RNA Synthesis, Processing & Modification Flashcards
RNA is a polymer composed of ribonucleotides connected through what bond?
3’-5’ phosphodiester bond
The central dogma of molecular biology:
DNA replication (DNA repair gentic recombination) –> RNA synthesis (transcription) –> protein syntesis (translation)
Ribonucleotides contain:
Hydroxyl groups on 2’- carbon of ribose sugar
Uracil (in place of thymine)
It is 80% of total RNA.
Ribosomal RNA (rRNA - rampant)
Involved in mRNA splicing and gene regulation.
small RNA (1%)
Working copies
The RNA are considered as _______ of DNA and it expresses the master plan contained in DNA.
It is the smallest of RNA species, excluding small RNA, and make up about 15%.
Transfer RNA (tRNA - transient/tiny)
Most heterogenous in terms of size and base sequence.
Messenger RNA (mRNA - massive) 2-5%
Measure of size based on molecular sedimentation rate during ultracentrifugation.
Svedberg unit
Prokaryotic rRNA:
23s
16s
5s
Give the type and stability of micro (miRNA - <1% total).
100’s-1000’s, stable
Stability of mRNA.
May vary from unstable to very stable (rRNA & tRNA are both very stable)
T or F: only DNA adhere to Watson-Crick base-pairing rules.
FALSE (both DNA & RNA)
Is a primer involved in RNA synthesis?
No (bec RNA polymerase have the ability to initiate synthesis de novo)
Which requires the entire genome to be replicated? RNA or DNA
DNA (RNA - only a portion is copied)
T or F: there is no proofreading function during RNA transcription.
TRUE
The template strand is always read in what direction?
3’ to 5’ direction
What do you call the opposite strand of the template?
Coding strand (non-template strand)
What is the enzyme responsible for polymerization of ribonucleotides into a sequence complementary to the template strand of the gene?
DNA-dependent RNA polymerase
The DNA-dependent RNA polymerase will attach to the ________ on the template strand, then initiation of RNA synthesis occurs.
Promoter
The ___________ of transcription corresponds to the 5’ nucleotide of the mRNA and is designated position +1.
Starting point of transcription
The nucleotide in the promoter adjacent to the transcription initiation site will be designated what number?
-1
Positive numbers will increase as sequence go ___________.
Downstream
_________ numbers will increase as sequence proceeds upstream, away fron the initiation site.
Negative
What are the 3 signals for transcription?
Initiation
Elongation
Termination
It is the RNA product, synthesized in 5’ to 3’ direction:
Primary transcript
It is defined as the region of DNA that includes initiation, elongation & termination:
Transcription unit
3 components of a transcription unit:
Promoter
Coding-region
Terminator
The enzyme responsible for 5’ -> 3’ RNA polymerase activity; has 4 subunits (plus an omega subunit):
Core enzyme
The core enzyme lacks _______. It cannot recognize the promoter on the DNA template.
Specificity
It enables RNA polymerase to recognize promoter regions on DNA:
Sigma subunit/factor contained in holoenzyme
Some regions of DNA that signal the termination of transcription are recognized by _______________.
RNA polymerase
On the other hand, termination of RNA synthesis in bacteria is signaled by a sequence in temolate strand, this signal is recognized by what termination protein?
rho factor
It is an auxiliary lrotein of RNA polymerase:
Termination factor
Primary transcripts generated by RNA polymerase II are promptly capped by:
7-methylguanosine triphosphate
Why are caps for transcripts necessary? Give 3 reasons.
For subsequent processing of primary transcript to mRNA
For translation of mRNA
For protection of mRNA against exonucleolytic attack
Binding of the RNA polymerase holoenzyme to a promoter region:
Initiation
It is a stretch of 6 nucloetides (5’-TATAAT-3’) centered around 8 to 10 nucleotides to the left of the transcription start site that codes for the initial base of mRNA:
Pribnow box
Consensus (general agreement/idea) of nucleotide sequences:
Pribnow box & -35 sequence
Highly conserved
Recognized by prokaryotic RNA polymerase sigma factors
Centered around 35 bases to the left of the transcription start site
-35 sequence
What is the possible effect of a mutation in Pribnow box or -35 sequence?
Can affect the transcription of the gene controlled by mutant promoter
T or F: Unlike DNA polymerase, RNA polymerase has no endo or exonuclease activity. (No repair capability)
TRUE
When would the RNA polymerase begin to synthesize a transcript of DNA sequence, and release signa subunit? (ELONGATION)
Once promoter has been recognized by holoenzyme
In elongation, the ribonucleotides are added to ________.
3’-OH end
T or F: the mechanism of RNA synthesis is NOT the same as that used for elongation of a DNA strand.
FALSE (same mechanism)
3’-OH acts as a _________, attacking -phosphate of incoming ribonucleoside triphosphate & releasing pyrophosphate.
Nucleophile
A rho factor protein is required for release of RNA product:
Rho dependent termination
Rho factor binds to a _____ region near 3’ end of newly synthesized RNA, migrate behind RNA polymerase in the _____ direction until termination is reached.
C-rich region, 5’-3’ direction
At termination, rho factor displaces DNA template strand thus facilitating ________ of RNA molecule.
Dissociation
Activity of Rho factor that allows it to hydrolyze ATP thus able to unwind the 3’ end of transcript from the template:
ATP-dependent RNA-DNA helicase activity
Give the 5 steps of Rho-dependent transcriptional termination:
- RNA polymerase transcribes DNA
- Rho attaches to recognition site on RNA
- Rho moves along RNA, following polymerase which would pause at terminator allowing rho to catch up
- Rho unwinds the DNA:RNA hybrid in transcription bubble
- Termination: RNA polymerase, rho & RNA are released
In Rho-INDEPENDENT termination, a stable ___________ slows down progress of RNA polymerase & causes it to pause temporarily.
Hairpin turn
A hairpin turn complementary to a region of DNA template near the termination region that exhibits 2-fold symmetry is due to _______.
Palindrome
A rho-independent terminator contains an ______________, which are transcribed into RNA and would fold into a hairpin loop which would cause RNA polymerase to pause.
Inverted repeat
In rho-independent termination, a transcription will terminate when inverted repeat form a ______ followed by a string of_________.
Hairpin, string of uracils
In transcription of eukaryotic genes, aside from RNA polymerase recognizing the promoter, supplemental _____________ bind to DNA in eukaryotes.
Transcription factors
How will RNA polymerase & transcription factors recognize & bind to specific DNA sequence?
Double helix must assume loose conformation & dissociate temporarily from nucleosome core
Most actively transcribed genes are found in a relaxed form of chromatin called:
Euchromatin
Refers to the interconversion of active & inactive forms of chromatin:
Chromatin remodeling
Most inactive segmenta are in highly condensed:
Heterochromatin
Acetylated histones would result to:
Looser chromatin structure
Inactive genes contain more:
Methylated DNA (5-methylcytosine)
T or F: mitochondrial RNA resembles bacterial RNA polymerase.
TRUE
________ promoters utilize a small number of ybiquitous transcription factors while ________ uses a latge variety of specific ones.
Pol I and III (small number) Pol II (large variety)
Fatal disease that results from autoimmune response where Px produces Abs against host proteins, including snRNPs:
Systemic lupus erythematosus
Mutation causing incorrect splicing of beta-globin mRNA:
Beta thalassemia
