Genetics Chapter 12 part 2
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What does eukaryotic RNA polymerase I do?
transcribes all genes that encode ribosomal RNA (rRNA) except 5S rRNA
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
What does RNA polymerase III do?
transcribes all tRNA and the 5S RNA gene
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
What are the 3 things in the core promoter?
- transcriptional start site (+1)
- TATA box (-25)
- regulatory elements
What are the two categories of regulatory elements?
What are enhancers? What are silencers?
- stimulate transcription
- inhibit transcription
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)
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
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
The core subunits form a(n) ______ shaped complex that partially wraps around RNA polymerase ___. It appears to regulate the ability of what?
- TFIIH to phosphorylate the CTD
The mediator plays a pivitol role in what?
the switch between transcription initiation and elongation
What is the role of chromatin structure in gene transcription?
compaction of DNA presents an obstacle to transcription
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
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
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
What is colinearity?
the one to one correspondence between the sequence of codons in DNA coding strand
What are exons?
the coding sequence
What are introns?
the noncoding sequence
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
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
- RNA has a lot of tRNA in strand and exonucleases and endonucleases come in and cut out all the tRNA strands
What is a ribozyme?
- piece of RNA that can catalyze the cutting out of tRNA
- no ATP required
What are maturases?
enhance the rate of splicing
Why do scientists think RNA predates DNA?
RNA can act like an enzyme and splice itself. DNA cant
How do group I and group II introns differ?
in the way the introns are removed and the exons joined
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
- 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
What are sNRPs?
subunit that contains Small Nuclear RNA and a set of Proteins
What are some alternative splicing methods?
- cassette exon
- mutually exclusive exons
- intron retention
- alternative 5' to 3' splice sites
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
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
What is the process of adding a string of A's to the end of an RNA molecule?
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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