DNA methylation
This is when a gene is expressed from only one parental allele, despite both alleles being identical in sequence. (looking for one word here)
Imprinting
These are complexes that are made of short RNA molecules and a set of proteins. Five of them assemble to carry out splicing.
snRNPs (small nuclear ribonucleoproteins)
True or false: In prokaryotes, translation initiation begins after the smaller ribosomal subunit binds the 5’ cap, scanning until it finds the Shine-Dalgarno (SD) sequence.
False - prokaryotic mRNA does not have a cap. The smaller subunit (30S) directly binds the SD sequence.
How does a nascent chain leave the ribosome?
Through the exit tunnel in the large subunit.
Name one type of small silencing RNA.
Possible answers: siRNA, piRNA, miRNA
Methylation can repress transcription in two ways. Name one.
Either directly, by blocking some transcription factors from binding, or indirectly where methyl-CpG binding proteins read the mark and recruit repressors
Name one mode of alternative splicing.
Possible answers: exon skipping, intron retention, alternative 3′ splice site, alternative 5′ splice site
What happens in translation termination?
A release factor recognises the stop codon in place of a tRNA and frees the finished chain from the tRNA holding it; the subunits then come apart.
Why do most RNA-seq library preparations utilize reverse transcription?
Most sequencers read DNA, so the RNA needs to be copied into cDNA first
True or false: A riboswitch is a regulatory protein that binds a metabolite and blocks the ribosome binding site in bacteria.
False - a riboswitch is mRNA. It contains an aptamer domain that binds the metabolite directly, with no protein involved
Two kinds of methylase do different jobs. What is the difference?
One maintains an existing pattern by marking the new strand after replication; the others create methylation on unmethylated DNA (de novo methylation)
Name two general ways RNA editing can change the protein an mRNA encodes.
Possible answers: changing an amino acid, introducing a stop codon (truncating the protein), inserting or deleting nucleotides
What does the ribosome actually check when a tRNA arrives?
The codon–anticodon pair. (It doesn’t inspect the amino acid attached)
Why does RNA have to be enriched or depleted before a library is made?
Most of the RNA in a cell is ribosomal, so without that step the reads are overwhelmingly rRNA.
Name two ways eukaryotes regulate translation.
Possible answers: cap-dependent vs. IRES-dependent initiation, small noncoding regulatory RNAs, riboswitches, repression by phosphorylation, secondary structure in 5’ UTR, uORFs, storage and destruction
What is a CpG island (explain what “CpG” is), and what does it usually mean if one is methylated?
CpG is a cytosine followed by a guanine on the same strand. A CpG island is a CpG-rich stretch of about a kilobase at roughly 60% of promoters. Methylation usually means the gene is silenced.
The signals defining an intron are described as weak. What does that mean, and why does it matter?
They are short and degenerate rather than strictly conserved, This makes alternative splicing possible.
What occurs in aminoacylation, and what is the result?
An amino acid gets activated and transferred to a tRNA, resulting in a charged aminoacyl-tRNA.
Long reads and short reads both measure isoforms. What is the difference in what they can claim?
Long reads observe whole isoforms directly; short reads only infer them from fragments.
What is an upstream open reading frame, and what does it do?
A short reading frame in the 5′ UTR that scanning ribosomes initiate at instead of the real start codon, lowering output from the gene below it.
After replication each daughter CpG carries the mark on one strand only. What is that state called, and how is the full pattern restored?
Hemimethylation. The maintenance methylase (Dmnt1) travels with the replication fork and acts specifically on sites marked on one strand.
Splicing removes an intron in two steps rather than cutting both ends at once. What holds the pieces in place between them?
The spliceosome, which has already paired its components to both ends of the intron before either cut is made.
Explain the results of peptidyl transfer and translocation.
Peptidyl transfer - growing polypeptide chain is transferred from the tRNA in the P site to the tRNA in the A site with the new amino acid
Translocation - the two tRNAs move one site over, and the ribosome moves one codon over on the mRNA
Name three differences between bacterial and eukaryotic mRNA.
Possible answers: (the following are true only of eukaryotes): monocistronic, has a 5’ cap, has a poly(A) tail, longer half-life, spatial and temporal separation from transcription, has to be exported from nucleus first, UTRs carry regulatory elements
Name and briefly describe the conditions of the 3 pathways to destroy faulty mRNAs.
Nonsense decay - premature stop codon
No-go decay - ribosome stalling
Non-stop decay - missing stop codon