Term
| Factor-independent termination |
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Definition
Of transcription
RNA stem loop + >4U's
Structure disrupts elongation complex, pulls from DNA
RNAP slower-> higher probability of stem loop form |
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Term
| Factor-dependent termination |
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Definition
Of transcription
Rho binds to RNA rut sites
Destabilizes complex in helicase-like activity is hits RNAP
Concurrent translation prevents this b/c ribosome blocks RNAP
Less precise than factor-independent |
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Term
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Definition
protein binds to rut sites in RNA for factor-dependent termination
hits RNAP to end transcription |
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Term
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Definition
| RNA sites that Rho initially binds to |
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Term
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Definition
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Term
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Definition
UAA, UAG, UGA
don't interact w/ tRNAs |
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Term
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Definition
non-standard AA inserted into UGA
found in antioxidant proteins |
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Term
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Definition
non-standard AA inserted into UAG stop
found in archaea methanogens |
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Term
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Definition
50S has 23S & 5S rRNA
30S has 16S rRNA |
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Term
| aminoacyl & RNA synthetase |
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Definition
charges tRNA w/ AA
1st step in translation
uses ATP to form an aminoacyl & tRNA-AA
only editing step in translation |
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Term
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Definition
on tRNA
added enzymatically at beginning of translation
not encoded in DNA
only properly folded RNA get CCA |
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Term
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Definition
ribosome binding site
base pairs with 16S rRNA in 30S ribosome subunit |
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Term
| translation initiation factors |
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Definition
IF-1: blocks A site
IF-2: helps put tRNA-fMet in P site (ATG), binds GTP
IF-3: blocks 50S until 30S properly positioned |
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Term
| translation elongation factors |
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Definition
EF-Tu: brings tRNA-AA to A site, binds GTP
EF-Ts: regenerates EF-Tu
EF-G: pushes ribosome 1 codon, binds GTP |
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Term
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Definition
carries out peptide bond formation
evidence of RNA world |
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Term
| translation release factors |
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Definition
mimic structure of tRNA & bind to A site
RF1: associate with UAA, UAG
RF2: associate with UAA, UGA |
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Term
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Definition
has tRNA & mRNA functions
interacts w/ open A site in case of stalled ribosomes (ex. mRNA cut in middle & doesn't have stop codon)
has tag codons for proteases & a stop codon |
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Term
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Definition
1961 Nature
tried to solve genetic code before sequencing
saw T4 phage rII mutant (derived by frameshift mutagens) could form plaques in EC B but not K12
r+ wild type could form plaques in either
+1 & -1 rII mutants could suppress e/o for r+ phenotype (+1,+1 and -1,-1 were still non-functional mutant) b/c deletion & insertion restores reading frame
3 +1 or 3 -1 together yielded r+ phenotype b/c addition of whole codon or deletion of whole codon restored reading frame
concluded triplet codon genes w/ no overlapping or commas/spaces and that is read from a specific starting point |
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Term
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Definition
1961
developed in vitro translation
fed mRNA to ribosomes & AAs
polyU->tyrosine |
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Term
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Definition
1962/63
mastered synthesis of oligonucleotides
made many RNAs & exposed them to in vitro translation to solve genetic codes |
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Term
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Definition
| 2nd site mutation restores wild type phenotype |
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Term
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Definition
| mutation upstream affects downstream gene expression |
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Term
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Definition
insert in gene may affect->
repression/activation of ds by us
transcription initiation & termination (ex. rut- decreases term)
translation
mRNA stability
promotor insertion |
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Term
| what happens if nonsense mutation before rut site |
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Definition
stop codon makes ribosome halt
can't block RNAP
Rho terminates transcription |
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Term
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Definition
translation of us gene allows translation of ds gene
RNA structure-> 70S at us stop codon prevents stem loop that would block RBS on ds |
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Term
| how to distinguish polarity change |
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Definition
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Term
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Definition
unfolded protein secretion
1. post-translational: protein translated in cytoplasm & secreted
N-terminal signal sequence cleaved
protein into periplasm
SecA/B/YEG
Co-Translational: signal sequence stops translation-> ribosome recruited-> translation pushes protein through SecYEG & into membrane
SS is not cleaved
must occur this way b/c hydrophobic proteins would aggregate in cytoplasm |
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Term
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Definition
binds to N-terminal signal sequence in post-translational Sec secretion
uses ATP |
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Term
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Definition
| many bind to protein in cytoplasm during post-translational Sec secretion |
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Term
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Definition
inter membrane protein involved in Sec system
transport of protein |
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Term
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Definition
Twin-Arginine Transports
fully-folded proteins modified in cytoplasm to be secreted
signal sequence gets cleaved
transport using PMF |
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Term
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Definition
multiple genes on 1 mRNA transcript
allows easy co-regulation of function
1 terminator & promotor
Diff RBS, start codon, & stop codon for each gene |
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Term
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Definition
RNAP has no editing function
rRNAs & tRNAs in operon must be cleaved apart by RNAases to be used in translation |
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Term
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Definition
creates pseudouridine from uridine
very regulated & specific
isomerization
protects RNA from damage |
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Term
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Definition
purine derived from adenine
sugar + hypoxanthine (deaminated adenine) attached
unique bp w/ C, U, or A
wobble |
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Term
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Definition
3rd base in codon has less stringent base pairing rules
inosine |
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Term
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Definition
| mutants deficient in making (anabolic) or using (catabolic) something |
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Term
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Definition
| probability of mutation for specific phenotype per generation |
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Term
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Definition
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Term
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Definition
mutagen that inserts in helix
creates a zone of inhibition, and then many colonies around on selection plate (ex. LB Amp)
downside: many irrelevant mutations |
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Term
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Definition
B-Lactam
allows isolation of mutants that can't grow in a certain condition (auxotrophs)
inhibits peptidoglycan synthesis, so only growing cells killed
grow in penicillin culture & plate w/o penicillin w/ molecule of interest (what auxotroph for)
may also get other mutants (pen-, persisters) b/c phenotypic heterogeneity |
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Term
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Definition
stops growing, can survive penicillin
not always a mutant
present in biofilms
high antibiotic resistance |
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Term
| conditional lethal mutations |
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Definition
essential gene nonfunctional in certain condition
1) temperature sensitive die at high T, easier isolation
2) cold sensitive die at low T |
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Term
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Definition
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Term
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Definition
after mutation, takes time for phenotype to be expressed
can lead to underestimation of mutation rate |
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Term
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Definition
| selection of random mutation |
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Term
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Definition
directed evolution
growing w/ antibiotic can lead to directed evolution of resistance |
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Term
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Definition
Fluctuation test
supports Darwinian evolution
1st grew EC & plated same culture on T1 phage plates -> similar colony counts
Then grew separately -> plates had different colony counts -> evolution occurred in flask before selective conditions |
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Term
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Definition
| purine to purine (A, G) or pyrimidine to pyrimidine mutation (C, T) |
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Term
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Definition
| purine to pyrimidine (or vice versa) mutation |
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Term
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Definition
| base change in ORF doesn't change AA (wobble) |
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Term
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Definition
base change alters ORF
silent: no phenotype change
null: non-functional protein
leaky: intermediate
gain of function |
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Term
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Definition
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Term
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Definition
reading frame disruption
rarely leaky
6 potential reading frames for any DNA |
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Term
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Definition
| homologous recombination between direct repeats causes end of us gene & beginning of ds gene to be deleted bc forms circular DNA w/ no oriC |
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Term
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Definition
DNA order switches due to homologous recombination between inverted repeats
inner portions of genes are switched & genes between invert order |
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Term
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Definition
mobile genetic element in gene by homologous recombination
usually produces null mutation
used in lab to generate knockouts |
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Term
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Definition
TN put on suicide plasmid
commonly use EC lambda(pir)
TN inserts in different places for each mutant |
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Term
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Definition
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Term
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Definition
| only allows growth of desired mutant |
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Term
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Definition
spontaneous mutation
replication error
base change into isomer |
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Term
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Definition
spontaneous mutation
superoxide or H2O2
8-oxoguanine (GO) is most common, can bp w/ A or C |
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Term
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Definition
combines TN mutagenesis & deep sequencing
large-scale identification of genes important for given condition
1. generate TN mutant library
2. expose to selective & non-selective conditions
3. isolate genomic DNA
4. sequence TN junctions
5. map back to genome
6. count # of sequence reads per junction to see how much mutation is represented in population
If mutation is unfavorable, selective condition will show lower frequency & vice versa |
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Term
| base deamination repair (2) |
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Definition
base deamination = loss of amino group of base
fixed by base excision
1. DNA glycosylases recognize deaminated base
2. base flipped out of helix & cut (apurinic or ayrimidic base is sugar w/o base)
3. AP endonuclease removes AP base
4. DNAPI & Ligase fills gap
fixed by Very Short Patch Repair when 5'methyl cytosine-> thymine causes T-G pairing mismatch
1. Dcm methylation
2. MutS recognizes mismatch
3. Vsr endonuclease cuts T strand
4. MutL & UvrD helicase removes cut strand
5. DNAPI & Ligase |
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Term
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Definition
G=O
fixed by MutM that removes GO from DNA when paired w/ C
fixed by MutY that removes incorrect A pairing
fixed by MutT that dephosphorylates GO so that it won't be incorporated |
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Term
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Definition
| determines proteins & genes in a pathway |
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Term
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Definition
methyl methane sulfate
low alkylation means bases damaged
high alkylation means phosphates damaged |
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Term
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Definition
fixed by Base Excision using AlkA & Tag
fixed by methyl transferases that transfer methyl groups to themselves & are destroyed
fixed by AkB that removes methyls from bases & releases CO2 |
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Term
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Definition
response to excessive alkylation
Ada: trigger/switch, methyl transferase
low alkylation: methyl destroyed from base
high alkylation: methyl moved from phosphates to N-terminus
Ada is renewed & becomes a transcriptional activator |
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Term
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Definition
UV causes covalent bonds in adjacent pyrimidines
commonly thymine dimers
Photolyase recognizes & removes bases, requires UV light
DNAPI & Ligase fills gap
not in humans (sunscreen!) |
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Term
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Definition
methyl-directed mismatch repair
1. Dam methylase methylates GATC sites after replication
2. MutS recognizes distortion, recruits MutL & MutH
3. DNA spooled until complex meets GATC
4. Much cuts unmethylated strand
5. UvrD degrades unmethylated strand back to damage
6. DNAPIII*** & Ligase
a dam null mutant would randomly cut a strand |
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Term
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Definition
| recognize deaminated bases |
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Term
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Definition
| remove sugar w/o base during base deamination repair |
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Term
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Definition
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Term
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Definition
| recognizes incorrect base pairing |
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Term
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Definition
| endonuclease that cuts damaged strands |
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Term
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Definition
| helicase spools DNA during MMR & Very Short Patch Repair |
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Term
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Definition
| removes bases on damaged strand |
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Term
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Definition
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Term
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Definition
| removes incorrect A=GO pairing during ROS repair |
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Term
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Definition
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Term
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Definition
| removes methyls from bases & releases CO2 |
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Term
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Definition
trigger of adaptive response
methyl transferase |
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Term
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Definition
| Recognizes & removes dimers from UV damage |
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Term
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Definition
| methylates GATC sites after replication |
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Term
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Definition
| cuts unmethylated damaged strand in MMR |
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