1. Lactose (allolactose) binds repressor
2. Repressor releases from operator
3. RNA polymerase transcribes genes
4. Lactose metabolized

Function: Inducible system - genes turned ON when substrate present

trp Operon (Repressible)

Tryptophan synthesis genes

Without tryptophan (ON):

1. Repressor inactive (can't bind operator)
2. RNA polymerase transcribes genes
3. Tryptophan synthesized

With tryptophan (OFF):

1. Tryptophan (corepressor) binds repressor
2. Activated repressor binds operator
3. Blocks transcription

Function: Repressible system - genes turned OFF when product present

Eukaryotic Gene Regulation

More complex than prokaryotes:

• Chromatin structure
• Transcription factors
• Alternative splicing
• mRNA stability
• Translation control
• Post-translational modifications

Chromatin Structure

Histone modifications:

• Acetylation: loosens chromatin (genes accessible - ON)
• Methylation: can activate or repress (depends on location)
• Phosphorylation: various effects

DNA methylation:

• Addition of methyl groups to cytosine
• Usually silences genes
• Heritable (epigenetic)

Chromatin remodeling:

• Euchromatin: loosely packed, genes active
• Heterochromatin: tightly packed, genes inactive

Transcription Factors

Activators:

• Promote transcription
• Help RNA polymerase bind
• Bind to enhancers (DNA sequences)

Repressors:

• Inhibit transcription
• Block activators or RNA polymerase
• Bind to silencers

Enhancers and silencers:

• Can be far from gene
• DNA loops bring them near promoter

Control Elements

Proximal control elements:

• Near promoter
• TATA box, CAAT box, GC box

Distal control elements:

• Far from promoter
• Enhancers and silencers

Epigenetics

Changes in gene expression without DNA sequence changes

Mechanisms:

1. DNA methylation: adds methyl groups to DNA
2. Histone modification: acetylation, methylation, etc.
3. Chromatin remodeling: changes DNA packaging

Characteristics:

• Can be heritable (passed to daughter cells)
• Can be reversible
• Influenced by environment
  • Diet, stress, toxins, behavior

Examples:

• X-inactivation in females (Barr body)
• Genomic imprinting: parent-specific expression
• Cancer: abnormal methylation patterns

Post-Transcriptional Regulation

mRNA processing:

• Alternative splicing (one gene → multiple proteins)
• 5' cap and poly-A tail additions

mRNA stability:

• Some mRNAs degraded quickly
• Others stable for long time
• Controlled by sequences in 3' UTR

microRNA (miRNA) and siRNA:

• Small RNAs that bind mRNA
• Block translation or cause degradation
• Gene silencing

Levels of Gene Regulation

1. Chromatin structure (access to DNA)
2. Transcription (RNA synthesis)
3. RNA processing (splicing, capping, tailing)
4. mRNA stability (degradation)
5. Translation (protein synthesis)
6. Post-translational (protein modifications)

Key Concepts

1. lac operon: inducible, turned ON by lactose
2. trp operon: repressible, turned OFF by tryptophan
3. Chromatin modifications control gene accessibility
4. Transcription factors (activators/repressors) control transcription
5. Epigenetics: heritable changes without DNA sequence change
6. Multiple levels of regulation in eukaryotes
7. miRNA and siRNA silence genes post-transcriptionally