| Term | Definition |
|---|
| Eukaryotes have | 20,000-50,000 genes |
| prokaryotes | genes group by fxn, reguated as operons |
| eukaryotic genes | genes are placed randomly, regulation more complicated. not continuous, have introns, diff mechanisms for for regulating genes |
| Rrna | 80-90% in cell, only 3 classes |
| MRNA | 1-5%, enocde a protein, most complex RNA |
| tRNA | 1-5%, carry amino acids, multiple TRNAs for each AA (isoacceptors), stable and heavily modified |
| in bacteria how many RNA pol | only 1 |
| universal properties of RNA | synthesize 5' to 3', require DNA template, does not require a primer |
| RNA pol uses what to produce RNA and PPi | rNTP and Mg++ |
| sigma subunits are required for | initiation of transcription |
| rho subunit is required for | termination at some sites |
| Diff btw RNA pol and DNA pol | DNA pol work on ssDNA with primer, RNA works on dsDNA |
| When RNA pol binds it creates a | single stranded DNA bubble which is where catalytic process occurs, about 17bp unwound |
| Topological problem:The rapid rate of synthesis causes supercoiled DNA to | transiently accumulate on either side of the transcription complex; need topoisomerases to relax the winding and unwinding |
| RNA polymerase accuracy | not as accurate as DNA |
| RNA polymerases and proofreading exonucleases | they do not have one, mistakes stay there but less of a problem bc it makes multiple copies |
| template strand of DNA | strand used for template for RNA POL |
| coding strand of DNA | corresponds to sequence of RNA transcript except for U's |
| Promoters | RNA Pol bind here to start transcription. defined sequence in bacteria, |
| -10 region and -35 region on bacterial promoters | binding sites for the sigma subunit; essential for initiation, found in all promoters |
| UP element | found on some promoters, binding site fo the alpha subunit of RNA Pol |
| strength of the promoter depends on | how close the sequence matches the optimal UP, -35 and -10 sequence |
| Dnase I | a nuclease that nicks dbl stranded DNA and produces a specific pattern of DNA frsgments. Protein binding usually inhibits it at a protected site. |
| Protein binding to Dnase I | can stimulate cleavage at adjacent sites (hypersensitive sites) |
| E. coli initiation of transcription | A closed complex is formed by the binding of RNA Pol-sigma complex to the promoter (sigma at -10 and -35 and alpha at UP) |
| In E. coli the open complex is formed during initiation of transcription by | the unwinding of DNA near -10 sequence, it is now ssDNA, after ~9nt are made, sigma is releases and POL is committed to elongation |
| Rifampin binds what part of what it inhibits | the beta subunit of prokaryotic RNA polymerase. used also to treat tuberculosis |
| Dactinomycin | made by streptomyces to inhibit RNA POL by intercalating between base pairs. also inhib DNA synthesis. toxic |
| alpha amanitin | inhibitor of euk RNA pol II. made by mushroom |
| AZT azidothymidine | thymidine analogue used antiviral agent. inhibits reverse transcriptase. HIV treatment. |
| Termination of transcription: Rho independent | weakened association btw RNA/DNA hybrid. Transcription of a palindromic region of DNA causes the formation of a hairpin structure from the RNA transcription looping and binding upon itself. followed by a string of A residues. Pol pauses at terminator |
| Termination of transcription: Rho dependent | forms hairpin and CA-rich sequence, rho is a 5'-3' RNA-DNA helicase. migrates along RNA until it reaches a transcribing pol paused at a termination site and then causes its release |
| Ribosomal RNAs and tRNA | derived from a single transcript processed by RNase II |
| tRNAs processing | give a specific 5' termini and have a number of modified bases |
| Eukaryotes specialized RNAs | snRNAs and Interfering RNA and microRNAs |
| POL I | synthesize pre ribosomal RNA |
| POL II | synthesize messenger RNA and some specialized RNAs |
| POL III | synthesize transfer RNA, 5SrRNA, some specialized RNAs |
| POL IV | found in plamts. special RNAs involved in silencing transposons and some repetitive DNAs |
| TBP in eukaryotes | TATA binding protein binds and recognizes the TATA box; necessary for all promoters; sequence differences result in different affinities for the initiation complex |
| TFIIH | has DNA helicase and kinase activity; it catalyzes opening of DNA and creates open complex; also required for in transcription coupled DNA repair and nucleotide excision repair |
| POL II has a CTD | This is phosphorylated by TFIIH and CDK9. Essesntial for initiation and other events in transcription |
| efficient transcription with POL II requires | activator proteins that usually bind DNA near start site and interact with TFs or POL |
| histone acetylases | needed to remodel or open chromatin for efficient transcription |
| mutations in TFIIH can lead to | xeroderma pigmentosum and Cockayne's syndrome |
| cap synthsizing complex binds to | 5' end and synthesizes a 5' cap which is a 5' triphosphate linkage where the 5' nucleotide is linked to a 7-methy-guanosine residue |
| Poly A complex interacts with | POL II CTD (C terminal domain) |
| Spliceosome | contains multiple snRNAs associated with proteins snRNP |
| snRNA recognize juntions and | orient RNA in spliceosome, ATP required for assembly |
| Interactions with spliceosome components make RNA | assume conformation necessary for splicing, activate internal A and promote other steps |
| Introns in eukaryotes | much longer than exons, alternate splicing can result in multiple messages from a single gene |
| mRNAs can be differently processed | ex) more than one poly A site or different splice sites; in different tissues, in response to growth or development status, or simultaneously in a cell |
| Ribosomal RNAs are synthesized by | POL I as a single transcript that is then methylated and cleaved into individual rRNAs |
| tRNAs are derived from | a long precursor by POL III, some bases are modified, splicing removes the small intron, CCA added tot he 3' end, cleavage at 5' and 3' termini |
| retrotransposons | similar life cycle to retroviruses but may not form virion like particles and if they are formed they remain in the cell |
| retroviruses | have RNA genome, copied into DNA and integrated, viral sequences transcribed into mRNA and viral RNA, most do not kill host cell |
| Reverse transcriptase | used by retrovirsuses to synthesize their genome, has no 3' to 5' exonuclease activity and has a high error rate, mutate at a high rate |
| retroviruses express their high number of genes as | polyproteins that are then cleaved by proteases to produce viral proteins |
| Long Terminal Repeat Sequences (LTR) | at both ends of retrovirus genomes. have regulatory elements and direct transcription of both viral genes and and host sequences |
| LTR can aberrantly express host genes | so it can cause cancer by causing abnormal expression of oncogenes if integrated near genes that control proliferation |
Combine with other sets
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