Chapter 7 (edited)

Overview of Transcription and Translation

Chapter Title: From DNA to Protein: How Cells Read the Genome

Goals: Upon completion, students will be able to:

• Describe the complex process of transcription in both prokaryotes and eukaryotes.

• Explain the intricacies of RNA processing in eukaryotes and its significance.

• Describe in detail the translation process and the molecular machinery involved.

Central Dogma of Molecular Biology

Definition:

The central dogma describes the flow of genetic information within a biological system whereby genetic information is transferred from DNA to RNA and ultimately to the protein. This is succinctly captured in the formula: DNA → RNA → Protein.

Articulated by:

Francis Crick in 1958 in collaboration with James Watson, this concept laid the foundation for understanding molecular biology.

Key Processes:

• Transcription: The process by which the nucleotide sequence of DNA is copied into RNA.

• Translation: The subsequent process that utilizes the information in RNA to synthesize proteins, which perform various functions in the cell.

Transcription

General Overview:

Transcription produces a single-stranded RNA molecule that is complementary to one of the DNA strands. The nontemplate strand, also known as the coding strand, has the same sequence as the RNA product (except for the substitution of uracil for thymine).

Enzymatic Process:

• Enzyme: RNA polymerase is the key enzyme that catalyzes the transcription process.

• Mechanism: RNA polymerase forms phosphodiester bonds linking ribonucleotides, unwinds the double-stranded DNA, and progresses along the template strand (the DNA strand being copied).

• RNA chain initiation: Specific nucleotide sequences known as promoters signal the start of transcription, while terminators signal when to stop.

RNA Structure and Differences from DNA:

• Chemical Composition:

  • Sugar: RNA contains ribose, which has an -OH group at the 2' carbon, unlike DNA, which contains deoxyribose.

  • Bases: RNA uses uracil (U) instead of thymine (T) found in DNA.

  • Base pairing: Uracil pairs with adenine, maintaining the same base-pairing rules as thymine in DNA.

RNA Folding and Structure:

The presence of intramolecular base pairing facilitates complex folding of RNA molecules into three-dimensional structures, which are critical for their specific functional roles within the cell.

Types of RNA

Transcription in Prokaryotes vs. Eukaryotes

• Bacterial (Prokaryotic) Process: In prokaryotes, a single RNA polymerase directly recognizes promoter sequences to initiate transcription without the need for additional factors.

• Eukaryotic Process: In eukaryotes, transcription involves three types of RNA polymerases (I for rRNA, II for mRNA, and III for tRNA and other small RNAs) and requires the participation of various transcription factors and regulatory sequences.

Eukaryotic Transcription Complex

• Components: The transcription process begins when the TATA box is recognized by transcription factor TFIID, allowing the further assembly of a pre-initiation complex, including other factors such as TFIIH, which unwinds DNA.

• RNA Processing Events: Post-transcriptional modifications, including 5’ capping, polyadenylation, and RNA splicing (removal of non-coding introns and joining of coding exons), prepare the RNA for translation.

RNA Splicing Mechanism

• Spliceosome: A complex structure made of small nuclear ribonucleoproteins (snRNPs) and proteins that precisely removes introns and ligates exons to produce mature mRNA ready for the translation phase.

Translation Overview

• Process: The mRNA is interpreted and translated into a corresponding amino acid sequence by ribosomes, employing a cyclic mechanism involving tRNA and codon recognition.

• Codons: Each codon consists of three nucleotide bases that specify particular amino acids; certain codons also serve as stop signals during translation.

Ribosome Function

• Ribosomes possess multiple binding sites for mRNA and tRNAs—namely, the A (aminoacyl), P (peptidyl), and E (exit) sites—which facilitate the orderly addition of amino acids to the growing peptide chain.

• Process of Translation: Steps include tRNA binding, peptide bond formation catalyzed by the ribosome, and the translocation of the ribosome along the mRNA strand.

Eukaryotic vs. Prokaryotic Translation

• In eukaryotes, the initiation of translation is more complex, beginning at the 5' cap of the mRNA molecule.

• In contrast, prokaryotic mRNA can encode multiple proteins simultaneously through arrangements known as operons, resulting in coordinated translational activity.

Final Proteins and Modifications

• Protein Modifications: Post-translational modifications such as protein folding, cofactor binding, and chemical modifications (e.g., phosphorylation, glycosylation) are critical for determining the functional state and activity of proteins.

• Degradation: Protein degradation is meticulously regulated and mediated by the Ubiquitin-Proteasome Pathway, which enables the cell to maintain appropriate levels of proteins and eliminate misfolded or damaged proteins.

Antibiotics and Protein Synthesis

• Many antibiotics function by selectively inhibiting the bacterial protein synthesis machinery, exploiting the differences in ribosomal structure and function between prokaryotic and eukaryotic cells to mitigate the impact on human cells while targeting pathogenic bacteria effectively.