Lecture 29 & 30 Flashcards
What are the 5 subunits of the spliceosome and what doe each subunit contain
U1, U2, U4, U5, and U6
Each subunit contains a small RNA and accessory proteins
U subunits
What is the spliceosome process (7 Steps)
- U1 binds the 5’ splice site
- U2 binds the branch site to make the A accessible
- U4/U5/U6 bind to U1
- U4 releases U6 so it can bind the splice site
- U1 is removed from the splice site
- U6 and U2 come together and bring 5’ splice site to the branch site to form the lariat
- U5 takes the 5’ exon (now liberated) to the 3’ splice site and the intron is release
More introns = _______
More complexity
___% of human genes contain an exon which does not include any open reading frame (doesn’t encode part of a protein)
30
___% of human genes are alternatively spliced
~60
What is the smallest exon is how many bases long
5 bases long
Longest exon in the human gene?
10kb in a gene called KIAAA1958
There are at least __ genes with a single intron above 0.5 Mbp and at least __ genes which produce a pre-mRNA over 1 Mbp
24
50
T/F you could fit the entire E. coli genome in the empty spaces wasted in a handful of human genes
True
T/F Size, # of exons and protein size are invariable
false
Median intron and exon sizes
Typically the first intron is the largest and the last exon is the largest
Last exon is the biggest because it contains the 3’ untranslated region
Dystrophin (size, # of coding & non-coding, # of introns)
2.5 million bases long
15, 000 are coding
2.485 million are non coding
78 introns
79 exons
What is dystrophin for
X-linked gene with 79 exons
1 in 3200 males have dystrophin mutation
causes Duchenne MD
Milder version is Becker MD
What are the different subunits for in splicing
U1/U2 spliceosome subunits recognize 5’SS and A-branch site
* U4/5/6 subunits displace U1, attach 5’-P of intron to 2’-OH of A-branch, releasing the 3’-OH end of the first exon
* U4/5/6 subunits swap linkage between the 3’ end of the intron & 5’ end of the second exon to be between the 3’ end of 1st exon & 5’ end of the 2nd exon – This liberates the intron as a lariat & completes the exon to exon connection
Are intron or exons longer
introns 10-20x
What are the 4 main type of introns? How are the each removed?
– Pre-mRNA introns are the “normal” introns in most genes
– Group I and Group II introns are autocatalytic introns
(self-splicing ribozymes)
– tRNA introns are cut out rather than spliced
How are group I and group II introns spliced? Do either need proteins to function in vitro
Neither need proteins to function in vitro
– Group II introns splice using the same 5’, 3’ and branch site sequences as pre-mRNA introns
– Group I introns use a free-floating GTP cofactor as the branch site instead of an intronic A and do not form a lariat structure
Which introns are structurally conserved
Group I
the spliceosome replicates the activity of which intron
group II introns
Why did the group II introns not retain their activity
initially the spliceosome may have evolved only to assist group II introns in their own removal but once an effective spliceosome was made, there was no fitness advantage to ensure Group II introns retained their activity
describe the relationship between DNA and Proteins
DNA need protein to function but Protein need DNA to exist
What is the RNA world hypothesis (3 reasons)
RNA kickstarted life and gave rise to life
Reasoning is because chains of RNA are found abundantly in all living cells, they are related to DNA, and can replicate, evolve and interact with the environment
How did RNA arise
arose from an earlier proto-RNA in the primordial soup
3 theories of the origin of introns
Introns First
Introns early
introns late
Describe the introns first theory
Self-splicing nature was a mechanism to link and rearrange primitive functional RNAs and were made before DNA
Describe introns early theory
Introns were present in LUCA
Functional RNAs gave rise to a mechanism for translation into proteins and copying to DNA
Self splicing introns were used to shuffle RNA & later protein subunits around like building blocks of mechanical life
Evidence for introns early theory
The majority of introns are “in phase” with the reading frame of a gene
They do not interrupt a codon
Introns are found in the same position in some evolutionarily ancient eukaryotic genes
Introns are present functional genes of the protein that could benefit from swapping
why don’t prokaryotes have introns
to decrease their metabolic load
Introns late theory
Introns arose after the prok/euk split, but still very early in eukaryotic evolution
A sequence arose that was both self-splicing and mobile (type II introns)
Once the spliceosome evolved, introns lost their abilities and the eukaryotic genome selected for the more stable spliceosome
Is the early or late theory correct
The answer is both
Some introns arose early which explains type II in some bacteria
Some introns are early-late which explains the introns which are in the same position as human orthologs
some introns arose late which explains the new arising introns being discovered
