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1 | KMPk
BIOLOGY NOTES
CHAPTER 6 : EXPRESSION OF BIOLOGICAL INFORMATION
SUBTOPIC 6.1: DNA and genetic information
LEARNING OUTCOMES: a) State the concept of Central Dogma
MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Central Dogma
Definition: The ‘Central Dogma’ is the process by which the
instructions in DNA are converted into a functional product. It
was first proposed in 1958 by Francis Crick, discoverer of the
structure of DNA.
The central dogma of molecular biology explains the
flow of genetic information, from DNA to RNA to make
a functional product, a protein.
The central dogma suggests that DNA contains the
information needed to make all of our proteins, and that
RNA is a messenger that carries this information to
the ribosomes.
The ribosomes serve as factories in the cell where the
information is ‘translated’ from a code into the
functional product.
The process by which the DNA instructions are
converted into the functional product is called gene
expression.
Gene expression has two key stages- transcription and
translation.
In transcription, the information in the DNA of every
cell is converted into small, portable RNA messages.
During translation, these messages travel from where the
DNA is in the cell nucleus to the ribosomes where they
are ‘read’ to make specific protein.
The central dogma states that the pattern of information
that occurs most frequently in our cells is:
o From existing DNA to make new DNA (DNA
replication)
o From DNA to make new RNA (transcription)
o From RNA to make new proteins (translation)
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Concept of Central Dogma: An illustration showing the flow of information between DNA, RNA
and protein.
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BIOLOGY NOTES
CHAPTER 6 : EXPRESSION OF BIOLOGICAL INFORMATION
SUBTOPIC 6.2 : DNA Replication
LEARNING OUTCOMES: a) Explain the semi-conservative replication of DNA.
b) Explain the enzymes and proteins involved in DNA replication.
c) Explain the mechanism of DNA replication and the enzymes involved.
MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Models of
DNA
replication:
Semi-
conservative
DNA replication is the biological process of producing two
identical replicas of DNA from one original DNA molecule.
DNA is made up of a double helix of two complementary
strands.
During replication, these strands are separated. Each strand
of the original DNA molecule then serves as a template for
the production of its counterpart, a process referred to
as semi-conservative replication.
This semi-conservative replication model has been
demonstrated by Meselson and Stahl.
As a result of semi-conservative replication, the new helix
will be composed of an original DNA strand as well as a
newly synthesize strand.
Cellular proofreading and error-checking mechanisms ensure
near perfect fidelity for DNA replication
Enzymes and
proteins
involved in
DNA
replication
No. Enzyme/Protein Function
1 Helicases
catalyzed the untwist the double
helix at the replication forks,
separating the two parental strands
and making them available as
template strands.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
2 Topoisomerase
The untwisting of the double helix
causes tighter twisting and strain
ahead of the replication fork.
Topoisomerase catalyzed in
relieving this strain by breaking,
swiveling and rejoining DNA
strands.
3 Primase
Catalysed the synthesis of short
RNA primer (using DNA strand as
a template), generally 5-10
nucleotides long.
4 DNA
polymerase I
Cataysed the removal of primer
from the 5’end and replacing it
with DNA nucleotides added one
by one to the 3’ end.
5 DNA
polymerase III
Cataysed the synthesizing new
DNA strand by adding nucleotides
to an RNA primer or a pre-
existing DNA strand by using
parental DNA strands as a
template.
6 DNA ligase
Cataysed the joining of Okazaki
fragments of lagging strand; on
leading strand, catalyzed the
joining of 3’ end of DNA that
replaces primer to rest of leading
strand DNA.
7 Single-strand
binding proteins
Bind to the unpaired DNA strands,
keeping them from re-pairing/
stabilized the unwound parental
strands.
• Special properties of DNA polymerase III:
• Cannot initiate the synthesis of a DNA strand all by itself.
• Need an RNA primer
• Complementary to the parental DNA strand
• Can only add new nucleotides in 5’ to 3’ end direction.
• Can only add a nucleotide to the 3' end of an already
growing chain
• Has important implications for antiparallel strands
running in opposite directions.
Mechanism of
DNA
replication and
the enzymes
involved
Step 1: Replication Fork Formation
• Before DNA can be replicated, the double stranded molecule
must be “unzipped” into two single strands.
• In order to unwind DNA, these interactions between base pairs
must be broken. This is performed by an enzyme known as DNA
helicase.
• DNA helicase disrupts the hydrogen bonding between base pairs
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
to separate the strands into a Y shape known as the replication
fork. This area will be the template for replication to begin.
• The replication fork is bi-directional; one strand is oriented in the
3' to 5' direction (leading strand) while the other is oriented 5' to
3' (lagging strand).
• After the parental strands separate, single-strand binding
proteins bind to the unpaired DNA strands, keeping them from
re-pairing.
• The untwisting of the double helix causes tighter twisting and
strain ahead of the replication fork. Topoisomerase helps relieve
this strain by breaking, swiveling, and rejoining DNA strands.
Step 2: Primer Binding
• Once the DNA strands have been separated, a short piece of RNA
called a primer binds to the 3' end of the strand.
• The primer always binds as the starting point for replication.
Primers are generated by the enzyme primase.
• Primase starts a complementary RNA chain from single RNA
nucleotide, adding more RNA nucleotides one at a time, using
DNA strand as a template.
• The completed primer, generally 5-10 nucleotides long.
• The new DNA strand will start from 3’ end of the RNA primer.
Step 3: Elongation
• Enzymes known as DNA polymerases are responsible creating
the new strand by a process called elongation.
• DNA polymerase III binds to the strand at the site of the primer
and begins adding new base pairs complementary to the RNA
primer and then continues adding DNA nucleotides,
complementary to the parental DNA strand template strand, to the
growing end of the new DNA strand.
• Because replication proceeds in the 5' to 3' direction on the
leading strand, the newly formed strand is continuous.
• The lagging strand begins replication by binding with multiple
primers. Each primer is only several bases apart.
• DNA polymerase III then adds pieces of DNA, called Okazaki
fragments, to the strand between primers.
• This process of replication is discontinuous as the newly created
fragments are disjointed.
• After Okazaki fragment forms, DNA polymerase I, replaces the
RNA nucleotides of the adjacent primer with DNA nucleotides.
Step 4: Termination
• Once both the continuous and discontinuous strands are formed,
an enzyme called exonuclease removes all RNA primers from the
original strands.
• These primers are then replaced with appropriate bases.
Another exonuclease “proofreads” the newly formed DNA to
check, remove and replace any errors.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
• Another enzyme called DNA ligase joins Okazaki fragments
together forming a single unified strand.
• The ends of the linear DNA present a problem as DNA
polymerase can only add nucleotides in the 5′ to 3′ direction.
• The ends of the parent strands consist of repeated DNA sequences
called telomeres. Telomeres act as protective caps at the end of
chromosomes to prevent nearby chromosomes from fusing.
• A special type of DNA polymerase enzyme called telomerase
catalyzes the synthesis of telomere sequences at the ends of the
DNA.
• Once completed, the parent strand and its complementary DNA
strand coils into the familiar double helix shape. In the end,
replication produces two DNA molecules, each with one strand
from the parent molecule and one new strand.
• Differences between leading strand and lagging strand.
Leading strand Lagging strand
Synthesized continuously
TOWARDS replication fork
Synthesized discontinuously
AWAY from replication fork
No formation of Okazaki
fragments
Formation of several Okazaki
fragments
BOTH require RNA primer to initiate replication
Mechanism of DNA replication and the enzyme involved.
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BIOLOGY NOTES
CHAPTER 6 : EXPRESSION OF BIOLOGICAL INFORMATION
SUBTOPIC 6.3: Protein synthesis : Transcription and translation
LEARNING OUTCOMES: a) Explain briefly transcription and translation
b) Introduce codon and its relationship with sequence of amino acid using genetic
code table.
c) Explain transcription and the stage involved (initiation, elongation and
termination) in the formation of mRNA strand from 5’ to 3’.
d) Explain translation and the stages involved in translation:
i. initiation
ii. elongation (codon recognition, peptide bond formation and translocation)
iii. termination
MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Roles of
transcription
and translation
Definition of protein synthesis:
the process by which amino acids are linearly arranged into proteins
through the involvement of ribosomal RNA, transfer RNA, messenger
RNA, and various enzymes.
Transcription:
Transcription is the first step of gene expression, in which a particular
segment of DNA is copied into RNA by the enzyme RNA polymerase.
Both DNA and RNA are nucleic acids, which use base pairs of
nucleotides as a complementary language.
Translation:
In translation, messenger RNA (mRNA) is decoded in a ribosome,
outside the nucleus, to produce a specific amino acid chain, or
polypeptide. The polypeptide later folds into an active protein and
performs its functions in the cell.
Importance of
Protein
Synthesis
There are many different types of proteins and associated functions.
Some more commonly used examples are:
Enzymes are protein molecules that catalyze biochemical reactions.
Common examples are enzymes involved in digestion. Amylase,
which breaks down starch into sugars and is present in the saliva of
mammals. Pepsin and trypsin are enzymes involved in the protein
digestion. Pepsin and trypsin cleaves the large protein molecules into
shorter polypeptides which can be passed through the lining of the
small intestine.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Hormones are proteins that are able to transmit signals from one body
location to another. Insulin is an extracellular protein and regulates the
metabolism of glucose controlling the levels of blood sugar.
Contractile proteins, like actin and myosin in the muscles, are
involved in movement.
Structural protein is usually filamentous and are used to provide
support. Keratin strengthen protective coverings such as hair and
nails. Collagen and elastin are important component of the connective
tissue, which build tendons and ligaments.
Transport proteins supply different cellular processes with the
required ions, small molecules, or macromolecules, such as another
protein. Most common transport proteins are integral membrane
proteins they are involved in the transport across a biological
membrane.
Antibodies are another class of protein which are involved in immune
response. Their primary function is to bind to foreign for the body
substances and thus to identify them for destruction. Antibodies are
usually anchored in the membranes of the immune response cells or are
excreted into the extracellular matrix.
Transcription
In transcription, a portion of the double-stranded DNA template gives
rise to a single-stranded RNA molecule. This process occurs in
nucleus as it copies DNA into mRNA.
Enzyme involved in this process is RNA polymerase.
Functions:
1. Select which gene to transcribe
2. Recognizes which of the 2 paired DNA strands it should copy
(act as template)
3. Identifies where it should begin and end transcription
4. Unwinds DNA double helix by breaking the hydrogen bonds
5. Adding new RNA nucleotides in 5’ – 3’ direction, doesn’t
requires a primer
6. Rewinds the DNA strands
Stages : 1. Initiation
2. Elongation
3. Termination
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
1. Initiaition:
The first step in transcription is initiation, when the RNA
polymerase binds to the DNA upstream (5′) of the gene at a
specialized sequence called a promoter.
The promoter of a gene includes within in the transcription start
point - the nucleotide where RNA polymerase actually begins
synthesis of the mRNA – and typically extends several dozen or
so nucleotide pair upstream from the start point.
RNA polymerase binds in a precise location and orientation on the
promoter. This in turn determines where transcription starts and
which of the two strands of DNA helix is used as the template.
In eukaryotes, a collection of protein called transcription factors
mediate the binding of RNA polymerase and the initiation of
transcription (Only after transcription factors are attached to the
promoter does RNA polymerase bind to it).
Once the appropriate transcription factors are firmly attached to
the promoter DNA and the RNA polymerase is bound to them in
the correct orientation on DNA, the enzyme unwinds the two
DNA strands and begins transcribing the template strand at the
start point.
2. Elongation:
As RNA polymerase moves along DNA, it untwists the double
helix, exposing about 10-20 DNA nucleotides at a time for pairing
with RNA nucleotides.
The enzyme adds nucleotides to the 3’ end of the growing RNA
molecule as it continues along the double helix.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Transcription progress at a rate of about 40 nucleotides per second
in eukaryotes.
A single gene can be transcribed simultaneously by several
molecules of RNA polymerase. The congregation of many
polymerase molecules simultaneously transcribing a single gene
increases the amount of mRNA transcribed from it, which helps
the cell make the encoded protein in large amounts.
3. Termination:
Bacteria and eukaryotes differ in the way they terminate
transcription.
In bacteria, transcription proceeds through a terminator
sequence in the DNA. The transcribed terminator functions as
the terminator signal, causing the polymerase to detach from
the DNA and release the transcript (requires no further
modification before translation).
In eukaryotes, RNA polymerase transcribed a sequence on the
DNA called polyadenylation signal sequence, which specifies
a signal to cut the RNA transcript free from RNA polymerase,
releasing the pre-mRNA.
The pre-mRNA then undergoes splicing process. During this
process, certain interior sections of RNA molecule / non-
coding region (intron) are cut out and the remaining parts/
coding region (exon) spliced together producing an mRNA
molecule that ready for translation.
How is pre-mRNA spicing carried out?
- The removal of introns is accomplished by a large
complex made of protein and small RNAs called
spliceosome.
- This complex binds to several short nucleotide
sequence along an intron, the intron is then release
(and rapidly degraded), and spliceosome joins together
the two exons that flanked the intron.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Relationship
between base
sequences in
codons with
specific amino
acids using
genetic code
table
Codon:
A triplets of nucleotides within mRNA that codes
for an amino acid. Codon are customarily written in the 5’ 3’
direction.
Characteristics:
• 1 codon consists of triplet nucleotide combination.
o There are 64 codons in genetic code table
o Only 61 codon specify amino acids
• One start codon, AUG o Encodes for Methionine (Met)
o Since AUG is the start codon and codes for methionine,
do all protein have methionine as the first amino acid?
Explain.
• 3 stop codons: UAA,UGA, UAG o Termination codons
o Do not specify amino acids.
• Non-overlapping - E.g : Codon 5’ AUGUCUAGU 3’ read as 5’ AUG, UCU,
AGU 3’ NOT 5’ AUG, GUC, CUA, AGU 3’
• 1 codon specify for particular amino acid
• 1 amino acid encoded by several (1/more) codon(s)
Translation
• During translation, the sequence of codons along an mRNA
molecule is decoded, or translated, into a sequence of amino acids
making up a polypeptide chain.
• This process occurs in cytoplasm.
• Fascilitates by transfer RNA/ tRNA.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
• Anticodon:
A nucleotide triplet at one end of a tRNA molecule that base pairs
with a particular complementary to codon on an mRNA molecule.
Anticodons are conventionally written 3’ 5’ to align properly
with codons written 5’ 3’.
• Before translation can takes place:
– Each amino acid is matched with the correct tRNA by a
specific enzyme called aminoacyl-tRNA synthetases.
– This process is known as: activation of amino acids.
Stages of translation:
1. Initiation:
The start codon (AUG) signals the start of translation (this is
important because it establishes the codon reading frame for the
mRNA)
In the first step of translation, small ribosomal subunit binds to
both the mRNA and specific initiator tRNA, which carries the
amino acid methionine.
In eukaryotes, the small subunit with the initiator tRNA
already bound, binds to the 5’ cap of the mRNA and then moves
(or scans), downstream along mRNA until it reaches the start
codon; the initiator tRNA then hydrogen-bonds to the AUG start
codon.
The first components to associate with each other during the
initiation stage of translation are mRNA, a tRNA bearing the
first amino acid of the polypeptide, and the small ribosomal
subunit.
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
This followed by the attachment of a large ribosomal subunit,
completing the translation initiation complex.
At the completion of the initiation process, the initiator tRNA
sits in the P site of the ribosome, and the vacant A site is ready
for the next aminoacyl tRNA.
2. Elongation:
In the elongation stage of translation, amino acids are added
one by one to the previous amino acids at the C-terminus of
growing chain.
The mRNA is moved through the ribosome in one direction
only, 5’ end first; this is equivalent to the ribosome moving 5’
3’ on the mRNA
Involve 3 process; codon recognition, peptide bond formation
and translocation.
During codon recognition: Anticodon of the 2nd aminoacyl-
tRNA base-pairs with the complementary 2nd codon in A site
Peptide bond formation: A peptide bond between the two
amino acids is formed. The reaction is catalyzed by rRNA
molecule of large ribosomal subunit
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MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Polypeptide from initiator tRNA in P site is removed and
attaches to the 2nd tRNA in the A site
During translocation: Ribosome moves along mRNA,
translocating the 2nd tRNA in the A site to P site
The initiator-tRNA is released and A site is occupied by the 3rd
aminoacyl-tRNA
The whole mechanism repeats several times until all the codes
has been translated
3. Termination:
The final stage of translation is termination where the
elongation continues until a stop codon in mRNA reaches the
A site.
The nucleotide base triplets UAG, UAA and UGA do not code
for amino acids but instead act as signals to stop translation.
A release factor (a protein shaped like an aminoacyl tRNA)
binds directly to the stop codon in the A site.
The release factor causes the addition of a water molecule
instead of an amino acid to polypeptide chain (water molecule
are abundant in the cytosol).
This reaction hydrolysed the bond between the completed
polypeptide abd the tRNA in the P site, releasing the
polypeptide through the exit tunnel of the ribosome’s large
subunit.
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The stages involved in translation.
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BIOLOGY NOTES
CHAPTER 6 : EXPRESSION OF BIOLOGICAL INFORMATION
SUBTOPIC 6.4: Gene regulation and expression – lac operon
LEARNING OUTCOMES: a) Explain the concept of operon and gene regulation.
b) State the components of operon.
c) Explain the components of lac operon and their functions in E.coli
c) Explain the mechanism of the operon in the absence and presence of
lactose.
MAIN IDEAS
/KEY POINT EXPLANATION NOTES
Concept of
operon and gene
regulation
• Operon is a genetic regulatory system found in bacteria
and their viruses in which genes coding for functionally
related proteins are clustered along the DNA.
• This feature allows protein synthesis to be controlled
coordinately in response to the needs of the cell.
• By providing the means to produce proteins only when and
where they are required, the operon allows the cell to
conserve energy (which is an important part of an
organism’s life strategy)
Components of
operon
• A typical operon consists of a group of structural genes that
code for enzymes involved in a metabolic pathway, such as
the biosynthesis of an amino acid.
• These genes are located contiguously on a stretch of DNA
and are under the control of one promoter (a short segment
of DNA to which the RNA polymerase binds to initiate
transcription).
• A single unit of messenger RNA (mRNA) is transcribed
from the operon and is subsequently translated into separate
proteins.
• The promoter is controlled by various regulatory elements
17 | KMPk
that respond to environmental cues.
• One common method of regulation is carried out by a
regulator protein that binds to the operator region, which
is another short segment of DNA found between the
promoter and the structural genes.
• The regulator protein can either block transcription, in
which case it is referred to as a repressor protein; or as an
activator protein it can stimulate transcription.
• Further regulation occurs in some operons: a molecule
called an inducer can bind to the repressor, inactivating it;
or a repressor may not be able to bind to the operator unless
it is bound to another molecule, the corepressor.
Components of
lac operon and
their functions
in E.coli
• Lac operon: a system that allows the Escherichia coli to
repress the production of enzymes involved in lactose
metabolism when lactose is present and glucose is absent.
• Regulator that turn the operon "on" and "off" in response to
lactose and glucose levels called repressor protein.
• The repressor protein acts as a lactose sensor. It normally
blocks transcription of the operon, but stops acting as a
repressor when lactose is present.
• The repressor protein senses lactose indirectly, through its
isomer allolactose.
• The lac operon contains three genes: lacZ, lacY, and lacA.
These genes are transcribed as a single mRNA, under control
of one promoter.
• Genes in the lac operon specify proteins that help the cell
utilize lactose.
o The lacZ gene encodes an enzyme called β-
galactosidase, which is responsible for splitting lactose
(a disaccharide) into readily usable glucose and
galactose (monosaccharides).
o The lacY gene encodes a membrane protein called
lactose permease, which is a transmembrane "pump" that
allows the cell to import lactose.
o The lacA gene encodes an enzyme known as a
transacetylase that attaches a particular chemical group
to target molecules.
• In addition to the three genes, the lac operon also contains a
number of regulatory DNA sequences. These are regions of
DNA to which particular regulatory proteins can bind,
controlling transcription of the operon.
• The promoter is the binding site for RNA polymerase, the
enzyme that performs transcription.
• The operator is a negative regulatory site bound by the lac
repressor protein. The operator overlaps with the
promoter, and when the lac repressor is bound, RNA
polymerase cannot bind to the promoter and start
transcription.
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Mechanism of
the operon in
the absence and
presence of
lactose.
In present of lactose
1. lactose converted to allolactose by transacetylase
allolactose bind to repressor protein and change the
confirmation of repressor protein.
Repressor protein cannot bind to operator
Lac operon swich on
2. RNA polymerase binds to the promoter and transcribes the
structural gene into mRNA.
3. mRNA is translated into three structural enzymes.
β-galactosidase hydrolyses lactose into glucose and
galactose
Permease transport lactose into E.coli
Transacetylase transfers an acetyl group from acetyl co-A to
β-galactosidase
In absent of lactose
1. Repressor protein binds to the operator and block promoter site
2. RNA polymerase cannot bind to the promoter to start
transcription.
3. Lac operon switches off.
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