Transcription and Processing

• gene expression: the creation of proteins from the genes encoded in the DNA of a cell
• DNA evolved to store genetic information because it is more stable, but RNA came first and stuck around because it makes gene expression more efficient (think of it like a giant recipe book)

  
• DNA is transcribed into mRNA (messenger RNA), which is then translated into proteins

  
• transcription: synthesis of RNA from a DNA template
• RNA polymerase: an enzyme (protein) that catalyzes the synthesis of RNA from DNA (catalyzes the formation of phosphodiester bonds between nucleotides during RNA synthesis)
• template strand: the strand of DNA that is being used as a template to synthesize against; the non-coding strand
• coding strand: the strand of DNA that opposes the template strand; the strand that the RNA will have the same sequence as
• the direction of transcription is 5' to 3' (ribonucleotides are added to the 3' end)

  
• three stages of transcription: initiation, elongation, and termination

  
• promoter: a sequence of DNA to which proteins bind to initiate transcription; usually near the start of the gene sometimes farther away
• TATA box: a non-coding DNA sequence that acts as a promoter element; starts with a sequence of TATA and is followed by varied subsequent T and A bases
• transcription factors: proteins that bind to promoters and recruit RNA polymerase (transcription initiation)

  
• ribonucleotide: a nucleotide that had ribose as its sugar
• RNA polymerase uses the template strand as a guide to determine which ribonucleotide to add next (transcription elongation)

  
• ribonucleotides are added to the 3' end as triphosphates (3 phosphate groups) - ATP, GTP, CTP, or UTP (nucleotide triphosphates; NTPs), 2 phosphate groups leave and a phosphodiester bond is created

  
• prokaryotic (bacteria) transcription termination: a termination sequence at the end of a gene signals RNA polymerase detachment
• eukaryotic transcription termination: an RNA sequence is recognized by proteins that cut it free and signal the RNA polymerase to stop and leave the DNA

  
• RNA processing: the preparation of mRNA transcripts for translation into proteins

  
• prokaryotic cells do not do RNA processing

  
• pre-mRNA: an RNA transcript that has not been processed yet (becomes mRNA after processing)
• RNA processing consists of 3 modification types to turn pre-mRNA into mature RNA: adding a 5' cap, adding a poly-A tail, and splicing
• a nucleotide is added to the 5' end, creating the 5' cap (a modified guanine nucleotide; 7-methylguanosine) soon after transcription starts

  
• the 5' cap prevents degradation of the mRNA, enable export of the mRNA from the nucleus into the cytoplasm, and helps ribosomes attach to start translation
• the termination of eukaryotic transcription occurs soon after AAUAAA is transcribed (the "polyadenylation signal")
• polyadenylation: 50-250 adenine nucleotides added to the 3' end of the mRNA to create the poly-A tail

  
• the poly-A tail prevents degradation of the mRNA, enables export from the nucleus to the cytoplasm, and helps ribosomes attach to start translation
• introns: non-coding sequences that are spliced out of pre-mRNA during processing
• exons: coding sequences (and other necessary mRNA) that remain in the mRNA after splicing
• introns can account for up to 95% of pre-mRNA
• most pre-mRNA is non-coding (not meant to be translated) and is spliced out

  
• heterogenous nuclear RNA (hnRNA): the collective unprocessed mRNA in the nucleus
• spliceosomes: large complexes of proteins and snRNAs (small nuclear RNAs) that catalyze the removal of introns from pre-mRNA (splicing)

  
• UTRs: untranslated regions in the first and last exons; important for guiding ribosomes in translation

  
• alternative splicing: exons from the same gene are joined in different combinations; allows a single gene to encode multiple proteins
• humans have about 21,000 genes, but cells can make about 100,000 different proteins through alternative splicing
• domains: regions of a protein that serve a particular role (e.g. DNA-binding domain, enzymatic domain, protein-binding domain, etc.)
• often an exon entails all the information for a domain

  
• removing an exon removes that domain

  
• every cell in a multicellular organism has the same genome, but cells can play many different roles or have many different jobs because

  expression of different genes -> different proteins -> different cell structure, function, types, activities, etc.
• humans have over 200 distinct cell types