1st SEMESTER | 2022-2023 SEPTEMBER 5, 2022

LESSON 3: DNA REPLICATION, TRANSCRIPTION, TRANSLATION

LECTURER: Mr. Stefan Paolo C. Jesalva

have a 1:1 stoichiometric ratio

TOPIC OUTLINE of purines and pyrimidines.
More specifically, A=T and G=C.
OVERVIEW These patterns are found in both
strands of the DNA.
THE BASIC PRINCIPLE
 DNA is a double-stranded helix
TRANSCRIPTION & TRANSLATION with
antiparallel strands.
BUILDING A POLYPEPTIDE *antiparallel strands- these
strands run on opposite
directions, one strand runs from
the 3’ to 5’ while the other one
OVERVIEW runs from the 5’ to 3’.
 The genetic material is stored in the form  Nucleotides in each strand are linked by
of DNA in most organisms. 5’ to 3’ phosphodiester bonds.
 In humans, the nucleus of each cell  Bases on opposite strands are linked
contains 3x109 base pairs of DNA by hydrogen bonding: A with T and
distributed over 23 pairs of G with C.
chromosomes, and each cell has
two copies of the genetic material.
 This is known collectively as the
“human genome.” The human
genome contains around 30,000
genes, each of which codes for one
protein.
 It is normally a stretch of DNA that codes
for a type of protein or for an RNA
chain that has a function in the
organism.
 Genes hold the information to build
and maintain an organism’s cells
and pass genetic traits to
offspring.
 “Gene” are also known as the unit
of heredity.
 The Central Dogma of Molecular
Biology states that DNA makes
RNA, and RNA makes proteins.
 The process by which DNA is copied
to RNA is called “Transcription”,
and that by which RNA is used to
produce proteins is called
“Translation.”
“In this figure, you have your sugar-
phosphate backbone and the bases. And
STRUCTURE OF DNA:
your whole DNA Nucleotide composed of
 DNA is composed of four nucleotides
phosphate, deoxyribose sugar, and your
each containing: Adenine, Cytosine,
base: Guanine, Cytosine, Adenine, or
Thymine, Guanine.
Thymine.”
 The amounts of A=T , G=C, and
Purines=Pyrimidines (Chargaff’s
Rule)
- This rule states that DNA from any
species of any organism should
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ORGANIZATION OF DNA: - The parent molecule unwinds,
and two new daughter strands
are built based on base-pairing
molecules.
- The parent molecule has two
complementary strands of
DNA. Each base is paired by
hydrogen bonding with its specific
partner, A with T and G with C.
- The steps of Replication are the
following:
o Separation of the two
DNA strands which is
the unwinding of the
“First you have your chromosome and parental strand.
then when you magnify that, you will be
able to observe the chromatin. If you
magnify that further, you can be able to
observe your nucleosomes which are
made up of 8 histone proteins. These
histone proteins are the site in which
the DNA wraps around. The blue color in
the picture is the DNA helix that is
wrapped around the histones. And
within the DNA Helix, we may be able to
see the base pairs: A with T and G with
C.”
o Parental strand as a
template.
THE BASIC PRINCIPLE
*dark blue= parental
THE BASIC PRINCIPLE: BASE PAIRING TO strand
A *light blue=
TEMPLATE STRAND daughter
 The relationship between structure strands
and function is manifested in the
double helix.
 Since the two strands of DNA are
complementary, each strand acts as a
template for building a new strand in
replication.

1) DNA REPLICATION

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 o Formation of the parental DNA strands serve as a
sugar- phosphate template for new
backbones of the new
stands.

1.a) MODELS OF REPLICATION

- Here we have the 3 suggested
models
of DNA Replication.

 Conservative Method – this suggests

that parental DNA remains
together, and the uniform daughter
strands are also together.
- The term “conservative” comes
from the fact that the two
strands of the parental DNA
are conserved or they stay
together.
 Semi-conservative Method – this
method suggests that the two
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 DNA and after replication, each
double stranded DNA contains one
strand from the parental DNA
and one new daughter strand.
- It is called “semi-
conservative” because only
one parental strand is
conserved.
 Dispersive Method – this
suggests that after replication, the
two daughter DNA’s have
alternating segments of both
parental and newly
synthesized DNA dispersed on
both strands.

*DNA REPLICATION IS ACTUALLY

SEMI- CONSERVATIVE.
 This was discovered by Meselson
and Stahl, using E. coli DNA,
which was determined that DNA
replicated via the semi-
conservative method of
replication.
 Each 2-stranded daughter
molecule is only half new and
the original strand was used as
a template to make the new
strand.
- The copying of DNA is
remarkable in its speed and
accuracy. It involves
unwinding the double helix
and synthesizing into two new
strands.
- More than a dozen enzymes
and other proteins
participate in DNA replication.
- The replication of a DNA
molecule begins at special
sites called “origins of
replication” where the two
strands are separated.

1.b) ORIGINS OF REPLICATION

- a eukaryotic chromosome may
have hundreds or even thousands
of replication origins.
- the DNA replication of a
eukaryote may begin at many
sites along the giant DNA
molecule of each chromosome.

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 - DNA synthesis on the leading strand
is continuous.
- The lagging strand grows in the
same general direction as the
leading strand (in the same
direction as the Replication Fork).
However, DNA is made in the 5’ to
3’ direction.
- Therefore, DNA synthesis on the
lagging strand Is discontinuous.
- DNA is added as short
*Replication fork- this is a structure that
fragments known as “Okazaki
forms within the long helical DNA during
fragments” that are
the process of replication. This is created
subsequently ligated together.
by the helicases that breakdown the
hydrogen bonds, folding the two DNA
strands together.

“As you can see there are three

bubbles that are formed: Bubble 1, 2
and 3.”

1.c)MECHANISM OF DNA REPLICATION

- DNA replication is catalyzed by DNA
polymerase which needs an RNA
primer.
- RNA primase synthesizes primer on
DNA strand
- DNA polymerase adds nucleotides
to the 3’ end of the growing strand.

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“This is the overall direction of
replication. It always goes to the
direction of the replication fork. We have
our leading strand and our lagging
strand.”

1.c)ENZYMES IN DNA REPLICATION

- Many proteins assist in DNA
- These are the different enzymes in
replication.
DNA replication:
- The DNA helicases unwind the
double helix, the template
strands are stabilized by other
proteins.
- Single stranded DNA binding
proteins make the template
available.
- RNA primase catalyzes the
synthesis of short RNA primers
to which nucleotides are
added.
- DNA polymerase III extends the
strand in 5’ to 3’ direction.
- DNA polymerase I removes the
RNA primer and replaces it
with DNA.
- DNA ligase joins the DNA
fragments into a continuous
daughter strand.

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 REPLICATION FORK OVERVIEW:

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 *PROOFREADING *dimers- are molecular lesions formed
- DNA must be faithfully replicated, from Thymine or Cytosine bases in DNA
however mistakes occur. via photochemical reactions. These
- DNA polymerase has a dimers can potentially lead to mutations
proofreading ability and can and even possibly cancer.
correct error, but it can also insert
the wrong nucleotide base in 1.d) ACCURACY OF DNA
1/10,000 bases. REPLICATION
CHROMOSOME CHROMOSOME
o Mismatch repair: OF OF
“wrong” inserted base
E.COLI HUMAN CELL
can be removed. contains about 5M The 46
o Excision repair: DNA base pairs chromosomes of a
may be damaged by human cell contain
chemicals, radiation, 6B pairs of
etc. Mechanism to cut DNA.
out the damaged DNA capable of copying Takes a cell a few
and replace with this DNA in less hours to copy this
correct bases. than an hour DNA
*MUTATIONS
With amazing
- A mismatching of base pairs can
accuracy – an
occur at a rate of 1 per 10,000
average of 1
bases.
per
- DNA polymerase proofreads and
repairs
accidental mismatched pairs.
- Chances of a mutation occurring at
any one gene is over 1 in 100,000.
- Because the human genome is so
large, even at this rate, mutations add
up. Each of us probably inherited 3-
4 mutations.
*PROOFREADING AND REPAIRNG DNA
- DNA polymerases proofread newly
made DNA, replacing any incorrect
nucleotides.
- In mismatch repair of DNA, repair
enzymes correct errors in base
pairing.
- In nucleotide excision DNA repair,
nucleases cut out and replace
damaged stretched of DNA.

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TRANSCRIPTION & TRANSLATION
2) TRANSCRIPTION AND TRANSLATION
o PROTEIN SYNTHESIS
- The information content of DNA is in
the form of specific sequences of
nucleotides along the DNA strands.
- The DNA inherited by an organism
leads to specific traits by dictating
the synthesis of proteins.
- The process by which DNA directs
protein synthesis, gene expression,
includes two stages called
transcription and translation.
o Cells are governed by a cellular chain
of command: DNA > RNA > PROTEIN
o TRANSCRIPTION
 Is the synthesis of RNA under
the direction of DNA
 Produces messenger RNA
(mRNA)
o TRANSLATION
 Is the actual synthesis of a
polypeptide which occurs
under the direction of mRNA
 Occurs in the ribosomes
o In a eukaryotic cell, the nuclear
envelope separates transcription
from translation.

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 o Extensive RNA processing occurs *DIFFERENT TYPES OF RNA:
in the nucleus. The nucleus
provides a separate compartment
for transcription. The original RNA
transcript, called “pre- mRNA”, is
processed in various ways before
leaving the nucleus as mRNA.

a.1) SYNTHESIS OF RNA TRANSCRIPT

a.) TRANSCRIPTION
- it is the DNA directed synthesis of
RNA
- RNA synthesis
 Is catalyzed by RNA
polymerase which pries the
DNA strands apart and
hooks together the RNA - The stages of transcription are:
nucleotides. o Initiation
 This process follows the same  Promoters signal the
base-pairing rules as DNA initiation of RNA synthesis
except that in RNA, Uracil and transcription factors
substitutes for Thymine. help eukaryotic RNA
polymerase
*MAIN DIFFERENCES BETWEEN RNA AND DNA:
RNA DN recognize promoter
A sequences.
Single stranded double stranded o Elongation
Short with only 1 gene Very long and  RNA polymerase
long contains many synthesizes a single strand
genes of RNA against the DNA
Uses sugar ribose Uses template strand (anti-
sense strand), adding
Deoxyribose nucleotides to the 3’ end
sugar of the RNA chain.
Uses the base Uracil Uses the base  As RNA polymerase moves
(U) Thymine (T) along the DNA, it continues
to untwist the double
helix, exposing about 10 to
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 20 DNA bases at a time
for pairing with RNA
nucleotides.

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 “Stage one which is Initiation where the
promoters signal the initiation of RNA
synthesis. Then the second stage,
Elongation where RNA polymerase
unwinds the DNA double helix and
synthesizes a single RNA strand against
the DNA template strand. And lastly, the
Termination stage where RNA
polymerase encounters specific DNA
sequences that signal the termination of
RNA transcription, and this RNA
transcript is finally released.”

a.3) POST TERMINATION RNA PROCESSING

- Most eukaryotic mRNAs are not ready to
o Termination be translated into protein directly after
 Specific sequences in the being transcribed from DNA. mRNA requires
DNA signal termination of processing.
transcription. - Transcription of RNA processing occurs
 When one of these sequences in the nucleus. After this, the messenger
is encountered by RNA moves to the cytoplasm for translation.
the - The cell adds a protective cap to one end,
polymerase, the RNA and a tail of Adenines to the other end.
transcript is released from These both function to protect the RNA
the DNA and the double from enzymes that degrade.
helix can zip up again. - Most of the genome consists of non-coding
a.2) TRANSCRIPTION OVERVIEW regions called “introns”.
o These non-coding regions
may have specific
chromosomal functions of
have regulatory purposes.
o Introns also allow for
alternative RNA splicing
- Thus, an RNA copy of a gene is
converted into mRNA by doing two things:
o Add protective bases to the ends
o Cut out the introns

*ALTERATION OF MRNA ENDS

- Each end of a pre-mRNA molecule is
modified
in a particular way:
o The 5’ end receives a
modified nucleotide cap (5’
cap)
o The 3’ end gets a poly-A tail
*These two makes the RNA more stable
and protect it from degradation.

*RNA PROCESSING – SPLICING

- The original transcript from the DNA is
called pre-mRNA and it contains
transcripts of both introns and exons.
- The introns are removed by a process called

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“splicing” to produce mRNA.

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 - Codons: 3 base codes for the
production of a specific amino acid,
sequence of the four different
nucleotides.
- Since there are 4 bases and 3
positions in each codon, there are
4x4x4 = 64 possible codons. 64
codons but only 20 amino acids,
therefore, most have more than 1
codon.
- 3 of the 64 codons are used as
“Here we have the DNA and the initial STOP signals which are found at
mRNA transcript that still contains the the end of every gene and mark
introns. And then it undergoes mRNA the end of the protein.
processing or splicing wherein there is - One codon is used as a START
the removal of the introns and finally we signal
can get our mature mRNA.” which is the start of every protein.
- Proteins often have a modular - This code is universal which is present
architecture consisting of discrete in all living organisms.
structural and functional regions called - A codon in mRNA is either
“domains.” translated into an amino acid or
- In many cases, different exons code for serves as a translational
the different domains in a protein. START/STOP signal.

b.) TRANSLATION
- It is the RNA-directed synthesis
of a polypeptide. It involves:
o mRNA
o Ribosomes – ribosomal RNA b.2) TRANSFER RNA (tRNA)
o tRNA
- consists of a single RNA strand
o Genetic coding – codons
that is only about 80 nucleotides
long.
b.1) THE GENETIC CODE
- each carries a specific amino acid
- Genetic information is encoded as a on one end and has an anticodon
sequence of base triplets, or on the other end.
codons.
- A special group of enzyme pairs
up the proper tRNA molecules with
their corresponding amino acids.
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 - tRNA brings the amino acids to if we see this, we can automatically know
the ribosomes which are the sites of that this is what represents the tRNA.”
protein synthesis.
b.3) RIBOSOMES
- these facilitate the specific
coupling of tRNA anticodons with
mRNA codons during protein
synthesis.
- The 2 ribosomal subunits are
constructed of proteins and RNA
molecules namely ribosomal RNA
(rRNA). A ribosomal unit is a collection
of rRNA molecules and proteins.

“Since the base of our anticodon is AAG,

bases that are in the mRNA molecule
would be UUC. This is because A is paired
with U and G is paired with C.”
BUILDING A POLYPEPTIDE

E P A

- A tRNA fits into a binding site

(ribosome) when its anticodon
base pairs with an mRNA codon.
The P site holds the tRNA
attached to the growing
polypeptide. The A site holds the
“The 3-dimensional tRNA molecule is
tRNA carrying the next amino
roughly “L”
acid to be added to the polypeptide
shaped. For the Symbol which are used in
chain. Discharged tRNA leaves the
books,
E site.
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*p site- “peptidyl site” is the second
binding site for the tRNA in the ribosome.
*a site- “amino acyl site” is the first binding
site in the ribosome
*e site- “exit site” is the third binding site.
- We can divide translation into three stages
namely:
o Initiation
 Brings together mRNA,
tRNA bearing the first
amino acid of the
polypeptide, and two
subunits of a ribosome.
o Elongation
 Amino acids are added one
by one to the preceding
amino acid.
o Termination
 When the ribosome reaches
STOP codon in the mRNA,
there is no corresponding
tRNA.
- The AUG START codon is recognized
by
methionyl-tRNA (Met)
- Once the START codon has been
identified, the ribosome
incorporates amino acids into a
polypeptide chain. *GTP- guanosine
- RNA is decoded by tRNA
molecules, which each transport triphosphate
specific amino acids to the
growing chain. ELONGATION STAGE
- Translation ends when a STOP
codon (UAA, UAG, UGA) is reached.

INITIATION STAGE

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 TERMINATION STAGE

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*A small protein called a “release factor”
attaches to the STOP codon.
*The release factor causes the whole
complex to fall apart: mRNA, the two
ribosome units, and the new polypeptide.
*The mRNA can be translated many times, to
produce many proteins copies.

POST-TRANSLATION
- The new polypeptide is now
floating loose in the cytoplasm, if
translated by a free ribosome.
- It might also be inserted into a
membrane, if translated by a
ribosome bound to the
endoplasmic reticulum.
- Polypeptides fold spontaneously
into their active configuration,
and they spontaneously join with
other polypeptides to form the
final proteins.
- Sometimes other molecules are
also attached to the
polypeptides: sugars, lipids,
phosphates, etc. All of these have
special purposes for protein function.

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