Central Dogma: Bacteria vs Eukaryotes

Prokaryotes

Operon and Regulon Structure

The organization of genes in prokaryotes is distinct, often involving operons and regulons that coordinate gene expression.

• Operon: A cluster of genes under the control of a single promoter, transcribed together as a polycistronic mRNA.

  • Monocistronic: mRNA encodes a single protein.

  • Polycistronic: mRNA encodes multiple proteins, typical in prokaryotes.

• Regulon: A collection of operons controlled by a common regulatory protein.

Transcription in Prokaryotes

Transcription is the process by which RNA is synthesized from a DNA template.

• Template vs Coding Strand: The template strand is used by RNA polymerase to synthesize RNA, which is complementary to the template and identical to the coding strand (except uracil replaces thymine).

• Initiation:

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

  • Sigma Factor: Protein that enables RNA polymerase to recognize promoter regions.

  • Sigma Factor Binding Sites: Specific DNA sequences recognized by sigma factors. Upstream refers to sequences before the transcription start site; downstream refers to sequences after.

• Elongation:

  • Uracil: In RNA, uracil (U) replaces thymine (T).

  • Primer: Not required for RNA polymerase to initiate synthesis.

• Termination:

  • RNA polymerase stops transcription at specific terminator sequences; the fate of RNA polymerase after termination varies.

Translation in Prokaryotes

Translation is the synthesis of proteins from mRNA by ribosomes.

• Codon: Three-nucleotide sequence on mRNA that specifies an amino acid.

• Stop Codon: Codons (UAA, UAG, UGA) that signal termination of translation.

• Start Codon: Usually AUG, signals the start of translation.

• Reading Frame: The way nucleotides are grouped into codons.

• Ribosome:

  • Composed of rRNA and proteins; has distinct structural forms in prokaryotes (70S ribosome).

  • Polyribosomes (polysomes) are multiple ribosomes translating a single mRNA simultaneously.

• tRNA:

  • Transfer RNA carries amino acids to the ribosome; contains an anticodon that pairs with the mRNA codon.

• Release Factor:

  • Proteins that recognize stop codons and promote release of the newly synthesized polypeptide.

• Initiation:

  • Shine-Dalgarno Sequence: Ribosome binding site in prokaryotic mRNA, located upstream of the start codon.

• Elongation:

  • Role of EPA sites: Exit, Peptidyl, and Aminoacyl sites on the ribosome facilitate tRNA movement and peptide bond formation.

  • Role of tRNA: Delivers amino acids to the growing polypeptide chain.

• Termination:

  • Release factors recognize stop codons and facilitate the release of the polypeptide.

Eukaryotes

DNA Transcription

Eukaryotic transcription is more complex, involving multiple RNA polymerases and regulatory factors.

• RNA Polymerases:

  • RNA Polymerase I: Synthesizes rRNA.

  • RNA Polymerase II: Synthesizes mRNA.

  • RNA Polymerase III: Synthesizes tRNA and other small RNAs.

• Transcription Factors: Proteins required for the initiation and regulation of transcription.

• Type of mRNA Product: mRNA is processed before translation (see below).

RNA Processing

After transcription, eukaryotic pre-mRNA undergoes several modifications.

• 5' Cap: Addition of a modified guanine nucleotide to the 5' end, aiding in mRNA stability and translation initiation.

• 3' Poly A Tail: Addition of a string of adenine nucleotides to the 3' end, enhancing stability and export from the nucleus.

RNA Splicing and Alternative Splicing

Splicing removes non-coding regions (introns) from pre-mRNA, joining coding regions (exons).

• Exons: Coding sequences retained in mature mRNA.

• Introns: Non-coding sequences removed during splicing.

• Alternative Splicing: Process by which different combinations of exons are joined, allowing for multiple protein products from a single gene.

mRNA Translation in Eukaryotes

Translation in eukaryotes involves additional regulatory sequences and factors.

• 5' Cap: Facilitates ribosome binding and translation initiation.

• Kozak Sequence: Consensus sequence surrounding the start codon, important for efficient translation initiation.

Comparison Table: Prokaryotic vs Eukaryotic Transcription and Translation

Key Equations

• Central Dogma:

• Codon-Anticodon Pairing:

Example

In Escherichia coli, the lac operon is a classic example of a polycistronic operon regulated by both positive and negative control mechanisms.

Additional info: Academic context was added to clarify definitions, processes, and comparisons between prokaryotic and eukaryotic systems.