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57 Cards in this Set
- Front
- Back
What are the stop codons?
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UAA, UAG, UGA
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what is the start codon?
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AUG
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There are six different codons for...
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Leu, Arg, Ser
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There are only one codon for...
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Trp, Met
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Pairing combinations with the wobble concept:
5' anticodon G can pair with ___ or ___ in the 3' base in CODON 5' anticodon base U can pair with ___ or ___ in the 3' base in codon in tRNA, 5' base I (ionosine) can base pair with ___, ___, or ___. |
U, C
A, G A, U, C |
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How many hydrogen bonds are in wobble base pairing?
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2
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Wobble allows the cell to have ______ tRNAs. It only occurs in the ____ base of the 3' mRNA or the first base in 5' tRNA for the base ___.
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fewer, last, ionosine
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Why is the base at the 5' end of the anti-codon (tRNA) allowed to wobble base pair?
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There is a large flexible bend in the RNA near that position.
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Suppresses the effect of an earlier mutation within the same gene
A second missense mutation in the same gene can bring back biological activity if it somehow restores the original configuration around the functional part of the molecule. |
intragenic suppressor mutation
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supresses the effect of an earlier mutation in another gene
review slide 9 |
intergenic suppressor mutation
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Mitochondrial genetic code:
Only ___ tRNAs are needed instead of the normal 32. This is because ___ can base pair with all 4 nucleotides in the mRNA. |
22, U
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Stop codons for the mitochondrial genetic code:
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UAA, UAG, AGA, AGG
AGA AND AGG are not arginine codons (as the usual) but specify chain termination. In fruit fly mtochondria, these codons encode for serine. |
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Mitochondria code:
Internal methionine is encoded by both ___ and ___. |
AUG AND AUA
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how was the genetic code cracked?
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Initial studies used the polynucleotide phosphorylase reaction to make homopolymers of poly-A, poly-C, and poly-U
(poly-G folded back on itself and could not be translated) |
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Preparing oligoribonucleotides from synthesized DNA led to what?
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more codon assignments
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Activators that stimulate this kind of promoter work by triggering a con- formational change in either RNA polymerase or DNA; that is, they interact with the stable closed complex and induce a conformational change that causes transition to the open complex (Fig. 18-2b). This mechanism is an example of _______________ (2).
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allosteric activation
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DNA ______________ fascilitates protein interaction from distant site. ~30-200 bases away. ex: activator protein needs to come in contact with RNA polymerase.
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bending
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Lac genes are expressed at high levels only when ________ is available, and ________—the preferred energy source—is not.
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lactose, glucose
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In the lac operon, what activates transcription and what binds to the operator?
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CAP activates transcription and Lac repressor binds the operator
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The lac operator is symmetric with two _________ sites on each end and a __:__ in the middle.
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Half site, G:C
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CAP and Lac repressor bind DNA using the common structural motif called
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helix-turn-helix
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The bacteriophage lambda repressor protein is an example of what motif
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helix-turn-helix
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Activation of the lac promoter by CAP.
When CAP binds to the CAP site on the mRNA, it is recognized by the _____ of the _____ subunits of RNA polymerase. This helps and guides RNA polymerase to bind to the promoter. |
CTD, alpha,
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_________ ACTIVATES CAP.
_________ INACTIVATES CAP by decreasing cAMP. |
cAMP, Glucose
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Whenever glucose and lactose is present, there is a ________ level of transcription.
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basal
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When there is glucose but no lactose, there is ______ transcription.
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no
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When there is no glucose but high lactose, there is an ___________ level of transcription and _____ levels of cAMP.
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activated, high
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What bacteriophage uses different sigma factors for its lytic life cycle when infecting Baccilus subtillus?
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SPO1.
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EARLY MIDDLE AND LATE GENES are regulated by SPO1 by transcribing a ______________ of ______________ factors.
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cascade, sigma
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NtrC and MerR are transcription activators that function
by ____________ instead of recruitment. They bind the promoter after RNA polymerase and induce the ____conformation. |
allostery, open
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_______ is an ATPase. What kind of genes does it transcribe?
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NtrC, used to transcribe genes involved in nitrogen metabolism.
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NtrC recruit the _____ protein that ______ DNA to help with transcription activation.
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IHF, bends
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What kind of genes do MerR transcribe?
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Transcribe genes involved in mercury resistance.
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What does MerR do to the DNA?
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it twist it to align the -10 and -35 sequences.
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The araBAD operon is controlled by two activators, what are they?
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AraC and CAP
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In the absence of the inducer ______________, AraC binds to ___ and ____ on the mRNA. AraC then dimerize and a ______ is formed with the mRNA. This _______________ transcription.
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Arabinose, I1, araO2
loop, inhibits |
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When arabinose is present, arabinose binds to ______ which binds to two sites on the mRNA: ____ and ____. This _______________ transcripion.
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AraC, i1, i2, stimulates
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In the control of gene expression in bacteriophage lambda, the lambda repressor when bound to the lambda genome, induces what kind of growth?
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lysogenic
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Bacteriophage lambda has a _____kb genome with ______ genes.
There are _____ operator sites in the genome that can be bound by ____ and _____ proteins. |
50, 50
cI, cro |
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The ___ protein is a lambda repressor that can activate or repress. ____ protein can only repress.
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cI, cro
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PRM (promoter for repressor maintenance) transcribes only the __ gene.
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cI
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PR and PL are _______ promoters; that is, they bind RNA polymerase efficiently and direct transcription without help from an ________.
PRM, in contrast, is a ______ promoter and only directs efficient transcription when an activator is bound just upstream. |
strong, activator, weak
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Lytic growth proceeds when PL and PR remain switched ____ while PRM is kept ____.
Lysogenic growth, in con- trast, is a consequence of PL and PR being switched ___ and PRM switched ___. |
on, off
off, on |
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cl repressor binds ____ 10 fold better than ____. cro binds ____ best.
� |
OR1, OR2, OR3
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Lambda repressor binds DNA ___________ and as a ________.
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cooperatively, dimer
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The amino (N) domain of the repressor contains two regions, what are they...
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DNA binding region, and activating region
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the sites on the carboxyl (C) domain of the repressor has two regions...
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dimer region and tetramer region
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During DNA damage, ______ is activated. In addition to stimulating homologous
Recombination, ______ stimulates proteolytic autocleavage of certain proteins including _____ involved in DNA repair and also the ___________ repressor. This removes the ___-terminal domain of repressor, so dimerization and cooperativity are lost. This prevents binding to OR1 and OR2. This allows activation of ___ and ___, which stimulates lytic growth! |
RecA, RecA, LexA, lambda, C, PR, PL
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The repressor bound to OR1 AND OR2 turns of transcription from _____ The repressor bound at OR2 contacts the _______________(2) at PRM, which activates the expression of the ___ repressor. This activity stimulates the ______________________ cycle. This is also an example of _____________ regulation as the repressor stimulates stranscription of it own protein
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PR, RNA polymerase, cI, lysogeny, positive
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OR3 lies within P__. Cro, when bound there, because it has highest affinity for it, repress transcription of ___. It makes more of its Cro gene (positive regulation.
This stimulates the __________cycle. |
RM, cI, Lytic
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Interaction of repressors at OR and OL allow ________ regulation.
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negative
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This negative autoregulation works as follows:
PRM being activated by repressor cI (at OR2) to make more repressor. But if the concentration gets too high, repressor will bind to _____ as well and repress____. cI starts blocking its own promoter when levels get to high |
OR3, PRM
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Interaction between the repressors on OL1, 2, 3 AND OR1, 2, 3 form an __________.
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octamer
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cII is on the right of cI and is transcribed from ___; cIII, on the left of cI, is transcribed from ___.
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PR, PL
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Like the l repressor, the CII protein is a ________________(2). It binds to a site _________ of a promoter called _____ (for repressor establishment) and stimulates transcription of the ____ (repressor) gene from that promoter.
Thus, the repressor gene (cI) can be transcribed from two different promoters (PRE and PRM) |
TRANSCRIPTIONAL ACTIVATOR, UPTREAM, PRE, cI.
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CII bind PRE and initially stimulates
transcription of the cI (repressor) gene from that promoter, which favors _______ growth. But the cro protein that stimulates ___________ growth is transcribed from the PR promoter initially. |
lysogenic, lytic
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The number of phage particles that enters the bacterium
determines if lytic or lysogenic growth occurs. If the average number of phage is _______________ per cell than lytic growth is favored. It the number is _____________ lysogenic growth is favored. |
one or fewer,
two or more |