COMPRESSED NOTES CHAPTER 6: EXPRESSION OF BIOLOGICAL INFORMATION SB015

6.1 DNA AND GENETIC INFORMATION

CONCEPT OF CENTRAL DOGMA

 The central dogma state that the flow of genetic information within a
biological system can only occur from DNA to RNA to protein.
 This concept was proposed by Francis Crick in 1956.
 General information transfer:
i. DNA  DNA (DNA replication)
ii. DNA  RNA (Transcription)
iii. RNA  protein (Translation) Protein synthesis
 Both transcription and translation occur during protein synthesis.
Transcription Translation
A process in which genetic A process of interpreting the
information in DNA is genetic information (codons) in
transcribed/ copied to form the mRNA into sequence of amino
mRNA acids.

6.2 DNA REPLICATION

 Definition: Process of producing two identical copies of DNA from one original DNA molecule. It
occurs in nucleus of eukaryotic cell during S phase (of interphase).
 1 chromosome consists of 2 sister chromatids bound to a centromere

(a) 3 Models of DNA replication:

Conservative Model Semi-conservative Model Dispersive model

 Two parental strands  Two parental strands of  Each strand of both daughter
recombine after acting as parental molecule separate, DNA molecules contains a
templates, thus restoring the each functions as a template mixture of old and newly
parental double helix. for synthesis a new DNA. synthesized DNA.
 Each DNA molecule consists  Each DNA produced consist of
of two intact old strands and one old strand and one new
two new strands. strand.

Experiments by Matthew
Meselson and Franklin Stahl
(1957) supported the semi-
conservative model.

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(b)The ENZYMES AND PROTEIN involved in DNA replication:

Enzyme Function
(DNA) Helicase Unwind the parental DNA double helix at replication fork. (by breaking the
hydrogen bond between nitrogenous bases)
Single-strand binding Binds to and stabilizes the single-stranded DNA to and avoid them from re-pairing
protein and this two single-stranded DNA will act as template for DNA replication.
Topoisomerase/ DNA Use to make sure that double stranded DNA outside of the replication fork does not
gyrase supercoil/ preventing supercoiling and knot formation during replication
Relieve the strain of unwound DNA by breaking, swiveling and rejoining DNA
strands
Primase Bind to the template strands and synthesize RNA primer (short sequence of RNA)
at the 5’ end of the strand.
DNA polymerase III Elongates new DNA strand by adding free DNA nucleotides by complementary
base pairing. A pair with T and G pair with C. The addition of new nucleotide
occurs at free 3’-OH. (The new strand is synthesized from 5’→3’ direction)
DNA polymerase I Replace RNA primer with DNA nucleotides.
DNA ligase Joins the DNA fragments (Okazaki fragments) by formation of phosphodiester
bond

(c)DNA replicates semi-conservatively. The mechanisms/steps involved in DNA replication:

Step Process Description
1 Unwinding of strand  Initiator protein binds to origin of replication
 Helicase unwinds the double helix strands of parental DNA at origin of
replication.
 Break the hydrogen bond between complementary nitrogenous bases
 2 polynucleotide strands separate
 Replication bubble consists of 2 replication fork formed.
2 Strands acts as template  Each of the single-strand of parental DNA will acts as template strands
for the new complementary DNA strands.
 Single-strand binding protein (SSB Protein) holds the separated DNA
strands apart and stabilize them while they act as template
 When double stranded DNA is unwound, it adds extra helical twist beyond
the unwound region
 DNA become more tightly twisted (overwinding/supercoil), creating a
strain to DNA strand
 Topoisomerase makes a nick by breaking the phosphodiester bond
 Topoisomerase helps relieve the strain of unwound double stranded DNA
and rejoin the DNA strands by reforming phosphodiester bond
3 Synthesis RNA primer  The primase will then synthesize RNA primers (about 10-60
nucleotides) at 5’end of leading strand and 5’end of each Okazaki
fragment of lagging strand (RNA nucleotide)
 RNA primer is synthesized to provide free 3’-hydroxyls end
 Which allow DNA polymerase III to start the synthesis of DNA strand
 by adding DNA nucleotide to the free 3’-hydroxyls end of these RNA
primers
4 Extension (DNA  After the synthesis of RNA primer, DNA polymerase III will add the free
nucleotides join up to nucleotide to the growing end (exposed bases at 3’ end) of RNA primer
the exposed bases by to synthesise a new DNA strands.
specific base pairing)  The nucleotide added is complementary to the bases of the template
strands.

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5 Formation of leading  At one of the DNA template, the DNA polymerase III synthesise a
and lagging strands complementary strands called the leading strands. The leading strands are
synthesized continuously towards the replication fork, using only one
RNA primer.
 Besides, the lagging strand elongates discontinuously, as a series of
segments called the Okazaki fragments. The direction is away from the
replication fork using several RNA primers.
 Other DNA polymerase (DNA polymerase I) replace the RNA primer
with DNA nucleotides in both strands. In lagging strands, this process
occur before DNA ligase can join the Okazaki fragments together.
6. Formation of new The new leading and lagging strands will only elongates from 5’-3’ direction
strand from 5’ to 3’ and thus resulting in two identical copies of the original DNA.

Basic rules of DNA

replication:
1. semi-conservative
2. starts at origin
3. new strand
synthesis from 5’
to 3’
4. primer is required
5. can be uni or
bidirectional

*Difference between LEADING AND LAGGING strand:

Leading strand Lagging strand
- New DNA copies toward the replication fork - Copies away from replication fork
- Continuous DNA synthesis - Discontinuous DNA synthesis
- Primase only add one RNA primer - Primase adds many RNA primers at various spots as
replication fork opens
- No formation of Okazaki fragments - Short fragments called Okazaki fragments formed

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Addition of nucleotides by DNA polymerase (III) during DNA replication at 3’-OH ends.

6.3 PROTEIN SYNTHESIS

(a) TRANSCRIPTION AND TRANSLATION
Transcription Translation
 Synthesis mRNA  Synthesis protein
 A process by which genetic information in DNA  The sequence of nucleotides in mRNA act as a
base sequence is copied or transcribed into template and is translated into sequence of
complementary sequence of pre-mRNA. amino acids.
 Pre- mRNA need to undergo RNA processing/
splicing in nucleus before mRNA exit to cytoplasm
and undergo translation.
 Pre-mRNA is longer than mature mRNA. During
RNA processing, spliceosome is used.
 The intron (non-coding sequence) is removed
 The exon (coding sequence that is to be translated
into protein/ polypeptide) is combine together
forming functional mRNA

(b) Properties of Genetic code

1. Composed of nucleotide triplets (triplet 2. Each codon represents 1 specific amino acid
code)  20 different amino acids commonly found in proteins
• 3 bases per codon  At least 20 different codons
• will result in 43 or 64 possible codons
3. The code is degenerate 4. Contain start & stop codons
• Most amino acids are coded by more • AUG is the start codon.
than one codon • UAG, UAA, UGA are the stop codons.
• Only 2 amino acids are coded by 1 codon • Do not code for any amino acid.
• 61 codons represent 20 amino acids Signals to terminate the coding sequence.
5. Almost universal 6. Non-overlapping
The same codon codes for the same amino  Each codon consists of 3 nucleotides
acids in all organisms  Sequence of codon is read continuously
 Until it reaches the termination point.

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7. Comma-free (commaless)
• There are no commas
• or other forms of punctuation
• within the coding regions of mRNA
• Codons are read consecutively

(b) Process in Protein synthesis (transcription)

i. TRANSCRIPTION
 Transcription process occurs in the nucleus. It is a process by which mRNA is synthesized using genetic
information from DNA.
 The enzyme involved is only RNA polymerase. Formation of mRNA strand is from 5’ to 3’.
 Transcription involves 3 main stages:
(a) Initiation
 RNA polymerase recognizes and binds to
DNA region called promoter, and then
unwind DNA double helix.
 Only one DNA strand acts as template
while the other strand is non-template
strand.
 RNA polymerase initiates RNA synthesis
at the start point of template DNA.
(b) Elongation
 As RNA polymerase moves along the
DNA template, it keep unwind the DNA
and adding free RNA nucleotides by
complementary base pairing.
 A pair with U and G pair with C. the
mRNA is synthesised from 5’ to 3’.
 Behind the point of mRNA synthesis,
double helix DNA reforms.
(c) Termination
 Transcription terminates when RNA
polymerase reaches terminator or ‘stop
signal’.
 The mRNA molecule is released from
template DNA strand.

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Basic rules of transcription:

- Only ONE strand of DNA act as template
- Single strand mRNA was produce
- The enzyme use is RNA polymerase

(d) Process in protein synthesis (Translation)

ii. TRANSLATION
 Translation process occurs in the cytoplasm of a cell. It is a process of translating the genetic information
from mRNA into a polypeptide/ protein. Translation involves 3 types of RNA that are:
Types of RNA Function
(a) mRNA  Function: Carries genetic information
transcript from DNA in nucleus to
cytoplasm.
 Characteristics of genetic code on mRNA:
 in the form of “triplets bases” called codon
 Non-overlapping- each codon codes for
one amino acid.
 Degenerate - more than one codon can
specify the same amino acid
 Almost universal in all living organism
 Start codon is AUG
 Stop codon are UAA, UAG and UGA and
do not code for any amino acid
Codon = triplet bases found on mRNA which  There are 64 possible combinations of
codes for a specific amino acid triplet bases.
(b) tRNA  Single strand RNA that folded into cloverleaf
shape by hydrogen bond.
 Function: Brings specific amino acids to the
particular codon on the mRNA. Amino acid
carried by tRNA determined by specific triplet
bases called anticodon.
 Anticodon region of tRNA will matches the
codon on mRNA
 Amino acid attach to tRNA by a process called
as activation of amino acids.
 The enzyme aminoacyl-tRNA synthetase
Anticodon = triplet bases found on tRNA which attaches a specific amino acid to tRNA

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form base pairs with a specific codon on  by using energy from ATP
the mRNA  forming aminoacyl-tRNA/ charged tRNA
 covalent bond formed between tRNA and
amino acid
(c) ribosome (rRNA+ protein)  Function: rRNA combines with proteins to
form organelles called ribosome. It plays
catalytic roles and structural roles in ribosome/
assist protein synthesis
 Ribosome consist of large and small subunit
 It facilitate the specific coupling of tRNA
anticodons with mRNA codons during
translation
 Ribosome have 3 site that are:
(a) E (exit) site
(b) P (Peptidyl-tRNA binding site): Holds the
tRNA carrying the growing polypeptide
chain.
(c) A (Aminoacyl-tRNA binding site): Holds
the tRNA carrying the next amino acid to
be added to the chain.

STAGES IN TRANSLATION PROCESS

Activation of Amino Acids  mRNA codon carries the code for amino
acids.
 Anticodon (of tRNA) has a specific
complementary binding sequence for the
codon (of mRNA).
 Each kind of tRNA binds to a specific
amino acid
 to form aminoacyl-tRNA,
 catalysed by aminoacyl-tRNA synthetase.
 ATP is used as energy source.
 There are 20 different aminoacyl-tRNA
synthetases.
 tRNA is re-activated many times.
 Amino acids are linked to their respective
tRNA molecules by the formation of ester
bond,
 at the 3’end of tRNA.
1. Initiation  Small ribosomal subunit binds to start
codon, AUG at mRNA
 An initiator tRNA with the anticodon,
UAC attaches to the start codon, AUG on
mRNA. This tRNA carries first amino acid
that is methionine.
 The arrival of large ribosomal subunit
E completes the initiation complex.
 Initiator tRNA occupies the P site. The A
site is available for the next tRNA.

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2. Elongation - Amino acid are added one by one to the initial i. Codon recognition
amino acid.  The next tRNA with specific amino acid
binds at the A site.
 The incoming tRNA anticodon has
complementary base pair with the mRNA
codon. Hydrogen bond form between
mRNA codon and the anticodon of tRNA.
ii. Peptide bond formation
 The growing polypeptide chain detached
from tRNA in P site, and attached to the
E amino acid carried by the new tRNA at the
A site.
 Peptidyl transferase (component of large
ribosomal subunit ) catalyses the
formation of peptide bond
 Result in empty tRNA in P site and
polypeptide attach to the tRNA in the A
site.
iii. Translocation
 The ribosome moves to the next codon of
the mRNA. It translocate the tRNA in the
A site to the P site.
E E
 The empty tRNA in the P site (uncharged
tRNA) then released to the E site while
the A site ready to accept new tRNA.
 The process is repeated until complete
polypeptide chain is formed.
3. Termination  When a ribosome reaches a stop codon
on mRNA, the A site of the ribosome
accepts a protein called release factor
 A release factor binds to stop codon &
hydrolyses the bond (by addition of
water molecule) between polypeptide &
tRNA in P site.
 Polypeptide is release from ribosome
while the ribosomal subunit dissociate.

POLYRIBOSOME
 Multiple ribosome bind to the single mRNA to form
polyribosome
 A single mRNA is used to make many polypeptide
chain simultaneously
 When the first ribosome moves past the initiation (start)
codon, the second ribosome will bind to the same
mRNA
 Significance: Produce many copies/ large amount of
polypeptide chains rapidly

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6.4 GENE REGULATION AND EXPRESSION: lac operon

 Operon is a cluster of genes regulated as a single unit. (Single mRNA produced contains genes that
produced a few enzymes simultaneously).
 Operon consist of a group of two or more structural genes having a related function
 Operon is regulated as a single transcriptional unit by a single promoter.
 These genes are transcribed into a single mRNA.
 To allow bacteria to synthesize all enzymes needed to metabolize a substrate at once if the substrate is
present.
 Lactose (lac) operon is introduced by Jacob and Monod (1961).
 lac operon contains genes that encode for enzymes used in the hydrolysis and metabolism of lactose in
E. coli bacteria. Only prokaryote has operon.
 lac operon consists of:

i. Structural genes ( lacZ, lacY and lacA)

Structural Function Function of enzyme produce
gene
lacZ Gene encoding for β- Hydrolyses/ break down lactose to glucose and galactose
galactosidase
lacY Gene encoding for lactose Facilitate the entry or uptake of lactose into E.coli //
permease Allow uptake of lactose and increase permeability of
membrane to lactose.
lacA Gene encoding for Transfer an acetyl group from acetyl-CoA to β-
transacetylase galactosidase
ii. Promoter gene
-Binding site for RNA polymerase to initiate the transcription (of structural genes)
iii. Operator gene
-Binding site for repressor protein
-Act as switch; which activate or inactivate the operon
 Regulatory gene (lacI) located outside the operon, codes for repressor protein.

MECHANISM OF LAC OPERON

LACTOSE ABSENT LACTOSE PRESENT
 No inducer (lactose)  Inducer is present (lactose)
 Repressor protein is synthesized by  Some lactose are converted into allolactose
regulatory gene  Allolactose binds to repressor protein
 The repressor protein binds to operator  Repressor protein change its conformation/ shape
 Repressor protein cannot binds to operator gene
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 RNA polymerase cannot bind to the  RNA polymerase binds to promoter gene
promoter  Lac operon is activated/ switch on :
 Lac operon is inactivated/ switch off :  structural genes ( lacZ, lacY and lacA) are
 structural genes ( lacZ, lacY and transcribed into mRNA
lacA) are not transcribed.  mRNA is translated by ribosome to produce enzymes
 enzymes β-galactosidase, β-galactosidase, permease and transacetylase are not
permease and transacetylase are produced
not produced.  lactose is broken down into glucose and galactose
 no broken down of lactose

State the differences between DNA replication and transcription.

DNA Replication Transcription
i) Involve copying the whole DNA molecule i) Involve copying specific regions of DNA
ii) Both DNA strands acts as a template ii) Only one DNA strand acts as template
iii) Produces two molecules of double stranded DNA iii) Produces a single stranded mRNA molecule
iv) Involves DNA polymerase iv) Involves RNA polymerase
v) Occurs during interphase only v) Occurs throughout the life of the cell
vi) RNA primer is required vi) RNA primer is not required

State the differences between transcription and translation.

Transcription Translation
Occurs in the nucleus Occurs in the cytoplasm/ cytosol
Only one DNA strand acts as template mRNA acts as template
Produces a single-stranded mRNA Produces a polypeptide chain

END OF TOPIC

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