EXON INTRON

Etty Widayanti, SSi. MBiotech.

Sub Bagian Biologi, Bagian Anatomi
Fakultas Kedokteran, Universitas
YARSI

Five different types of RNA, each encoded by different genes:

1. mRNA

Messenger RNA, encodes the amino acid sequence of

a polypeptide.

2. tRNA

Transfer RNA, transports amino acids to ribosomes

during translation.

3. rRNA

Ribosomal RNA, forms complexes called ribosomes

with protein, the structure on which mRNA is
translated.

4. snRNA

Small nuclear RNA, forms complexes with proteins

used in eukaryotic RNA processing (e.g., exon
splicing and intron removal).

5. miRNA/siRNA

Micro RNA/small interfering RNA, short ~22 nt RNA

sequences that bind to 3 UTR target mRNAs and
result in gene silencing.

Three Steps to Transcription:

1. Initiation
2. Elongation
3. Termination
Occur in both prokaryotes and eukaryotes.
Elongation is conserved in prokaryotes and eukaryotes.
Initiation and termination proceed differently.

Step 1-Initiation, E. coli model:

Fig. 5.3

Each gene has three regions:

1.

5 Promoter, attracts RNA polymerase

-10 bp 5-TATAAT-3
-35 bp 5-TTGACA-3

2.

Transcribed sequence (transcript) or RNA coding sequence

3.

3 Terminator, signals the stop point

Step 2-Elongation, E. coli model:

1.

After 8-9 bp of RNA synthesis

occurs, sigma factor is released
and recycled for other reactions.

2.

RNA polymerase completes the

transcription at 30-50 bp/second
(and order of magnitude slower
than DNA polymerase).

3.

DNA untwists rapidly, and reanneals behind the enzyme.

4.

Part of the new RNA strand is

hybrid DNA-RNA, but most RNA
is displaced as the helix reforms.

Step 3-Termination, E. coli model:

Two types of terminator sequences occur in prokaryotes:
1.

Type I (-independent)
Palindromic, inverse repeat forms a hairpin loop and is believed to
physically destabilize the DNA-RNA hybrid.

2.

Type II (-dependent)
Involves factor proteins that break the hydrogen bonds between the
template DNA and RNA.

Prokaryotes possess only one type of RNA polymerase

transcribes mRNAs, tRNAs, and rRNAs
Transcription is more complicated in eukaryotes
Eukaryotes possess three RNA polymerases:
1.

RNA polymerase I, transcribes three major rRNAs 12S, 18S, 5.8S

2.

RNA polymerase II, transcribes mRNAs and some snRNAs

3.

RNA polymerase III, transcribes tRNAs, 5S rRNA, and snRNAs

*S values of rRNAs refer to molecular size, as determined by sucrose gradient

centrifugation. RNAs with larger S values are larger/have a greater density.

Production of the mRNA molecule (Fig. 5.8)

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

mRNA differences between prokaryotes and eukaryotes:

Prokaryotes
1.

mRNA transcript is mature, and used directly for translation without

modification.

2.

Since prokaryotes lack a nucleus, mRNA also is translated on ribosomes

before it is transcribed completely (i.e., transcription and translation are
coupled).

3.

Prokaryote mRNAs are polycistronic, they contain amino acid coding

information for more than one gene.

Eukaryotes
1.

mRNA transcript is not mature (pre-mRNA); must be processed.

2.

Transcription and translation are not coupled (mRNA must first be

exported to the cytoplasm before translation occurs).

3.

Eukaryote mRNAs are monocistronic, they contain amino acid sequences

for just one gene.

Fig. 5.9. Prokaryotes and Eukaryotes

Production of mature mRNA in eukaryotes:

1.

2.

3.

5 cap

After 20-30 nucleotides have been synthesized, the 5-end of the

mRNA is capped 5 to 5 with a guanine nucleotide (See Fig. 5.10).

Results in the addition of two methyl (CH3) groups.

Essential for the ribosome to bind to the 5 end of the mRNA.

Poly (A) tail

50-250 adenine nucleotides are added to 3 end of mRNA.

Complex enzymatic reaction.

Stabilizes the mRNA, and plays an important role in transcription

termination.

Introns (non-coding sequences between exons) are removed and exons

(amino acid coding sequences) are spliced.

EXON INTRON
Introns and exons are parts of genes. Exons code for proteins, whereas
introns do not. A great way to remember this is by considering introns as
intervening sequences and exons as expressed sequences.
exons: the sequences in the DNA molecule that code for the amino
acid sequences of corresponding proteins.
intron: the DNA sequence in a eukaryotic gene that is not translated
into a protein.

Introns and exons:

Eukaryote pre-mRNAs often have intervening introns that must be

removed during RNA processing (as do some viruses).
intron = intragenic region made of non-coding DNA sequences between
exons in a gene.
exon = expressed DNA sequences in a gene, code for amino acids.
Fig. 5.12

1993: Richard Roberts (New England Biolabs) & Phillip Sharp (MIT)

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 10s of base
pairs to 1000s 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.

INTRON
It has been suggested that the number of
introns an organisms genes contains is
positively related to its complexity. That is
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

Splicing signal
Most introns start from the sequence GU and end with the sequence
AG (in the 5' to 3' direction). They are referred to as the splice donor
and splice acceptor site, respectively. However, the sequences at
the two sites are not sufficient to signal the presence of an intron.
Another important sequence is called the branch site located 20 - 50
bases upstream of the acceptor site. The consensus sequence of the
branch site is "CU(A/G)A(C/U)", where A is conserved in all genes.
In over 60% of cases, the exon sequence is (A/C)AG at the donor
site, and G at the acceptor site.
Figure 5-A-4.

The consensus sequence for splicing.

Pu = A or G; Py = C or U.

RNA Splicing
RNA splicing, also known as RNA processing, occurs at
special splice sites. These tend to begin with the
dinucleotide GU at the 5 end and AG at the 3 end.
The process is carried out by small nuclear
ribonucleoproteins (snRNPs), which are commonly
known as snurps. They bind to both the 5 and 3 ends of
the intron and cause the intron to form a loop. The intron
is then removed from the sequence and the two
remaining exons are linked together.

Eukaryotes: Organization of DNA within a single gene; Exons and

introns
Primary transcript
Exon

Intron

Exon

Intron

Intron

Exon

Intron

Primary transcript
Exon

modification

Exon Exon
Splicing

Cap

poly A tail

RNA PROCESSING

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.

Splicing mechanism
The detailed splicing mechanism is quite complex. In short, it involves
five snRNAs and their associated proteins. These ribonucleoproteins
form a large (60S) complex, called spliceosome. Then, after a two-step
enzymatic reaction, the intron is removed and two neighboring exons
are joined together. The branch point A residue plays a critical role in the
enzymatic reaction.

Schematic drawing for

the formation of the
spliceosome
during
RNA splicing. U1, U2,
U4, U5 and U6 denote
snRNAs
and
their
associated
proteins.
The U3 snRNA is not
involved in the RNA
splicing, but is involved
in the processing of
pre-rRNA.

Fig. 5.12

Fig. 5.13

-globin gene
Expression of the -globin gene is a typical process. This gene contains
two introns and three exons. Interestingly, the codon of the 30th amino
acid, AGG, is separated by an intron. As a result, the first two nucleotides
AG are in one exon and the third nucleotide G is in another exon.
Expression of
the human globin gene.
U5 and U3
represent
untranslated
regions at the
5' and 3' end,
respectively.
Note that the
mature
globin protein
does
not
contain the
initiating met
hionine
for protein
synthesis.