GENE EXPRESSION:

TRANSCRIPTION &
TRANSLATION
Indwiani Astuti
Dept of Pharmacology & Therapy
Fac of Medicine
Universitas Gadjah Mada

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DNA and Gene Expression

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DNA

Deoxyribonucleic Acid
Double helix
Carries genetic information
Located in the nucleus
The monomer is a
nucleotide
A phosphate
A ribose sugar
A nitrogenous base

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What are the bases in DNA

A adenine
T thymine
C cytosine
G guanine
Base pair rules

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Where is DNA located in the

Cell?

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Where are the genes located?

Genes are located
on the
chromosomes.
Every species has a
different number of
chromosomes.
There are two types
of chromosomes:
autosomes and sex
chromosomes
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 Genes are located on the chromosomes

which are found in the nucleus of a cell.
When a cell is undergoing cell
reproduction, the chromosomes are
visible. Chromosomes appear when the
chromatin condenses and become
visible.
Most of the time (90%) the genetic
material in the form of chromatin.
A genome is the complete genetic
information contained in an individual.
(gene + chromosome)
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What is gene expression?

Gene expression is the activation of a
gene that results in a protein.
Biological processes, such as
transcription, and in case of proteins, also
translation, that yield a gene product.
A gene is expressed when its biological
product is present and active.
Gene expression is regulated at multiple
levels.
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DNA is embedded in chromatin

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Regulation of gene expression at the level o

Sequence-independent

linker histones: control DNA compaction and accessibility to transacting factors

post-translational modifications of histone tails: control
compaction of DNA and serve as docking sites for trans-acting
factors
Range: Can act at the level of a single gene, often acts over
groups of genes and over larger domains (20-200kb), and can
affect gene expression over an entire chromosome

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Eukaryotic Chromosome
Structure
Eukaryotic DNA is packaged into
chromatin.
Chromatin structure is directly related to
the control of gene expression.
Chromatin structure begins with the
organization of the DNA into
nucleosomes.
Nucleosomes may block RNA polymerase
II from gaining access to promoters.
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Eukaryotic Chromosome
Structure
Methylation (the addition of CH3) of
DNA or histone proteins is associated
with the control of gene expression.
Clusters of methylated cytosine
nucleotides bind to a protein that
prevents activators from binding to DNA.
Methylated histone proteins are
associated with inactive regions of
chromatin.
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Regulation of gene
expression
Promoter Gene (red) with an intron (green)
1. DNA replication

Plasmid

single copy vs. multicopy

plasmids

2. Transcription
Primary
transcript
3. Posttranscriptional
processing

mRNA degradation

Mature
mRNA

4. Translation
inactive
protein
5. Posttranslational
processing

active
protein
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Protein degradation

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Control of Gene Expression

Controlling gene expression is often
accomplished by controlling
transcription initiation.
Regulatory proteins bind to DNA
to either block or stimulate
transcription, depending on how they
interact with RNA polymerase.
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Gene expression regulation at the level

Sequence-dependent

cis-acting factors: promoters/regulatory sequences of genes

trans-acting factors: proteins and RNAs that bind cis-elements
and promote or
repress gene expression
DNA methylation: methylation of CpG islands promotes silencing
Range: Usually functions at level of single gene, or at most a local
group of genes

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Control of Gene Expression

Prokaryotic organisms regulate gene
expression in response to their
environment.
Eukaryotic cells regulate gene
expression to maintain homeostasis
in the organism.

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Gene expression takes place

differently in prokaryotes and
eukaryotes.
What is a prokaryotes?
Eukaryotes?
Prokaryotes

Eukaryotes

No membrane
Membrane bound
bound organelles
organelles ( specialize in
function nucleus,
(nucleus)
mitochondria,
More primitive
chloroplast)
organisms
Chromosomes are in
Only one circular
pairs and not circular
chromosome
All organisms that are
Bacteria are the
not bacteria: protist,
only organisms that
fungi, plants and animals
are prokaryotes.
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Expression of Genetic Information

Production of proteins requires two steps:
Transcription involves an enzyme (RNA polymerase) making an
RNA copy of part of one DNA strand. There are four main
classes of RNA:
i. Messenger RNAs (mRNA), which specify the amino acid
sequence of a protein by using codons of the genetic code.
ii. Transfer RNAs (tRNA).
iii. Ribosomal RNAs (rRNA).
iv. Small nuclear RNAs (snRNA), found only in eukaryotes.

Translation converts the information in mRNA into

the amino acid sequence of a protein using
ribosomes, large complexes of rRNAs and
proteins.
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Proteins Regulate Gene Expression

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Gene structure relevant to

metabolic regulation

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In Eukaryotes, following mitosis or meiosis,

DNA recoils but certain regions remain
relaxed for transcription. The areas of
relaxed DNA are called euchromatin.
Transcription is the
Reading of the DNA and
Changing the code to
mRNA.
Translation is changing
The mRNA into a trait by
Using tRNA to interpret
the
mRNA (The synthesis of
a polypeptide chain
using the genetic code
on the mRNA molecule
as its guide).
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 DNA in eukaryotes has regions of coding

and noncoding DNA. The regions of DNA
that code for proteins or traits are called
EXONS, while the regions that do not code
for proteins are called INTRONS.

cytoplasm
cytoplasm

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Eukaryotic Transcription
General transcription factors bind to
the promoter region of the gene.
RNA polymerase II then binds to the
promoter to begin transcription at the
start site (+1).
Enhancers are DNA sequences to
which specific transcription factors
(activators) bind to increase the rate
of transcription.
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Intron Splicing in Eukaryotes

Exons: coding regions

Introns: noncoding regions
Introns are removed by splicing

GU
at 5 end
of intron

AG
at 3 end
of intron

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Splicesomes Roles in Spicing out Intron

RNA splicing occurs in small nuclear ribonucleoprotein
particles (snRNPS) in spliceosomes

Spliceosomes:
protein +
small RNAs
(U1-8)
complementar
y to the
splice
junctions

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Eukaryotic Transcription
Coactivators and mediators are
also required for the function of
transcription factors.
coactivators and mediators bind to
transcription factors and bind to other
parts of the transcription apparatus

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Enhancer Control
Eukaryote genes on
a DNA strand also
have noncoding
control sequences
that facilitate
transcription.
These are called
enhancers.
Transcription factors
are additional
proteins that bind to
RNA polymerase and
enhancers to help
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 In prokayotes, transcription and

translation occur in the cytoplasm.
In eukaryotes, transcription occurs
inside the nucleus in a two step
sequence of events.
Pre-mRNA includes both introns and
exons for the gene.
mRNA is only the coding portion (exons).

Translation occurs in the cytoplasm at

the ribosomes.
Reminder: The are three (3) types of RNA
Messenager (mRNA)
Transfer (tRNA)
Ribsomal (rRNA)
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RIBONUCLEIC ACID (RNA)

Found all over the cell (nucleus,
mitochondria, chloroplasts, ribosomes
and the soluble part of the cytoplasm)

2007 Paul Billiet ODWS

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Types

Messenger RNA
(mRNA) <5%
Ribosomal RNA (rRNA) Up to 80%
Transfer RNA
(tRNA) About 15%
In eukaryotes small nuclear
ribonucleoproteins (snRNP)

2007 Paul Billiet ODWS

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Structural characteristics of
RNA molecules
Single polynucleotide strand
which may be looped or coiled (not a
double helix).
Sugar Ribose (not deoxyribose).
Bases used: Adenine, Guanine,
Cytosine and Uracil (not Thymine).

2007 Paul Billiet ODWS

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mRNA

A long molecule 1 million Daltons

Ephemeral
Difficult to isolate
mRNA provides the plan for the
polypeptide chain

2007 Paul Billiet ODWS

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rRNA
Coiled
Two subunits:
a long molecule 1 million Daltons
a short molecule 42 000 Daltons
Fairly stable
Found in ribosomes
Made as subunits in the nucleolus
rRNA provides the platform from
protein synthesis
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2007 Paul Billiet ODWS

tRNA
Short molecule about 25 000 Daltons
Soluble
At least 61 different forms each has a
specific anticodon as part of its structure.
tRNA translates the message on
the mRNA into a polypeptide chain

2007 Paul Billiet ODWS

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Transcription: The synthesis of a

strand of mRNA (and other RNAs)
Uses an enzyme RNA polymerase
Proceeds in the same direction as replication
(5 to 3)
Forms a complementary strand of mRNA
It begins at a promotor site which signals
the beginning of gene is not much further
down the molecule (about 20 to 30
nucleotides)
After the end of the gene is reached there is
a terminator sequence that tells RNA
polymerase to stop transcribing
NB Terminator sequence
terminator codon
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Editing the mRNA

In prokaryotes the transcribed mRNA goes
straight to the ribosomes in the cytoplasm
In eukaryotes the freshly transcribed mRNA
in the nucleus is about 5000 nucleotides long
When the same mRNA is used for translation
at the ribosome it is only 1000 nucleotides
long
The mRNA has been edited
The parts which are kept for gene expression
are called EXONS (exons = expressed)
The parts which are edited out (by snRNP
molecules) are called INTRONS
2007 Paul Billiet ODWS

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Posttranscriptional
Regulation
Control of gene expression usually involves
the control of transcription initiation.
But gene expression can be controlled after
transcription, with mechanisms such as:
RNA interference
alternative splicing
RNA editing
mRNA degradation

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Posttranscriptional
Regulation
RNA interference involves the use
of small RNA molecules
The enzyme Dicer chops double
stranded RNA into small pieces of
RNA
micro-RNAs bind to complementary
RNA to prevent translation
small interfering RNAs degrade
particular mRNAs before translation
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Posttranscriptional
Regulation
Introns are spliced out of pre-mRNAs to
produce the mature mRNA that is
translated.
Alternative splicing recognizes different
splice sites in different tissue types.
The mature mRNAs in each tissue possess
different exons, resulting in different
polypeptide products from the same
gene.
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Posttranscriptional
Regulation
RNA editing creates mature mRNA
that are not truly encoded by the
genome.
For example
apolipoprotein B exists in 2 isoforms
one isoform is produced by editing the
mRNA to create a stop codon
this RNA editing is tissue-specific
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Posttranscriptional
Regulation
Mature mRNA molecules have
various half-lives depending on the
gene and the location (tissue) of
expression.
The amount of polypeptide produced
from a particular gene can be
influenced by the half-life of the
mRNA molecules.
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Translation
RNA
Single stranded
Does not contain
thymine but has uracil
instead.

tRNA carries 3 base

pair code for specific
amino acid.
Amino acids compose
polypeptid chains.
One or more
polypeptide chains
compose a protein
proteins provide the
blueprints for our
characteristics and
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functions.

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Transcription plan
Nucleus
Gene

DNA
Transcripti
on messenger
RNA

2007 Paul Billiet ODWS

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Translation plan
Complete protein
Polypeptide chain
TRANSLATIO
N

Ribosomes

Stop codon
2007 Paul Billiet ODWS

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Start codon
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SKEMA TRANSLASI

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Translation
Location: The ribosomes in the
cytoplasm that provide the
environment for translation
The genetic code is brought by the
mRNA molecule

2007 Paul Billiet ODWS

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What is the genetic

code?
The genetic code consists of the
sequence of bases found along the
mRNA molecule
There are only four letters to this
code (A, G, C and U)
The code needs to be complex
enough to represent 20 different
amino acids used to build proteins
2007 Paul Billiet ODWS

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How many combinations?

If one base represented one amino acid this would
only be able to produce
4 different combinations. (A, C, G and U)
If pairs of bases represented each amino acid this
would only be able to produce
4 x 4 = 16 combinations. (AA, AC, AG, AU, CA, CC,
CG, CU etc)
If triplets of bases represented each amino acid,
this would be able to produce
4 x 4 x 4 = 64 combinations
This is enough combinations to code for the 20
amino acids but is the code actually made of
triplets?
2007 Paul Billiet ODWS

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Nature is logical!
Over 10 years biochemists synthesised
bits of mRNA with different
combinations
Then they used them to synthesise
polypeptides
The results proved the logical answer
was correct
The genetic code is made of triplets of
bases called codons
2007 Paul Billiet ODWS

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Ribosomes initiate translation at ribosome-binding sites

in polycistronic procaryotic mRNAs, which can encode
more than one protein

07_33_mRNA.encode.jpg

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07_35_polyribosome.jpg

A polyribosome from a
eucaryotic cell

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Initiation of Translation in
Eukaryotes
AUG----------------Stop

Cap
5UTR

3UTR

AAAAAAAAA

Important points:
No direct binding between mRNA and rRNA
Small ribosome subunit binds directly to cap requires
specific initiation factor eIF4e
Other initiation factors can unwind double stranded regions
in the mRNA eIF4 group
Small subunit scans mRNA till it finds correct AUG
Correct AUG is embedded in preferred sequence
GccAccAUGG
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Proteins
Essential for all biological events

DNA carries the information

Protein does the business
Enormous diversity
functional
structural

Simple building-blocks L-amino acids

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 Kuliah Selanjutnya Protein

Selamat Belajar

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