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Chapter 16

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University of British Columbia
BIOL 112
Karen Smith

Chapter 16 Notes DNA – transcription--> mRNA –translation--> Proteins 16.1-Transcription in Bacteria - RNA polymerase (preform template-directed synthesis from 5’3’ and no primer needed to begin transcription) synthesize mRNA - Transcription occurs when: 1. RNA polymerase matches the base of ribonuculeotide triphosphate with a complementary base in gene (gene: section of DNA that codes for a protein or RNA) 2. RNA polymerase catalyzes formation of phosphodiester bond between 3’ end of growing mRNA and the new ribonucleotide 3. RNA that is complementary to the gene is synthesized - RNA Polymerase Structure and Function * structure found by using: crystallography which allows biologists to obtain 3-D images of molecules * shape: large, globular, many channels running through interior * active site: located where several channels intersect * DNA fits into one of the enzyme’s channels two strands of DNA in double-helix separate inside the enzyme to produce single stranded template at active site Initiation: - Polymerase can’t do it on their own = Sigma (detachable protein subunit) must bind to polymerase - Polymerase + Sigma = holoenzyme (“whole enzyme”) which is made of core enzyme (polymerase) which contains active site and other needed proteins - Sigma: guides RNA polymerase to specific location where transcription should begin = promoter - promoters: 40-50 nucleotide base sequence on non-template strand of DNA, binds to RNA polymerase, lets transcription start (prokaryotic- a single promoter for several genes, eukaryotic- each gene has own promoter) - TATAAT: -10 box (centered 10 bases upstream from where RNA polymerase starts transcription) - Downstream: direction RNA polymerase moves during transcription, Upstream: opposite direction - +1 site: place where transcription beings - TTGACA: -35 box, located 35 bases upstream from +1 site - Sigma binds to -10 and -35 boxes – sigma makes first contact with DNA to start transcription in bacteria, = sigma is regulatory protein that tells RNA polymerase where and when to start synthesis - After sigma binds, DNA helix opens up and single strand is threaded through active site, ribonucleoside triphosphates (NTP’s) enter channel and diffuse into active site, NTP pairs with complementary base on template strand of DNA, polymerization beings! - entire process is spontaneous and exergonic (NTP’s have a lt of PE) Elongation: - RNA polymerase move along DNA template from 3’5’, synthesizing RNA in 5’3’ direction - Inside the enzyme, group of projecting amino acids = enzyme’s zipper help open double helix upstream - Rudders (amino acids) steer template/non-template through correct channels inside the enzyme - At active site, addition of nucleotides to 3’ end of the growing RNA molecule at 50 nucleotide/sec*Note: During transcription, all main channels of enzyme are filling. DNA double-helix goes in and out of one groove, NTP’s enter from another and growing RNA leaves through another Termination: - transcription stops when RNA polymerase hits stop codon - as soon as synthesized, RNA sequence folds back on itself and forms short double-helix (held together by complementary base pairing) = secondary structure = hairpin - formation of hairpin disrupts interaction between RNA polymerase and RNA transcript = the physical separation of enzyme and product 16.2-Transcription and RNA Processing in Eukaryotes Similarities to Bacteria Transcription: RNA polymerase does not bind direction to promoter. Basal Transcription Factors: initiate eukaryotic transcription by matching enzyme with appropriate promoter region in DNA Basal Transcription Factors –same as—Sigma, BUT they interact with DNA independent of RNA polymerase Differences to Bacteria Transcription: Eukaryotes Bacteria Many Basal Transcription Factors are required to Different versions of sigma bind to different initiate transcription (machinery to start promoters transcription is complex) 3 Distinct RNA polymerase: Only has one type of RNA polymerase 1. RNA pol I: genes that code for most large RNA molecules (rRNA) found in ribosomes 2. RNA pol II: protein-coding gene (mRNA) RNA molecules found in snRNPs 3. RNA pol III: genes that code for tRNA, one of the small RNA molecules (rRNA) found in ribosomes Promoters are much more diverse Simple promoter Promoters recognized by Pol II: Contain TATA Box Contains a -10 and -35 box = located 30 base pairs upstream of transcription start site, some do not Pol I and Pol III have entirely different promoters Transcription is followed by several RNA Transcription and translation occur at the same processing steps to make a mRNA that may leave time as there is no nucleus to travel to. No RNA nucleus. 1)
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