Part 2: RNA Processing

Question 1

Do bacteria have introns and exons?

Answer 1

• No.

Question 2

Exons:

Answer 2

• nucleic acid sequences that are transcribed and retained in the corresponding mature mRNA

Question 3

Introns:

Answer 3

• nucleic acid sequences that are transcribed but spliced from the primary transcript to yield the mature mRNA
• removed BEFORE translation

Question 4

Transcription:

Answer 4

DNA → RNA

Question 5

Translation:

Answer 5

mRNA → protein

introns REMOVED before translation

Question 6

Start and stop codons are in which portion of a gene: introns or exons?

Answer 6

• exons
• start and stop codons are utilized by the ribosome during translation (protein synthesis)
  
  • since splicing of introns occurs before translation, start and stop codons must be in the exons in order to reach the ribosome

Question 7

Splicing:

Answer 7

• the removal of introns from mRNA
• occurs before translation
• splices adjacent exons to each other

Question 8

When does splicing occur?

Answer 8

• co-transcriptionally or post-transcriptionally
• BEFORE translation

Question 9

Schematic summary of splicing:

Answer 9

Question 10

How are introns recognized by spliceosomes?

Answer 10

• GU always at 5’ splice site of intron
• AG always at 3’ splice site of intron
• consensus sequences
• branch-site (conserved sequence)

Question 11

Length of introns is highly variable, ranging from:

Answer 11

<100 to several thousand nucleotides

Question 12

Consensus sequences:

Answer 12

• conserved, but not invariant sequences found at 5’- and 3’-ends of introns
• used for intron recognition and splicing

Question 13

Branch-point:

Answer 13

• conserved sequence 20 – 50 nucleotides from the 3-end of the intron
• used for intron recognition and splicing
• an adenine residue that is catalytic/nucleophilic

Question 14

How does splicing occur?

Answer 14

• two transesterification reactions:
  
  1. cleaving of phosphodiester bond between exon 1 and intron 1
  2. cleaving of phosphodiester bond between intron 1 and exon 2

Question 15

Splicing Mechanism (Text):

Answer 15

1. 2’-OH of an adenylate residue at the branch site attacks phosphate at 5’ intron splice site
   
   • new 2’– 5’ phosphodiester bond formed
2. 3’-OH of exon 1 attacks phosphate at 3’ intron splice site
   
   • cleaves phosphodiester bond between the intron and exon 2
3. Exon 1 and Exon 2 now joined
4. Intron forms lariat structure - degraded

Question 16

Splicing Mechanism (Draw):

Answer 16

Question 17

The splicing reaction is catalyzed by:

Answer 17

• the spliceosome
  
  • assembly of ribonucleoprotein particles (SNURPs) that recognize the 5’ splice site, the 3’ splice site and the branch site.

Question 18

The spliceosome is:

Answer 18

• an assembly of ribonucleoprotein particles (SNURPs) that recognize the 5’ splice site, the 3’ splice site, and the branch site.

Question 19

Spliceosome assembly:

Answer 19

• de novo
• SNURPs come together on pre-mRNA
• requires ATP

Question 20

SNURPs that make up a spliceosome:

Answer 20

1. U1 and U2
2. U4-U5-U6 complex

Question 21

The U1 SNURP of the spliceosome recognizes:

Answer 21

• the GU sequence at the start of an intron
  
  • U1 then binds to GU

Question 22

The U2 SNURP of the spliceosome recognizes:

Answer 22

• the 2’-OH adenylate residue of the branchpoint
  
  • U2 then binds to branchpoint

Question 23

Steps of spliceosome assembly (Text):

Answer 23

1. U1 binds to GU sequence at intron start
2. U2 binds to 2’OH adenylate residue branch point
3. U1 and U2 come together with the U4-U5-U6 complex to form a complete spliceosome

REQUIRES ATP

(ATP HYDROLYSIS)

Question 24

Steps of spliceosome assembly (Draw):

Answer 24

Question 25

A conserved GU sequence is always at:

Answer 25

• the 5’ splice site of an intron (the start)

Question 26

A conserved AG sequence is always at:

Answer 26

• the 3’ splice site of an intron (the end)

Question 27

Alternative splicing:

Answer 27

• can produce multiple, related proteins from a single gene
• although structurally related, can have completely different functions

Question 28

There are 100,000 proteins in the human body, but only 20,000 genes. This difference is accounted for partly by:

Answer 28

alternative splicing