Structural motif

Common structures found in regulatory proteins that allow interactions between protein amino acids and nucleotides in major and minor grooves

Enhancers

Regulate the timing and spatial patterns of gene expression

Strong purifying selection

Reduced rate of evolution of enhancers at regions that bind to protein; prevents evolutionary change.

Sonic hedgehog (SHH)

Important regulator in several developmental pathways, including limb development

Insulator sequences

cis-acting, protein-binding sequences that prevent enhancers from turning on the wrong genes and turning on the right genes at the right time.

Chromatin packagin is caused by....

Interactions between DNA and histones, forming nucleosomes.

What do Covered promoters do?

Characterize genes that are regulated, and require the remodeling or movement of nucleosomes to allow transcription activators to bind.

What does Chromatin remodelers do?

Reorganize nucleosomes by sliding, moving, or modifying their protein composition.

What does Chromatin modifiers do?

Add acetyl or methyl groups to histones to activate or repress gene activity, respectively.

DNA histone interactions are weak and regulatory sequences are accessible; transcription proceeds

Open chromatin

DNA histone interactions are strong and regulatory sequences are not accessible; transcription is silent.

Closed chromatin

DNase I hypersensitivity

can identify open and closed chromatin

Methylated histones; Unmethylated histones

Close chromatin; Open chromatin

In negative control, what molecule would you expect to find bound to the operator if there is no transcription?

A) activator

B) repressor

C) inducer

D) corepressor

E) RNA polymerase

B) repressor

You want to design a repressor protein mutant. Which protein domain is the best target for preventing binding of the corepressor?

A) DNA-binding domain

B) allosteric domain

C) promoter domain

D) helix-turn-helix domain

E) activator binding site

B) allosteric domain

The presence of which combination of molecules would lead to active transcription of an operon?

A) activator + corepressor

B) activator + repressor

C) inducer + corepressor

D) repressor + corepressor

E) activator + inducer

E) activator + inducer

In the lac operon, what acts as the inducer?

A) glucose

B) permease

C) allolactose

D) β-galactosidase

E) transacetylase

C) allolactose

The enzyme β-galactosidase catalyzes what reaction?

A) allolactose → glucose + lactose

B) lactose → glucose + fructose

C) lactose → galactose + glucose

D) glucose → galactose + lactose

E) galactose → glucose + lactose

C) lactose → galactose + glucose

A bacterium is unable to transport lactose into the cell to be broken down. Which gene is likely mutated in this bacterium?

A) lacZ

B) lacY

C) lacI

D) lacP

E) lacO

B) lacY

Which region of the lac operon would you target if you want to disrupt the -10 and -35 consensus sequences?

A) lacZ

B) lacY

C) lacI

D) lacP

E) lacO

D) lacP

In the presence of glucose, where is the lac repressor bound?

A) lacZ

B) lacO

C) lacP

D) lacI

E) The lac repressor is not bound to the operon.

B) lacO

Which structural gene of the lac operon can be mutated without affecting the cell's ability to break down lactose?

A) lacZ

B) lacY

C) lacA

D) lacP

E) lacO

C) lacA

Which of the following are constitutive mutants of the lac operon?

A) lacZ and lacP

B) lacZ and lacI

C) lacO and lacI

D) lacO and lacZ

E) lacI and lacY

C) lacO and lacI

Which mutants are noninducible?

A) lacIS

B) lacI-

C) lacI+

D) lacOC

E) lacO+

A) lacIS

Which of these haploid strains produce β-galactosidase constitutively but do not produce permease?

A) I- P+ O+ Z+ Y+

B) I+ P+ O+ Z- Y-

C) I- P+ O+ Z-Y+

D) I+ P+ O- Z+ Y+

E) I- P+ O+ Z+ Y-

E) I- P+ O+ Z+ Y-

Which of these haploid strains produce permease but do not produce β-galactosidase?

A) I- P+ O+ Z+ Y+

B) I+ P+ O+ Z-Y+

C) I- P+ O+ Z-Y-

D) I+ P+ O- Z+ Y+

E) I- P+ O+ Z+ Y-

B) I+ P+ O+ Z-Y+

During the attenuation of the trp operon, which stem loop leads to polycistronic mRNA synthesis during tryptophan starvation?

A) 1-3 (antitermination) stem loop

B) 3-4 (termination) stem loop

C) 1-2 (pause) stem loop

D) 2-3 (antitermination) stem loop

E) 2-4 (termination) stem loop

D) 2-3 (antitermination) stem loop

In the absence of tryptophan,

A) the inactive repressor cannot bind trpO, so operon gene transcription occurs.

B) the active repressor binds trpP, so operon gene transcription is repressed.

C) the inducer cannot bind trpO, so operon gene transcription occurs.

D) the active repressor cannot bind trpO, so operon gene transcription is attenuated.

E) the repressor binds the corepressor, and operon gene transcription occurs.

A) the inactive repressor cannot bind trpO, so operon gene transcription occurs.

Which sigma factor, encoded by the rpoH gene, is active at high temperatures?

A) σ70

B) σ32

C) σ45

D) σ37

E) σ50

B) σ32

Which enzyme is responsible for integration of a temperate phage into a host genome?

A) β-galactosidase

B) transposase

C) integrase

D) transacetylase

E) permease

C) integrase

Which region of the lambda phage genome enables the linear chromosome to circularize when it enters a host cell?

A) cohesive (cos) site

B) IS10

C) early operators

D) integrase (int) gene

E) excisionase (xis) gene

A) cohesive (cos) site

If you wanted to prevent a cell from entering the lysogenic pathway, which gene controlled by PRM would you target?

A) cro

B) Q

C) cI

D) cII

E) O

C) cI

In λ phage, which protein, the product of the cI gene, blocks the transcription required to initiate the lytic cycle?

A) cro

B) repressor

C) enhancer

D) integrase

E) operator

B) repressor

Regulation of transcription of bacterial genes takes place at which two levels?

Answer: initiation and amount

What are the two active sites or "domains" on a repressor protein?

Answer: DNA-binding and allosteric

If a corepressor is inhibited, what effect would you expect to see in the operon?

Answer: Transcription will occur.

Which proteins facilitate RNA polymerase binding at promoters?

Answer: activator proteins

Catabolite repression refers to the repression of the lac operon in the presence of which catabolite?

Answer: glucose

Binding of which complex increases the ability of RNA polymerase to transcribe the lac operon?

Answer: CAP-cAMP

Which enzyme is the product of the lacZ gene?

Answer: β-galactosidase

Which part of the lac operon is cis-dominant?

Answer: lacO

Which part of the lac operon produces a regulatory protein that is trans-acting?

Answer: lacI

In the absence of both glucose and lactose, the presence of which molecule is capable of inducing basal transcription?

Answer: cAMP

Which protein in the arabinose operon is responsible for both positive and negative regulation of transcription?

Answer: araC

In the trp operon, where is the attenuator region located?

Answer: trpL

Which molecule functions as the corepressor in the trp operon?

Answer: tryptophan

What are the three possible alternative stem loops that can form in mRNA?

Answer: pause, antitermination, and termination

Mutations of trpL decrease the efficiency of transcriptional regulation by disrupting the formation of which stem-loop structure?

Answer: 3-4 (termination) loop

Bacteria grown at 45°C initiate expression of which two types of proteins?

Answer: heat shock and chaperone

Antisense control of translation involves the regulation of which enzyme produced by bacterial insertion sequence IS10?

Answer: transposase

The genetic switch controlling whether a bacterium enters the lytic or lysogenic cycle relies on the binding of which two proteins?

Answer: cro and λ repressor

What is the process by which a bacterium switches from a lysogenic to lytic cycle?

Answer: induction

What protein cleaves the λ repressor monomers to inactivate the repressor protein, and is activated by DNA-damaging agents?

Answer: RecA

Most of the regulation of gene expression in bacteria occurs at the ________ level.

Answer: transcriptional

Changing conformation at the active site as a result of binding a substance at a different site is known as ________.

Answer: allostery

Expression of a(n) ________ alters gene transcription in E. coli by activating transcription of specialized heat stress response genes.

Answer: alternative sigma factor

Bacterial translation is inhibited by ________ RNA, which is complementary to a portion of a specific mRNA.

Answer: antisense

In λ phage, entry into the ________ cycle requires transcription of late genes.

Answer: lytic