Chapter 10

Question 1

Control of mRNA stability

Answer 1

mRNAs levels regulated by RNase activity (degradation)

Question 2

posttranslational control

Answer 2

when proteins are made, their activity is controlled by modifying protein structure
• Cleavage, phosphorylation, methylation, acetylation

Question 3

regulatory proteins

Answer 3

help a cell sense internal changes and alter its gene expression to match
• Bind ligands (specific, low- MW compounds)

Question 4

repressors

Answer 4

repress transcription of target genes. blocks part of promoter; prevents sigma factor from binding.

Question 5

repressor scenario 1

Answer 5

repressor binds dna, inducer causes repressor to release.

Question 6

repressor scenario 2

Answer 6

repressor-corepressor complex binds dna, ligand concentration decreases and releases from repressor
• Known as derepression

Question 7

Activators (transcriptional control)

Answer 7

bind DNA; activates transcription by interacting w/ RNAP
•activators bind poorly unless inducer is present
• Removal of inducer–>stops transcription

Question 8

lactose

Answer 8

• Used as C and energy source

* LacY imports lactose from extracellular environment

Question 9

lac operon

Answer 9

lacZ, lacY, lacA –1 promoter (lacZYA)

• Role of lacA is unclear

Question 10

lacI

Answer 10

repressor upstream of lacZYA. has diff promoter

•Operator sites (binding sites) – lacO

Question 11

cAMP

Answer 11

cyclic AMP. AMP–>adenosine monophosphate

Question 12

Cyclic AMP (cAMP) accumulates

Answer 12

when a cell is starved for carbon

• cAMP-CRP complex binds to specific DNA sequences near bacterial genes (CRP= cAMP receptor protein)

Question 13

cAMP activation

Answer 13

• cAMP-CRP binds to DNA (as activator)
• RNAP can get stuck even in absence of LacI
• cAMP-CRP causes DNA to bend
• CRP interacts w/alpha subunit of RNAP
-Helps initiate open complex formation
• cAMP-CRP can only bind when LacI is not bound

Question 14

glucose

Answer 14

represses the lac operon by keeping lactose out of cell. FAVORABLE C source.
•glycolysis enzymes always being produced
• If there is glucose, no need to use lactose

Question 15

other operons

AraC

Answer 15

both activation and repression
• Arabinose is absent-AraC represses production of genes for catabolism
• Arabinose is present-AraC activates same set of genes

Question 16

other operons

Tryptophan operon

Answer 16

repression and attenuation

• Example of derepression

Question 17

Tryptophan binds to

REPRESSION

Answer 17

TrpR (repressor protein)-converts it to active repressor (holorepressor) that binds to operator sequence (blocks RNAP)
• Low tryptophan – derepression of repressor and transcription of genes for trp biosynthesis

Question 18

Attenuator RNA base pairing options
• 1:2 and 3:4

2:3

Answer 18

• 1:2 and 3:4
-3:4 = intrinsic terminator hairpin
• 2:3 called anti-terminator (more stable)
-Prevents terminator from forming–>transcription of trpE

Question 19

What controls which hairpins form?

Answer 19

• High trp – ribosome translates, but stops at the stop codon (sequesters region 2) –>3:4 forms
• Low trp – ribosome stalls at double trp codons
• Region 2 binds to region 3

Question 20

rnas can also bind

Answer 20

metabolites (riboswitches)
-Amino acids, vitamins, SAM, Mg, etc.
• Found in 5’-untranslated region of gene
• Conformational changes in RNA structure when metabolite is bound

Question 21

regulatory circuits

Answer 21

analagous to electrical circuits

-multiple switches

Question 22

How does cell know its reached an attractant?

Answer 22

• Methyl-accepting chemotaxis proteins (MCP)
• Cytoplasmic domains bind to CheA w/ protein CheW
• Binding of attractant to MCP causes conformational change that inhibits CheA activity (less tumbling)

Question 23

of tumbles are supressed by

Answer 23

lower conce–> higher conc.

Question 24

Quorum sensing

Answer 24

Aliivibrio fischeri – a marine microbe that colonizes a squid
•is bioluminescent but only at high cell densities

Question 25

Which one gets expressed? cro or cii High nutrients low nutrients dna damage

Answer 25

* High nutrients –cleave CII leaving Cro to start lytic cycle * Low nutrients – CII * DNA damage – lysis

Question 26

Phage enters cell; transcription from PL and PR

Answer 26

Lysis vs Lysogeny depends on which regulation happens first

Question 27

laz z

Answer 27

also cleaves X-gal-->color change-->blue colonies

Question 28

If E. coli are treated with ATC

Answer 28

colonies are blue

Question 29

another name for B galactosidase

Answer 29

lac Z

Question 30

Lac Operon – no lactose

Answer 30

lac operon is transcribed at low levels (<10 molecules LacZ) • Repressed by LacI -Tetramer of LacI binds to two lacO, causes DNA to loop and prevents RNAP access

Question 31

Lac Operon – high lactose

Answer 31

100-fold higher expression • LacY to be expressed and let in lactose • Low concentration of LacZ doesnt cleave the glycosidic bond of lactose; rearranges to allolactose • Allolactose binds LacI and unlocks protein (removes repressor)

Question 32

Trp operon ATTENUATION

Answer 32

* transc/translation happen at same time * ribosome-sensor of amino acid levels * dna bw operator and trpE

Question 33

small rnas

Answer 33

* typically post-transcriptional control * Repress and activate translation * controls mrna degration * require chaperone Hfq

Question 34

How does cell know if concentrations of attractant are increasing?

Answer 34

CheR methylates MCP, reactivate cheA. cell tumbles until higher conc of attractant is encountered. then, no attractant. reset by CheB-P.