Term
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Definition
| alter single nucleotide in DNA sequence, simplest just switch bases |
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Definition
| pyrimidine to pyrimidine or purine to purine, 10x more frequent |
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Definition
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Definition
| results in no change of the protein function |
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Definition
| causes a change in amino acid sequence of a polypeptide |
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Definition
| produce premature stop codons, will cause truncated protein |
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Definition
| one or more base pairs added to the wild-type sequence |
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Definition
| due to loss of one or more base pairs |
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Definition
| insertion and deletions within the open reading frame, repeated sequences prone to this |
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Definition
| insertions or deletions within the open reading frame of a gene, often causes truncated protein |
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Term
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Definition
| first line of defense against mutation but not foolproof |
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Term
| Triplet Expansion Disease |
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Definition
| most involve codon for glutamine (CAG) |
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Term
| Chromosomal Abnormalities |
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Definition
| chromosomes under large deletions or duplication, inversions of large stretches can also occur |
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Term
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Definition
| sometimes regions from one chromosome transferred to other, sometimes non-homologous chromosomes can exchange large stretches of DNA |
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Definition
| happens during normal operations of cell, hydrolysis reactions play an important role |
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Definition
| removal of amino group (cytosine, guanine, and adenine can all be deaminated) cytosine produces uracil |
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Definition
| common result of hydrolysis, the N-glycosyl bond holding base to sugar is broken, leaves missing base abasic site, occurs at high rates for purines |
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Definition
| DNA damage caused by outside chemical or physical agents |
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Term
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Definition
| react with As and Cs, results in deamination |
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Term
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Definition
| H2O2, OH-, O2 can be attached to various bases or backbone of DNA, often result in transversions |
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Term
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Definition
| addition of alkyl groups to bases or backbone of DNA, can happen at many different positions |
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Term
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Definition
| any substance involved in promoting cancer, benzo apyrene of cigarette smoke |
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Term
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Definition
| DNA reactive compounds that cause chemical changes in DNA |
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Definition
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Definition
| screens compounds to see if mutagenic, uses strains of salmonella typhimurium, bacteria exposed to agent and screened for reversion mutations back to wild-type |
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Term
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Definition
| light at 260nm strongly absorbed by DNA, forms thymine dimers |
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Term
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Definition
| create oxygen species which can break one or both strands of DNA |
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Term
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Definition
| catches mistakes proofreading misses, conserved in all cell types, must discriminate between strands, will even catch small indels |
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Term
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Definition
| methylates it adenines in sequence GATC to mark old strand of DNA, work of protein dam methylase, new DNA isn't methylated, corrected as though the old strand is correct |
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Term
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Definition
| in E. Coli the genome is scanned by this protein for mismatches, MutL is recruited to the spot which activates MutH, MutH cuts the DNA, exonucleases digest the damaged, Pol I fills the gap and ligase seals the last nick |
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Term
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Definition
| DNA photolyase captures energy of light and breaks thymine dimers, present in almost all cells |
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Term
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Definition
| transfer methyl groups off bases |
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Term
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Definition
| most prevalent type of DNA repair |
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Term
| Base Excision Repair (BER) |
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Definition
| sees a single damaged base, in bacteria it is recognized by DNA glyosylase which breaks the glycosidic bond holding the base to the sugar, leaves abasic site |
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Term
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Definition
| recognized by AP endonuclease which cleaves DNA creating a nick, can be removed by nick translation ability of DNA pol I |
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Term
| Nucleotide Excision Repair (NER) |
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Definition
| don't recognize particular lesion but distortions in the double helix, short segment removed |
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Term
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Definition
| 2 incisions made on one DNA strand |
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Term
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Definition
UvrA- detects distortions in double helix
UvrB- creates a ss bubble around helix
UvrC- creates a two nick flanking the lesion
DNA pol I- removes fragment and fills gap as DNA ligase comes and seals nick |
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Term
| Transcription-coupled Repair |
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Definition
| damage recognized by RNA polymerase, will repair damage within genes |
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Term
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Definition
| repaired by double-stranded break repair pathway, retrieves information from sister chromatid, probably the selective force behind crossing over |
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Term
| Translesion Synthesis (TLS) |
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Definition
| happens when DNA comes across damage, special DNA pol (Ypol) comes in and sticks something in, do not read anything and prone to error |
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Term
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Definition
| copying sequences of DNA into RNA molecule, occurs in nucleus of eukaryotic cell, catalyzed by RNA polymerase |
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Term
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Definition
-don't need a primer
-identified from E. Coli in 1960s
-product doesnt stay
-large complex |
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Term
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Definition
| sixth polypeptide sigma actor binds transiently to core and directs enzyme to promoters, sigma plus core forms the RNA polymerase holoenzyme in E. Coli |
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Term
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Definition
pol I ribosomal RNA
pol II hn RNA (mRNA)
pol III tRNA and other small RNAs
***overall shape like crab claw, 2 large units make up pincers of the claw with activation site containing regions from both |
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Term
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Definition
begins at defined sites called promoters (DNA sequences which mark the beginning of gene)
-2 strands of DNA: template strand serves as a pattern for RNA synthesis, the non-template or coding strand is identical to the RNA sequence |
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Term
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Definition
| short distance that DNA is unwound for transcription, usually 17bp in bacteria, +supercoils in front and -supercoils form behind |
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Term
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Definition
| binding of the RNA polymerase to the promoter, DNA stays double stranded, enzyme bound to one face of the helix |
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Term
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Definition
| DNA opened up over distance of 14bps, first 10bases made relatively inefficiently and often short transcripts are released to start over, called initial transcribing complex |
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Term
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Definition
| when an enzyme has added more than 10 bases to the transcript |
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Term
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Definition
| RNA polymerases don't require a primer, two rNTPs in place to get started, during first 10 bases there is high probability that transcription will start over, after 10 bases RNA more stable |
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Term
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Definition
| RNA polymerase binds to DNA and completes transcription of the gene, after 10bp, 8-9bp of RNA bound to DNA |
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Term
| RNA polymerase inhibitors |
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Definition
| Actinomycin D, Acridine, rifampicin inhibits bacterial transcription, alpha aminitin blocks RNA pol II |
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Term
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Definition
| occur between -40 and -60, strong in promoters |
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Term
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Definition
| probabilities, initially defined by 2 types of mutations (promoter up made promoter more efficient, promoter down made less) |
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Term
| Pyrophosphorolytic editing (kinetic proofreading) |
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Definition
| enzyme uses its active site to remove incorrect bases by reincorporating a Ppi, enzyme pauses a little over incorrect bases |
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Term
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Definition
| enzyme will backup after a mistake, the RNA product is cleaved and the enzyme tries again, balance between pausing and moving on |
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Term
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Definition
| less accurate than DNA polymerases, can cause elevated mutation rate in RNA |
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Term
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Definition
E. Coli has 2 classes of termination
Rho independent- most common type of terminator, work solely on basis of shape, composed of GC rich stem loop structure followed by run of Us
Rho dependent- need protein factor called Rho to work, may consist of stem loop to slow down, uses ATP |
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Term
| Specific Transcription factors |
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Definition
| bind DNA at long distance from various genes |
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Term
| General transcription factors |
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Definition
| bind at the promoters of all genes |
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Term
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Definition
| each polymerase requires TATA binding protein as part of machinery, binds sequence called TATA box if present but only present 1/4 of time |
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Term
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Definition
| transcribes only one gene encoding the precursor to ribosomal RNAs, many copies of this gene, has 2 transcription factors |
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Term
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Definition
| have 2 parts to core element and UCE (upstream control element), located near start site |
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Term
| UBF (upstream binding factor) |
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Definition
| transcription factor, binds upstream to control element, UBF recruits factor called SL1 to complex |
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Term
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Definition
| binds near the core element and contain TBP and 3 TAFs for pol I, this recruits RNA pol I |
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Term
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Definition
| promoters refer to minimal set of sequence elements required to activate transcription (usually 40-60bases) |
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Term
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Definition
| many located downstream from start site of transcription, promoters contain two sequence boxes, requires 2 transcription factors TFIIIC and TFIIIB |
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Term
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Definition
| combine with RNA polymerase to form pre-initiation complex, contains RNA pol II and 6 general transcription factors |
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Term
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Definition
| binds near TATA box, complex protein with many subunits, TATA associated factors (TAFs), TBP associates with about 10 TAFs, bind other promoter elements like Inr and DPE |
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Term
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Definition
| highly conserved, binds TATA box, contacts minor grove of DNA, distorts and bends the double helix |
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Term
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Definition
| doesn't seem to always be essential, may stabilize binding between TFIID and promoter |
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Term
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Definition
| binds next makes some contacts with DNA and BRE as well as downstream of the TATA box, needs TFIID to bind |
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Term
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Definition
| comes in with polymerase, loosens non specific attractions between DNA and pol II |
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Term
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Definition
| bind to create closed promoter complex |
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Term
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Definition
| has helicase activity that unwinds the DNA to form open complex |
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Term
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Definition
| will form few abortive transcripts then enter elongation, pol III is phosphorylated on its CTD to leave promoter, TFIIE and TFIIH are released |
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Term
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Definition
| aid general transcription factors at most genes, seem to have modular design in both yeast and humans, may aid in assembly of general transcription to activate genes |
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Term
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Definition
| terminates at a T rich sequence located short distance from 3' end of the mature RNA and requires several proteins |
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Term
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Definition
| terminates at a terminator sequence downstream of the rRNA precursor and requires several helper proteins |
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Term
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Definition
| can terminate anywhere from a few base pairs to several KB away from end of a mature transcript |
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Term
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Definition
| many RNAs synthesized as biologically inactive precursors |
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Term
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Definition
| more extensive in eukaryotes than bacteria |
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Term
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Definition
| capped, tailed, have introns removed, many enzymes involved in processing |
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Term
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Definition
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Term
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Definition
| coding sequences in genes |
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Term
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Definition
| methylation on 5' ends, extra nucleotide linked by 5'-5' linkage |
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Term
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Definition
| last phosphate clipped off the 5'PO4 new RNA, GMP added, then methylated, can be early even, happens within first 20-30 bases, only done on mRNA |
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Term
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Definition
| typically 80-250 bases long, protects mRNA from enzymatic destruction |
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Term
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Definition
| happens after primary transcript triggers cleavage then occurs, there is sequence AAUAAA about 10-30bp before the poly A tail, sequences 20-40 downstream of this tend to be GU or U rich |
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Term
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Definition
| further processing of RNAs including removal of introns |
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Term
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Definition
| huge role in alternative splicing, splice sites may be hidden or marked |
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Term
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Definition
| different pol A sites many also used to cause production of different gene products |
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Term
| 3 Sites Important in Splicing |
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Definition
-5' splice site marks the 5' end of intron
-3' splice site marks the 3' end of the intron
-branch point site found close to 3' end |
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Term
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Definition
used for most nuclear genes, 2 steps
1st step-2'OH groups of A attacks phosphodiester bond between first exon and G at beginning
2nd step-3'OH group at the left end of the 1st exon attacks phosphodiester bond between G and end base of second exon |
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Term
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Definition
| mediates reactions of nuclear splicing, contains 5 small nuclear ribonucleoproteins or snurps |
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Term
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Definition
| contain small nuclear RNA, about 100-200 bases long, each one binds to proteins called Sm proteins |
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Term
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Definition
| part of spliceosome but not part of snRNP, proteins play important roles in selecting splice sites |
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Term
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Definition
| introns have GU on the 5'end and AG on the 3'end, surrounding sequences and structure of the primary transcript may all pay important roles |
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Term
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Definition
| base pairing between snRNA and primary transcript to select splice sites |
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Term
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Definition
| recognizes the GU at the 5' splice site, U2AF binds AG at the 3' splice site, this recruits U2 to branch point (ATP dependent) |
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Term
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Definition
| binds and replaces U1 at the 5' splice site, U6 binds U2, U4 is released |
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Term
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Definition
| of the A at the branch point attacks the 5' splice site, catalyzed by U6 and U2 |
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Term
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Definition
| base pairs with the 5' exon and 3' splice site, 3' splice site is attacked, joins exons together and liberates |
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Term
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Definition
| some introns removed by alternative spliceosome which recognizes slightly different signals |
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Term
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Definition
| some introns capable of removing themselves without any help, first discovered in tetrahymena, 2 groups |
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Term
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Definition
| splice by totally different pathway, instead of A in the branch point they use free guanine nucleotide and its 3’OH, the free G attacks the 5’ splice site, the G is added to the intron and the exon broken off, shape of key, internal guide sequence aligns the splice sites in particular way to react |
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Term
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Definition
| chemistry of splicing and RNA intermediates same as nuclear splicing, RNA still has to fold precise way, may be evolutionary intermediate |
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