Genetics BCQ CH16

1: Why is gene regulation important for bacterial cells?

• helps bacteria respond quickly to the environment

• saves energy by making proteins when needed

2: Name six different levels at which gene expression might be controlled.

(1) Alteration of DNA or chromatin structure.

(2) Transcription

(3) mRNA processing

(4) mRNA stability

(5) Translation

(6) Posttranslational modification of the synthesized protein

3: Draw a picture illustrating the general structure of an operon, and identify the operon’s parts.

• Promoter – where RNA polymerase binds

• Operator – where regulatory proteins bind

• Structural genes – the actual genes being turned on/off

• Regulator gene (sometimes nearby) – makes a repressor or activator protein

4: What is the difference between positive and negative control? What is the difference between inducible and repressible operons?

Positive vs. Negative Control

• Positive control: Needs an activator to start transcription

• Negative control: Uses a repressor to block transcription

Inducible vs. Repressible Operons

• Inducible operon: Usually off, turned on when needed

• Repressible operon: Usually on, turned off when not needed

5: Briefly describe the lac operon and how it controls the metabolism of lactose.

What is the lac operon?

• A group of 3 genes (lacZ, lacY, lacA) that help break down lactose in E. coli

• Controlled by a single promoter and operator

• Regulated by the lacI repressor protein

When lactose is absent:

• The repressor binds to the operator

• Blocks RNA polymerase → no transcription

• Lac genes are OFF

When lactose is present:

• Some lactose is turned into allolactose

• Allolactose binds to the repressor and inactivates it

• Repressor can't bind the operator

• RNA polymerase transcribes lac genes

• Lac genes are ON → lactose is broken down

6: What is catabolite repression? How does it allow a bacterial cell to use glucose in preference to other sugars?

What is catabolite repression?

• A way for bacteria to prefer glucose over other sugars

• When glucose is present, genes for using other sugars are turned off

How it works:

• Glucose ↓ → cAMP ↑ → CAP-cAMP binds DNA → transcription ON

• Glucose ↑ → cAMP ↓ → CAP can't bind → transcription OFF

8: What is antisense RNA? How does it control gene expression?

What is antisense RNA?

• A small RNA that is complementary to mRNA

How does it control gene expression?

• Binds to mRNA and blocks the ribosome from attaching

• Or it can cause the mRNA to be cut and destroyed

• Result: Stops translation → no protein made

9: What are riboswitches? How do they control gene expression?

What are riboswitches?

• Regulatory RNA sequences that change shape when a molecule binds

• Found in the 5′ UTR of some mRNAs

How do riboswitches control gene expression?

• Regulatory molecule binds → RNA folds into a new shape

• This can:

  • Stop transcription early (by forming a terminator)

  • Block ribosome binding (preventing translation)

  • Or allow expression in some cases

14: The blob operon produces enzymes that convert compound A into compound B. The operon is controlled by a regulatory gene S. Normally, the enzymes are synthesized only in the absence of compound B. If gene S is mutated, the enzymes are synthesized in the presence and in the absence of compound B. Does gene S produce a regulatory protein that exhibits positive or negative control? Is this operon inducible or repressible?

Blob Operon Summary (Simplified)

• ✅ Operon makes enzymes when compound B is absent

• 🛑 No enzyme made when compound B is present (normal)

• ⚠ Mutation in gene S → enzymes made always (on with or without B)

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What does this mean?

• Gene S makes a repressor → Negative control

• Compound B helps the repressor work → it's a corepressor

• Operon is normally ON, turned OFF by B → Repressible operon

15: A mutation prevents the catabolite activator protein (CAP) from binding to the promoter in the lac operon. What will the effect of this mutation be on transcription of the operon?

• CAP helps RNA polymerase bind to the lac promoter when glucose is low and lactose is present.

• A mutation preventing CAP binding means RNA polymerase binds poorly.

• This causes lower transcription of the lac operon, even if glucose is absent.

• Transcription still occurs, just not as much—better than with the repressor bound, but not fully active.

17: Under which of the following conditions would a lac operon produce the greatest amount of β-galactosidase? The least? Explain your reasoning.

	Lactose present	Glucose present
Condition 1	Yes	No
Condition 2	No	Yes
Condition 3	Yes	Yes
Condition 4	No	No

• Condition 1 (Lactose yes, Glucose no) → Maximum β-galactosidase

  • Lactose inactivates the repressor → operon turned on

  • No glucose → high cAMP → CAP-cAMP enhances transcription

• Condition 2 (Lactose no, Glucose yes) → Minimum β-galactosidase

  • No lactose → repressor stays active → blocks transcription

  • Glucose → low cAMP → no CAP activation → further reduces transcription

19: A mutant strain of E. coli produces β-galactosidase in both the presence and the absence of lactose. Where in the operon might the mutation in this strain be located?

• Mutation likely in the operator region of the lac operon:

  • If the mutation prevents the lac repressor from binding to the operator, transcription of the lac genes happens continuously (constitutive expression), regardless of lactose presence.

• Alternative mutation:

  • In the lacI gene (produces the repressor), if mutated to be inactive or unable to bind the operator, it would also lead to constitutive expression of β-galactosidase.

25: The mmm operon, which has sequences A, B, C, and D (which may be structural genes or regulatory sequences), encodes enzymes 1 and 2. Mutations in sequences A, B, C, and D have the following effects, where a plus sign (+) indicates that the enzyme is synthesized and a minus sign (–) indicates that the enzyme is not synthesized.

	mmm absent		mmm present
Mutation in sequence	Enzyme 1	Enzyme 2	Enzyme 1	Enzyme 2
No mutation	+	+	–	–
A	–	+	–	–
B	+	+	+	+
C	+	–	–	–
D	–	–	–	–

a. Is the mmm operon inducible or repressible?

b. Indicate which sequence (A, B, C, or D) is part of the following components of the operon:

a. Is the mmm operon inducible or repressible?

Solution:

The data from the strain with no mutation indicate that the mmm operon is repressible. The operon is expressed in the absence of mmm, but inactive in the presence of mmm. This is typical of a repressible operon, where mmm acts as a corepressor (see Figure 16.5).

b. Indicate which sequence (A, B, C, or D) is part of the following components of the operon:

Solution:

Regulator gene B

When sequence B is mutated, gene expression is not repressed by the presence of mmm.

Promoter D

When sequence D is mutated, no gene expression occurs either in the presence or

absence of mmm.

Structural gene for enzyme 1 A

When sequence A is mutated, enzyme 1 is not produced.

Structural gene for enzyme 2 C

When sequence C is mutated, enzyme 2 is not produced.

what is an operon?

• group of genes controlled together by a single promoter and regulatory region

• These genes are transcribed together into one mRNA and usually work in the same pathway (like breaking down or making something).

How do riboswitches differ from RNA-mediated repression?

Feature	Riboswitches	RNA-Mediated Repression
Mechanism	Change RNA structure	Self-cleavage of RNA
Effect	Blocks or allows expression	Destroys the mRNA
Regulation site	5′ UTR	5′ UTR with ribozyme activity
Trigger	Binding of small molecule	Binding of small molecule triggers cleavage