FOM 5.4.1

Question 1

What are the three forms of RNA processing?

Answer 1

Capping, splicing, and polyadenylation

Question 2

What two forms of RNA processing happen co-transcriptionally?

Answer 2

Capping and splicing

Question 3

Tell me about capping. What is it? Where? What type of bond? What is important about this bond?

Answer 3

7-methyl Guanosine cap, 5’ end, 5’->5’ triphosphate bond, impenetrable to exonuclease activity

Question 4

What are the four way that capping influences function of mRNA?

Answer 4

increase stability, export to cyto, req’d for tln, identification of mRNA as cellular (not viral)

Question 5

Polyadenylation. PolyA signal sequence? Two steps? # of A added? What is not required?

Answer 5

AAUAAA signal, cleavage then polyadenylation, 150-200A, no DNA template required

Question 6

What are the four way that polyadenylation influences function of mRNA?

Answer 6

export to cyto, stabilize mRNA

Question 7

Do all genes have introns? Examples?

Answer 7

No, histone proteins don’t have introns. Distrophin holds record w/ 79 exons and enormous amounts of introns

Question 8

What are the two ways that the complexity of hnRNA conversion to mRNA leads to diversity?

Answer 8

alt splicing and terminaiton/polyA

Question 9

Baby M.S. has hypotonic posture, inactivity and poor sucking, elevated creatinine kinase, then at 4 mo cannot control head/respiration. What’s the diagnosis, doc?

Answer 9

Spinal muscular atrophy

Question 10

What is spinal muscular atrophy (SMA)? What gene expression is altered?

Answer 10

Primarily motor neuron degenerative dz, SMN1 (survival of motor neuron 1)

Question 11

What is SMN1 typically involved with?

Answer 11

snRNP (small nuclear ribonucleo-protein) assembly

Question 12

Which exon is typically not expressed in SMN2 that is normally expressed in SMN1?

Answer 12

Exon 7 ( prolly out of the scope, but Miles needs humbled every now and again)

Question 13

What is the role of snRNP in mRNA splicing?

Answer 13

Recognition of conserved nucleotide sequences and creation of splicing assembly

Question 14

What are the 3 steps of lariat structure/splicing?

Answer 14

PIC

Question 15

Which snRNPs find recognize exon/intron boundary and A at the “branch point” of lariat

Answer 15

U1: donor exon/intron boundary U2: A at the “branch point”

Question 16

What are the components of the spliceosome:

Answer 16

U1, U2 (Sean’s favorite band), U4, U5, U6

Question 17

What are the four examples of alternative exon usage?

Answer 17

Cassette (exon skip), mutually exclusive, internal acceptor, alternative promoter

Question 18

What % of human genes are alternatively spliced?

Answer 18

>90%

Question 19

What splice variants of what gene lead to increased prostate cancer risk?

Answer 19

KLF6, a tumor supressor gene

Question 20

What type of effect does KLFP-SV1 have on KLF6?

Answer 20

dominant-negative, it binds DNA preventing KLF6 from binding & blocking txn

Question 21

If a prostate cancer is found to have a higher potential to metastasize, what can be said about the ratio of KLF6-SV1 /KLF6

Answer 21

High ratio

Question 22

Is different usage of alt splicing always an indication of something gone wrong?

Answer 22

No, alternative splicing of glucocorticoid receptor to (+)/(-)

Question 23

In B(not)-thalassemia, no B-chain synthesis occurs. What is the mutation mechanism?

Answer 23

Mutation kills acceptor site of splicing, so a cryptic splice site (best alternative) is used

Question 24

What are the three mutations that alter splicing location?

Answer 24

1) kill acceptor, use cryptic (no good protein) 2) new, strong acceptor (a little good) 3) new donor splice site (frameshit; decent amt of good)

Question 25

What are the three general types of mutation mechanisms that lead to splice variants for specific genes?

Answer 25

1) SNP alters splice donor/acceptor (B-thal) 2) SNP alters binding factor that regulates splicing (prostate CA) 3) SNP alters splicing machinery (SMA)

Question 26

What are core elements?

Answer 26

demarcate where splicing occurs and are bound by snRNPs and other general factors that influence splice site utilization

Question 27

What are Auxiliary splicing reg elements?

Answer 27

lie within introns or exons and bind proteins that promote or repress the choice of splice site, these are analogous to transcriptional enhancers/silencers