Controlling Gene Expression

7.4 Controlling Gene Expression

Definition of Gene Expression Control

• Not all proteins are required by all cells at all times; thus, it is inefficient for cells to continuously transcribe and translate all genes.
• Gene expression is regulated based on life cycles and environmental conditions of cells, occurring in both prokaryotic and eukaryotic cells.
  • Example: Human insulin is produced when blood glucose levels are high.
  • Example: E. coli synthesizes lactose-degrading enzymes only when lactose is present in the environment.
• Optimal function requires genes to be expressed at the correct times, even though all cells contain the complete genome.
• Cells utilize complex regulatory systems evolved to fine-tune gene expression, ensuring expression of necessary genes only.

Types of Genes

• Housekeeping genes:
  • Continuously transcribed and translated to regulate vital processes (metabolism, growth, DNA replication).
• Specialized genes:
  • Present in specific cell types or activated under certain environmental conditions.
  • Example: Repair enzymes in liver cells, hemoglobin genes only in red blood cells.

Mechanisms for Regulating Gene Expression

• Understanding these mechanisms is essential as they allow molecular biologists to manipulate gene expression in various cells (bacteria, viruses, cancer cells).

Prokaryotic Gene Control Mechanisms

Gene Expression and Feedback Control

• Gene expression in prokaryotes is primarily regulated by the concentrations of molecules like lactose and tryptophan through negative feedback control.

The Lac Operon

• The lac operon is a cluster of three genes responsible for metabolizing lactose:
  • Structure includes:
  • Promoter: Site where transcription begins.
  • Operator: Sequence controlling transcription.
  • Coding regions: Genes for lactose-metabolizing enzymes.
• An upstream gene encodes a repressor protein (lacI or lac repressor), which responds to environmental cues (lactose concentration).

Function of the Lac Operon

• The lac repressor is always present as its coding genes are continuously transcribed.
• When lactose is absent:
  • The active lac repressor binds to the operator, preventing RNA polymerase from accessing the promoter.
• When lactose is present:
  • Lactose binds to the lac repressor, rendering it inactive and allowing RNA polymerase to transcribe lactose-metabolizing genes.
• Lactose acts as an inducer, initiating enzyme production, resulting in a direct correlation between lactose concentration and enzyme synthesis.

The Trp Operon

• The trp operon regulates tryptophan production:
  • Structure similar to the lac operon: contains a promoter, operator, and genes coding for tryptophan-synthesizing enzymes.
  • Includes the trp repressor, always synthesized.

Function of the Trp Operon

• When tryptophan is absent:
  • The trp repressor is inactive, allowing transcription of genes for tryptophan synthesis.
• When tryptophan is present:
  • Tryptophan binds and activates the trp repressor, which then binds to the operator and inhibits transcription.
• Tryptophan acts as a corepressor in this system, functioning to reduce gene expression related to its synthesis.
• Negative feedback mechanism observed as environmental tryptophan level affects gene transcription.

Eukaryotic Gene Control Mechanisms

• Eukaryotic gene expression is more complex; does not use the operon system. Control mechanisms fall into four categories:
  1. Transcriptional: Regulation during mRNA synthesis.
  2. Post-transcriptional: Regulation during mRNA processing.
  3. Translational: Regulation during protein synthesis.
  4. Post-translational: Regulation after protein synthesis.

Transcriptional Regulation

• Most common regulation occurs during transcription.
• Eukaryotic chromatin structure prevents access to gene promoters; genes must be unwound for transcription.
  • Activator molecules bind upstream, signaling chromatin remodeling complexes to expose promoters.
  • Addition of acetyl groups (–COCH3) to histones loosens their DNA association, promoting transcription.
• General transcription factors bind to specific promoter regions (TATA box), initiating transcription with RNA polymerase forming a transcription initiation complex.
  • Activators and repressors further modify transcription rates.
• Methylation of cytosine bases in promoter regions inhibits transcription, a process referred to as silencing.

Methylation

• Inactive genes can be "put on hold" via methylation until needed, such as hemoglobin production in red blood cell precursors.
• Certain chemical triggers (like bisphenol A) can influence gene methylation and expression, affecting phenotypes in organisms (example: agouti mice with differing traits).

Post-transcriptional Regulation

• Involves mechanisms like alternative splicing, where different mRNAs arise from the same pre-mRNA by splicing combinations of introns/exons.
  • Useful in varying protein production based on cell type.
• Binding of masking proteins to mRNA can inhibit protein synthesis until necessary.
• Degradation rates of mRNAs can be influenced by regulatory molecules such as hormones.
  • Example: Prolactin extends mRNA lifespan for casein in mammary glands.

Translational Regulation

• Alters the poly(A) tail length of mRNA, affecting translation speed and efficiency; mechanisms are still being understood.

Post-translational Regulation

• Processes proteins into active forms and modifies them chemically.
  • Hormonal presence can regulate the lifespan of these functional proteins.
• Short-lived proteins are tagged with ubiquitin, marking them for degradation; adding/removing these tags modifies their functional lifespan to manage protein availability.

Summary of Gene Expression Controls in Eukaryotes

Cancer and Gene Regulation

• Cancer cells disregard regulatory mechanisms that control cell growth, often linked to mutations in genomic sequences that result in oncogenes (genes promoting unchecked cell division).
• Cancer cells tend to have longer telomeres, which contributes to their uncontrolled growth.
• Mutations can arise from cumulative exposure to mutagens, increasing the likelihood of cancer as organisms age.
• When cells deviate from normal division, they can form tumors:
  • Benign tumors: Grow slowly, remain localized.
  • Malignant tumors: Grow uncontrollably and invade nearby tissues, requiring treatments such as chemotherapy.

Questions for Review

1. Define the following terms:
   • (a) Operon
   • (b) Operator
   • (c) Corepressor
   • (d) Repressor
   • (e) Housekeeping genes
   • (f) Inducer
2. Why do eukaryotes have a more complex gene regulation system than prokaryotes? Provide an example.
3. Compare and contrast the lac and trp operons.
4. Summarize the regulation of the lac operon.
5. Describe the trp operon activities when tryptophan levels are low and what happens when tryptophan is available.
6. Provide eukaryotic regulatory mechanisms for transcription, translation, and post-translation.
7. Hypothesize why eukaryotic transcription is influenced by regulatory proteins rather than modifying RNA polymerases.
8. Analyze the agouti gene relationship with environmental chemicals such as bisphenol A.
9. Discuss mechanisms leading to cancerous cells.

Summary Points

• Cells adjust gene expression based on environmental changes.
• Prokaryotes utilize operons to regulate gene expression, while eukaryotes have a multifaceted approach.
• Gene regulation in eukaryotes occurs throughout the transcriptional process, during mRNA processing, translation, and post-translation.
• Changes in gene expression can result in cancer due to the absence of regulatory controls in malignant cells.