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
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