EXON & INTRON

Tri Panjiasih S
 Eukaryotic genes have introns and exons.
 Exons contain nucleotides that are
translated into amino acids of proteins.
 Exons are separated from one another by
intervening segments of junk DNA called
introns
 Exons vs Introns
 Introns do not code for protein. They are
removed when eukaryotic mRNA is processed.
 Exons make up those segments of mRNA that
are spliced back together after the introns are
removed;
 the intron-free mRNA is used as a template to
make proteins.
What’s the difference between exons and coding
sequence?
 Exons often are described as short segments of protein
coding sequence.
 Exons are those segments of sequence that are spliced
together after the introns have been removed from the
pre-mRNA.
 the coding sequence is contained in exons, but it is
possible for some exons to contain no coding sequence.
These are the untranslated regions or UTRs. UTRs are
found upstream and downstream of the protein-coding
sequence.
 EXON
• Exons are parts of DNA that are converted into mature
messenger RNA (mRNA). The process by which DNA is
used as a template to create mRNA is called transcription.
• This mRNA then undergoes a further process called
translation where the mRNA is used to synthesize proteins,
via another type of molecule called transfer RNA (tRNA)
• Transcription
– DNA – preRNA – mRNA
• Translation
– mRNA - Proteins
 INTRON
 Introns are parts of genes that do not directly
code for proteins.
 Introns can range in size from 10’s of base pairs
to 1000’s of base pairs.
 Introns are commonly found in multicellular
eukaryotes, such as humans. They are less
common in unicellular eukaryotes, such as yeast,
and even rarer in bacteria.
 the more introns an organism contains, the
more complex the organism is.
• It is vital for the introns to be removed precisely, as any
left-over intron nucleotides, or deletion of exon
nucleotides, may result in a faulty protein being
produced. This is because the amino acids that make up
proteins are joined together based on codons, which
consist of three nucleotides. An imprecise intron removal
thus may result in a frameshift, which means that the
genetic code would be read incorrectly.

• This can be explained by using the following phrase as a

metaphor for an exon: “BOB THE BIG TAN CAT”. If the
intron before this exon was imprecisely removed, so that
the “B” was no longer present, then the sequence would
become unreadable: “OBT HEB IGT ANC AT…”
 INTRON

 Introns are present in the initial RNA

transcript, known as pre-mRNA. They
need to be removed in order for the
mRNA to be able to direct the production
of proteins. Pre-mRNA, therefore,
undergoes a process, known as splicing,
to create mature mRNA
 Introns and Exons
 DNA is interrupted by short sequences that
are not in the final mRNA
 Called introns
 Exons = RNA kept in the final sequence
 Introns and Exons
 Introns--Untranslated
intervening
sequences in mRNA
 Exons– Translated
sequences
 Process-RNA splicing
 Heterogeneous
nuclear RNA
(hnRNA)-Transcript
before splicing is
complete
 Splicing Overview
 Occurs in the nucleus
 hnRNAs complexed with specific proteins,
form a ribonucleoprotein particle (RNP)
 Primary transcripts assembled into hnRNP
 Splicing occurs on spliceosomes consist of
 Small nuclear ribonucleoproteins (SnRNPs)
 components of spliceosomes
 Contain small nuclear RNA (snRNA)
 Many types of snRNA with different functions
in the splicing process
Spliceosome
 Splice Site Recognition

 Introns contain invariant 5’-GU and 3’-AG

sequences at their borders (GU-AG Rule)
 Recognized by small nuclear ribonucleoprotein
particles (snRNPs) that catalyze the cutting and
splicing reactions.
 Internal intron sequences are highly variable even
between closely related homologous genes.
 Alternative splicing allows different proteins from
a single original transcript
mRNA splicing of exons and removal of introns:

1. Introns typically begin with a 5’-GU and end with

AG-3’.
2. Cleavage occurs first at the 5’ end of intron 1
(between 2 exons).
3. The now free G joins with an A at a specific
branch point sequence in the middle of the intron,
using a 2’ to 5’ phosphodiester bond.
 Intron forms a lariat-shaped structure.
4. Lariat is excised, and the exons are joined to form
a spliced mRNA.
5. Splicing is mediated by splicosomes, complexes of
small nuclear RNAs (snRNAs) and proteins, that
cleave the intron at the 3’ end and join the exons.
6. Introns are degraded by the cell.
 Simplified Splicing Mechanism

1. 2’ hydroxyl group of an A nt within the intron attacks the phosphodiester bond

linking the first exon to the intron. This attack breaks the bond between exon 1
and the intron, yielding the ree exon and a lariat exon-intron intermediate, with
the GU linked to the internal A via a phosphodiester linkage to C-2 of ribose.
2. Free 3’ –OH on exon 1 attacks phosphodiester bond between intron and exon
2.
3. Yields spliced exon1-exon2 and lariat shaped intron. Phosphate at end of exon
2 becomes the phosphate linking the 2 exons.
 Alternative
Splicing I

 Exon removed
with intron
 Alternative
Splicing II

 Multiple 3’
cleavage
sites
 EX. AG
found at 5’
end of exon
2 and inside
exon 2
Three main parts:

1. 5’ untranslated region (5’ UTR) or leader

sequence
2. Coding sequence, specifies amino acids to be
translated
3. 3’ untranslated region ( 3’ UTR) or trailer
sequence may contain information that signals
the stability of the particular mRNA
Five Classes of Introns
 Generic Splicing Reaction
5’ splice junction 3’ splice junction

Intron
Exon 1 Exon 2

Intron

Exon 1 Exon 2

Two Steps (“Scissors than Tape”):

Step 1: Break phosphodiester bonds at the exon-intron boundaries
(splice junctions). 5’ bond broken before 3’ bond
Step 2: Formation of a new phosphodiester bond between 3’ end of upstream exon
and 5’ end of downstream exon
 Transesterification
• Splicing of Group I, II, and Pre-mRNA introns
results from two sequential transesterification
reactions

• “Transesterification” occurs when a hydroxyl group

makes a nucleophilic attack on a phosphodiester bond
to form a new phosphodiester bond while displacing a
hydroxyl group

• The reaction requires no energy (ATP-independent)

• Phosphate is conserved
 Pre-mRNA Splicing

 Requires ~100 proteins and 5 RNAs

 Occurs in a large RNP assembly known as
the “Spliceosome”
 Catalytic component unknown but may be
RNA-catalyzed
 Splicing via sequential transesterification
reactions (same chemical steps as Group
II intron splicing)
Pre-tRNA Splicing

Splice
 Endonuclease OH P Splicing of
Ligase Nuclear
Pre-tRNA
or ATP Introns
‘Kinase’
3’ phosphodiesterase
‘Cyclic Phosphodiesterase’
(in Yeast )

‘Adenylase’ Protein-catalyzed
1) endonuclease
2) ‘ligase’with 5
‘Ligase’
activities

‘2'-Phospho transferase’
 Summary of Intron Splicing Mechanisms

Catalytic Mechanisms: nucleophiles, introns, catalysts

Splice-site Selection: splice junctions, recognition