Gene Expression

from DNA to Protein

D. Renovaldi, M.Sc. (Biomed)
Faculty of Medicine & Health
Universitas Muhammadiyah Jakarta
THE GENE

Source: National Human Genome Research Institute.

 GENE STRUCTURE

 Eukaryotic gene structure:

 The average gene 7-10 exons spread over 10- 16kb of DNA.
 The gene must have (Exon; start signals; stop signals; regulatory
control elements).

Gene structure
Exons (The coding sequences)
 Introns (The non coding sequences).

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 GENE STRUCTURE

The genes consist of; short coding sequences or exons are interrupted
by a longer intervening noncoding sequence or introns; although a
few genes in the human genome have no introns.
From DNA to Protein
DNA does not direct protein synthesis itself, but acts rather like a manager, delegating the
various tasks to a team of workers. When a particular protein is needed by the cell, the
nucleotide sequence of the appropriate section of an immensely long DNA molecule in a
chromosome is first copied into another type of nucleic acid—RNA (ribonucleic acid).

These RNA copies of short segments of the DNA are then used to direct the synthesis of the
protein. Many thousands of these conversions from DNA to protein occur each second in every
cell in our bodies.

The flow of genetic information in cells is therefore from DNA to RNA to protein (Figure 7–1). All
cells, from bacteria to humans, express their genetic information in this way—a principle so
fundamental that it has been termed the central dogma of molecular biology.
Central dogma of
Molecular
Biology
 GENE EXPRESSION

Transcription
RNA polymerase makes a copy of information in the gene (complementary
RNA) complementary to one strands of DNA.

Translation

Occurs on ribosomes, messenger RNA decoded or translated to determine

the sequence of amino acid in the protein being synthesized.
TRANSCRIPTION
From DNA to mRNA
 Transcription
● The first step a cell takes in reading out one of its many thousands of genes is to copy the nucleotide
sequence of that gene into RNA.
● The process is called transcription because the information, though copied into another chemical form, is
still written in essentially the same language of nucleotides
● Transcription is controlled by regulatory DNA sequences and protein transcription factors.
● RNA polymerase is the enzyme responsible for making mRNA copies of genes. DNA unzips at the site of the
gene that is needed.
 Transcription
The process of production of RNA from DNA is called transcription; it
consists of three stages:

1) Initiation – the RNA polymerase enzyme binds to a promoter site on the

DNA and unzips the double helix.
2) Elongation – free nucleotides bind to their complementary pairs on the
template strand of the DNA elongating the RNA chain which is identical
to the informational strand of DNA, except that the nucleotide thymine
in DNA is replaced by uracil in RNA. The polymerase moves along the
DNA in the 3’ to 5’ direction, extending the RNA 5’ to 3’.
3) Termination – specific sequences in the DNA signal termination of
transcription; when one of these is encountered by the polymerase, the
RNA transcript is released from the DNA and the double helix can zip up
again.
 Activators Promoter
Gene
DNA
Enhancer Distal control TATA
element box
General
transcription
factors
DNA-bending
protein

Group of
mediator proteins

RNA
polymerase II

RNA
polymerase II

Transcription
initiation complex RNA synthesis
– Most eukaryotes have a TATA box promoter.
– Enhancers and silencers speed up or slow down the rate of
transcription.
– Each gene has a unique combination of regulatory
sequences.
 mRNA processing includes three major steps.

– Introns are removed and exons are spliced together.

– A cap is added.
– A tail is added.
RNA Processing (Pre-mRNA → mRNA)
Capping

The cap structure is added to the 5' of the newly transcribed mRNA precursor in the
nucleus prior to processing and subsequent transport of the mRNA molecule to the
cytoplasm.

Splicing

Joining of exons; it takes place on a special structure called spliceosomes.

Addition of poly A tail

Synthesis of the poly (A) tail involves cleavage of its 3' end and then the addition of
about 40- 200 adenine residues to form a poly (A) tail.
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 Splicing
● The original transcript from the DNA is
called heavy nuclear RNA (hnRNA).
● It contains transcripts of both introns
and exons.
● The introns are removed by a process
called splicing to produce messenger
RNA (mRNA) and the ends of the RNA
molecule are processed.
TRANSCRIPTION

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 ALTERNATIVE SPLICING

 Alternative splicing: is a very common phenomenon in higher

eukaryotes. It is a way to get more than one protein product out of the
same gene and a way to control gene expression in cells.

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TRANSLATION
From mRNA to Protein
 Translation
• Special molecules called transfer RNAs (tRNAs) recognise both
an amino acid and a triplet of nucleotides (a codon). The tRNA
molecule has an anticodon on one end which binds to a codon on
the mRNA and to a specific amino acid on the other end. It thus
enforces the genetic code in which a codon codes for a specific
amino acid.
• Protein synthesis takes place on the ribosomes. The tRNAs position
themselves for reading the genetic message in the mRNA. The first
tRNA binds to a start codon (AUG) on the mRNA and then each
tRNA adds an amino acid to a growing polypeptide (protein)
chain.
Three tRNA binding
sites:
A site = amino-acyl
tRNA binding site

P site = peptidyl-tRNA
binding site

E site = exit site

Translation
Initiation begins with a tRNA
bearing methionine (met) attaching
to one of the ribosomal units.

The codon for methionine is a

universal “start” codon for “reading”
the mRNA strand.
Translation
The ribosomal unit binds to
mRNA where the code for met is
located (AUG).

The anticodon (UAC) of the

tRNA matches the “start” codon
on mRNA (AUG).
Translation
The larger ribosomal subunit
now binds to the smaller unit,
forming a ribosomal complex.

The tRNA binds to the first active

site on the ribosome. Translation
may now begin.
Translation
The second codon in mRNA
(GUU) matches the anticodon of
a tRNA carrying the amino acid
valine (CAA).

The second tRNA binds to the

second active site on the large
subunit.
Translation
A catalytic site on the larger
subunit binds the two amino
acids together using dehydration
synthesis, forming a peptide
bond between them.
Translation
The first tRNA now detaches
and goes of to find another met
in the cytoplasm.

The mRNA chain shifts over one

codon, placing the second codon
(CAU) over the second active
site.
Translation
A tRNA with an anticodon (GUA)
matching the exposed codon
(CAU) moves onto the ribosome.

This tRNA carries histidine (his).

Translation
A new peptide bond forms
between val and his on the
catalytic site.

The tRNA that carried val will

detach and find another val in
the cytoplasm.

The mRNA strand will then shift

over one more codon.
Translation
The process continues until the
ribosome finds a “stop” codon.

The subunits detach from one

another, the mRNA is released,
and the polypeptide chain moves
down the ER for further
processing.

The initial met is removed and

the chain is folded into its final
shape.
PROTEIN
 Protein
• A protein is a linear polymer of amino acids linked together
by peptide bonds.
• The average protein is c. 200 amino acids long, but some
can contain thousands of amino acids.
• Proteins are the main functional chemicals in the cell,
carrying out many functions, for example catalysis of the
reactions involved in metabolism.
• Proteins have a complex structure which can be thought of
as having four structural levels.
 Primary structure
• Primary structure of a protein is simply the linear sequence of
amino acid in its polypeptide chain(s)
(NB proteins are written in order from the amino-teminal end to
the carboxy-terminal end, so Ala-Cys-Phe is different from Phe-
Cys-Ala)

• Eg. first 100 (of 457) amino acids in hexokinase:

AASX DXSLVEVHXXVFIVPPXILQAVVSIATTRXDDXDS
AAASIPMVPGWVLKQVXGSQAGSFLAIVMGGGDLEVILIXLAGY
Q E S S I X A S R S L A A S M X T ……
MUTATION
 MUTATION
• Any mistakes in the DNA code can result in a
“broken” (non-functional) protein.
• A mutation affecting only a few somatic cells
(body cells) might not have any effect, unless
the mutation turns the cell cancerous.
• A mutation affecting a sex cell can be passed
on to the offspring.
 Types of Mutation
• Point mutation: base substitution that may or
may not code for a different amino acid.

• Insertion mutation: one or more bases is

inserted into the DNA strand.

• Deletion: one or more bases is deleted from

the DNA strand.
 Hemoglobin Mutation
Properties of Effect on
DNA mRNA Amino Acid Disease
AA protein
Original
CTC GAG Glutamic Acid Hydrophilic Normal None
codon 6

Mutation 1 CTT GAA Glutamic Acid Hydrophilic Neutral None

Mutation 2 GTC CAG Glutamine Hydrophilic Neutral None

Loses water Sickle Cell

Mutation 3 CAC GUG Valine Hydrophobic
solubility Anemia
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from DNA to PROTEIN