L03 DNA Transcription Flashcards
What is transcription
synthesis of RNA (mRNA)
What is translation
synthesis of protein using mRNA
What is the function of ribosomes?
sites of translation
they bind messenger RNA and transfer RNA to synthesize polypeptides and proteins.
What is primary transcript
RNA transcript before processing
The coding strand of DNA has a different sequence from that of mRNA. (T/F)
False, the sense/coding strand of DNA has the same sequence as the mRNA (T instead of U).
The anticoding strand of DNA is complementary to mRNA and is used as the template for mRNA synthesis. (T/F)
True.
DNA being read = template, antisense, anti coding
RNA Transcript = same
DNA not being read = sense strand, coding strand
__________ ensures the proper location of transcription initiation
PROMOTER region of proykarytotic gene: located upstream of the RNA coding sequence, and ensures the proper location of transcription initiation.
Which direction does RNA polymerase catalyzes the synthesis of mRNA?
Which direction does it travel on the template strand?
RNA polymerase catalyzes the synthesis of an RNA molecule in the 5’ to 3’ direction along the 3’ to 5’ template/antisense/antiocoding strand of the DNA.
The coding strand or sense strand has the same sequences as the RNA. (T/F)
True
The prokaryote promoter sequences are generally found at ________________ bp from the transcription start site.
The prokaryote promoter sequences are generally found at -35 and -10 bp from the transcription start site.
What is the Pribnow box?
-10 consensus sequence: 5’-TATAAT-3’ (part of a promoter site on DNA for transcription to occur in bacteria
A primer is required for DNA and RNA (T/F)
False. A primer is only required for DNA.
What’s an holoenzyme?
core polymerase plus sigma factor used to synthesize PROKARYOTIC RNA
RNA polymerase I:
A. 5.8S, 18S, and 28S (rRNA genes)
B. all protein-coding genes (mRNA) and some snRNAs
C. tRNA genes and some snRNAs
RNA polymerase I: 5.8S, 18S, and 28S (rRNA genes)
RNA polymerase II:
A. 5.8S, 18S, and 28S (rRNA genes)
B. all protein-coding genes (mRNA) and some snRNAs
C. tRNA genes and some snRNAs
RNA polymerase II: all protein-coding genes (mRNA) and some SRNs
RNA polymerase III:
A. 5.8S, 18S, and 28S (rRNA genes)
B. all protein-coding genes (mRNA) and some snRNAs
C. tRNA genes and some snRNAs
RNA polymerase III: tRNA genes and some snRNAs
What is the significance of the RNA hairpin loop in prokaryotic RNA?
- The RNA hairpin loop causes physical stress on the enzyme complex which destabilizes the core polymerase’s hold on the RNA (prokaryotes)
- RNA is released
- Double helix reforms
What is the difference between prokaryotic and eukaryotic promoters?
Prokaryote’s promoter region:
- 35 consensus sequence = 5’-TTGACA-3’
- 10 consensus sequence = 5’-TATAAT-3’ (also called the Pribnow box)
Eukaryote Region:
GC box = GGGCGG (-70 to -200 bp)
CAAT box = CCAAT (-20 to -35)
TATA box = TATAAA (-80)
Not to be confused with DNA replication:
13-nucleotide sequences (three in tandem array)
9-nucleotide sequences (four are present).
TFIIE:
A. Causes a distortion in the DNA helix allowing the recruitment of other transcription factors.
B. Involved in RNA polymerase interactions and start site recognition (before polymerase)
C. Contains a DNA helicase to unwind DNA and activates RNA polymerase by phosphorylation
E. Involved in positioning RNA polymerase
E. Involved in positioning RNA polymerase
TFIIB:
A. Causes a distortion in the DNA helix allowing the recruitment of other transcription factors.
B. Involved in RNA polymerase interactions and start site recognition (before polymerase)
C. Contains a DNA helicase to unwind DNA and activates RNA polymerase by phosphorylation
E. Involved in positioning RNA polymerase
B. Involved in RNA polymerase interactions and start site recognition (before polymerase)
TFIIH:
A. Causes a distortion in the DNA helix allowing the recruitment of other transcription factors.
B. Involved in RNA polymerase interactions and start site recognition (before polymerase)
C. Activates RNA polymerase by phosphorylation
E. Involved in positioning RNA polymerase
C. Contains a DNA helicase to unwind DNA and Activates RNA polymerase by phosphorylation
TFIID:
A. Recruitment of other transcription factors.
B. Involved in RNA polymerase interactions and start site recognition (before polymerase)
C. Activates RNA polymerase by phosphorylation
E. Involved in positioning RNA polymerase
A. Causes a distortion in the DNA helix allowing the recruitment of other transcription factors.
__________________ are recruited to the promoter and transcription initiation site in eukaryotes.
RNA polymerase, TFIIE, and TFIIH
The RNA pol II and the transcription factors TFIIB (TAFs and TBP), and other transcription factors form the basal transcriptional machinery. (T/F)
False, The RNA pol II and the transcription factors “TFIID” (TAFs and TBP), and other transcription factors form the basal transcriptional machinery.
What is the difference between intrinsic and extrinsic termination sequences?
Intrinsic termination factors are found in the RNA molecule (Palindromic regions) that that can form a hairpin structure. They vary in length (7-20bp) and are G-C rich followed by a bunch of Us.
Extrinsic factors are proteins that can bind to RNA (Rho Proteins)
This concept says that cells are governed by a cellular chain of command.
The central dogma
Transcription and translation in prokaryotes and eukaryotes are
a) coupled
b) coupled in prokaryotes and separated by the nucleus in eukaryotes
c) separated by nucleoid in prokaryotes and coupled in eukaryotes
d) both separated
B
In Eukaryotes, what must take place between transcription and translation?
RNA processing from pre-RNA to mRNA and transport from nucleus to cytosol
What is transcription vs translation?
Trancription is the synthesis of RNA under direction of DNA, while translation is the synthesis of a polypeptide, using information in mRNA.
Where is the site of translation?
ribosomes
What is the bridge between genes and proteins the genes code for?
RNA
Choose the most correct answer(s).
a) in prokaryotes, translation can occur before transcription finished
b) in prokaryotes and eukaryotes translation can only occur once transcription has finished
c) in eukaryotes translation must occur after transcription has finished.
d) in prokaryotes, translation can only occur once transcription has finished.
A & C
What is the initial transcript from any gene prior to processing called?
primary transcript
T/F. Both strands of DNA can code for genes.
True
In which direction does RNA Polymerase read DNA and synthesis DNA?
Reads in 3’ –> 5’synthesizes 5’ –> 3’
Which is (are) true?
a) the template strand and RNA transcript has the same coding.
b) the anticoding strand and sense strand are complementary.
c) the antisense and coding strand have the same coding.
d) the RNA transcript and the sense strand have the same coding.
B & D
In relation to the RNA-coding sequence, the promoter and the terminator are location where on the template strand?
promoter = upstreamterminator = downstream
What are the 3 staged of transcription?
Initiation
Elongation
Termination
Where are the prokaryotic promoters found on the anti-sense (template) strand?
at -35bp and -10bp from transcription start site.
Sequence of -35 consensus.
5’ - TTGACA - 3’
Sequence of Pribnow box.
aka. -10 consensus5’ - TATAAT - 3’
What is the consequence of a variation in either consensus sequences of prokaryotic promoter?
affects the ability of RNA polymerase to bind and the rate of transcription.
What is the only difference between the coding strand and the RNA transcript?
thymine bases of coding strand are replaced by uracil on RNA transcript
Why is proofreading of synthesized RNA unnecessary?
because the volume of transcriptions occurring by various RNA polymerases, negates the 1:10,000 chance of an error
Function of each:
mRNA
tRNA
rRNA
snRNA
mRNA: encodes amino acid sequence of a polypeptide
tRNA: brings amino acids to ribosome during translation process
rRNA: combines with ribosomal proteins to form ribosome
snRNA: combines with certain proteins and is involved in RNA processing (in eukaryotes; i.e. mRNA splicing)
In bacteria, what is needed in addition to RNA polymerase?
sigma factor
What is the function of the 3 RNA polymerases in eukaryotes?
RNAP I: rRNA genes
RNAP II: mRNA, some sn
RNARNAP III: tRNA, some snRNA
mnemonic: 1 Rat, 2 Mice, 3 Traps
What are the 3 main sites of the RNA polymerase core enzyme?
- ribonucleoside triphosphate uptake channel
- active site
- RNA exit channel
When RNA polymerase and sigma factor join together, what is this called?
A holoenzyme
At what point doe the holoenzyme bind tightly to the DNA?
once it reached the promoter regions (-10 & -35 consensus)
What is the function of the prokaryotic holoenzyme?
to open and expose a short stretch of DNA
How many base pairs of DNA are unwound by sigma factor?
17 bp
When does the sigma factor dissociate from the DNA?
after RNA polymerase has synthesized 10 nucleotides
What characteristic of the newly synthesized RNA causes RNA polymerase to end transcription and release from DNA?
the “self complementary” portion of RNA causes it to form a hairpin loop which places stress on RNA polymerase, destabilizes its hold on DNA
What 3 sequence elements are located near the transcription start site in eukaryotes and at what approx. position?
GC box (GGGCGG) at -70 to -200TATA box (TATAAA) at -20 to -35CAAT box (CCAAT) at -80
The TATA box binding protein is a subunit of which transcription factor for polymerase II?
TFIID
Which transcription factor is considered “the recruiter” of the other transcription factors?
TFIID
Which transcription factor serves to recognize the start site before polymerase can bind?
a) TFIID
b) TFIIH
c) TFIIF
d) TFIIB
e) TFIIE
d) TFIIB
This transcription factor activates RNA polymerase by phosphorylation and contains helicase.
TFIIH
What is the function of TFIIE?
positioning of RNA polymerase
