Regulation of Gene Expression in Bacteria (Lectures 13-14)

A set of QUESTION_AND_ANSWER flashcards covering lac and arabinose operons, cis/trans regulation, promoters and sigma factors, consensus sequences, and global gene regulation concepts from the lecture notes.

What two conditions must be satisfied for maximal lac operon expression (catabolite repression) in E. coli?

Lactose present (to relieve repression via allolactose) and glucose absent (high cAMP to activate CAP; CAP-cAMP enhances RNA polymerase binding).

What is the role of the lac repressor (lacI) and its effector?

lacI binds the operator to repress transcription; allolactose (from lactose) binds lacI to inactivate it and relieve repression.

What is an Oc mutation in the lac operon and what is its effect?

Oc is a constitutive operator mutation; the repressor cannot bind the operator, so the operon is always on.

What is a lacI- mutation and its consequence for operon expression?

lacI- is a mutation that produces a defective repressor that cannot bind the operator; the operon is constitutively on.

Explain cis-acting vs trans-acting elements with examples from lac regulation.

Cis-acting elements (e.g., Oc) affect only nearby DNA; trans-acting elements (e.g., lacI repressor) are diffusible proteins that can act anywhere in the cell.

What are the canonical promoter elements in E. coli and their roles?

-35 region: TTGACA; -10 region: TATAAT; they are binding sites for RNA polymerase to initiate transcription.

Why is spacing between the -35 and -10 promoter elements important?

Optimal spacing allows RNA polymerase to contact both regions; changes in spacing affect binding and transcription efficiency.

What is a sigma factor and what does it do?

Sigma factor is a subunit of RNA polymerase that directs promoter binding; it is released after transcription starts and different sigma factors recognize different promoter sequences (e.g., sigma70 recognizes canonical promoters).

What is a consensus sequence and how is it determined?

A consensus sequence is the most common nucleotide at each position across multiple sequence alignments; it reflects binding preferences and is used to describe common promoter/ binding-site motifs.

Give an example of a strong promoter and a weak promoter in E. coli as mentioned in the notes.

Strong promoter: recA; Weak promoter: araBAD (based on the typical -35/-10 sequences and spacing shown in the notes).

Describe the regulatory architecture of the arabinose (ara) operon.

Dual positive and negative control: AraC activates transcription by binding to araI (positive control) and CAP-cAMP also provides positive control; in the absence of arabinose, AraC binds araO and araI to form a loop and repress transcription.

What are the two key DNA-binding features of regulatory proteins involved in transcription control?

DNA-binding site (where the protein binds DNA) and allosteric site (where effector binding changes protein conformation to enable or prevent DNA binding).

What is the role of CAP and cAMP in lac operon regulation?

CAP-cAMP acts as an activator that enhances transcription; cAMP levels rise when glucose is scarce, linking glucose presence to lac operon expression via CAP.

What is the effect of the CAP-cAMP complex on RNA polymerase during lac operon activation?

CAP-cAMP bends DNA and interacts with RNA polymerase to improve binding to the -10/-35 promoter regions, promoting transcription initiation.

What is a genetic switch in bacterial regulation?

Regulatory proteins at promoters (repressors and activators) control transcription; presence/absence of effectors alters DNA binding and gene expression.

What are the two components of the ara operon’s regulation, and how do they interact?

AraC (activator) binding to araI (and in presence of arabinose activating) plus CAP-cAMP positive control; in absence of arabinose AraC binds araO/araI to repress transcription via looping.

What happens to AraC’s binding and operon activity in the presence vs absence of arabinose?

With arabinose: AraC adopts a conformation that activates transcription by binding araI (and promoting DNA looping away from araO); without arabinose: AraC binds both araO and araI and represses transcription.

How does the lac operon illustrate cis- and trans-acting elements in action?

Cis element (operator Oc) controls its own operon on the chromosome; trans element (lacI repressor) produced in the cell can regulate lac operons elsewhere if present in the cell.

What is the typical half-life of bacterial mRNA and how does this relate to gene regulation?

Approximately 2 minutes; rapid turnover allows quick regulation of gene expression in response to environmental changes.

What is the relationship between gene copy number and expression potential as discussed in the notes?

More gene copies (e.g., plasmid copies) generally lead to higher potential output, influencing overall transcription and protein production.

What is the role of mRNA stability in post-transcriptional control?

mRNA stability determines how long transcripts persist for translation; stability is a key factor in post-transcriptional regulation of gene expression.

What does the term ‘post-translation effects’ refer to in the context of gene regulation?

Regulatory influences after translation that affect protein folding, modification, stability, and activity, thereby altering final function.