Exam 3 Flashcards
- regulates the expression of a structural gene
- does not encode RNA or protein
- includes promoters and binding sites for regulatory proteins
DNA control sequence
- all the genetic information that defines an organism
- consists of one (usually) or more DNA chromosomes
genome
made up of contiguous packets of information called genes
chromosomes
produces a functional RNA, which usually encodes a protein
structural gene
- identifies conserved sequences
- the consensus sequence for sigma-70 promoters is called
the -10/-35 box
- subunit that directs RNA pol to different genes as needed to initiate transcription
- dissociates
sigma factors
always transcribing (s70 in E. coli)
housekeeping sigmas
recognize different promoters
specialized sigma factors
recognize promoters for genes that encode nitrogen metabolism and other functions
sigma 54
recognize promoters for genes that are heat shock-induced
sigma 32
recognize promoters for genes that encode motility and chemotaxis
sigma 28
recognize promoters for genes that encode stationary-phase and stress responses
sigma 38
what is the function of the omega subunit of the RNA polymerase holoenzyme
helps to protect the integriity of the complex in stressful situations
act as scaffolding proteins in the RNA polymerase holoenzyme
alpha 1 and alpha 2
what is the function of the Beta (and Beta prime) subunits of the RNA polymerase holoenzyme
catalyzes the synthesis of RNA
when the sigma factor is bound to the core enzyme, the six-subunit complex is termed
the RNA polymerase holoenzyme
RNA polymerase DNA and lays down a complementary and antiparallel strand of RNA
transcription
stages of transcription
- initiation
- elongation
- termination
RNA transciption begins at which nucleotide
+1
in bacteria, a gene can operate independently or in tandem with other genes in
an operon
1 gene under control of a single promoter
monocistronic RNA
more than one gene under control of a single promoter
polycistronic RNA
occurs when a bacteriophage accidentally packages a fragment of host cell DNA
transduction
steps to transduction
- P22 phage DNA infects a host cell and makes subunit components for more phage
- DNA is packaged into capsid heads, some capsids package host DNA
- new phage assembly is completed
- cell lyses; phage is released
- transducing phage particle injects host DNA into new cell, where it may recombine into the chromosome; recombination crossover events exchange host DNA for donor DNA
what genome characteristics would be useful for computationally identifying genes acquired by HGT
- guanine-cytosine content
- codon usage
benefits of fast replication of bacteria
- competitive advantage
- rapid evolution
- rapid colonization
- biofilm formation
- survival under stress and changing conditions
what features enable prokaryotes to replicate rather quickly
- small genomes that contain only essential genes
- genes lack introns
- only short control sequences between genes (high gene density)
- form when an integrated F plasmid is inaccurately excised from the genome
- some host cell DNA is excised and ends up on the plasmid
F’ plasmid
what happens when the F’ plasmid conjugates
sends host cell DNA to recipient
- the F factor loops out of the chromosome with thr and leu genes in the loop
- a crossover excises the F factor carrying the thr and leu genes, producing an F’ thr leu
can transfer chromosomal genes between cells
integration of the F- plasmid
which type of genome has a lot less non-coding DNA
bacterial genomes
methods of gene transfer
- vertical gene transfer
- horizontal gene transfer
- allows the introduction of new genes into an organism that may be of selective advantage
- segments of DNA can move between bacteria
horizontal gene transfer
the introduction of extracellular DNA directly into an organism
transformation
cells express machinery for DNA uptake (proteins are encoded in the genome)
natural competence
researchers make cells competent through electrical or chemical manipulation
induced/artifical competence
the transfer of DNA from cell to cell via direct contact/sex pilus formation
conjugation
steps to conjugation
- the F+ plasmid donor extends the sex pilus component of its T4SS, making contact with the F- recipient cell
- contraction of the pilus draws the two cells together. Relaxase unwinds the DNA at oriT; a second relaxase is recruited to this bubble
- one strand of the F factor is nicked at the nic site in oriT. one relaxase attaches to the 5’ end of the nicked strand and trasnfers it through teh T4SSS. the other relaxase remains in the donor and unwinds the DNA
- the strand remaining in the donor replicates by DNA pol III
- once in the recipient, the transferred strand circularizes and replicates by DNA pol III
- the recipient has been converted to a donor
the sequential addition of ribonucleotides
elongation
relies on a protein called rho and a strong pause site at the 3’ end of the gene
Rho-dependent transcription termination
requires a GC-rich region of RNA, as well as 4-8 consecutive U residues (terminator haripin loop and RNA being built)
Rho-independent transcription termination
functions as ATPase and RNA-DNA helicase activity
Rho
steps to rho-dependent termination
- Rho binds to C-rich regions
- Rho is threaded through Rho hexamer, pulling Rho toward RNA polymerase
- contact between Rho and RNA polymerase causes termination
contact between hairpin, NusA protein, and RNA polymerase cause termination
Rho-independent termination
70S
prokaryotic ribosome
80S
eukaryotic ribosome
happens at ribosomes
translation
match amino acids to mRNA
tRNAs
amino acids are linked to this region of tRNA through charging
acceptor end
when is translation initiated in bacteria
when the 16S rRNA recognizes the Shine-Dalgarno sequence
AGGAGG at the 5’ end of bacterial mRNA; positions the start codoon into catalytic site for translation
Shine-Dalgarno sequence
how do eukaryotes initiate translation
through recognition of the 5’ cap and start codon
what happens in eukaryotes vs prokaryotes if there is a start codon mutation
- eukaryotes: keeps scanning
- prokaryotes: ribosome gets stuck and translation does not begin
after inititation, the ribosome moves along the RNA until
it reaches a stop codon
what prevents the degradation of mRNA in prokaryotes
coupling of transcription and translation
have multiple Shine-Dalgarno sequences
polycistronic mRNAs
accepts the incoming aminoacyl-tRNA
A site of ribosome
holds the tRNA with the peptide attached, which is to be transferred to the new amino acid residue in the course of the peptidyltransferase reaction
P site of ribosome
which type of control system is most efficient in resource usse
transcriptional control
which type of genomic control is fastest
post-translational
bind DNA near the promoter, affects transcription
regulatory proteins
DNA sequences recognized by regulatory proteins
sequence motifs
what is the effect of an activator on transcription
increases transcription (positive regulation)
what is the effect of a repressor on transcription
decreases transcription (negative regulation)
protein binds to DNA, assisting binding of RNAP
activator
protein binds to DNA, blocking RNAP
repressor
effects on transcription when the activator binding site is occupied
increases transcription
effects on transcription when the operator is occupied
decreases transcription
DNA sequence bound by activator
activator binding site
DNA sequence bound by repressor
operator
small molecules that bind to regulator proteins to modify their activity; help regulatory proteins to modify their activity
effectors
enable activators or disable repressors
inducers/coactivators
enable repressors or disable activators
corepressors
what type of operon utilzes corepressors
repressible operons
decreases transcription when present
what type of operon utilizes inducers/coactivators
inducible operons
increase transcription when present
true or false:
gene transcription is all or nothing: off is zero
false
located in E. coli genome, encodes the proteins needed to catabolize lactose
Lac operon
- plays as an inducer
- breaks lactose into monosaccharides
- encoded by LacZ
B-Galactosidase
- brings lactose into cell, transport protein
- encoded by LacY
lactose permease
- moves acetyl group
- not really understood
- encoded by LacA
thiogalactoside transacetylase
encodes Lac repressor
LacI
compared to the eukaryal genome, the bacterial genome
contains a larger percent of DNA that encodes for functional proteins
characteristics of HGT
- transduction, conjugation, transformation
- genes from one independent mature organsim transferred to another mature organism
Suppose a microbe has died and lysed, exposing its DNA to the environment. Some of this DNA was taken up by another unrelated microbe and incorporated into its genome. This is an example of which process(es)?
transformation (HGT)
carries genes responsible for formation of sex pili, has several insertion elements to assist plasmid integration into host cell’s chromosome
F plasmid
following an F+ x F- mating, the donor is … and the recipient is …
F+, F+
the order of gene transfer in a completed Hfr x F- mating is best represented by
part of the plasmid followed by the chromosome followed by the rest of the plasmid
suppose a strain of E. coli is identified as an Hfr strain. In a conjugal experiment between the donor Hfr strain and a recipient E. coli strain that is F-, what would you expect to result
the recipient to remain F-