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Micro Test
2nd exam
146
Microbiology
Undergraduate 2
02/27/2012

Additional Microbiology Flashcards

 


 

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