Lecture 15

Question 1

Self-splicing introns:

Answer 1

RNA-catalysed reactions compared to spliceosomal-based

Question 2

Linear intron (group 1):

Answer 2

• eg) protozoan rRNA genes

- these are not covalently closed

Question 3

Lariate introns (group 2):

Answer 3

• eg) some mitochondrial genes
• Generates a lariate
• Doesn’t require a snurp for splicing

Question 4

Two theories of intron evolution:

Answer 4

• Introns evolved and proliferate early, but are being lost in some genes over time
• Introns evolved late and are proliferating, increasing in number

Question 5

Comparison of intron positions in related genes in closely related species shows

Answer 5

• Conservation of introns in amidase genes of Aspergillus species
• A conserved intron is observed in almost all species, so there is evidence of the introns slowly being lost over time
• Single introns between species provide evidence for introns arising in sequences.

Question 6

Intron evolution:

Answer 6

• An intron present in the cell that has been excised is reinserted into the DNA by reserve splicing, reverse transcription and recombination.
• Introns can also be lost from sequences

Question 7

Intron sliding:

Answer 7

• Change in intron position
• An intron is spliced out, then reinserted into a different location of the gene. It has the same sequence but moves around at a slower rate

Question 8

Are introns conserved?

Answer 8

• Intron sequences are often not conserved in sequence or length
• Intron sequences can show regions of conservation, and then we would expect some function such as a conserved regulatory site or an unsuspected coding region eg) In Drosophila, the Adh locus has another gene

Question 9

Introns may code for snoRNA:

Answer 9

• Small nucleolar RNA that modify target RNAs, including tRNA
• Transcribed by RNAPIII
• Modify bases in rRNA and tRNA

Question 10

Presumably RNA involved first then DNA evolved as it is more stable and complex. RNA is matured:

Answer 10

• pre-mRNA that is spliced to produce mature mRNA
• pre-rRNA is cleaved to produce a mature rRNA
• pre-tRNA is cleave to produce mature tRNA

Question 11

Alternative splicing:

Answer 11

• Splicing of different introns and exons
• Different cell types
• Different functions
• The same DNA strip can create different products by splicing together different parts of the gene

Question 12

Example of alternative splicing: SV40, simian virus 40, T antigen gene encodes two proteins (T and t)

Answer 12

• T: viral growth
• t: Stops cell apoptosis, so promotes viral proliferation
• From the same gene but are different splice forms and have different functions

Question 13

Example of alternative splicing: Drosophila DSCAM:

Answer 13

• Down Syndrome Cell Adhesion Molecule
• 24 alternatively spliced exons
• 38, 016 combinations of mature mRNAs
• Can do more with the genes that you have, don’t necessarily need lots and lots of genes

Question 14

Transcript splicing, repression:

Answer 14

• This process must be controlled

- The spliceosomal complex can’t see the splice site due to a protein present in some cells blocking the splice site

Question 15

Transcript splicing activation:

Answer 15

• Splicing doesn’t usually happen
• The splicosomal complex doesn’t usually recognise the splice site
• A different cell type expressing an activator may recruit the splicing machinery to the splice site

Question 16

RNA editing:

Answer 16

• Post-transcriptional modification of mRNA sequence
• DNA sequence differs from mRNA sequence
• Protein sequence differs from that predicted from DNA sequence

Question 17

Two mechanisms of RNA editing:

Answer 17

• Nucleotide modification, site specific deamination

- Nucleotide insertion by guide RNAs

Question 18

Nucleotide modification by specific enzymes:

Answer 18

• Cytosine deamination by cytidine deaminase (converts C to U)
• Adenine deamination by adenine deaminase (ADAR)
• Different amino acids can be inserted into the same transcript

Question 19

Nucleotide insertion by guide RNAs:

Answer 19

• Insertion or deletion of U’s
• RNA in mitochondria of some protozoans
• Insertion of U’s to RNA by guideRNAs

Question 20

Pre-mRNA is retained in the nucleus and must be transported out for translation:

Answer 20

• Mature mRNA must be exported out of the nucleus

- RNA’s are bound to proteins that allows transport through the membrane into the cytoplasm