Gene Expression, Regulation, and Viral-Host Interactions: Study Notes for Cell Biology

Gene Expression I: The Genetic Code, Transcription, and RNA Processing

Genetic Code and Translation

The genetic code is the set of rules by which information encoded in mRNA is translated into proteins. It is universal and degenerate, meaning multiple codons can code for the same amino acid.

• Codon: A sequence of three nucleotides in mRNA that specifies an amino acid.

• Degeneracy: Most amino acids are encoded by more than one codon.

• Start Codon: AUG (methionine) signals the start of translation.

• Stop Codons: UAA, UAG, UGA signal termination of translation.

• Types of RNA: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

Example: The codon UUU codes for phenylalanine.

Transcription: DNA to RNA

Transcription is the process by which RNA is synthesized from a DNA template. It involves several steps and regulatory elements.

• Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

• Transcription Factors: Proteins that regulate the binding of RNA polymerase.

• Stages of Transcription:

  1. Initiation

  2. Elongation

  3. Termination

• Prokaryotic vs. Eukaryotic Transcription: Eukaryotes have more complex regulation, multiple RNA polymerases, and additional processing steps.

Example: The TATA box is a common promoter element in eukaryotes.

RNA Processing

After transcription, eukaryotic pre-mRNA undergoes several modifications before becoming mature mRNA.

• 5' Capping: Addition of a methylated guanine cap to the 5' end.

• Polyadenylation: Addition of a poly(A) tail to the 3' end.

• Splicing: Removal of introns and joining of exons.

Example: Spliceosomes are complexes that carry out splicing.

Gene Expression II: Protein Synthesis and Sorting

Translation: Protein Synthesis

Translation is the process by which ribosomes synthesize proteins using mRNA as a template.

• Ribosome Sites:

  • A site: Aminoacyl-tRNA binding site

  • P site: Peptidyl-tRNA binding site

  • E site: Exit site

• Initiation: Assembly of ribosome on mRNA and first tRNA.

• Elongation: Addition of amino acids to the growing polypeptide chain.

• Termination: Release of the completed polypeptide when a stop codon is reached.

Example: The ribosome moves along the mRNA, reading codons and adding corresponding amino acids.

Protein Sorting

Proteins are sorted to their correct cellular locations after synthesis.

• Signal Sequences: Short amino acid sequences that direct proteins to specific organelles.

• Post-translational Modifications: Chemical changes to proteins after synthesis, such as phosphorylation or glycosylation.

Example: Proteins destined for secretion have a signal peptide that directs them to the endoplasmic reticulum.

Regulation of Gene Expression

Levels of Regulation

Gene expression is regulated at multiple levels to ensure proper cellular function.

• Transcriptional Regulation: Control of gene expression at the level of transcription initiation.

• Post-transcriptional Regulation: Control after RNA is made, including splicing and stability.

• Translational Regulation: Control of protein synthesis from mRNA.

• Post-translational Regulation: Control after protein synthesis, including modifications and degradation.

Example: Enhancers and silencers are DNA elements that increase or decrease transcription.

Regulatory Elements

• Enhancers: DNA sequences that increase transcription when bound by activator proteins.

• Silencers: DNA sequences that decrease transcription when bound by repressor proteins.

• Insulators: DNA elements that block the interaction between enhancers and promoters.

Additional info: The combination of regulatory elements and transcription factors determines the specific expression pattern of each gene.

Viral-Host Cell Interactions (HIV Focus)

HIV Life Cycle and Host Adaptation

Viruses such as HIV must adapt to their host cell environment to replicate and propagate.

• Reverse Transcription: HIV uses reverse transcriptase to convert its RNA genome into DNA.

• Integration: Viral DNA is integrated into the host genome.

• Transcription and Translation: Host machinery is used to produce viral proteins.

• Assembly and Release: New viral particles are assembled and released from the host cell.

Example: HIV infects CD4+ T cells and uses host enzymes for replication.

Key Steps in HIV Infection

• Entry into host cell

• Reverse transcription of viral RNA

• Integration of viral DNA into host genome

• Production of viral proteins and assembly of new virions

• Release of new viruses to infect additional cells

Additional info: HIV evades the immune system by integrating into host DNA and mutating rapidly.

HTML Table: Comparison of Prokaryotic and Eukaryotic Transcription

Feature	Prokaryotic Transcription	Eukaryotic Transcription
Location	Cytoplasm	Nucleus
RNA Polymerases	One type	Three types (I, II, III)
RNA Processing	Minimal	Extensive (capping, polyadenylation, splicing)
Promoter Elements	-10 and -35 regions	TATA box, enhancers, silencers
Transcription Factors	Few	Many