central dogma

Transcription

• One strand of DNA acts as a template for the production of an RNA strand by the enzyme RNA polymerase.
• RNA polymerase unwinds DNA locally and assembles complementary RNA nucleotides along the DNA template strand, linking them with phosphodiester bonds into a polynucleotide.
• RNA polymerase can only add to the 3’-end of the growing polymer.
• Unlike DNA polymerases, RNA polymerases do not need a primer.

Stages of Transcription

• Initiation: RNA polymerase interacts with the promoter at the TATA box to establish a transcription complex.
• Elongation: the RNA polymerase extends the new RNA by adding to the 3' end.
• Termination: a sequence in the DNA (terminator) halts transcription.

Transcription in Eukaryotes

• Transcription in eukaryotes makes "pre-mRNA" that must be processed to mature mRNA for translation.
• A 5’ cap, a 3’ polyA tail, and splicing are all required for maturation.
• Once these processes are complete, the mRNA can be exported to the cytoplasm.

mRNA Processing

• The 5' cap and 3' polyA tail both protect the mRNA, aid in export of mature mRNA to the cytoplasm, and improve translation efficiency by the ribosome.
• Splicing removes introns, which are extra nucleotides in the transcribed region of genes, and ligates together exons to make a mature mRNA with a correct protein coding sequence.

Translation

• mRNA has a protein coding sequence using codons which are translated using tRNA.
• There is a different tRNA and associated enzyme for each of the 20 amino acids.
• A tRNA hydrogen bonds with the proper codon on mRNA through its anti-codon using strict base pairing.
• Codons represent a degenerate code, with more than one codon representing the same amino acid.

Stages of Translation

• Initiation: the small ribosomal subunit binds to mRNA near the 5'-end.
• Elongation: a charged tRNA enters the A-site, and ribosomal enzymes cut the growing polypeptide free from the P-site tRNA, and attach it to the new amino acid on the tRNA in the A-site with a peptide bond.
• Termination: a stop codon lines up with the A-site and binds to a release factor, halting translation.

Gene Structure

• The information encoding proteins is organized as genes on DNA, and all genes have the same basic structure.
• A transcription start site denoted as "+1" corresponding to the first nucleotide at the 5' end of the RNA product.
• A transcribed region that acts as the template for the transcribed RNA, located "downstream" of the transcription start site.
• A regulatory domain called a promoter located "upstream" of the transcription start site.

Regulation of Gene Expression

• Prokaryotes depend largely on negative regulation, using repressor proteins to control gene expression.
• Eukaryotes depend on positive regulation of gene expression, but also regulate gene expression with transcription factors acting as activators or repressors of RNA polymerase activity.
• Basal transcription factors bind to the promoter to recruit RNA polymerase, with their presence or absence acting as an on/off switch for transcription.
• Regulatory transcription factors including both activators and repressors can bind to proximal control elements upstream of the promoter, modifying transcription at different times, or in different cells.
• Position-independent elements called enhancers greatly increase transcription when bound by transcriptional activators.