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rRNA processing is carried
out in the nucleolus by _____________that are associated with
proteins to form particles called ___________.
small, nucleolar RNAs (snoRNAs),
snoRNPs (small, nucleolar ribonucleoproteins)
Most genes in eukaryotes are _________ which means they contain both introns (intervening sequences) and exons.
split genes
Transcription factors effect:
What are:
• whether transcription is initiated
• rates of new rounds of transcription
• differential expression, tissue specific expression
TFIIH has two enzymatic functions:
1. Helicase – unwinds DNA (uses ATP) at start
site
2. Kinase – phosphorylates Pol II at specific AA
in the CTD --> required for movement of RNA
Pol II
One promoter, multiple genes
What is Polycistronic DNA?
In the processing of rRNAs, most pre-RNAs are modified right after transcription at specific positions using these modifications.
• Isomerization --> some uridines are
modified to pseudouridine
• Methylation --> methyl group attached to
the ribose
This technique used to prove introns are removed from mRNA uses a DNA-RNA hybrid and can be observed using electron microscopy.
R-loop formation
Eukaryotic mRNA has what modifications on it's 5' and 3' end?
5' methylated guanosine cap
3' poly(A) tail (50-250 adenosines)
What phosphorylates RNA Polymerase II and where?
TFIIH on serine residues in its C-terminal domain (CTD).
What does RNA Polymerase II require in order to bind to many different promoters?
What are general transcription factors?
The rRNA transcription unit resembles a ____________. The region between the structures is the ________________.
A Christmas tree, non-transcribes spacer.
Describe how the R-loop formation experiment works
In mature mRNA, DNA:RNA hybrids base pair in
most areas but lacks complementarity with
some regions of the gene, forming double-
stranded loops.
Conclusion: The looping region was missing
in mRNA molecules – represents intervening
sequences (introns)
Name the three functions of the 5' cap
• Prevents 5’ end from being digested by
exonucleases
• Plays a role is transport out of nucleus and
initiation of mRNA translation to protein
• Helps cells to distinguish mRNA from other
types of RNA molecules
What is thought to be the trigger that allows RNA Polymerase II to escape the promoter?
Phosphorylation
The TATA box.
What is a consensus sequence similar or identical to 5'-TATAAA-3'
There is an RNA polymerase for every ____ bp along the rDNA template.
100
What types of DNA sequences encode tRNA?
• Encoded by repeated DNA sequences (tDNA) located in small clusters
scattered around the genome (tandem repeated array)
• Internal promoter transcribed by RNA pol III
• Lots of non-transcribed spacer sequences
The capping enzyme has two active sites for each of these two functions.
triphosphatase and guanylyl transferase
Where to GTFs go after RNA Polymerase II begins transcription?
They are either left behind at the
promoter (TFIID) are simply released from the complex (TFIIB)
The binding site of the TATA binding protein (TBP)
What is the minor groove of DNA.
The S value (Svedberg unit) is a measure of the
sedimentation rate during centrifugation and is affected by both ____ and _____.
mass and shape.
What are the four types of eukaryotic rRNAs and which one of them is not like the rest?
28S, 18S, 5.8S, 5S
5S is different because it is made from a separate cluster of genes and does not need chemical modifications. It is synthesized by RNA Polymerase III.
In mammalian cells, polyadenylation begins ~20 nucleotides downstream of this special
sequence
5’-AAUAAA-3’
Which other proteins get associated with RNA Polymerase as it moves along the template?
What are:
• Elongation factors
• RNA modifying proteins
• RNA processing proteins
The assembly of the preinitiation complex occurs in a
step-wise manner:
TFIID --> TFIIA and TFIIB --> RNA Pol II and
TFIIF --> TFIIE and TFIIH