3

Subject:
Gene Expression

Instructional objective :
After attending this course,
students will be able to describe
the Gene Expression.
Sub Subject:

3.1. Regulation of Expression

3.2. Protein Synthesis
3.1. Regulation of Expression

The effect of a gene can be

visually observed for instance in
grape fruit color from green, lilac
to dark purple in color. The
appearance of fruit bunches from
poor, dense to very dense.
All the differences are caused by
different gene expression.
dark purple lilac green
very dense poor dense
bunch bunch bunch
The effect of a gene can also be
distinguished from the level
expression intensity. For example
the differences in expression
intensity of ox gene of rice that
control dwarf characters, stunted,
causing differences in plant height.
The higher the intensity of ox gene
expression will resulted causing
lower rice growth.
Expression
intensity
Expression take place in nuclear and
cytoplasm

DNA
Transcription
nuclear
hnRNA
RNA processing
mRNA

Translation Ribosome
cytoplasm
Protein

Phenotypic Expression
Based on their end result, the genes
are grouped into 3 class of:

1. Class I Gene:
Genes of this class makes a large
precursor to the major rRNA
(ribosome RNA) of 5.8S,and18S,
or 28S rRNA in vertebrates).
2. Class II Gene :
Genes of this class involved in
synthesis of protein that work as an
enzyme in physiological pathway
and responsible to phenotype of
individual organism. The
transcription product of the gene
named as mRNA (messenger RNA).
It also make most small nuclear
RNAs (snRNAs).
3. Class III Gene:
Genes of this class involved in
synthesis of protein that bring
amino acid in cytoplasm
ribosome in translation process
for polypeptide chain synthesis.
The transcription product of the
gene named as tRNA (transfer
RNA). Also produce other small
RNAs (5s rRNA, snRNAs)
Based on expression pattern, the
class II genes could be divided
into two groups of :
1. Constitutive expression genes
2. Specific expression genes
1. Constitutive expression genes.
The genes expressed constitutively on
most tissues or organelles, since the
protein products are necessary for
basic living mechanism, such as
respiration to generate energy for cell
metabolism. The genes also named as
housekeeping genes, and shared
about 10% of entire gene of an
organism.
2. Specific expression genes.
The genes are expressed in specific
tissue or organelle in response to
specific growth and development stage
(germination, flowering, fruiting, and
seed development) as well as certain
environment circumstance (biotic and
abiotic stresses). The genes also
named as inducible genes, and shared
about 90% of entire gene of an
organism.
Process Expression of a gene that occurs
in the cell nucleus is two stages of:

1. The transcription.
At this stage, the coding strand / positive
strand of DNA was replicated using
complementation mechanism with other
strand as a template (negative strand).
The result of this process is hetero-
nuclear RNA (hnRNA)
2. RNA Processing.
At this stage hnRNA experienced three
processes of, capping at 5’ ends;
discarding intron fragment , shielding 3’
with poly A fragment. The result is RNA
fragment that is ready translated into
amino acid chain, called as messenger
RNA (mRNA).
Transcription Steps
a. Template recognition)
b. Initiation
c. Elongation
d. Termination
 a c Coding Strand
b d Template Strand
Promoter +1 Terminator
Upstream Downstream
a. Template recognition
At this stage the enzyme RNA
polymerase II bind to the double
stranded DNA of the target gene,
and recognizes a promoter, which
lies upstream of the gene.
There are many types of promoters,
but the most common is a TATA box
located 10 bases before the initiation
site(10 base pairs upstream)
1. TATA box (TATAAA, 10 bp);
2. CAAT box (GGCCAATCT, 22 bp);
3. GC box ( GGGCGG, 20 bp);
4. Octamer (ATTTGCAT, 20 bp);
5. kB (GGGACTTTCC, 10 bp);
6. ATF (GTGACGT, 20 bp).
b. Initiation
The polymerase binding causes the
unwinding of the DNA double helix.
This is followed by initiation of RNA
synthesis at the start site.
After the first nucleotide is in place,
the polymerase joins a second
nucleotide to the first, forming the
initial phosphodiester bond in the
RNA chain
 TGC
A C G T A Coding strand
RNA
T T G G C AT Template strand
A G
C
c. RNA Elongation
RNA polymerase directs the sequential
binding of ribonucleotides to the growing
RNA chain in the 5`-3` direction.
Each ribonucleotide is inserted into the
growing RNA strand following the rules of
base complementation. This process is
repeated till the desired RNA length is
synthesized
d. Termination
Other regions at the end of genes; called
terminators, signal termination. These work in
conjunction with RNA polymerase to loosen the
association between RNA product and DNA
template. The result is that the RNA dissociate
from RNA polymerase and DNA and so stop
transcription. The product is hnRNA

Start site Transcribed region Poly A tailing site

regulator promoter Termination site
TATA EXON INTRON EXON AAUAA

UTR ORF UTR

AUG UGA,UAA,UAG
RNA processing
a. Capping at 5’ end of hnRNA
fragment
b. Splicing to remove intron from
the fragment
c. Adding Poly-A fragment to 3’ end
(Polyadenylation)

a c b
a. Capping
Special structure called a cap added to the 5`
end. The cap consist of a 7- methylguanosine
(m7G) residue linked to transcript by three
phosphate groups. The cap protects the
mRNA from being degraded by enzymes;
enhancement of mRNA translatability.
b. Splicing
Step-by-step removal of introns present in
the pre-mRNA and joining of the
remaining exons. The removal of introns
and joining of exons takes place on a
special structures called spliceosomes.
c. Polyadenylation
Adding of the poly (A) tail involves
cleavage of its 3' end and then the
addition of about 200 adenine residues
to form a poly (A) tail; This completes
the mRNA molecule (mature mRNA),
which is now ready for export to the
cytosol for protein synthesis.
.
A A A AA A
 Coding Strand
Template Strand
Exon Intron Exon
hnRNA Strand
a. Capping
mGppp

b. Splicing
mGppp

c. Polyadenylation
mGppp AAAAAA
mRNA Strand
3.2. Protein Synthesis
Protein Synthesis consist of 4 steps:
1. mRNA transport from nucleus
2. mRNA attachment to ribosome
3. mRNA Translation to make
polypeptide chain with tRNA
participation
4. Development polypeptide chain
into active protein
1. mRNA transport
to initiate translation process the
processed mRNA should be
brought from nucleus to cytoplasm
which protein machine ribosome
located.

nucleus ribosome
2. mRNA attachment to ribosome
mRNA yang sudah berada dalam
sitoplasma selanjutnya berikatan
dengan ribosome sebagai tahap awal
dari proses sintesis protein (translasi)
3. mRNA Translation
one amino acid encoded by 3
bases, since only 4 bases available
will be resulted 64 (43). However,
due to the 3 combinations encode
stop codons, then the remaining 61
combination.
There were 20 amino acid that’s
composed the protein is 20, and
61 codons available, therefore
several amino acid should be
encoded by more than1codon.
No. 3 letters 1 letter Codon No. 3 letters 1 letter Codon
1 Met M AUG 11 Tyr Y UA C/U
2 Trp W UGG 12 Ile I AU A/C/U
3 Asn N AA C/U 13 Ala A GCI
4 Asp D GA C/U 14 Gly G GCI
5 Cys C UG C/U 15 Pro P GCI
6 Glu E GA A/G 16 Thr T ACI
7 Gln Q CA A/G 17 Val V GUI
8 His H CA C/U 18 Arg R A/C GI
9 Lys K AA A/G 19 Leu L C/U UI
10 Phe F UU C/U 20 Ser S A/U G/C I
Ribosome as protein biosynthesis
machine using the mRNA as a
template, the ribosome traverses
each codon of the mRNA, pairing it
with the appropriate amino acid.
This is done using molecules of
transfer RNA (tRNA) containing a
complementary anticodon on one end
and the appropriate amino acid on
the other.
The protein synthesis started by polypeptide
chain synthesis that occur in 3 phases:
1. Accurate and efficient initiation occurs, the
ribosome binds to the mRNA, and the first amino
acid of Methionine attached to its tRNA. To make
M-tRNA for initiating polypeptide chain synthesis
2. Chain elongation, the ribosome adds one amino
acid at a time to the growing polypeptide chain .
3. Accurate and efficient termination, the ribosome
releases the mRNA and the polypeptide after
reach the first stop codon in the mRNA
fragment.
UTR ORF UTR
AUG UGA, UAA, UAG
UAC
M-tRNA
MWNDCEQHKFYIAGPTVRLS

Since start codon is Methionine

(M), the polypeptide chain
always started by Methionine,
and called as Nitrogen end. The
end of polypeptide chain named
as carboxyl end
4. Protein Development
The produced polypeptide chain, will
be used as precursor to construct an
enzyme or together with other chain
composed active enzyme.
Starting from enzyme synthesis, the
subsequent physiological pathway
will occurs and responsible to
determine plant phenotype