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Micro Test II
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58
Microbiology
Undergraduate 3
02/17/2012

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Term
Topoisomerases
Definition
Type I: reactive, cut one strand, and reattach to reduce torsion
Type II: preemptive, cut both strands and twist negatively, to preempt torsion
Term
Prokaryotic DNA Replication Regulation
Definition
1) Methylation of origin (Hi = go)
2) SeqA (association = no go)
3) clamp loader concentration (Hi = go)
Term
helicase loader
Definition
recruits helicase and allows it to bind origin
Term
DNA organization types in Bacteria
Definition
linear/circular/mix; also plasmids, and/or chromids (sinorhizobia)
Term
Regulon
Definition
all the operons/genes affected by a regulatory element
Term
rolling circle model
Definition
DNA pol displaces one strand, synthesizing a new one in its place. Displaced strand gets replicated independently
Term
shuttle vector
Definition
usually a plasmid, built to propagate in 2+ species
Term
metagenomics
Definition
the study of multiple genomes found in a single environment simultaneously, helps study diversity
Term
PCR
Definition
requires two polymerases, gene in question, NTPs, and 2 primers; melt (95), anneal (55), synthesize (72), repeat
Term
DNA melting point
Definition
depends on GC content: more GC higher melting point
Term
Shot-gun sequencing
Definition
Dideoxynucleotides added to truncate at random places, giving you oligo’s that overlap, giving you contigs and possibly the full sequence
Term
Open Reading Frame (ORF)
Definition
gene or series of genes (mono/polycistron), which code for protein(s)
Term
promoter
Definition
prokaryote: -35 and -10 consensus sequences that recruit sigma factor
Term
sigma factor
Definition
RNP which locates/binds promoter and recruits holoenzyme; different sigmas for different kinds of genes
Term
Initiation (translation)
Definition
1) 30S unit binds start codon with help
2) Met-charged tRNA is recruited
3) 50S subunit encompasses tRNA w/ help
Term
Elongation (translation)
Definition
1) new tRNA enters A site, peptidotransferase acitivity moves protein chain to its amino acid (ATP)
2)50S unit is shifted down one codon, tRNAs are shifted down one site (ATP)
3) 30S unit is shifted afterward
Term
Termination (translation)
Definition
1) RF1/2 enters A site, PTase releases protein (ATP)
2) 50S and 30S are separated (ATP)
Term
how antibiotics affect transcription
Definition
intercalation into DNA proper (actinomycin D)
binding active sites in RNA pol (rifamycin B)
Term
tmRNA
Definition
adds tags to proteins of stop-less mRNA; chaperones take tagged proteins to ATP-dependent proteases
Term
TAT
Definition
secretory protein complex; secretes entire folded proteins to periplasm
Term
direct secretion
Definition
three part secretory protein complex that transports amino acid chains through both cell membranes without it ever coming in contact with the periplasm
Term
proteosomes
Definition
hetero (eu), or homoheptameric (pro) rings of protein which degrade tagged proteins. Hetero has an unwinding cap (sometimes)
Term
list the major types of RNA in order of increasing half-life
Definition
mRNA, tRNA, then rRNA
Term
how we know codons are 3 bps
Definition
alternating bp's gave two different amino acids: ATA and TAT; if 2: it would be the one, over and over: AT and AT
Term
Merodiploid
Definition
haploid organism with an extra copy of part of its own genome; occurs through Hfr conjugation
Term
Competance and quorum sensing
Definition
CF excreted and, at high enough concentration, reenters, begins pathway for gene transcription of transformation
Term
Pheromones and conjugation
Definition
pheromones produced by recipient, enter donor, induce genes which code for enzymes on conjugation pathway
Term
specialized vs. generalized transduction
Definition
S: few close genes are transduced (lysogenic virions)
G: any set/number of gense can be transduced (lytic virions)
Term
Holliday Structure
Definition
Rec D causing the recombination of donor and recipient DNA such that one strand of the donor is paired with the complementary strand of the recipient and vice versa (+)
Term
Cointegrate (noun)
Definition
intermediate molecule during generalized recombination; D + R (Holliday)
Term
Cotransduction
Definition
two genes are simultaneously added to host genome during transducive recombination: the closer they are on the donor genome, the more likely they are to be cotransduced
Term
Six mutation repair mechanisms
Definition
NER, Methylation mismatch, BER, Recombination, Translesion bypass synthesis, Photoreactive
Mnemonic: NuMBeR TraP
Term
Griffith
Definition
Microbiologist who discovered transformation: live non-virulent strain + dead virulent strain = death
Term
Competence of Bacteria Based on Gram Staining
Definition
Gram positive: naturally competent
Gram negative: requires membrane compromising mechanisms
Term
Transformation
Definition
CFs --> dsDNA --> recombination
Term
Starved F+ E. Coli...
Definition
...will cease maintenance of unnecessary mechanisms (including plasmids)
Term
Sex Pilus
Definition
DNA is transferred through hollow tube rather than relaxosome
Term
macrolesions (5)
Definition
Inversions, mass insertions/deletions, translocations, and duplications
Term
Positive selection
Definition
Poisoning a population to select for mutants resistant to poison (pen + screening)
Term
Indirect selection example
Definition
tryptophan auxotrophs, replica plating
Term
Ames test
Definition
His - in limited Histidine, healthy colonies are REVERTANTS; mutagen testing: more revertants, more mutagenic; Benzpryene, only mutagenic when metabolized: add rat liver homogeny
Term
Recombination
Definition
generalized: considerable homologous DNA, RecA mediated
specialized: site specific, recombination enzyme mediated (no RecA)
Term
Transition
Definition
substitution of purine for purine, or pyrimidine for pyrimidine
Term
Transversion
Definition
substitution of purine for pyrimidine, or pyrimidine for purine
Term
Transcriptional Attenuation
(example)
Definition
as w/ trp attenuation: high [trp], ribosome stalls to polymerize, allowing 3:4 attenuation loop to form, and release RNA pol; low [trp] 2:3 loop forms allowing time for RNA pol to begin transcription of functional genes
Term
Sigma Factor Regulation
Definition
Transcriptional regulation, Anti-/anti-anti-sigma factor activity (sporulation), Methylation, conditional Proteolysis
Mnemonic: TAMP(on)
Term
Major pro and con to transcriptional modification
Definition
ideal energetically, very slow
Term
operon
Definition
regulator--operator--promoter--SG--SG--SG
Term
Synthesize protein from one prokaryotic org's gene in another prokaryotic org (6)
Definition
PCR, restrict stock plasmid and gene with same RE, ligate gene into plasmid, detect its presence, denature wall of recipient (if incompetent) and transform plasmid, select for F+ strain
Term
Ways to detect presence of gene in plasmid
Definition
mass spec before and after or a good gel; re-restrict: 1 or 2 pieces?
Term
Polyethylene glycol
Definition
induces competence in E. coli by denaturing outer wall
Term
Specify the gene for a particular protein
Definition
Sequence the amino acids of protein, predict the sequence, probe endonuclease polymorphisms for the sequence, PCR that morphism (use same endonuclease to introduce said morphism into a plasmid, transform)
Term
synthesize a eukaryotic protein in a prokaryote
Definition
buy stock mRNA for that protein(no introns), use viral reverse transcriptase to create ds cDNA, PCR, plasmid, transform
Term
Mechanism of Gene Therapy
Definition
buy cDNA for gene, transduce; may kill patient
Term
Mechanism of Vaccine Therapy
Definition
specify the gene for the primary antigen (a.a. sequence, predict, probe), insert into plasmid for E. coli and replicate (denature, transform, conjugate), isolate protein from E. coli, innoculate
Term
RNA dependent DNA polymerase
Definition
used to make cDNA from mRNA in gene studies
Term
Steps of Plasmid Genetic Engineering
Definition
1: Restrict/Digest DNA in question
2: Isolate Gene
3: cleave plasmid
4: transform
5: ligate
Term
Promoters Serve what specific purpose?
Definition
To attract RNA Pol, to synthesize RNA strands. Period.
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