Transcription RNA Synthesis Flashcards
what is the synthesis of RNA from a DNA template
transcription
what do RNA polymerases do?
they catalyze the synthesis of RNA from a DNA template; more specifically, they catalyze the formation of ester bonds between nucleotides that base pair with the complementary nucleotides on the DNA template.
do RNA polymerases require a primer?
no
T/F, RNA polymerases lack a 3’-5’ exonuclease activity and do not perform rudimentary proofreading via other means?
Lack 3’-to-5’ exonuclease activity although they do perform rudimentary proofreading via other mechanisms.
what direction does the RNA polymerase move on the DNA template?
DNA copied in 3’-to-5’ direction and synthesized in a 5’-to-3’ direction
what are the substrates of the RNA polymerase?
ribonucleoside triphosphates (ATP, CTP, GTP, UTP) [T:A, C:G, G:C, A:U] DNA:RNA
cleavage of the high energy bond in the nucleoside triphosphate and release of pyrophosphate provides energy, T/F?
T
what is the overall error rate for RNA polymerases?
1 in 100,000
what is the purpose of transcription?
segment of DNA copied that functions as a unit to generate an RNA product or eventually a polypeptide chain through the process of translation
what 2 things must the RNA polymerase do?
recognize the start point and appropriate strand of DNA
and
be sensitive to signals that reflect need and control frequency of transcription
how does the RNA polymerase start?
with a promoter and other regulatory sequences all upstream of the start point, closer to the 5’ end
what is the promoter in terms of usage for the RNA polymerase?
region of regulatory sequences that controls the binding of RNA polymerase to DNA and identifies the start point.
what are the other regulatory sequences in terms of usage for the RNA polymerase?
Control frequency of transcription and stabilize polymerase to promoter
what is the RNA polymerase in prokaryotes?
a single RNA polymerase that generates all types of RNA (mRNA, rRNA, tRNA)
how many subunits do the RNA polymerase subunits contain?
4 (α2ββ’) that form the core
how is the σ (sigma) factor important for RNA polymerase in prokaryotes?
it binds to the core enzyme and directs RNA polymerase to the promoter
the RNA polymerase has many different types
the major σ (sigma) factor is σ70 relating to its molecular weight of 70,000 Da
what are the types of RNA polymerase in Eukaryotes?
3 RNA polymerases
All have the same mechanism of action but recognize different types of promoters
RNA polymerase I,II,III
product of RNA polymerase I in Eukaryotes?
rRNA
product of RNA polymerase II in Eukaryotes?
mRNA + micro RNA
product of RNA polymerase III in Eukaryotes?
tRNA + other small RNA’s
what is α-amanitin? side effects?
an inhibitor of eukaryotic RNA polymerases; particularly RNA polymerase II; : Gastrointestinal disturbances, electrolyte imbalance, and fever. Eventually the patient will have liver and kidney dysfunction.
A family, while on a picnic, picked some wild mushrooms to add to their picnic salad. Shortly after, all the members of the family became ill, with the youngest child showing the most severe symptoms. The family is suffering these effects owing to a primary inability to accomplish which one of the following in their cells and tissues?
a) Synthesize proteins
b) Synthesize lipids
c) Synthesize DNA
d) Synthesize carbohydrates
e) Repair damage in DNA
a)Synthesize proteins
what does the dsDNA consist of?
coding strand and template strand
of the coding strand and template strand, what does the RNA polymerase use for transcription?
the DNA template strand
how can we relate the DNA coding (nontemplate) strand with the RNA transcript?
identical in base sequence and direction to the RNA transcript
what can the base sequence of the coding strand be used for?
to determine the amino acid sequence of the protein.
what does a eukaryotic gene consist of?
a transcribed region and regions that regulate transcription of the gene like the promoter and enhancer regions
what must a Eukaryotic RNA polymerase do?
start point of transcription
which genes to transcribe
cell type and physiologic conditions
what is unique about the prokaryotic gene?
Several protein producing genes may be linked together and controlled by a single promoter. This genetic unit is called an operon and the result is a polycistronic mRNA.
what is a cistron?
a region of DNA that encodes a single polypeptide
what is the promoter region in prokaryotes?
this is the TATA box which is A-T rich consensus sequence in the promoter that determines the start point of transcription by binding proteins that facilitate the binding of RNA polymerase
recognized by the sigma factor σ70 and located -10 region upstream from the start site
Bacteria promoter also contain the sequence TTGACA in the _____ region?
-35 region
what is the effect with RNA polymerase binds activators or repressors?
it stimulates or inhibits transcription
just like the prokaryotes what are the promoter regions for the eukaryotes?
TATA Box (Hogness-Goldberg Box)
TF element BRE, -35
Promoter and Enhancer elements further upstream, enhancer furtherest upstream
In Eukaryotes, how is transcription initiated?
General transcription factors (basal factors, TFIIs) bind to the TATA box and facilitate binding of RNA polymerase II
In prokaryotes, how is transcription initiated?
Binding of RNA polymerase with σ-factor to the promoter region of DNA causes the two DNA strands to unwind and separate.
in transcription for prokaryotes, when is the sigma factor released?
when the growing RNA chain is ~10 nucleotides long
how long does the elongation reaction continue in the transcription of the RNA polymerase?
until the RNA polymerase encounters a transcription termination signal
T/F, Bacterial mRNA is usually generated from an operon as a polycistronic transcript?
T
is the polycistronic transcript in prokaryotes translated as it is transcribed?
yes
is the prokaryotic transcript modified or trimmed?
no
in the transcription of prokaryotic genes, more specifically, rRNA, how is it produced?
a single, long transcript that is cleaved to produce the 16S, 23S, and 5S rRNAs
what is the name of the enzyme that catalyzes the cleavage reaction in prokaryotes?
RNase P
what is the specific RNA cleaved from the larger transcripts in prokaryotes?
tRNA
what are the major differences in transcription of Eukaryotes with Prokaryotes?
Elaborate mechanism for processing transcripts, particularly mRNA.
3 RNA polymerases (versus one)
Eukaryotic mRNA usually contains the coding information for one polypeptide chain
RNA is transcribed in the nucleus and migrates to the cytoplasm for translation
what is an exon?
nucleotide codons that dictate amino acid sequence
what is an intron?
non-coding nucleotide region; removed
in the capping of mRNA in Eukaryotes, where does the capping happen?
5’-end as its being transcribed
what is the purpose of the 5’ cap in Eukaryotes?
“Seals” the 5’ end of the transcript and decreases rate of degradation. Also serves as a recognition site for the binding of mRNA to a ribosome.
what is the purpose of the Poly A tail in Eukaryotes?
a protein binding site that protects mRNA from degradation
Background information
RNA polymerase continues to transcribe DNA until it passes a sequence called the polyadenylation signal (AAUAAA)
As primary transcript is released, an enzyme complex binds to polyadenylation signal and cleaves the transcript forming the 3’-end.
After the cleavage, a poly (A) tail (>200 nt) is added to the 3’-end
NOTE: There is no poly(dT) sequence in the DNA template
ATP serves as the precursor for the addition of the adenine nucleotides.
Added one at a time by poly(A) polymerase
in the removal of introns in the transcription of eukaryotic genes how are the sequences recognized so they can be spliced?
through consensus sequence at the intron/exon boundary of the pre-mRNA consisting of AGGU
what do introns in the eukaryotes begin with?
5’-GU and end with a 3’-AG
what is the name of the enzyme that removes the introns?
spliceosome
what is a spliceosome made of?
small ribonucleoproteins (snRNPs)
briefly describe the removal of introns in the transcription of Eukaryotic Genes?
U1 binds near the 1st exon/intron junction and U2 binds to an adenine residue within the intron
U4, U5, U6 then bind to the complex and a loop is formed
Cleavage occurs and the exons are joined together.
Intron (shaped like a lariat) is released and degraded to nucleotides.
what can we take away from the formation eukaryotic rRNA?
its made similarly to mRNA, transcript comes out, edited, folded together with structure and then trimmed and sent out. Sent out as a blob as oppose to an mRNA being sent out as a straight piece
what part of the tRNA in eukaryotes recognizes mRNA? what part of the tRNA do the amino acids attach? what is the shape of the tRNA?
the anticodon recognizes the mRNA; 3’end; clover leaf structure
what are the important recognition elements in the tRNA?
dihydrouridine, ribothymidine, pseudouridine which help for recognition and placement
how many different tRNA’s are there?
20 for each of the amino acids
what is tRNA synthesis in eukaryotes?
in tRNA synthesis, the tRNA is produced from RNA poly III, tRNA precursors are generated, it then assumes a cloverleaf shape and cleaved at the 5’-3’ end. The bases are modified simultaneously with endonucleolytic cleavage. Finally, the addition of CCA sequence at the 3’-end by nucleotidyltransferase
