Lecture 29 & 30

Question 1

What are the 5 subunits of the spliceosome and what doe each subunit contain

Answer 1

U1, U2, U4, U5, and U6

Each subunit contains a small RNA and accessory proteins

Question 2

U subunits

What is the spliceosome process (7 Steps)

Answer 2

1. U1 binds the 5’ splice site
2. U2 binds the branch site to make the A accessible
3. U4/U5/U6 bind to U1
4. U4 releases U6 so it can bind the splice site
5. U1 is removed from the splice site
6. U6 and U2 come together and bring 5’ splice site to the branch site to form the lariat
7. U5 takes the 5’ exon (now liberated) to the 3’ splice site and the intron is release

Question 3

More introns = _______

Answer 3

More complexity

Question 4

___% of human genes contain an exon which does not include any open reading frame (doesn’t encode part of a protein)

Answer 4

30

Question 5

___% of human genes are alternatively spliced

Answer 5

~60

Question 6

What is the smallest exon is how many bases long

Answer 6

5 bases long

Question 7

Longest exon in the human gene?

Answer 7

10kb in a gene called KIAAA1958

Question 8

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

Answer 8

24
50

Question 9

T/F you could fit the entire E. coli genome in the empty spaces wasted in a handful of human genes

Answer 9

True

Question 10

T/F Size, # of exons and protein size are invariable

Answer 10

false

Question 11

Median intron and exon sizes

Answer 11

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

Question 12

Dystrophin (size, # of coding & non-coding, # of introns)

Answer 12

2.5 million bases long

15, 000 are coding

2.485 million are non coding

78 introns

79 exons

Question 13

What is dystrophin for

Answer 13

X-linked gene with 79 exons

1 in 3200 males have dystrophin mutation

causes Duchenne MD

Milder version is Becker MD

Question 14

What are the different subunits for in splicing

Answer 14

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

Question 15

Are intron or exons longer

Answer 15

introns 10-20x

Question 16

What are the 4 main type of introns? How are the each removed?

Answer 16

– 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

Question 17

How are group I and group II introns spliced? Do either need proteins to function in vitro

Answer 17

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

Question 18

Which introns are structurally conserved

Answer 18

Group I

Question 19

the spliceosome replicates the activity of which intron

Answer 19

group II introns

Question 20

Why did the group II introns not retain their activity

Answer 20

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

Question 21

describe the relationship between DNA and Proteins

Answer 21

DNA need protein to function but Protein need DNA to exist

Question 22

What is the RNA world hypothesis (3 reasons)

Answer 22

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

Question 23

How did RNA arise

Answer 23

arose from an earlier proto-RNA in the primordial soup

Question 24

3 theories of the origin of introns

Answer 24

Introns First
Introns early
introns late

Question 25

Describe the introns first theory

Answer 25

Self-splicing nature was a mechanism to link and rearrange primitive functional RNAs and were made before DNA

Question 26

Describe introns early theory

Answer 26

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

Question 27

Evidence for introns early theory

Answer 27

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

Question 28

why don’t prokaryotes have introns

Answer 28

to decrease their metabolic load

Question 29

Introns late theory

Answer 29

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

Question 30

Is the early or late theory correct

Answer 30

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