How genes work and such Flashcards
What modifications happen to mRNA after transcription? (post-transcriptional modifications)
5’ Capped and 3’ tailed.
5’Cap added to protect 5’ end and allow ribosome binding for translation.
3’ poly(A) tail added to protect tail. (tail circles back onto cap for translation)
Introns spliced out.
mRNA transported to cytoplasm
What is a retrovirus and what are some of its ssRNA components?
A ssRNA virus like HIV that carries out reverse transcription, inserting viral DNA into host genome.
Contains Repeat regions at either end for insertion purposes, gag, pol, env
Packaging signal for assembling new viruses from proteins such as:
Gag (group specific antigen): capsid protein
Pol: codes reverse transcriptase
Env: envelope protein.
How is the RNA in RNA viruses translated?
(and define ambisense genome)
Either through reverse transcription to DNA in retroviruses or directly translated from RNA.
Direct translation can only occur if the ssRNA is sense (+) orientation, (runs in correct direction, start codon to stop codon)
If the ssRNA is antisense (-) then the sense + strand is made by viral enzyme RNA-dependent RNA polymerase. RdRp (making dsRNA)
Ambisense genome contains sense and antisense ssRNA.
Describe Genome, Transcriptome, Proteome:
Genome is all DNA, coding or not.
Transcriptome is an organism or specific cell’s repertoire of transcribed RNAs (differs between cells/tissues)
Proteome is a cell’s repertoire of translated proteins.
What are enhancer regions?
Regions that alter (normally enhancing) the expression of a gene by interacting with it.
They can be near to, inside, or far from the enhanced sequence but must interact physically interact with the enhanced sequence.
What is the role of small nuclear RNAs (snRNA)
They form the spliceosome to splice introns from pre-mRNA.
What is a twintron?
An intron within an intron! (intronception)
Small one spliced out first, then surrounding intron.
What is the role of small nucleolar RNAs? snoRNA
Found in the nucleolus, where Ribosomes are made from rRNA.
snoRNA facilitates modification of rRNA.
By pairing with rRNA it induces methylation of cytosine bases.
Guide RNAs?
Guide RNAs are small RNAs found in some species (?humans?) that edit the sequence of other mRNA.
Role of microRNAs? miRNA
Post-transcriptional regulation of gene expression.
Bind to mRNA to inhibit translation, and speeds up deadenylation (removal of polyA tail and so destruction)
Production of micro RNAs?
miRNAs produced in the form of large stem-loop structures which are transported out of the nucleus and then diced into tiny sequences by dicer.
siRNA?
Small interfering RNA, causes RNAinterference RNAi.
Enters as dsRNA (synthetic or viral) diced by Dicer in cytoplasm.
Binds to mRNA. causing its destruction by RISC (RNA induced silencing complex)
How to use/create synthetic siRNA to artificially silence genes?
Create dsRNA identical to the target gene (by incorporating promoters its transcription on both strands of dsDNA)
This dsRNA produced will be diced by Dicer and the segments incorporated into RISC which will then help siRNAs bind and degrade target gene.
What is the C-value paradox?
and how is it resolved?
C-value represents the total amount of DNA in the haploid genome.
The C-value paradox is the apparent lack of correlation between phenotypic/morphological complexity of an organism and the size of its c-value.
The paradox is explained because of variable amounts of ‘repetitive/”junk” DNA’
(doesn’t happen in bacteria and viruses because very little repetitive DNA)
Describe some ways some bacteria (and other organisms) can have small genomes (<1Mbp)
Simplistic metabolism/life cycle (e.g. endosymbiotic bacteria) Few regulatory genes etc.
Small intergenic regions, and overlapping genes!
Why do some important bacterial chromosomal genes have increased copy number during DNA replication?
Because bacterial chromosomes (circular and typically 1 per bacteria) have only 1 origin of replication (ori) for the whole chromosome, genes closer to the origin are duplicated, relative to more distant genes.
[Genes often oriented in direction of replication (5’–>3’ away from ori (so half on + and half on - strand) so that replication and transcription machinery don’t collide.]
Why does DNA contain Thymine (as a pyrimidine pair for Adenine) whereas RNA contains Uracil?
Because Cytosine can be spontaneously deaminated to Uracil.
So if Uracil is found in DNA sequence it can be identified as wrong and fixed.
(RNA mutations don’t matter so much as they’re short lived, and Uracil costs less to make than Thymine)
