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48 Cards in this Set

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Define Transcription
The process in which single-stranded RNA with a base sequence complementary to the template strand of DNA or RNA is made.
What are the 3 classes of RNA formed? What are their Fxn's?
rRNA-components of Ribosomes
mRNA-bears the message for protein synthesis
tRNA-carries AA during protein systhesis
By what mechanism are rRNA components made in equimolar amounts? Are the transcripts of tRNA and rRNA genes processed in any way?
?
What enzyme is responsible for transcription in prokaryotes?Eukaryotes?
RNA Polymerase
What are the components of the pro. holoenzyme(5) and apoenzyme(core enzyme)(4)?
holo-2α,β,β’,σ
core-α,β,β’
What is the Direction of the enzymes activity?
5' to 3'
(RNA Poly)What is the promoter? What are two elements of the prok. promoter?Euk?
Prok-Pribnow box=TATAAT. σ specific (TTGACA). σ falls off afterward.
Euk-TATA box(Goldberg-Hogness): bends DNA to make it more accessable. Enchancer sites at 50 to 500
What component of the prok RNA polymerase recognizes the promoter?How does the use of different sigma factors affect the repertoire of genes being expressed in the cell?
Sigma factors needed to start (recognizes promoter for transcription), then falls off. ?
What is constitutive gene expression?What factors determine the rate of expression for these genes?
Rate determined by -35 and Pribnow consensus. The closer to consensus the more often transcribed. Never regulated. 10,000 fold diff in constitutive expression. Sigma factors determine gene expression
What are the componenets of rho dependent and independent terminators?
rho independant-GC rich hairpin loop. Poly U-rich sequence(weakest bonding w/ U)
rho dependent-GC rich hairpin loop proceeded by rho factor binding sites.
Describe the conversion of hnRNA to mRNA.
only in euk, post-transcriptional modification: 5' cap, poly-A tail, splicing of exons and introns
What are ribozymes?
Self-splicing RNA
What are exons and introns?
Introns removed by RNA splicing
How can the same sequence encode different proteins (not in book)?
Redundancy of AA table
Why is euk mRNA more stable than prok. mRNA?
?
Define translation (where does it take place in Prok/Euk)
Protein systhesis. the process by which the genetic message carried by mRNA directly copied from DNA codes for protiens. takes place in the cyto
codon, anticodon, sense and nonsense codons
Seq. of 3 nucleotides in mRNA that directs the incorporation of an AA; The base triplet on tRNA that is complimentary to mRNA; direct AA incorporation into protein; stop codons
What is the role of the shine-dalgarno sequence?What constituent of the ribosome recognizes it?How?
Shine-Dalgarno=ribosome binding site in prok. fpr translation start. First thing to be transcribed.
Met with the AUG
What is the most common codon for the initiation of translation? How is translation stopped?
AUG; UGA,UAG,UAA
What is meant by tRNA charging?
binds ATP and the cognate amino acid
What are molecular chaperones? What induces their increased production? What are their fxns?
Proteins found in all cells which fold newly formed proteins & partially denatured proteins.They are increased in concentration under high temps.,metabolic poisens, and other stressful conditions.
What are inteins and exteins?
Exteins are flanking regions which are not spliced out in protien splicing.
Interins are intervening regions which are removed.
Can you explain the diauxic growth curve of E. coli growing in glu and lac?
glu prevents use of lactose. glu used in lap period, when its used up you enter the lag period in which lac is used.
In E.coli, CAP is an activator for operons involved in the catabolism of sugars in addition lactose. Would you expect these operons to show catabolite repression? Would you expect these operons to be inducible?
?
What is the DNA-binding regulatory molecule in negative control of operons (induction/repression)?
regulatory proteins-repressors bind to operator near promoter which decrease the ability of RNA Poly to bind or leave the promoter and decrease transcription.
What site does a repressor bind? What site is this located near?
The repressor binds to operator near promoter.
Define corepressor and inducer. How do they differ?
Corepressor activates repressor gene and inturn decreases transcription.
Inducer inactivates repressor and inturn increases transcription.
What is the DNA-binding regulatory molecule in positive control of operons? What is done in Euk. systems(from lecture)?
Prok-activators
Euk-transcription factors bind at enhancers
What are the roles of CAP, cAMP, and glucose in the positive regulation of the lac operon? Why does the operon require positive control (activation)?
CAP-activator; cAMP-determines CAP binding to Plac;Glu-none then EIIBglu is phosphorylated and turns on cAMP
Is the repressor normally active or inactive for inducible genes? Repressible genes?
Inactivates repressor(transcription rises); activates repressor(transcription decreases).
Is there a specific DNA-binding regulatory protein in attenuation? What is the attenuator?
Common in AA anabolic pw. Involves the conditional termination of transcription before the 1st structural genes. Attenuator looks like a terminator. On trp operon.
Using sections 1,2,3 and 4 of the trp operon:what is the effect of no translation? Where is there a high freq. of tryp codons? What pairs form if there is lots of tryptophane?
no translation-then 1:2 and 3:4(termination); high then ribosome stalls @UAG and stops 2:3 allows 3:4(termination);if low then ribosome stalls in 1 2:3 and no 3:4 polymerase moves through operon (no termination)
What are regulons and stimulons?
collection of operons controlled by the same regulatory molecule;a collection of operons responding to the same ennironmental stimulus.
How do sigma factors affect the process of sporulation in Bacillus subtilis?
?global regulatory systems controlled by sigma factors
What is meant by antisense RNA?How can it regulate gene expression at the level of translation?
Base sequence complementary to a segment of another RNA molecule and specifically binds to another RNA molecule. Binding can block DNA replication, mRNA synthesis, or translation.
What are the components of a two-component regulatory system? What do each of these molecules do?
Two-component pphosphorelay system:signal transduction involving transfer of phosphoryl grp. Sensor kinase-"senses" environment and phosphorylates other molecules.
Response regulator-changes activity with phosphorylation.
How does replication affect cell divison? How can a cell that requires 40' to replocate its DNA divide every 20?
Inhibition of replication stops septation.
-two forks can be used to divide faster.
Can you identify the regularoty elements in the neg. control of the lac and trp operons?
lac-w/ glu lactose is not used. (lac operon is inducible with lac as inducer)Repressor binds operator.(O) 3' of P
trp:repressible;trp operon=P,O,and structural genes that code for tryptophan(corepressor).trpR binds O only in presence of typtophan
What is the DNA-binding regulatory molecule in positive control of operons?
The DNA-binding regulatory molecule in positive contorl of operons is catabolite activator protein (CAP)
What is done in eukaryotic systems (in lecture)?
???
What are the roles of CAP, cAMP, and glucose in the positive regulation of the lac operon?
CAP binds to the CAP site on the promoter when complexed with cAMP; this binding allows RNA polymerase to bind to the promoter and begin transcription. Glucose???
Why does the operon require positive control (activation)?
The operon requires positive control (activation) to upregulate mRNA synthesis (???)
Is there a specific DNA-binding regulatory protein in attenuation?
No, there is not a specific DNA-binding regulatory protein in attenuation.
What is the attenuator?
The attenuator is a rho-independent termination site in the leader sequence that is involved in attenuation.
Using sections 1,2,3, and 4 of the trp operon: a) What is the effect of no translation?
If there is not translation of the mRNA after the RNA polymerase has begun copying the leader region, segments 3 & 4 form a hairpin loop, and transcription terminates before the poymerase reaches the trpE gene (RNA poly dissociates)
Using sections 1,2,3, and 4 of the trp operon: b) Where is there a high frequency of trp codons?
There is a high frequency of trp codons in the leader peptide sequenc (section 1).
Using sections 1,2,3, and 4 of the trp operon: c) What pairs form if there is lots of tryptophan?
(short answer: 3 & 4) If there is lots of tryptophan, the ribosome synthesizes the leader peptide and stops at terminator codon between sections 1 & 2; the ribosome pauses & prevents 2 from pairing w/3; segments 3 & 4 form a hairpin loop, and the RNA polymerase terminates at the attenuator just as if no translation had taken place.
What are regulons and stimulons?
A regulon is a collection of operons controlled by the same regulatory molecule. A stimulon i sa collection of operons responding to the same environmental stimulus.