AP Bio: Biotechnology

Gene Expression and Regulation in Prokaryotes

• Coupled Transcription and Translation: In prokaryotes, transcription and translation occur simultaneously in the cytoplasm due to the absence of a nuclear membrane.

• Operon Concept: An operon is a cluster of genes under the control of a single promoter and regulated together.

• Inducers and Repressors: Inducers activate gene transcription by disabling repressors, while repressors prevent transcription by binding to operator regions.

Lac Operon Regulation

• Presence of Glucose: Low transcription due to catabolite repression.

• Absence of Glucose: Increased transcription as cAMP levels rise, promoting CAP binding to the promoter.

• Mutations:

  • Operator Sequence Mutations: Can lead to constitutive expression.

  • Promoter Mutations: May prevent RNA polymerase binding, halting transcription.

  • Repressor Protein Mutations: Non-functional repressors result in constant operon activity.

Trp Operon Regulation

• Presence of Tryptophan: Trp binds to the repressor, blocking transcription.

• Absence of Tryptophan: Repressor remains inactive, allowing gene expression.

• Attenuation: A regulatory mechanism using leader peptide sequences to halt transcription based on tryptophan availability.

• Mutations:

  • Operator or Promoter Mutations: Can lead to loss of repression.

  • Repressor Mutations: May cause constant expression of tryptophan biosynthesis genes.

Gene Expression and Regulation in Eukaryotes

• Levels of Gene Regulation:

  • DNA Availability: Chromatin remodeling controls gene accessibility.

  • Epigenetics: DNA methylation (silencing) and histone acetylation (activation).

  • Transcription Factors: General vs. specific transcription factors regulate transcription.

  • Enhancers: DNA sequences that increase transcription efficiency.

  • Post-Transcriptional Processing: Cap and tail addition, splicing, alternative splicing.

  • RNA Interference: MicroRNA and siRNA inhibit gene expression.

  • Translation Control: Availability of ribosomes, initiation factors.

  • Protein Fate: Misfolded proteins are tagged by ubiquitin and degraded by proteasomes.

Biotechnology

1. Gel Electrophoresis: Separates DNA fragments by size; used in evolutionary studies.

2. Restriction Enzymes: Cut DNA at specific sequences, enabling genetic modifications.

3. PCR (Polymerase Chain Reaction): Amplifies DNA sequences for analysis.

4. Plasmids in Cloning: Circular DNA molecules used for gene transfer in genetic engineering.

5. Transformation: Introduction of foreign DNA into bacteria, utilizing selective media.

6. DNA Sequencing: Determines nucleotide order; crucial for evolutionary studies.

7. Sequence Alignments in Cladograms: Helps establish evolutionary relationships.

8. Virus Life Cycles:

   • Lytic Cycle: Immediate viral replication and host cell destruction.

   • Lysogenic Cycle: Viral genome integrates into host DNA, remaining dormant.

Evolution

1. Mechanisms of Evolution:

   • Phenotype and Genotype: Observable traits vs. genetic composition.

   • Phenotypic Variation: Essential for natural selection.

   • Fitness: Reproductive success of an organism.

   • Types of Mutations: Beneficial, neutral, or deleterious changes in DNA.

   • Mechanisms: Natural selection, genetic drift, gene flow, mutation.

   • Selective Pressures: Environmental factors driving evolution.

   • Directional Selection: Favors one extreme trait.

   • Artificial Selection: Human-directed breeding.

2. Evidence of Evolution:

   • Fossil records, anatomical structures (homologous vs. analogous), molecular evidence.

   • Convergent vs. Divergent Evolution: Similar traits due to similar pressures vs. common ancestry.

3. Population Genetics:

   • Allele and Allele Frequency: Measure of genetic variation.

   • Hardy-Weinberg Equilibrium: Conditions for no evolution.

   • Genotypic Frequencies: p, q, p^2, q^2, 2pq.

4. Phylogenetics and Cladograms:

   • Shared Derived Characters: Unique traits defining evolutionary relationships.

   • Common Ancestor: Determined through branching points.

5. Speciation:

   • Reproductive Isolation: Prezygotic (before fertilization) vs. postzygotic (after fertilization) barriers.

   • Allopatric vs. Sympatric Speciation: Geographic vs. non-geographic isolation.

   • Punctuated Equilibrium vs. Gradualism: Rapid bursts vs. slow changes.

6. Origin of Species:

   • Extinction Causes: Environmental changes, competition.

   • Miller-Urey Experiment: Simulated early Earth conditions, proving organic molecules could form.

   • RNA World Hypothesis: Suggests RNA was the first genetic material.