Gene Expression

dr. I Wayan Surudarma, M.Si.

Biochemistry Dept. of Medicine Faculty

Udayana University
 Definition of the Gene
 A hereditary unit consisting of a sequence
of DNA that occupies a specific location on
a chromosome and determines a
particular characteristic in an organism.
 A segment of DNA that is involved in
producing a polypeptide chain.

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 Gene expression

 Gene expression is the process by which

information from a gene is used in the
synthesis of proteins.

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 Steps in the gene expression
Steps in the gene expression:
1. Transcription
• Post-transcriptional modification
2. Translation
• Post-translational modification

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 Transcription
 Transcription: the synthesis of RNA
using DNA as a template.
 Key Factors
1. DNA Template
2. RNA Polymerase
3. NTP : ATP, GTP, CTP, UTP
4. Transcription Factors (eukaryotes)

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 DNA Template
The stretch of DNA that will be transcribed
 Transcription Unit

3 critical regions of Transcription Unit :

1. Promoter
2. RNA Coding Region
3. Terminator

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Transcription Unit

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 Promoter
 Promoter: region of DNA (transcription
unit) where RNA polymerase attaches
and initiates transcription.

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 RNA Polymerase
 RNA polymerases are large multimeric
enzymes that transcribe defined segments
of DNA into RNA.

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 Eukaryotic
RNA Polymerase
 Eukaryotes
have 3 different RNA
polymerases
 RNA polymerase I, II, III
 Each transcribes a different set of genes

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 Stages of Transcription
1. Initiation
 RNA polymerase recognizes promoter and
attached to DNA
2. Elongation
 The RNA polymerase travels along the DNA
adding ribonucleotides that pair with the
DNA template
3. Termination

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 Termination
 Transcription ends after a terminator is
transcribed
 Two types termination:
 Rho-independant
 Rho-dependant

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Rho-independent Termination

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 Eukaryotic Transcription
 Eukaryotic Transcription is more
complicated!
 Three different polymerases

 Many proteins required

• Transcription factors
• Activator
• Repressor

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 Enhancer is a short region of DNA that
can be bound with activator proteins to
enhance transcription levels of genes.
 Silencer is a DNA sequence capable of
binding repressors protein that
suppressing transcription levels of genes.
 Activator is a protein that increases gene
transcription.
 Repressor is a protein that suppress gene
transcription.
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 Post Transcriptional Modification

 RNA processing achieves three things:

1. Addition of a 5’ cap
2. Addition of a 3’ tail
3. Removal of introns  splicing

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Translation
 Translation
 Process of converting information stored in
mRNA into proteins
 Key Factors
 Template - mRNA

 Ribosomes

 tRNAs

 Amino acids

 Release Factor

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 mRNA
 Molecule of RNA that encodes sequence
of the polypeptide.
 3 regions of mRNA:
• 5’ end has binding sites for translation

initiation
• Middle is a coding sequence

• 3’ end regulates stability of mRNA

 mRNA bases read as triplets (codons).

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Codon

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 The genetic code
 The genetic code is the set of rules by
which information encoded in mRNA is
translated into proteins by living cells.

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Genetic code

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 Genetic code
1. Universal: all organisms use the same
code in the formation of protein
2. Degenerate: some amino acids are
specified by more than one codon
3. Unpunctuated
4. Not ambiguous
5. Not overlapping

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 The start codons
 In bacteria: usually AUG, sometimes GUG,
even UUG
 In eukaryotic cells: always AUG
 Defines the reading frame for all
subsequent codons

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 The stop codons
 Define the end of the open-reading frame
and signal termination of polypeptide
synthesis.
 Three kinds:
 UAA
 UAG
 UGA

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 Anticodon
 Anticodon is a triplet of nucleotides in a
tRNA molecules that aligns by
complementary base pairing with an
mRNA codon.

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 tRNA
 Deliveramino acids to the translational
complex
 as adapters between codons in mRNA
and amino acid
 L-shaped secondary structure
 Anticodon and amino acid are at the
opposite arm of the L-shaped

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 Ribosomes
 Nucleoprotein
 Composed of small and large subunit
 Subunits bind together for translation

 Decoding and synthesis takes place in the

cavity between subunits

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 Stages of Translation

1. Initiation
2. Elongation
3. Termination

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 Initiation
 The small sub unit binds to both the
mRNA and a special initiator tRNA (met-
tRNA)
 The large ribosomal subunit attaches to
the small subunit such that the first codon
is aligned at the P binding site.
 This inititates elongation.

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 Elongation
 Attachment of amino acid-tRNA to A
binding site.
 Peptide transfer and peptide bond
formation between the peptide & the amino
acid carried at the A binding site.
 Ribosome moves in the 3' direction down
the mRNA  by three bases or one codon.
 tRNA ejected from the E binding site.

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 Termination
 The polypeptide chain is at the P site. The
stop codon at the A site.
 A Release factor protein binds to the stop
codon at the A binding site.
 Release factor protein initiates separation
of polypeptide chain
 Separation of translation machinary.

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 Post-translational modifications
 A newly synthesized polypeptide chain must
undergo post-translational processing to
generate the final protein
 Post-translational modifications include:
 Targeting to the appropriate cell compartment
 Folding
 Addition of sugar chains
 Formation of disulfide bonds

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