BMS100 BCH1-07 Central Dogma Notes PDF

Transcriptional unit • The transcription unit outlines the 3 general region found in all genes: § Promotor region – contains consensus sequence § Coding region • Transcribed into mRNA § Terminator region • Specifies end of transcription 5’ 3’ Promoter RNA-coding region TATA Transcription start...

Transcriptional unit • The transcription unit outlines the 3 general region found in all genes: § Promotor region – contains consensus sequence § Coding region • Transcribed into mRNA § Terminator region • Specifies end of transcription 5’ 3’ Promoter RNA-coding region TATA Transcription start site Terminator 3’ 5’ Template strand • The strand of DNA that is transcribed into RNA is referred to as the template strand. § It can also be referred to as the anti-sense strand • The template strand’s complimentary partner is referred as the non-template strand. § It can also be referred to as the sense strand RNA polymerase • RNA polymerase is the main key enzyme for transcription: § It moves along the DNA, unwinding the DNA helix just ahead of the active site for polymerization § Catalyzes a new phosphodiester bond on the newly-forming strand of RNA RNA polymerase cont. • RNA polymerase § Works in the 5’ à 3’ direction Template (aka non-sense strand) 3’ 5’ 5’ 5’ 3’ Non-template (aka sense strand) 3’ Steps of transcription • Transcription can be divided into 4 stages: § Initiation § Elongation § Processing § Termination Step 1 - Initiation • In order to begin transcription, RNA polymerase must recognize where to start. § Transcription initiation factors help with this process: • In prokaryotes there is just one: sigma factor • In Eukaryotes there are many different types, we will consider the role of general transcription factor TFII § Needed for RNA Polymerase II which transcribes all protein-coding genes in eukaryotes Step 1a – Initiation • A) TFII recognizes and binds a consensus sequence in the promoter region § In Eukaryotes one example is called the TATA box • Located ~25 nucleotides upstream from the transcription start site. • TFIID is the specific TFII that binds the TATA box Step 1bàd - Initiation • B) Other transcription factors join § Names of additional transcription factors are FYI • C) RNA Polymerase II joins • D) Transcription initiation complex is complete & transcription can begin Step 1 – Initiation: regulation • The TATA box (or other consensus sequences) aren’t the only binding site on DNA that influences initiation of transcription § Repressor proteins bind upstream sequences called silencers (aka negative regulatory elements) • Inhibit gene transcription Step 1 – Initiation: regulation cont. • Transcriptional activator proteins bind upstream sequences of DNA called enhancers (aka positive regulatory elements) § Increase the rate of transcription by attracting the RNA polymerase II enzyme. • Q: What might happen if there was a mutation in an enhancer sequence of DNA? Step 2 - Elongation • Once RNA Polymerase begins transcribing DNA, most of the general transcription factors (TFII) are released § These transcription factors are then available to initiate another round of transcription with new RNA Polymerase molecule Step 2 - Elongation • RNA polymerase moves downstream along the DNA, transcribing the coding region. § Various elongation factors are needed to help reduce the likelihood that RNA polymerase dissociating from DNA before it reaches the end of a gene. Step 2 - Elongation • In addition to elongation factors, eukaryotes also require: • Chromatin remodeling complexes help the RNA polymerase navigate the chromatin structure • Histone chaperones partially disassemble & reassemble nucleosomes as an RNA Polymerase passes through Step 2 - Elongation • As RNA polymerase move along the DNA double helix it generates supercoils. § In Eukaryotes DNA topoisomerase removes this super-helical tension DNA topoisomerase • The enzyme DNA topoisomerase relieves the super-helical tension by breaking the phosphodiester bond. • This allows the two sections of the DNA helix to rotate freely & relieve tension. • The phosphodiester bond will reform as DNA topoisomerase leaves. Step 3 - Processing • In eukaryotes, during elongation, the pre-mRNA transcript is processed in 3 main ways: • 1) Splicing • 2) Capping the 5’ end • 3) Polyadenylation of 3’ end • Once these modifications are complete the transcript is called mRNA Step 3 – Processing within elongation • 1. 7-methyl guanosine cap § A modified guanine nucleotide is added to the 5’ end of the transcribed premRNA • This occurs early, once ~25 nucleotides of RNA have been transcribed § This 5’ cap facilitates export of the mRNA into the nucleus and is involved in translation • More to come! Step 3 – Processing within elongation • 2. Splicing § Both intron and exon sequences are transcribed into RNA • Introns are then removed in a processes called RNA splicing. § Splicing is performed by spliceosomes • Spliceosomes require a special form of RNA (snRNA) and proteins complexed into snRNPs § snRNA = small nuclear RNA § snRNP = small nuclear ribonucleoprotein • snRNP is referred to a spliceosome once it has complexed with the pre-mRNA Why does splicing occur? • 95% of human genes are spliced in more than one way § Splicing allows the same gene to produce a variety of different proteins § For example: Step 4 – Processing & termination • The 3’ end of the mRNA molecule is specified by signals encoded in DNA. § These signals are transcribed into RNA and then bind to proteins that facilitate cleavage of mRNA from RNA polymerase • FYI – CPSF & CstF Step 4 – Processing & termination cont. • 3. Poly A tail: § Once cleaved, ~200 A nucleotides are added to the mRNA § FYI - This catalyzed by an enzyme called Poly-A Polymerase (PAP) • Poly A tails protects the mRNA from degradation and facilitates export from the nucleus • Poly A binding proteins then bind the poly-A tail Prokaryotes • Up to this point we have been discussing eukaryotic transcription. § The steps of transcription in prokaryotes are the same, however the mRNA transcript produced in prokaryotes is a little different: • No processing is required for the prokaryotic mRNA transcript § No 5’ cap, splicing, or poly-A tail • No export from nucleus § Thus translation can begin right away • mRNA transcript is polycistronic § Codes for more than one protein