Term
|
Definition
| stable, some variation allowed within structure, polymerizable, easy to replicate, easy to compress |
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Term
|
Definition
|
|
Term
| which carbon is -oh in rna and -h in dna |
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Definition
|
|
Term
|
Definition
|
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Term
|
Definition
| have 2 rings, connect to 1' sugar carbon through 9' nitrogen |
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|
Term
| which bases are pyrimidines |
|
Definition
|
|
Term
| how are pyrimidines connected to the sugar carbon |
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Definition
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Term
|
Definition
| right handed, bases stacked .34 nm apart, helix turns every 3.4 nm, 10.1 bp per turn |
|
|
Term
| what are the two grooves in DNA and which are accessible to DNA binding proteins |
|
Definition
| major, minor grooves. both accessible to binding proteins |
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Term
|
Definition
| right handed, more compact, exist in RNA-DNA hybrids, RNA-RNA duplexes |
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Term
|
Definition
| left handed, found with lots of alternating cs and gs, cellular function unclear |
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|
Term
| why is dna more stable that rna |
|
Definition
| lacks -oh on 2' carbon so less charge to deal with |
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Term
|
Definition
| heat, salt, h-bond destabilizing reagents, exreme pH |
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|
Term
| melt temp for dna definition |
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Definition
| Tm= temp at half the bases in sample of dsDNA have denatured |
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|
Term
| equation to find melt temp of strand of DNA |
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Definition
| 4* # g-c bonds+ 2* # a-t bonds |
|
|
Term
| what things help dna renature |
|
Definition
| lower temp, increased ion concentration, neutral pH |
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|
Term
| how is torsional stress released in DNA |
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Definition
|
|
Term
|
Definition
| creates phosphodiester bond break in one strnd then religates strand together |
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Term
|
Definition
| creates phosphodiester bond breaks in both strands, then re-ligates |
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|
Term
| which experiment showed dna replication is semiconservative |
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Definition
| messelston-stahl used heavy and light nitrogen and checked to see how bands appeared |
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|
Term
| what direction does dna synthesis happen |
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Definition
|
|
Term
| where does dna helicase bind |
|
Definition
| a-t rich sequences in parental dna replication origin of replication (ORI) |
|
|
Term
| what does dna helicase do |
|
Definition
| unwinds dsDNA of parent strands |
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|
Term
| how is rna primer for dna replication formed |
|
Definition
| through primase and RNA polymerase |
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Term
|
Definition
| creates short strand of rna for rna pol |
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|
Term
| rna polymerase action in dna replication |
|
Definition
| adds more nucleotides to strand created by primas |
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|
Term
| leading strand dna synthesis |
|
Definition
| proceeds from single rna primer in same direction of fork movement |
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|
Term
| what is the model organism for dna replication |
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Definition
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|
Term
|
Definition
| unwinds DNA at replication fork |
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Term
|
Definition
| keeps ssDNA in uniform conformation optimal for copying. leaves dna once pol begins |
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Term
|
Definition
| connects together okazaki fragments |
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|
Term
| what happens in euakaryotes before helicase can bind |
|
Definition
| origin replication complex binds to each ORI sequence in the dna |
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|
Term
| what can cause spontaneous cleavage of dna bonds |
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Definition
| uv/ionizing radiation, genotoxic chemicals, mutations during dna replication |
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|
Term
| does dna polymerase have proofreading ability? |
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Definition
|
|
Term
| which dna polymerase ahs exonuclease activity |
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Definition
|
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Term
|
Definition
| spontaneous, involves single base change |
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|
Term
| what are the three types of ssDNA excision repair systems |
|
Definition
| base, mismatch, nucleaotide excision repair |
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|
Term
| what is comoon between the process of all dna repair systems |
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Definition
|
|
Term
|
Definition
| replaces mutation with new base |
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Term
|
Definition
| what cleaves DNA backbone in base excision repair |
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Term
|
Definition
| removes deoxyribose-phosphate base in dna base excision repair |
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Term
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Definition
|
|
Term
| what two proteins first bind to dna in mismatch excision repair |
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Definition
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|
Term
| what two things recruit helicase and exonuclease in MER |
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Definition
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|
Term
| which dna polymerase adds nucleotides back in MER |
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Definition
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|
Term
| what defects in MER can cause raised colon cancer |
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Definition
|
|
Term
| what does nucleotide excision repair recognize in DNA |
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Definition
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|
Term
| what recognizes wrong shape in NER |
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Definition
| XP-C/23B protein complexes |
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|
Term
| what is the second step in NER |
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Definition
| TF2H is recruited and XP-G RPH proteins bind and unwind helix |
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|
Term
| which two XP proteins cut out strand of bases in NER |
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Definition
|
|
Term
| how many bases are cut out in NER? |
|
Definition
| about 28 before and after |
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|
Term
| how does non homologous end joining occur |
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Definition
| KV proteins and dna-dependent protein kinases bind the ends and form synapse |
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|
Term
| how does homologous recombination occur |
|
Definition
| dna lesions are replaced by segments of dna copied from homologous/sister chromatids |
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|
Term
| is information lost in holliday junction process |
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Definition
|
|
Term
|
Definition
| DNA and all associated proteins |
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Term
|
Definition
| nucleoprotein complexes of dna, histones, and non histone protiens |
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|
Term
| what is chromatin's composition by mass |
|
Definition
| half dna and half protein |
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Term
|
Definition
| abundand nuclear proteins that compact and organize dna |
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Term
|
Definition
| protein core octamer: 2X H2A, H2B, H3, H4 |
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Term
|
Definition
| holds dna to core histone proteins |
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|
Term
| which histones have flexible N-terminals of amino acids |
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Definition
|
|
Term
| which histones have flexible c terminus |
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Definition
|
|
Term
| what are some post translational modifications of histones |
|
Definition
| acetylation, methylation, phosphorylation, ubiquitination |
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|
Term
| histone acetylation effects |
|
Definition
| less condensed, conductive to dan rep/trans |
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|
Term
| histone methylation effects |
|
Definition
| occurs in n-terminal histone tail lys/arg and prevents acetylation. promotes condensed sequence |
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Term
|
Definition
| protein kinases add, phosphatases reove. adds negative charge, with many different functions |
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Term
|
Definition
| particular set of histone modification within a nucleosome |
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|
Term
| Euchromatin histone tail status |
|
Definition
| more acetylated, less condensed |
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|
Term
| heterochromatin histone tail status |
|
Definition
| more methylated, more condensed |
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Term
|
Definition
|
|
Term
|
Definition
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|
Term
| heterochromatin protein 1 (HP1) |
|
Definition
| binds N-terminal tail of histone H3, trimethylated at lys 9 |
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|
Term
| how does HP1 chreate heterochromatin |
|
Definition
| HP1 binds adjacent HP1's, bind histone methyltransferase H3K9 HMT, which methylates H3K9 |
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|
Term
| Transcription factor TFIID |
|
Definition
| contains bromodomains, binds acetylated histone tails. associated with transcriptionally active euchromatin |
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|
Term
| non histone proteins affect structure |
|
Definition
| proein scaffold present w/o histones |
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|
Term
| protein scaffold for chromatin |
|
Definition
| chromatin is arranged in loops, attached to scaffold |
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Term
|
Definition
| sequences located at base of DNA loops |
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Term
|
Definition
| promote transcription of neighboring genes, insulate transcription units from each other |
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Term
|
Definition
| maintain morphological structure of chromosome |
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Term
| Head domain of SMC proteins |
|
Definition
| formed from N and C termini of polypeptides, linked by kleisins |
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Term
|
Definition
| link n and c termini of polypeptides in head domain of SMC proteins |
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|
Term
| what domain links head/hinge domains of of SMC proteins |
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Definition
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|
Term
|
Definition
| dont'bind directly to DNA, associate with DNA regions between genes |
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|
Term
| High mobility group proteins |
|
Definition
| regulate/facilitate DNA related activities. bind to nucleosomes, little is known |
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|
Term
| low long is a metaphase chromadid |
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Definition
|
|
Term
|
Definition
| selectively stain regions of chromosomes; distinguish size, shapes |
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|
Term
| how are dna regions of low GC content revealed using giemsa dyes |
|
Definition
|
|
Term
| how are dna regions of high gc content revealed |
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Definition
|
|
Term
| what does multi color FISH detect |
|
Definition
| chromosomal translocations |
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Term
|
Definition
| genes occur in same order on chromosome in two different species |
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|
Term
| what are the 3 functional elements of chromosome |
|
Definition
| ORI, centromere, telomere |
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|
Term
| what is the ARS in yeast cell similar to |
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Definition
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Term
|
Definition
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|
Term
|
Definition
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|
Term
| which regions of CEN sequence regulate attachment of chromosome to spindle apparatus (yeast) |
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Definition
|
|
Term
| what does CEN region 2 do |
|
Definition
| binds histone h3 variant that is essential for proper chromosome function |
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|
Term
| what are alphoid dna sequences |
|
Definition
| bound by nucleosomes containing histone h3 variants CEMP-T |
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|
Term
|
Definition
| repeat of ttaggg thousands of times |
|
|
Term
| why are telomeres present |
|
Definition
| the lagging strand cant replicate all the way to the end |
|
|
Term
| what is the function of telomerase and what is it comprised of |
|
Definition
| protein/rna complex that adds telomere sequences to end of chromosomes |
|
|
Term
| what types of cells have telomerase active |
|
Definition
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|
Term
|
Definition
|
|
Term
|
Definition
| discovered enzyme that can synthesize rna in the laboratory |
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Term
|
Definition
| discovered RNA can be catalytic and proposed RNA came before DNA |
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Term
|
Definition
| pairing of bases within 5-10 nucleotides of each other |
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Term
|
Definition
| pairing of bases seperated by more than 10 bp |
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|
Term
|
Definition
| structured domains that have catalytic activity |
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|
Term
| Sidney Altman/ Thomas Cech |
|
Definition
|
|
Term
|
Definition
| site in DNA where RNA polymerase starts |
|
|
Term
| where is the first rNTP added |
|
Definition
|
|
Term
| what is downstream of the +1 site |
|
Definition
|
|
Term
| what is upstream of the +1 site |
|
Definition
|
|
Term
| what is RNA pol comprised of in bacteria |
|
Definition
| two subunits B and B' and 2 small alpha subunits and 1 w subunit |
|
|
Term
| How does RNA pol initiate transcription |
|
Definition
| binds promoter with transcription factor's help, seperates dsDNA to expose base pairs, creates transcription bubble, catalyzes phosphodiester bond between rNTP's |
|
|
Term
| how is RNA transcription elongated |
|
Definition
| RNA pol dissociates from promoter DNA then moves along template |
|
|
Term
| how is RNA transcription terminated |
|
Definition
| sequence signals RNA pol to stop; transcript released, then RNA polymerase release |
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Term
|
Definition
| genes encoding proteins that function together and are located in a continuous array |
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Term
|
Definition
| 7-methyl guanylate attached via a 5' triphosphate linkage |
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Term
|
Definition
| cleaved by endonuclease to yield 3' OH, a's added by poly-a polymerase |
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Term
|
Definition
| adds A's to 3' end of RNA transcript |
|
|
Term
| what are some functions of the 5' UTR |
|
Definition
| is binding site for proteins, affect stability, promote/inhibit translation, regulate export |
|
|
Term
| what are some functions of the 3' UTR |
|
Definition
| same as 5' UTR- is binding site for proteins, affect stability, promote/inhibit translation, regulate export but include miRNA's |
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|
Term
|
Definition
| increases number of proteins from single eukaryotic gene |
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|
Term
|
Definition
| multiple/ related proteins are produced |
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Term
|
Definition
| type/ region of expression controlled by alternative splicing |
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Term
|
Definition
| sticky, stays in area of translation. fibronectin gene alt. splicing product |
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|
Term
|
Definition
| travel in blood, fibronectin gene alt. splicing product |
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|
Term
|
Definition
| entire sequence needed for functional gene product |
|
|
Term
|
Definition
| each RNA encondes a single protein |
|
|
Term
| simple transcription unit |
|
Definition
| primary RNA transcript is processed to yield a single mRNA that encodes a single protein |
|
|
Term
| complex transcription unit |
|
Definition
| primary RNA transcript can be processed in more thatn one way |
|
|
Term
|
Definition
| same exons are originally processed, but one or more are not included |
|
|
Term
|
Definition
| cut at different sites because of poly-a recognition. affects which exon is present on end |
|
|
Term
|
Definition
| affect where cap site is placed. changes which exon is present in the beginning of the transcript |
|
|
Term
|
Definition
| 25-50% of protien coding genes, represented only once in haploid genome |
|
|
Term
|
Definition
| close, ont identical sequences |
|
|
Term
|
Definition
| encoding genes with similar AA sequences |
|
|
Term
| what do gene families make up |
|
Definition
|
|
Term
| how does exon duplication occur |
|
Definition
| unequal crossing over in meiosis by repetitive elements lining up |
|
|
Term
| what is the B globin gene family comprised of |
|
Definition
|
|
Term
| how did the b globin gene family arise? how about the pseudogenes? |
|
Definition
| from gene duplication by unequal crossing over. two psudogenes are where crossing over occured |
|
|
Term
|
Definition
| multiple copies of rRNA's on same gene, one after another. identical gene products |
|
|
Term
|
Definition
|
|
Term
|
Definition
| lies between transcription units, not repeated anywhere else in genome |
|
|
Term
|
Definition
| from ancient transposable elements that accumulated many mutations |
|
|
Term
| what does spacer dna contain? |
|
Definition
| transcription control regions |
|
|
Term
|
Definition
| multiple copies of non coding dna sequences |
|
|
Term
|
Definition
| composed of near perfect repeats of short sequence. originated by backward slippage |
|
|
Term
|
Definition
| most common, composed of larger repeat sequences, consist of transposable elements |
|
|
Term
|
Definition
| have many CAG repeats. suffer from various conditions |
|
|
Term
| how can dna be fingerprinted using satellite sequence dna |
|
Definition
| the sequence of the repeats are highly conserved, but the number varies widely between individuals |
|
|
Term
| transposable dna elements |
|
Definition
| interspersed regions that can move |
|
|
Term
|
Definition
| move directly from one region to another- cut and then reinserted |
|
|
Term
|
Definition
| transpose via RNA intermediate and reverse transcription |
|
|
Term
|
Definition
| name for dna transposons in prokaryotes |
|
|
Term
|
Definition
| enzyme required for transposition of IS element |
|
|
Term
| what is the structure of transposons |
|
Definition
| outside of sequence is inverted repeats on both sides. outside of those are direct repeat sequences |
|
|
Term
| what is the mechanism of transposase |
|
Definition
| excises IS element out of donor DNA, makes staggered cut in short sequence of target DNA, ligates termini of IS element into DNA strand. host dna polymerase fills in any gaps, ligase finishes insertion |
|
|
Term
| retrotransposon classification |
|
Definition
| either LTR (long terminal repeat) containing or lacking |
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|
Term
|
Definition
| promoter that directs host cell to RNA replicate |
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Term
|
Definition
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|
