
most pathogens really want it |
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Term
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Definition
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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Term
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Definition
Final e- acceptors are organic molecules
Buildup of NADH
pyruvate and NADH available
implies anaerobic catabolism |
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Term
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Definition
From organic compounds
From NO3-
From NH4+
SOME can use nitrogen fixation (from N2) |
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Term
| Limited nutrient Adaptation strategies |
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Definition
Go where nutrients are (habitat selection)
Adhere to surface, form biofilm |
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Term
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Definition
Grows 20-45 degrees C
Most pathogens |
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Term
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Definition
Heat denaturation (94-96 C)
Annealing (55-65 C)
Elongation (68-72 C)
REPEAT |
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Term
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Definition
| Histidine is an amino acid, must be given histidine to live, can't synthesize it |
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Term
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Definition
| In the RBS, where ribosome binds to mRNA, 8 base pairs upstream from start codon |
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Term
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Definition
| LOVES to grow at high pressures (up to 590 atm) |
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Definition
| Likes to grow under 15 degrees C |
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Definition
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Definition
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Definition
Obtain from preformed organic compounds
often get H, N, O from same organic compounds |
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Term
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Definition
Promotes growth of desired organisms
Almost ALWAYS DEFINED media |
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Term
| Water availability (AsubW) |
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Definition
Pure water =1
Saturated salt water= .75
Dried fruit= .5
Most organisms need above .98 |
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Term
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Definition
RNA polymerase + sigma factor all together
unwinds DNA, Elongation can begin |
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Term
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Definition
| Repressor protein inhibits transcription (binds downstream) |
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Term
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Definition
Seaweed extract
melts at 100 degrees C, solidifies at 44 degrees C |
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Term
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Definition
Serve as cofactors for many enzymes
Usually plentiful, supplied in lab from glassware contamination |
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Term
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Definition
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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Term
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Definition
Staph. aureus is a good example (salt on skin)
Usually salt plasmolyzes cells in hypertonic solutions (water leaves cell) |
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Term
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Definition
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Term
| Plasmids hold these informations |
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Definition
Transmittance
Virulence
Antibiotic resistance
Xenobiotic degradation (eating something not usually eaten) |
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Term
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Definition
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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Term
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Definition
| Type of positive control in which protein promotes transcription initiation |
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Term
| Can translation begin before transcription is complete? |
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Definition
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Definition
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Definition
| addition/removal of base, always deleterious |
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Definition
adds nucleotides
E Coli has 5 polymerases (i-v), only iii and i are important |
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Term
| when sigma factor falls off |
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Definition
| after elongation starts, sigma factor is recycled |
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Term
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Definition
aka lithotrophs
reduce simple chemical compounds
H2S, CH4, NH4+ |
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Term
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Definition
| all chemical reactions within organisms |
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Term
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Definition
| always, like an alarm clock |
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Term
| Oxidative phosphorylation |
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Definition
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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Term
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Definition
| back mutation, reverses 1st mutation |
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Definition
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Definition
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Definition
| can grow under high pressure |
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Term
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Definition
central aspect of metabolism in some bacteria
Produces NADH, FADH, ATP, CO2 |
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Term
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Definition
| chemical reactions occurring within |
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Term
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Definition
| common pathway for proteins to exit cell |
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Term
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Definition
discovered transposons in Indian corn in 1940s
Won Nobel prize in 1983 |
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Term
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Definition
| either way, doesn't give a damn with or without air |
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Definition
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Term
| Substrate level phosphorylation |
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Definition
| enzymatic reaction coupled directly to ATP production, seen in glycolysis |
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Term
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Definition
| enzymes can have chemical groups added, can turn enzyme on or off, removed when conditions change |
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Term
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Definition
| error in replication, very low 1 in a million per gene |
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Term
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Definition
| experiment w/ bacteria, know mutation rate |
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Term
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Definition
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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Term
| Pentose Phosphate Pathway |
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Definition
| generates ribose, NADPH for biosynthesis, Erythrose-4-P |
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Term
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Definition
| glucose (6C's) + 2ADP + 2 Pi + 2NAD+ ---- 2 pyruvate +2NADH + 2 ATP |
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Term
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Definition
| glycolysis, entner doudoroff, pentose phosphate |
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Term
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Definition
| group of genes put together because they're used around the same time (TRANSCRIBED FROM SINGLE PROMOTER) |
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Term
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Definition
| grow above 45 degrees celsius |
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Term
| Exponential (log) phase- phase of growth curve |
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Definition
growing exponentially
food and space good, doing great |
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Definition
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Term
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Definition
grows in pH 5.5-8
HUMAN PATHOGENS |
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Definition
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Definition
happens after replication
Old DNA methylated, new DNA hasn't, recognizes incorrect base pairs |
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Term
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Definition
| helps RNA polymerase see and find promoter, pushes along |
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Term
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Definition
in vitro replication of target DNA
Single DNA molecule amplified
Heating, cooling, heating |
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Term
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Definition
initiation, elongation, termination
(replication, transcription, translation) |
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Term
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Definition
| iron boomerang, cell sends it out to environment, grabs iron, comes back |
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Term
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Definition
| is created by RNA polymerase, starts the job, gives polymerase something to grab |
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Term
| Elements required for life- micronutrients |
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Definition
| just need very small amounts of Mn, Fn, Cu |
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Term
| Gyrase and Topoisomerases |
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Definition
| keeps DNA from getting twisted, uncoils DNA before helicase comes through |
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Term
| Two component phosphorelay system |
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Definition
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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Term
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Definition
| loss of flagella, loss of function of flagella |
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Term
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Definition
| made from bacteria, cuts DNA into chunks, used to destroy viral DNA that invades, won't chop up methylated DNA |
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Term
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Definition
many aerobic bacteria undergo
replaces first phase of glycolysis |
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Definition
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Term
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Definition
methionine normally
1st amino acid in EVERY bacterial protein- N-formylmethionine (fMET)
Goes back to normal after 1st AUG |
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Term
| What do bacteria do with energy |
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Definition
| motility, membrane transport, biosynthesis (anabolism) |
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Term
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Definition
moves growing chain
catalyzed by peptidyl transferase
Occurs between P and A sites |
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Term
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Definition
| new compounds can be produced, engineer avirulent organisms for vaccines |
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Term
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Definition
not chemically defined
made from plant or animal name
Digest- clue
Used just to get shit to grow in lab |
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Term
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Definition
| nucleotides, template, needs 3' OH to grab onto |
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Term
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Definition
nutrient agar, nutrient broth
used for general growth
many organisms will grow on it |
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Term
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Definition
nutrients limited
spore formation in bacteria
ultramicrobacteria-small forms of larger bacteria that are dormant, remain viable for years |
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Term
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Definition
nutrients ran out
growth rate=death rate |
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Term
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Definition
nutritional mutant that requires an additional growth factor
PARENT of auxotroph = PROTOTROPH |
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Term
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Definition
one essential nutrient limiting
fresh medium added as waste removed
mimics nature, used in food and industrial microbiology |
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Term
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Definition
organisms usually stressed
viable, non culturable
less than 1 percent or organisms can be cultured |
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Term
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Definition
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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Term
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Definition
| pathogens develop, antibiotic resistance spreads |
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Definition
| picky, needs just enough air to be happy |
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Definition
| plural (like bacteria, bacterium) |
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Definition
polymers often insoluble, must be solubilized to take in, secrete enzymes, break down, bring monomers in
Cellulose--cellobiose---glucose |
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Definition
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Term
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Definition
proton motive force
Proton into the cell drives turbine in flagellar basal body, ROTATION |
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Definition
pure chemicals, known concentrations
nutritional studies |
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Term
| Plasmid joining to chromosome |
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Definition
| random event, rarely occurs |
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Term
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Definition
regulation in large # of genes
can involve sigma factors
involves quorum sensing (pop. density, talking with chemicals) |
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Term
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Definition
| regulatory protein promotes transcription initiation |
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Definition
| requires glasses, synthesizes RNA, has 5 subunits |
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Term
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Definition
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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Definition
| sense environmental change, change 3d conformation to not fit in regulatory region |
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Definition
| separates, unwinds starting at the origin |
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Definition
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Definition
| some photosynthetic organisms (cyanobacteria) |
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Term
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Definition
some still dividing
death rate > growth rate |
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Definition
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Term
| Phase of growth curve- Lag phase |
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Definition
starting out, not shit happening
waking up and getting ready |
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Term
| Termination of translation |
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Definition
stops at nonsense codon (UAA, UAG, UGA)
Final bond made, peptide released, ribosomes dissociate from mRNA |
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Term
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Definition
| strong has good spacing in promoter, weak doesn't |
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Term
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Definition
| tests for chemical carcinogen, quickly determines mutagenecity, observes reversion rate, uses need for histidine in media, observes growth |
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Term
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Definition
transcriptional control based on DNA sequence/folding
Coupled to translation (trp operon) |
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Term
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Definition
type of translational control (post transcriptional)
end product ends biosynthesis by binding to allosteric site and tells slow down |
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Definition
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Definition
| used all of the time, 2 copies to start with, often ribosomal |
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Definition
| water wheel motor used in oxidative phosphorylation to crank ADP into ATP |
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Definition
| what forms after oriC is split open |
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Term
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Definition
| when 2 bacteria connect w/ sex pilus and transfer plasmid shit |
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