Transcription, Translation, and DNA Repair Flashcards
As you observe a cell committing its daily life, you note there is a presence of an RNA polymerase at work among a gene. What process is it undertaking?
DNA transcription. [note: remember transcription means to convert DNA -> RNA, and this making of RNA is achieved by RNA polymerase]
Upon discovery of a new microbe, you note that during the cell cycle, the mRNA transcribed is translated immediately as it comes from the genome. What domain of life is this organism? How would other domains of life undergo the process after transcription?
This is a bacteria or archaea - they have no nucleus and can readily transcribe their mRNA after translation. Eukarya has a membrane bound nucleus, therefore after the transcription of the DNA, the mRNA undergoes a processing phase before it is transported out of the nucleus to be translated.
Contrast the how transcription starts vs how replication starts
In transcription, RNA polymerase attaches to the promoter present before the gene to unzip and add in nucleotides - RNA polymerase is more complex and can carrying more roles. During replication (much harder with more players) Helicase unwinds the helix, primers are set down for DNA polymerase to bind onto DNA polymerase recognizes the primers and begins synthesis.
Identify the two different strands of DNA as the RNA polymerase is transcribing. What does the mRNA strand mirror?
The DNA strands are termed template and coding strand. The template is the strand the RNA polymerase attaches to code and the mRNA - the functioning unit - shares mirroring sequences to the other strand AKA the codon strand.
Even as RNA polymerase is extremely versatile, how does it still mirror DNA polymerase in nucleotide synthesis.
Like DNA polymerase, they can only read from the 3’ -> 5’ and produce nucleotides from 5’ -> 3’
What nucleotides should follow this template in transcription: 3’ TACTAG 5’
5’ AUGAUC 3’
As you’re observing the transcription of a gene, you notice the mRNA has formed some sort of loop at where the RNA polymerase is at. What should you expect to happen?
This falls under the theory of how RNA polymerase terminates its transcription. The hairpin loop is created by complementary codons at the end - this shape is thought to impair the RNA polymerase’s shape, causing it to let go of the template.
Instead of the hairpin theory for termination of transcription, what other theory also exists to argue for the termination?
Sequences of parts of the gene are recognized by the polymerase complex. This again causes a confirmation change resulting in the enzyme to let go.
What occurs to an mRNA eukaryotic cell before it diffuses out into the cytoplasm?
3 processing methods occur: A 5’ cap, a Poly-A tail, and splicing of introns
Contrast the additional sequences fused onto an mRNA after transcription. How are their purposes different?
Both processes protect the mRNA from exonucleases (these are responsible for degrading foreign RNA) and Also promotes ribosomal binding and helps with nuclear export of the mRNA
Addition of a 5’ cap (modified guanine) to the beginning - this helps with the translation process
Addition 3’ Poly-A tail to the end of the mRNA - a bunch of adenines, help in translation, assures the information is more robust, and a physical protection to prevent ends of mRNA from being damaged.
What would be the RNA strand from the template strands 3’ - TACTAG - 5’ A. 5’ - AUGAUC - 3’ B. 5’ - ATGATC - 3’ C. 5’ - GAUCAU - 3’ D. 5’ - GACTAT - 3’
A. 5’ - AUGAUC - 3’
Identify which term does not belong: A. Coding Strand B. Nontemplate Strand C. Sense Strand D. Transcribed Strand
D. Transcribed Strand. This is the Strand RNA Polymerase is working with to produce mRNA. All other terms are used for the opposite strand not used by RNA polymerase
All of these have the same definition except: A. Antisense Strand B. Transcribed Strand C. Nontemplate Strand D. Anticoding Strand
C. Nontemplate Strand. Template Strand - Noncoding Strand, Anticoding strand, Antisense Strand, Transcribed Strand while Coding strand also called: Coding Strand, Sense Strand, Non template strand
The method in which RNA polymerase and DNA polymerase synthesizes their nucleotides is called A. Perpendicular B. Anti-Perpendicular C. Parallel D. Antiparallel
D. Antiparallel. Read 3’ -> 5’ and mRNA is made 5’ -> 3’ (this method is called antiparallel)
During your work in a biochem lab, you observe an enzyme processing a newly transcribed mRNA. You find that it has bound onto some nucleotides and is attempting to loop these together. What do you expect to happen next? What is this process called?
This protein, called a spliceosome, binds onto either ends of an intron and loops the sequences, cleaves the intron, and ligates the neighboring exons together. This process is called Splicing
Which protein is not important in the processing of mRNA. A. Exonuclease B. Spliceosome C. Polyadenylate polymerase D. Adenosine deaminase
A. Exonuclease - these proteins degrade foreign RNAs in the cytoplasm and can potentially degrade the cell’s own RNA as well. All other enzymes are seen at work during RNA processing: Spliceosome - splicing introns. Polyadenylate polymerase - Adds poly A tail to mRNA. Adenosine deaminase - converts Adenosine of mRNA to inosine
Mnemonic to remember which molecule is on which end of nucleotide polymer chains
F - Five prim and for fosphate. Therefore the 3’ end has the OH end
What occurs when guadanine is added onto a phosphate of an mRNA chain?
This process is a portion of mRNA processing. Capping at the 5’ end converts the 5’ end to be similar to a 3’ end by a 5’ to 5’ linkage which basically protects the mRNA from exonucleases (these are responsible for degrading foreign RNA)
As you continue to observe the newly transcribed mRNA, you see another molecule working on some hydroxyl groups of the mRNA. What is occurring? How is this achieved?
Polyadenylate polymerase is adding adenosine onto 3’ end AKA OH end of the mRNA. This is achieved through the use of ATP to catalyze the reaction and this continues until the tail is about ~250 nucleotides long.
What other purpose is seen in the poly A tail not seen in the 5’ cap?
Helps with transcription termination of RNA polymerase
The mRNA is ready to be shipped out into the nucleus!! As you observe the process of the transport, you note that the mRNA strand does not reflect the coding strand of the DNA. The coding strand has a sequence of AGCT while the mRNA strand has AGUU. What occurred? Where exactly did this change occur in the sequence?
There appears to be some RNA editing, which is commonly seen in viral RNA, where deamination of nucleotides lead to other nucleotides to replace it. In this case, the Cytosine has been converted to Uridine. This process is achieved through cytidine deaminase
You analyze the gene again and find that in another section of the mRNA, there is yet another change in the mRNA not present in the genome! The template reads 3’ - AGGCT - 5’
While the mRNA reads 5’ - UCCGI - 3’. What occurred? Where exactly did this change occur in the sequence?
There appears to be some RNA editing again. The mRNA should read 3’ - UCCGA - 5’ however due to substitution of adenosine to inosine by adenosine deaminase, this is not what is present. These processes result in sequence variation in the RNA molecule. This process is catalyzed by various enzymes. This process is relatively rare and these event include: insertion, deletion, substitution of nucleotides within the edited RNA molecules
What is a common theme shared among most noncoding RNAs?
A common theme: most of these ncRNA participate in transcription or translation. [Note: ncRNA - function RNA that skips last step into a protein. They go from transcription to form vital functions in the step]
As you are observing the transcription and translation process of a cell, you note that the mRNA simply floats around and doesn’t enter into the next step of the process. Further analysis demonstrates that there is something bound onto it! What is this? What occurred as a result of this binding?
MicroRNA - miRNA - function in transcriptional and post transcriptional regulation of gene expression. They can bind to mRNA through complementary base pairs and as a result, silences it momentarily
