Is The Genetic Code Always Correct? Flashcards
How can we identify the exons if we have both the gDNA and cDNA sequences?
Align them together and the sequences should only match at the positions of the exons. The intron sequences will only be present in th gDNA. The cDNA represents the mature mRNA transcript where the introns have been removed and the exons spliced together.
There is a programme called ‘Spidey’ at the NCBI that can do this.
When comparing cDNA to gDNA we may get mismatches, why might this be?
They could be polymorphisms, especially if the sequences are derived from different individuals, or they may represent errors in either of the sequences that have arisen during the PCR or cloning process.
What programme could you use to identify the correct open reading frame for translation from an mRNA sequence?
ORF-finder from the NCBI.
What enzyme is responsible for editing A to G in RNA?
Enzymes known as adenosine deaminases.
What is the importance of RNA editing?
This additional layer of regulation allows the cells to produce many more protein isoforms from the relatively small number of genes that are in our genome.
Describe the diversity of RNA editing.
The diversity of RNA editing phenomena includes nucleobase modifications such as Cytidine>Uridine and Adenosine>Inosine deaminations, as well as non-templated nucleotide additions and insertions.
RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from the predicted genomic DNA sequence.
Describe RNA editing by insertion or deletion.
Pan-editing.
Pan-editing starts with the base pairing of the unedited primary transcript with a guide RNA (gRNA) which contains complementary sequences to the regions around the insertion/deletion points.
The newly formed double stranded region is then enveloped by an editosome to catalyse editing. The editosome opens the transcript at the first mismatched nucleotide and starts inserting uridines. The inserted uridines will base pair with the gRNA, and insertion will continue as long as A or G is present in the guide RNA and will stop when a C or U is encountered. The inserted nucleotides cause a frameshift and result in a translated protein that differs from its gene.
Describe C>U editing.
C>U editing involves Cytidine Deaminase that deaminates a Cytidine base into a Uridine base.
An example of C>U editing is with the apolipoprotein B gene in humans. Apo B100 is expressed in the liver and Apo B48 is expressed in the intestine. In the intestine, the mRNA has a CAA sequence edited to be a UAA, a stop codon, thus producing the shorter B48 form.
Describe A>I editing.
A>I editing is the main form of RNA editing in mammals and occurs on regions of dsRNA. Adenosine Deaminases acting on RNAs (ADARs) are the enzymes involved.
A>I editing can be specific (a single adenosine is edited within a stretch of dsRNA) or promiscuous (up to 50% of the adenosines are edited).
Specific editing occurs within short duplexes while promiscuous editing occurs within longer regions of duplex.
There are many effects of A>I editing, arising from the fact that I behaves as if it is a G both in translation and when forming secondary structures. These effects include alteration if coding capacity, altered miRNA or siRNA target populations, heterochromatin formation, nuclear sequestration, altered splicing etc.
