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What does eukaryotic RNA polymerase I do?
transcribes all genes that encode ribosomal RNA (rRNA) except 5S rRNA
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What does eukaryotic RNA polymerase II do? What is it responsible for?
- 12 subunits
- transcribes all structural genes and certain snRNA genes needed for pre-mRNA splicing
- responsible for the synthesis of all mRNA
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What does RNA polymerase III do?
transcribes all tRNA and the 5S RNA gene
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What are the 3 features of a promoter sequence?
- core promoter itself can produce low level of transcription called basal transcription
- regulatory element between -50 and -100
- promoter at -25
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What are the 3 things in the core promoter?
- transcriptional start site (+1)
- TATA box (-25)
- regulatory elements
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What are the two categories of regulatory elements?
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What are enhancers? What are silencers?
- stimulate transcription
- inhibit transcription
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What three categories of proteins are needed for basal transcription at the core promoter? (initiation stage)
- RNA polymerase II
- general transcription factors
- mediator (protein complex)
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Describe the pre-initiation complex.
- TATA box at -25
- TFIID recognizes TATA box (largest of transcription factors)
- TFIIA & B binds to TFIID
- TFIIF binds to TFIID
- H acts like a helicase
- Polymerase II
- once TFIIA & B are dropped it releases the complex (polymerase H, E, & TFIIF) and it can transcribe now
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What is the mediator?
a large protein complex that mediates interactions between RNA polymerase II and regulatory transcription factors that bind to enhancers or silencers
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The core subunits form a(n) ______ shaped complex that partially wraps around RNA polymerase ___. It appears to regulate the ability of what?
- elliptical
- II
- TFIIH to phosphorylate the CTD
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The mediator plays a pivitol role in what?
the switch between transcription initiation and elongation
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What is the role of chromatin structure in gene transcription?
compaction of DNA presents an obstacle to transcription
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What is the first mechanism used in alteration of chromatin structure? Give example.
- amino terminal ends of histone proteins can be covalently modified in a variety of ways including acetlyation of lysines, methylation of lysines, and phosphorylation of serines
- acetylation of lysine residues at the N terminus of histone proteins removes positive charges, thereby reducing the affinity between histone and DNA
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What is ATP-dependent chromatin remodeling?
- second mechanism used in the alteration of chromatin structure
- energy of ATP hydrolysis is used to drive a change in the structure of nucleosomes making DNA more accessible for transcription by shifting or changing the spacing between nucleosomes
- SWI/SNF
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What are SWI/SNF?
- large family of proteins found in all eukaryotes that catalyze ATP-dependent chromatin remodeling
- came from a strain of yeast from which they discovered it
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What is colinearity?
the one to one correspondence between the sequence of codons in DNA coding strand
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What are exons?
the coding sequence
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What are introns?
the noncoding sequence
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Describe RNA modification/splicing.
- DNA transcription, an RNA is made corresponding to the entire gene sequence
- the sequences in the RNAthat correspond to the inrons are removed, while the RNA sequences derived from the exons are connected (spliced) in a process called RNA splicing
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What is the enzymatic process of RNA?
- transcribed 45S rRNA must be cleaved at several points to produce three fragments that play a key role in creating the structure of the ribosome
- occurs in the nucleolus
- exonucleases
- endonucleases
- RNA has a lot of tRNA in strand and exonucleases and endonucleases come in and cut out all the tRNA strands
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What is a ribozyme?
- piece of RNA that can catalyze the cutting out of tRNA
- no ATP required
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What are maturases?
enhance the rate of splicing
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Why do scientists think RNA predates DNA?
RNA can act like an enzyme and splice itself. DNA cant
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How do group I and group II introns differ?
in the way the introns are removed and the exons joined
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What are group I introns? What are group II introns?
- external G initiates splicing
- internal A initiates splicing
- group II have a lariat (lasso) structure
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Describe pre-mRN.
- aka heterogenous nuclear RNA (hnRNA)
- must be altered before leaving the nucleus
- NOT self-splicing; requires the aid of a splicosome
- composed of several sNRPs
- found only in nucleus
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What are sNRPs?
subunit that contains Small Nuclear RNA and a set of Proteins
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What are some alternative splicing methods?
- cassette exon
- mutually exclusive exons
- intron retention
- alternative 5' to 3' splice sites
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What is capping?
- at the 5' end, most mature mRNA have a 7-methylguanosine covalently attached
- this event is known as capping
- it is neeed for the proper exit of certain RNAs from the nucleus
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Most mature have a adenine nucleotides called what at the 3' end? What is it important for?
- polyA tail
- the stability of mRNA and the translation of polypeptides
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What is the process of adding a string of A's to the end of an RNA molecule?
polyadenylation
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What is the process of polyadenylation?
- polyA polymerase attaches many adenine nuleotides
- once mature RNA leaves the nucleus the polyA tail give stability in case a nuclease chews at the end of the tail
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