DNA SYNTHESIS ● Represented by a table w/c contains the

corresponding amino acid for every combination

I. DIFFERENCE BETWEEN DNA AND RNA of nucleotides starting from the 5’ end of the
mRNA molecule

Codon

● triplet of mRNA nucleotide that codes for a

specific amino acid
● complimentary to the anticodon (found on tRNA
molecule)
● Made of A, G, C, U. The 4 nucleotide bases are
used to produce the 3-base codons. Hence, 4 3=
64 codons
● Sequences are always written from 5'-end (left)
to the 3'-end (right) in a linear configuration
● Special codons
o START CODON:AUG

Main structural differences between RNA and DNA are as

● signals the beginning of translation
follows:
● ENCODES FOR METHIONINE, hence all
nascent polypeptides produced will start
a. RNA is single-stranded while DNA is double-
with METHIONINE.
stranded.
● However, this is post-translationally
b. RNA contains uracil while DNA contains thymine.
cleaved such that the final protein will
c. RNA has the sugar ribose while DNA has the
not have methionine as the first amino
sugar deoxyribose.
acid.
d. RNA is not stable under alkaline condition while
DNA is stable.
o TERMINATION CODON:UAG, UGA, UAA

● a.k.a. nonsense codons/ stop codons:

do not code for any amino acids
● signals the end of polypeptide synthesis

II. GENETIC CODE

“The Dictionary”
Figure 3: The genetic code
● “letters”/bases in the mRNA sequence are
translated into “letters”/amino acids in the ● The difference among codons: third base position
polypeptide chain
(at the 3’ end)
 ○ The FIRST TWO letters of each codon are
the PRIMARY DETERMINANTS OF
SPECIFICITY
○ The THIRD BASE (WOBBLE BASE) of each
codon plays a lesser role in specifying an
amino acid than the first two – Changing
the third base will not drastically change
the type of AA that needs to be
incorporated
● The central dogma of molecular biology states
that te flow of genetic information in all living
cells is from DNA à RNA à Protein (Transcription to
Translation)
● The cell uses a genetic code that translate the
sequence of nucleotides on the RNA molecule
into the corresponding sequence of amino acids
on the polypeptide chain
● Four facts about genetic code
○ A 3 nucleotide sequence called Codon
is used to encode each amino acid
○ The code does not overlap
○ The code is read continuously
○ The code is degenerative
● Codon encodes each amino acid
○ A 3 nucleotide sequence will code for
amino acids
○ There are only 4 nucleotides and 20
amino acids
○ The combination of 3 nucleotides will
yield 64 possible combinations
○ 61 of the combinations will code for
amino acid and 3 will be stop codons
● The code does not overlap
○ When the RNA molecule is read by the
ribosomes, the codons do not overlap
○ UUG UUA CGU GGU AUU
● The codon is read continuously
○ The codon on the RNA are read by the
ribosome is a sequential manner from
the start to the end
○ There is no pause, or skip when reading
● The genetic code is degenerative
○ Because of the possible different
combinations, an amino acid will be
encoded by different codons. (The are
64 possibilities and only 20 amino acid)
○ The degeneracy of the code minimizes
the effects of mutations
III. DNA REPLICATION
● Involves all the chemical events that are involved
in generating a new DNA molecule from a
template
● It occurs in the INTERPHASE, specifically the S
phase of the cell cycle (CLUE: S for synthesis)
● Chromosomes are converted to 2 daughter DNA
molecules
● It is a highly coordinated process
● Simultaneous DNA unwinding and replication
occurs
Fundamental Rules in DNA Replication
1. REPLICATION REQUIRES A TEMPLATE
● The template is the parent DNA
● There is a need to copy the information from an
original
● Both strands of a DNA double helix are
complements of each other. The sequence of a
new strand being synthesized is dependent on
the sequence of the template strand
● Mediated by strict base pairing rules (A-T, G-C)
2. REPLICATION BEGINS AT AN ORIGIN AND
PROCEEDS BIDIRECTIONALLY
● Direction of synthesis and opening (separation of
hydrogen bonds) of the daughter strands should
be bidirectional
● Synthesis begins by making a NICK (a break in
the phosphodiester bond) first on the DNA double
helix at the origin of replication. From there, DNA
synthesis proceeds in opposite directions,
creating a replication bubble
● The bases before and after the replication
bubble are still bonded
○ Opening of the bases must proceed on
both the left and right side
simultaneously
○ Important in maintaining a fast rate of
replication – to avoid errors in replication
● REPLICON – area where replication bubbles are
formed
● ORIGIN OF REPLICATION (A-T-RICH REGION)
○ Specific region where replication will start
○ Also called the DNA winding element
(Lehninger)
○ Adenine – Thymine is loosely bonded
due to the presence of only 2 hydrogen
bonds; this makes it easier to cleave as
compared to Guanine – Cytosine with 3
hydrogen bonds
● REPLICATION FORKS
 ○ Present on either end of the replication
bubble
○ Where unwinding of parent DNA and
synthesis of daughter strand occur

3. REPLICATION IS SEMIDISCONTINUOUS
● 2 strands are not both continuously synthesized
● The LEADING STRAND (running in the 3’-5’
direction of the template) is synthesized
continuously while the
LAGGING/SEMIDISCONTINUOUS STRAND (running
in the 5’-3’ direction of the template) is
synthesized in fragments called OKAZAKI
FRAGMENTS
○ This occurs because reading of the
template strand is only possible in the 3 ’
to 5’ direction
● In the lagging strand, the enzyme has to wait
until there is a free 3 ’ end before it can start
replication

4. REPLICATION PROCEEDS IN A 5’ TO 3’ DIRECTION

● As opposed to the reading of the template V. COMPLEMENTARY BASE PAIRING
which occurs in the 3’ to 5’ direction
Chargaff rule - any sample of dsDNA, amount of A
equals the amount of T, the amount of G equals the
5. REPLICATION IS SEMICONSERVATIVE amount of C and the total amount of purines equals the
● The newly synthesized dsDNA has one strand from total amount of pyrimidines.
the parent DNA and another newly-synthesized
Base pairs - perpendicular to helical axis.
strand
● Each of these can be separated and used as a ● Adenine (A) - Thymine (T)
template for synthesis of a new complement ● Guanine (G) - Cytosin (C)
● Half of the information from the parent strand is
conserved in each new DNA strand synthesized *Stabilizes the structure of double helix

1. Hydrogen bonds

IV. STRUCTURE OF DNA NUCLEIC ACIDS A-T = 2 hydrogen bonds

G-C = 3 hydrogen bonds

2. Hydrophobic bonds

VI. DIRECTIONALITY

DNA polymerase – responsible for copying DNA

templates.

3’ 5’ direction - “reading” of parental

nucleotide sequences.
 5’ 3’ (antiparallel) direction - “synthesizing”
new DNA strands.
● Leading strand - being copied in the direction of
the advancing replication fork and is synthesized
continuously.
● Lagging strand - being copied away from the
direction of the advancing replication fork and is
synthesized discontinuously, with small fragments
of DNA being copied near the replication fork
(Okasazi fragments), that is ligated forming a
single continuous strand.
VII. ENZYMES
1. Helicase – open the DNA double helix
● Binds to a single strand of DNA near the
replication fork, which moves to a
double-stranded region and separates
the strands leading to the unwinding of
the double helix
● Breaks the hydrogen bonds between the
bases
● Requires ATP
● DnaB is the principal helicase of
replication in E. Coli
2. DNA polymerase – matches and adds new
nucleotides to form daughter DNA strand
● Catalyzes the addition of
mononucleotides to a growing chain
● For elongation of the strand
● Adds nucleotides to an existing primer
that provides a free 3’-OH group
3. Primase – forms RNA primer
● DNA-Dependent RNA Polymerase/DnaG)
● Synthesizes short RNA strands that are
complementary and antiparallel to the
DNA template (Makes the primer)
4. DNA Ligase – joining together of Okazaki
fragments on lagging strand
● Catalyze the joining of the sugar
phosphate backbone of the Okazaki
fragments of DNA
● Requires ATP
● Causes formation of a new
phosphodiester bond
5. Topoisomerase – relieves the three generated by
unwinding of DNA
● Introduces a transient break or nick in
the DNA via a transesterification reaction
to relax the torsion then reseal it
● Breaks the phosphodiester bond
● Mechanism of action
○ Transesterification reaction: a
phosphodiester bond is formed
between 3’ or 5’ carbon of 1
residue and the tyrosine residue
of topoisomerase
○ Rotation of the strand with free
-OH group unwinds the DNA to
allow proteins to gain access to
the bases
VIII. TRANSCRIPTION
● DNA is not directly involved in protein synthesis
● It has to be transcribed to form the RNA molecule
● The advantage of using RNA is that the cell does
not have to worry about damaging or mutating
the DNA
● DNA is found in nucleus and mitochondria. It is
only in these regions where transcription can
happen.
● Transcription involves 3 process:
1. Initiation
2. Elongation
3. Termination
A. Initiation
● The first step in transcription is to locate the
initiation point and unwind the DNA helix
● Initiation factor (group of proteins) moves along
the DNA until they find a promoter region
● The promoter region is a special sequence of
nucleotides that signals the RNA polymerase to
join the protein complex and begin synthesis of
the RNA strand
● Consensus sequence
B. Elongation
● RNA polymerase unwinds the DNA strand and
creates a bubble that exposes the single strand
of DNA
● Only 1 of these strands is used to synthesize RNA
● Template strand: antisense strand
● Coding strand: sense strand
● RNA polymerase can only read from 3`-5`
● The elongation of the daughter strand depends
on the template strand. The leading strand has to
base pair with the 3’-5' parent strand and the
 lagging strand will base pair with the 5’-3’ parent
strand.

C. Termination

● There is also a sequence of nucleotides that

signals end of transcription
● When RNA polymerase reaches this sequence, a
special protein helps the RNA to dissociate

IX. Types of RNA Polymerase

● Promoters control the binding of RN polymerase

to DNA to initiate the transcription of genes.
There are three types of RNA polymerases that all
transcribe different genes

a. RNA polymerase I – transcribes

genes encoding ribosomal RNA (rRNA)
which is a main component of a cell`s
ribosome structure. Ribosomes are the
site of protein synthesis where mRNA is
translated into a protein

b. RNA polymerase II – transcribes

messenger RNA (mRNA) which is the RNA
responsible for providing a stable
template for the translation of a protein

c. RNA polymerase III – transcribes

genes encoding transfer RNA (tRNA), the
adaptor molecules that are responsible
for bringing amino acids to the
ribosomes when proteins are being
synthesized. RNA polymerase III also
transcribes small RNAs, such as shRNAs
and gRNAs

References:
● Dr. Caculitan Lecture
● Nelson, David L., Michael M. Cox, and Albert L.
Lehninger. Lehninger: Principles of Biochemistry.
New York: W. H. Freeman . 5th ed.