Chapter 3: Transcription and RNA Processing Flashcards
Which strand of the DNA molecule is copied by RNA polymerase?
template strand
RNA polymerase synthesizes RNA in what direction?
5’ to 3’ direction
RNA polymerase moves along the template strand of DNA in what direction? (What direction does it read DNA)
3’ to 5’ direction
What is the purpose of rRNA?
ribsomal RNA
used as a structural component of the ribosome; ribsomal RNA associates with ribosomal proteins to form the complete functional ribosome
What is the purpose of tRNA?
transfer RNA; functions to carry amino acids to the ribsome, where they will be linked together during protein synthesis
What is mRNA?
messenger RNA carries the information specifying the amino acid sequence of a protein to the ribosome
What is the most abundant type of RNA?
rRNA
What is the 2nd most abundant type of RNA?
tRNA
What does hnRNA stand for? What is another name for it?
heterogenous nuclear RNA or pre-mRNA
Where is hnRNA found?
in the nucleus of the eukaryotic cells
What is pre-mRNA?
represents precursors of mRNA, formed during its posttranscriptional processing
snRNA is found where?
in the nucleus of eukaryotes
Major function of snRNA?
one major function is to participate in splicing (removal of introns) mRNA
What does snRNA stand for?
small nuclear RNA
What are ribozymes?
RNA molecules with enzymatic activity
Are ribozymes only found in eukaryotes?
found in both prokaryotes and eukaryotes
Describe the RNA polymerase responsible for making all types of RNA in the prokaryotic cell? (its structure)
α2ββ’
In prokaryotic cells, what is the protein required for initiation of transcription via RNA polymerase at the site of the promoter?
a protein factor called sigma factor σ
In prokaryotic cells, what is the protein that allows for termination of transcription?
rho (p) factor
Where is RNA polymerase I located?
in the nucleolus of eukaryotes
What does RNA polymerase I mainly synthesize?
rRNA except 5S rRNA
What does RNA polymerase II synthesize?
hnRNA/mRNA and some snRNA
Where is RNA polymerase II located in the cell?
the nucleoplasm of the eukaryotic cell
Where is RNA polymerase III located?
in the nucleoplasm of eukaryotic cells
What does RNA polymerase III synthesize?
tRNA, and some snRNA, and 5SrRNA
What are the transcription factors that help initiate transcription in eukaryotes?
TFIID for RNA polymerase II
How does actinomycin D inhibit transcription?
it inhibits RNA transcription by binding to DNA and stopping RNA polymerase from transcribing
RNA polymerase II is inhibited by what toxin?
α-amanitin (a toxin from certain mushrooms)
Which strand of DNA is identical to the sequence of the RNA molecule except that RNA contains uracil instead of the thymine found in DNA?
the coding (anti-template) strand
To the left (5’, or upstream) of the starting point for transcription, describe the numbering system?
-3, -2, -1, etc.
What are the 2 types of transcription terminators commonly found in prokaryotic genes?
rho and stem loop
Describe Rho-independent termination?
newly formed RNA folds back on itself to form a GC-rich hairpin loop closely followed by 6-8 U residues
these 2 structural features of the newly synthesized RNA promote dissociation of the RNA from the DNA template.
Describe Rho-dependent termination?
Requires participation of rho factor
this protein binds to the newly formed RNA and moves toward the RNA polymerase that has paused at a termination site
Ribosomes bind to what sequence in RNA to begin translation? (in prokaryotes)
Shine Dalgarno sequence (5’UTR) sequence
What direction does the ribosome translate the RNA message ?
5’ to 3’ direction
Which genes are expressed? Exons or introns?
exons
What is the purpose of the cap on the pre-messenger RNA? When is the cap added to the pre-messenger RNA?
5’ cap serves as a ribosome-binding site and also helps to protect the mRNA chain from degradation
7-methylguanosine cap is added to the 5’ end of the RNA molecule while it is still being synthesized
What is the purpose of adding the tail on the pre-mRNA?
protects the message against rapid degradation and aids in its transport to the cytoplasm
What part of the RNA molecule is the poly-A tail added? How is this carried out?
to the 3’ end; an endonuclease cuts the molecule on the 3’ side of the sequence AAUAA, then poly-A polymerase adds the poly-A tail (about 200 As) to the new 3’ end
What is a major genetic bases for the cause of B-thalassemia?
mutations in splice site;
mutations that interfere with proper splicing of B-globin mRNA are responsible for some cases of B-thalassemia
What are “snurps”?
aka snRNP “ small nuclear ribonucleotides” which are spliceosomes which are responsible for removing introns from hnRNA
Where do spliceosomes act to cut out introns?
- The hnRNA molecule is cut at splice sites at the 5’ (donor) and 3’ (acceptor) ends of the intron.
- Intron is excised in the form of a lariat structure and degraded.
- Neighboring exons are joined together to assemble the coding region of the mature mRNA
What is the technique used that can detect alternative splicing?
Northern blot
What are the large and small subunits for the prokaryotic ribosomes?
50 S is the large subunit
30 S is the small subunit
70S is the entire subunit
What are the large and small subunit for the eukaryotic ribosome?
60 S is the large subunit
40 S is the small subunit
80S is the complex
What is the MOA of Shiga Toxin?
Shigella dysenteriae and Verotoxin, a shiga-like toxin (enterohemorrhagic E. coli), inactivates the 28S rRNA in the 60S subunit of the eukaryotic ribosome.
The A subunits of these toxins are RNA glycosylases that remove a single adenine residue from the 28S rRNA
This prevents aminoacyl-tRNA from binding to the ribosome, halting protein synthesis.
What part of the cell do the tRNAs combine with their appropriate amino acids?
combine with the appropriate amino acids in the cytoplasm
What are some post transcription editing events?
- insertion
- deletion
- base alterations
What is an example of base alterations of nucleotides?
adenine deamination
Give an example of cytosine to uracil deamination?
in the apoprotein B gene
apo B100 is expressed in the liver, and apoprotein B48 is expressed in the intestines.
in the intestines, the mRNA is edited from a CAA sequence to be UAA a stop codon, thus producing the shorter apoprotein B48 form
Is there posttranscriptional processing of hnRNA (pre-mRNA in prokaryotic cells?
no
Describe the acceptor arm of tRNA?
5’ - CCA - 3’ which carries the amino acid
