control of gene expression: rna

Question 1

isoforms

Answer 1

different proteins produced from a single gene

Question 2

What is Dscam

Answer 2

gene specifying neurons in the brain to give rise to neural complexity. most alternatively spliced gene.

Question 3

how do b lymphocytes produce the long transcript isoform of an antibody?

Answer 3

1st stop codon in an intron is spliced out
results in translation of transmembrane domain
==> membrane bound antibody

Question 4

how do b lymphocytes produce the short transcript isoform of an antibody?

Answer 4

cleavage upstream the intron results in no acceptor site. intron is not spliced out due to no acceptor site. 1st stop codon is not lost.
results in translation of shorter protein with no transmembrane domain
=====> secreted antibody

Question 5

kozak sequence

Answer 5

ACCAUGG

Question 6

what is the purpose of the kozak sequence

Answer 6

provides a stronger signal for the small ribosome unit to stop at AUG + assemble the full ribosome

Question 7

how does Rev protein work during regulated nuclear transport of HIV RNA

Answer 7

• full length RNA required to make new virions
• unspliced RNA blocked at nuclear pore
• Rev goes back into nucleus + binds to intron of HIV RNA to protect from splicing + interacts with the nuclear pore to enable exit of unspliced RNA

Question 8

how does subcellular localisation of RNA occur within a cell

Answer 8

• intermolecular base pairing in the 3’UTR region forms stem loops
• stem loops recognised by rna binding proteins
• rna binding proteins localised at one side of cell
  mrna trapped on that side of the cell —> more protein made on that side of the cell

Question 9

ferritin

Answer 9

protein storing iron in the cell. reduces available iron.

Question 10

transferrin

Answer 10

receptor sitting in membrane importing iron into the cell. increases available iron.

Question 11

Regulating iron levels in the cell: Low iron?

Answer 11

aconitase binds to 5’ utr stem loop of ferritin –> blocks cap from small ribosomal subunit so cannot scan start codon
less ferritin made
aconitase binds to 3’ utr stem loop of transferrin –> stabilises mrna
more transferrin receptors made

Question 12

regulating iron levels in the cell: high iron?

Answer 12

aconitase binds iron in the cytoplasm –> conformational change causing aconitase to release the mRNAs
small ribosomal subunit can bind to cap scan mRNA for start codon —> more ferritin made
transferrin degraded —> less transferrin receptors made

Question 13

how is translation globally regulated to increase translation levels?

Answer 13

• eIF-2 bound to gtp binds to small ribosomal subunit & Met tRNA to start scanning mRNA
• eIF2B binds to eIF-2 + promotes dissociation of gdp from eIF-2 and allows gtp to bind
  ====> eIF-2 active + translation levels increase

Question 14

how is translation globally regulated to decrease translation levels?

Answer 14

• eIF-2B phosphorylated
  eIF-2B binds to eIF-2 very tightly, blocking its recycling
  decrease in levels of active eIF2 in cytoplasm

Question 15

what is IRES

Answer 15

stem loops in RNA that eIF-4G binds to ==> initiates formation of ribosome independent of cap/polyA initiation complex. imitates cap structure to allow small ribosomal unit to bind.

Question 16

what is DAN

Answer 16

protein factor competing with eIF-4E for binding to 5’ cap. degrades polyA tail

Question 17

how is Drosophila male sex determined?

Answer 17

• sxl and tra transcripts are spliced to give rise to inactive sxl and tra isoforms
• dsx undergoes non-regulated splicing to give rise to dsx transcript repressing transcription of genes required for female development

Question 18

how is Drosophila female sex determined?

Answer 18

has 2 X chromosomes so alternative promoter produces small amount of Sxl protein
sxl = splice repressor. binds to its own transcript to block U2AF from binding to splice site
more active sxl protein made
sxl blocks splice acceptor site on tra to activate tra
tra = splice activator. tra and tra-2 bind to dsx mRNA and activates splice acceptor site to give rise to transcript repressing male differentiation genes

Question 19

DEFINE: leaky scanning

Answer 19

small ribosomal subunit scans past 1st AUG because of a less than perfect kozak sequence

Question 20

high levels of ________ favour the 1st AUG

Answer 20

eIF-4F

Question 21

what is aconitase

Answer 21

cytosolic RNA binding protein

Question 22

how is the translation of a 2nd ORF favoured?

Answer 22

eIF-4G cleaved into a form that cannot bind eIF-4E but still binds IRES

Question 23

Where does polyadenylation take place?

Answer 23

nucleus

Question 24

where does readenylation take place?

Answer 24

cytoplasm