Nucleic Acid Chemistry

Nucleic Acid
• Nucleic acids are called as such because they were first
discovered in the nucleus
• They are complex organic acids that are composed of chains of
nucleotide units

Roles of Nucleic Acids

• They participate in the energy transduction that accompany
interconversions and oxidative phosphorylation
o ATP and ADP as the donor and acceptor of phosphoric group
• They play a role in a variety of metabolic functions such as:
protein synthesis, energy metabolism, signal transduction, and
regulation of enzymes
• They are also part of many coenzymes and when associated
with sugars and lipids, the nucleotides form key biosynthetic
• It is a 5 Carbon Sugar
intermediates
• Being linked to a heterocyclic ring by a Beta N-Glycosidic Bond
• They are also used as synthetic purine and pyrimidine analogs
in chemotherapy and in the treatment of AIDS • Could either be a Pentose Ribose or a Pentose 2’ Deoxyribose
o Immunosuppressors in organ transplants o The difference between these 2 sugars occur at Carbon 2’
o Ribose: has -OH group
• Most Important Function of Nucleotides
o Deoxyribose: has -H atom only (DEOXYribose = no oxygen)
o They are constituents of nucleic acids
▪ Nucleic Acids – molecular storage of the genetic • The one that determines the identity of the nucleic acid is the
information which allows living cells to produce replicas Pentose Sugar
of themselves o If the nucleic acid has a 2’ deoxydiribose → DNA
o If the nucleic acid contains a ribose sugar → RNA

History
• 1869: isolated DNA from salmon sperm (Friedrich Miescher)
• 1944: proved DNA is genetic materials (Avery et al)
• 1953: discovered DNA double helix (Watson and Crick)
• 1968: invented DNA sequencing method (Gilbert and Sanger)
• 1987: launched the human genome project
• 2001: accomplished the draft map of human genome

Two Types of Nucleic Acids

1. Deoxyribonucleic Acid (DNA)
2. Ribonucleic Acid (RNA) • Pentose Ring Atoms are designated with Primed Numbers
o The carbon atoms in the sugar are being identified by a
primed number (ex. carbon 1’), it just tells us that the primed
number carbon belongs to the sugar of a nucleotide
• The Nitrogen-containing Ring Atoms are designated with
Unprimed Numbers

• Describes the differences in

phosphorous-base distance;
displacement of the 2’, 3’-
carbons above the plane of the
C1’-O4’-C4’ atoms
• C3’ Pucker
o Prevalent in RNA and A-Form
DNA
• Monomer of a polymeric nucleic acid o Produces shorter phosphate-
• Considered as the building blocks of nucleic acids phosphate distance resulting
• Composed of: in a more compact helical
o Pentose Sugar → Deoxyribose or Ribose conformation
o Phosphate Group → Reason why the DNA is negatively • C2’ Endo
charged o Prevalent in B-Form DNA
o Base → Nitrogenous Base o More stable conformation
• Nitrogenous Base is linked to the Carbon 1’ of the sugar; Almost
always to the N-1 atom of the Pyrimidine or N-9 atom of Purine Remember: the farther apart the molecules, the more stable it
• Phosphate Group is linked to the Carbon 5’ of the sugar is
• If we have a chain of nucleotides, we will form Nucleic Acids

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 Note:
There are 4 possible RNA nucleotides and 4 possible DNA
nucleotides depending on the base that is present

Nucleoside
• A base linked to a sugar
without a phosphate group
• When you phosphorylate a
nucleoside → becomes a
Nucleotide → contains a base,
sugar, and phosphate
• 2 Groups of Bases: • Nucleosides are derivatives of
o Pyrimidine the bases that have a sugar
▪ A monocyclic base with a 6-membered ring being linked to a nitrogen of
o Purine either a purine base or
▪ A bicyclic base with fused 5 and 6-membered rings pyrimidine base
• These are heterocyclic structures that contain other atoms such • Nucleosides are named by changing the nitrogen base ending
as nitrogen, in addition to carbon atoms to -osine for purines and -idine for pyrimidines

Note:
o The smaller pyrimidine molecule has a longer name and
the larger purine molecule has a shorter name
o Their 6 atom rings are numbered in opposite directions
o These atoms are designated with unprimed numbers
To convert the base into a nucleoside → you add the purine or
pyrimidine base with a sugar (base + sugar). The linkage is
glycosidic bond.
o For Purines → The connection is between N9 of Purine
and C1 of sugar
o For Pyrimidines → The connection is between N1 of
Pyrimidine and C1 of sugar

EXAMPLE 1:

• There are 5 Nitrogen-Containing Heterocyclic Bases in Nucleic

Acids
• 3 are derivates of Pyrimidine:
o Cytosine
o Thymine
o Uracil • Nucleoside that has Cytosine as the base, linked to the sugar
• 2 are derivatives of Purine: without a phosphate group on its C-5’
o Adenine • Since Cytosine is a pyrimidine base, this nucleoside is named
o Guanine as Cytidine
• It will be named as Deoxycytidine if it has a deoxyribose sugar
Note:
o These bases are represented by the first letter of its EXAMPLE 2:
name • Base: Adenine
o A and G are seen in both DNA and RNA; C is seen in both • Linked to a sugar without a phosphate
DNA and RNA group
o T is only seen in DNA • Adenine is a purine base → Adenosine
o U is only seen in RNA

• The planar character of purine and pyrimidine facilitates their

close association or stacking which stabilizes the double
stranded DNA

• Derived from Phosphoric Acid;

gives nucleic acid their acidic
property
• Under cellular pH condition,
the Phosphoric Acid loses 2 of
its hydrogen atoms to give a
Hydrogen Phosphate Ion • There are 2 conformations of the Nucleosides
• The Phosphate Group is o Syn Conformation
attached to the sugar at the C- o Anti Conformation
5’ position through a
Phosphate-Ester Linkage

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 Syn Conformation Anti Conformation Structure of Nucleic Acid
Base is in parallel with the Base is being projected away
sugar from the sugar, occupying a
bigger space
More stable

• Base + Sugar + Phosphate Group

• A nucleotide is named using the name of the nucleoside
followed by the phosphate group
EXAMPLE:
• Nucleoside: Adenosine
• Nucleotide: Adenosine 5’ Monophosphate (AMP)
o 5’ indicates the phosphate group being linked to the C5’ of
the sugar
Nomenclature of Nucleotides
• 5’-monophosphate – indicates that only 1 phosphate group is
being linked to the C5’ of the sugar and it will be changed
accordingly to the number of phosphate group present
• PREFIX: identify the sugar present, if deoxyribose → use deoxy;
if ribose → no prefix will be added
• Name of Base comes before monophosphate; use -osine for
purine and -idine for pyrimidine
• Abbreviations: One letter symbol for the bases (A, C, G, T, and
U); MP for Monophosphate; a lower case “d” at the start if sugar
is deoxyribose
• Polymers of repeating nucleotide units as its monomers
• The nucleotide units within the polymer are linked together
through a Sugar-Phosphate Bond
• The Primary Structure of Nucleic Acids includes a chain of
alternating phosphate group and a sugar with a base attached
to the chain at regular intervals
• Each non-terminal phosphate group of the backbone is bonded
to 2 Sugar Molecules through a 3’ to 5’ Phosphodiester Linkage
• There is Phosphoester Bond that is linked to the 5’ Carbon of a
sugar unit and another Phosphoester Bond to the 3’ Carbon of
the next sugar
• The Nucleotide Chain has directionality
o The 5’ End carries a Free Phosphate Group linked to 5’
Carbon atom of the sugar
o The 3’ End has a Free Hydroxyl Group attached to the 3’
Carbon atom
o The sequence of the bases of the nucleic acid is being read
from the 5’ End to the 3’ End

Base Ribonucleoside Ribonucleotide Abbrev.

Adenine Adenosine Adenosine 5’- AMP
(A) monophophate // • RNA is a polymer with each monomer containing a Ribose, one
Adenylate of the Bases (Adenine, Cytosine, Guanine, Uracil), and a
Guanine Guanosine Guanosine 5’- GMP Phosphate Group
(G) monophosphate //
Guanylate
Cytosine Cytidine Cytidine 5’- CMP • DNA is a polymer with each monomer containing a Deoxyribose,
(C) monophophate // one of the Bases (Adenine, Cytosine, Guanine, Thymine), and a
Cytidylate Phosphate Group
Uracil (U) Uridine Uridine 5’- UMP
monophosphate // The alternating Sugar-Phosphate Chain in the structure serves
Uridylate as the backbone and is constant through the entire structure of
Base Deoxy- Deoxyribonucleotide Abbrev the nucleic acid.
ribonucleoside
Adenine Deoxyadenosine Deoxyadenosine 5’- dAMP The variable portion of each structure is the sequence of bases
(A) monophosphate // attached to the sugar units of the backbone
Deoxyadenylate
Guanine Deoxyguanosine Deoxyguanosine 5’- dGMP
(G) monophosphate // 1. The base composition of DNA generally varies from one
Deoxyguanylate species to another
Cytosine Deoxycytidine Deoxycytidine 5’- dCMP 2. DNA specimens isolated from different tissues of the same
(C) monophosphate // species have the same base composition
Deoxycytidylate 3. The base composition of DNA in a given species does not
Thymine Deoxythymidine Deoxythymidine 5’- dTMO change with an organism’s age, nutritional status, or
(U) monophosphate // changing environment
Deoxythymydylate 4. In all DNA molecules, the number of Purines is ALWAYS
EQUAL to the number of Pyrimidines

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 and hydrophobic ring structure very close together and is
perpendicular to the axis
o The size of the interior of the helix limits the base pairs that
can form hydrogen bonds with each other

Chargaff’s Rule serves a key in creating a 3D structure of DNA
and provided hints on how the genetic information is being
encoded in DNA and transferred form one generation to the next
generation.
Watson and Crick showed that the base pairs illustrated in this
figure (Guanine pairing with Cytosine and Adenine pairing with
Thymine) are those that fit best in the structure → validating the
Chargaff’s Rule that in any DNA, GC base pairs and AT base pairs
There are 3 Hydrogen Bonds that can be formed between the
GC Base Pair.
There are 2 Hydrogen Bonds that can be formed between the AT
Base Pairs.
o This makes the separation of paired DNA strands with
higher GC base pairs more difficult

• The pairing of Thymine with Adenine and Cytosine with Guanine

are said to be complementary, making the 2 strands of the DNA
Double Helix complementary with each other
• The Hydrogen Bonds between base pairs provide stabilization
of the DNA Double Helix
o Although they are weak forces, each DNA molecule has
many base pairs and collectively, these hydrogen bonds are
a force of significant strength
• In addition, Base Stacking interaction involving a given base
and the parallel bases directly above and below it also
contributes to the stabilization of the Double Helix structure
• The bases are hydrophobic in nature so their stacking
• Refers to the DNA Double Helix interactions are those associated with hydrophobic molecules,
mainly the London Forces
• Composed of two strands polynucleotides wound around each
o The London dispersion force is a temporary attractive force
other which forms → Helix (Right-Handed Double Helix)
that results when the electrons in two adjacent atoms
o Bases are sandwiched on the inside, while the sugar—
occupy positions that make the atoms form temporary
phosphate backbone are on the outside
dipoles
• Sequence of the bases is important since they determine the
• The strands of the DNA Double Helix are antiparallel, having a
genetic information of the molecule
5’ End and a 3’ End at both ends of the Double Helix
• The distance between 2 Base Pairs is at 0.34 nm
• In the early 1950s: • There are 10 base pairs per helical turn
o Maurice Wilkins and Rosalind Frank used the method of X-
Ray diffraction and they were able to show that the DNA
molecules are helical in structure, containing 2 periodicities
along their long axis: • The coil parking of these strands forms a Major Groove and a
▪ Primary one measuring 3.4 Å Minor Groove on the surface of the helix
▪ Secondary one measuring 34 Å o Major Groove – formed where the backbones are farther
apart
• In 1953:
o Minor Groove – formed when the backbones are closer
o James Watsons and Francis Crick described a 3D Model of
together
DNA structure
o The model is composed of 2 Helical DNA strands winding • These grooves are important for the binding of certain proteins
around the same axis and forming a Right-Handed Double to organize or change its structure or to regulate transcription
Helix or during replication
• It makes it easier for the DNA binding proteins to interact with
the bases one these grooves
• Facing the aqueous
environment are the Forms of DNA
hydrophilic sugar • The Double Stranded DNA may exist in 6 Forms: A, B, C, D, E,
phosphate backbones of and Z
the 2 polynucleotide
strands – outer part of the • The Watson and Crick Model is being referred to as the B Form
double helix DNA
• The Furanose Ring of the • This form is considered to be the most stable found under
Deoxyribose is on the C2’ physiologic conditions and in the studies of the properties of the
End Conformation DNA molecules
• The bases of each • It serves as the standard point of reference
backbone extend inward • A single turn of the B DNA along the axis of the molecule
toward the bases of the contains 10 Base Pairs
other strand • One turn spans the distance of 3.4nm
• The bases are inside the • Width: 2nm
double helix in between the 2 strands with their nearly planar

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• Favored in solutions which are devoid of water
• Also arranged in a Right-Handed Double Helix
• The helix is wider and shorter
• 11 Base Pairs for every helical turn
• The plane of the base pairs is somewhat bended around 20 0 in
relation to the axis of the helix
• When the inverted repeat occurs within each individual strand
of DNA
• Do not have complementary sequences within the same strand
• Contrary to the A DNA and B DNA, the helical rotation of the Z
and cannot form hairpin or cruciform structures
DNA is Left-Handed
• 12 Base Pairs in each helical turn
Mirror Repeat
• The structure appears more elongated and more slender It is characterized by the presence of identical pairs equidistant
from a center of symmetry within the DNA segment.
A Form B Form Z Form It looks like it is facing the mirror.
Helical Sense Right-Handed Right-Handed Left-Handed o Strand on Top (5’ to 3’): TTAGCAC
Diameter ~26 Å ~20 Å ~18 Å o Strand on Top (3’ to 5’): TTAGCAC
Base Pairs 11 10.5 12 o Strand Below (5’ to 3’): AATCGTG
per Helical o Strand Below (3’ to 5’): AATCGTG
Turn
Base tilt 200 60 70
normal to the
helix axis
Sugar Pucker C-3’ Endo C-2’ Endo C-2’ Endo for
Conformation pyrimidines;
C-3’ Endo for
Purines
Glycosyl Anti Anti Anti for
Bond Pyrimidines;
Conformation Syn for
Purines

Unusual Structures of DNA • Formed in DNA regions with continuous string of purine bases,
that is homopurine-homopyrimidine regions
• Generated by the hydrogen bonding of a 3rd strand into the
major groove of B-DNA
• The 3rd strand forms hydrogen bonds with another surface of
the double helix through Hoogsteen Pairs (Non-Watson-Crick
Pairing)
• The atoms that participate in hydrogen bonding of Triplex DNA
are referred to as Hoogsteen Positions
• Limited to only 4 Triplet Bases: TAT, CGC, GGC, AAT

• A sequence that is read the same way in either direction

• This sequence can exist in regions in DNA having an inverted
repeat of the Base sequences with twofold symmetry over the 2
strands of DNA molecule which can be complimentary with each
other and therefore can lead to a formation of a Hairpin Loop or
a Cruciform Structure within the DNA molecule
• EXAMPLE: REDIVIDER, ROTATOR

Inverted Repeat (Palindrome)
The strand on top is the same as the strand below when it is
inverted
o Strand on Top (5’ to 3’): TTAGCAC
o Strand Below (5’ to 3’): TTAGCAC
• Occurs readily for DNA sequences with a very high proportion of
guanosine residues
• The Guanosine Tetraplex/G Tetraplex is quite stable over a wide
range of conditions
• Tom Cech and Aaron Klug’s laboratories have demonstrated
that sequences found at the ends of t eukaryotic cell (at
telomeres) chromosomes form G-Tetraplex
• Involved in holding chromosome ends together during mitosis

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 Eukaryotes vs Prokaryotes • Organization results from the interaction of the arginine
residues of the core histone and the phosphodiester backbone
of the linear DNA
• H1 Histone facilitates the
coiling of the beaded fiber
into higher-order structures
such as chromatins
• As chromatin is compacted
to form Chromosomes, the
nucleosomes are coiled into
higher order structures like
the 30-nm fiber and is
further coiled to form 200-
nm filaments until it forms a
chromosome
• A eukaryotic cell contains
• The circular DNA in prokaryotes is contained in a 23 pairs of chromosomes
nonmembrane-bound nucleoid material
• The linear DNA in eukaryotes is found in its nucleus

• In prokaryotes, the DNA forms Supercoils

• When the DNA is negatively supercoiled (right-hand direction),
it winds around itself to form Interwound Supercoil
• Positive Supercoil (left-hand direction), it coils around a protein
core to form Toroidal Supercoil
• These supercoils are held together by anchoring proteins so it
can be compressed in a small space

DNA vs RNA

• The linear DNA are complexed with histones to form

Nucleosomes
• One nucleosome has 8 histone molecules (2 molecules for each
of the histone classes H2A, H2B, H3, and H4)

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 the ribosome and help stabilize the mRNA by not allowing
• Sugar: Ribose the activity of 5’ exonuclease
• Bases: Uracil, Cytosine, Guanine, Adenine • Polyadenine tail at the 3’ end
• Single-Stranded, but this does not prevent portions of an RNA o Prevents the activity of the 3’ exonuclease maintaining its
molecule from falling back upon itself and forming double intracellular stability
helical regions o Facilitates translation
• If the base sequences along the 2 portions of an RNA strand are • These structures protect the two ends of the mRNA from the
complementary, it results in a structure with a hairpin-like loop degradation of exonuclease
• Smaller than DNA
• Genetic Code – sequence of nucleotides in mRNA that is
transcribed from the DNA
I. Protein Coding RNAs – messenger RNA (mRNA)
• Codon – triplet of bases along the sequence of nucleotides in
II. Nonprotein Coding RNAs (ncRNAs)
mRNA that codes for a particular amino acid
a. Large ncRNAs – Ribosomal RNA (rRNA)
o Each of the 20 amino acids needed to synthesize a protein
b. Long ncRNAs
has at least 2 codons
c. Small ncRNAs
o There are codons that signal the “start” and “end” of the
• Small ribosomal RNAs polypeptide chain
• Transfer RNAs (tRNA)
• Small nuclear RNAs (snRNA)
• Micro/silencing RNAs (mi/siRNA)
Class of Primary Function
RNA
mRNA, Directly involved in protein synthesis
rRNA, tRNA
snRNA mRNA splicing
mi/siRNA Modulation of gene expression by altering mRNA
function
lncRNA Modulation of gene expression by altering mRNA
expression

Reading the Genetic Code

• Suppose we want to determine the amino acid sequence being
encoded by the following section of mRNA
o 5’ CCU AGC GGA CUU 3’
• According to the Genetic Code, the amino acid for these codons
are:
o CCU: Proline, AGC: Serine, GGA: Glycine, CUU: Leucine
• The mRNA section codes for the amino acid sequence of:
o Pro-Ser-Gly-Leu

• Acts as accessory for the

translation of mRNA in to a
specific sequence of the
amino acids
• Contains 4 main arms
1. Acceptor Arm
2. D Loop
3. T Loop
4. Anticodon Loop
• Conveys information in a gene to the protein synthesizing • Acceptor Arm
machinery (ribosome) where it serves as a template on which a o Terminates in a
sequence of amino acids is polymerized to form a specific nucleotide CCA
protein molecule sequence where the
appropriate amino acid
is affixed to the 3’ OH
group of the adenosine
• Methylguanosine Triphosphate cap at the 5’ end
molecule of the CCA
o The 5’ end of mRNA is capped by 7 Methylguanosine
sequence found on the
Triphosphate, which serves as recognition site of mRNA by
acceptor arm

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• Anticodon Loop • Involves processing of the premature mRNA to become a
o Opposite the Acceptor Arm mature mRNA
o Have a trinucleotide that is complementary to the codon • The premature mRNA contains both the introns and the exons
present on the mRNA o Introns – noncoding sequences
o In the figure, the anticodon at the bottom of the tRNA have o Exons – coding sequences
a trinucleotide GAA • During this process the introns are spliced off the premature
• D Loop and T Loop mRNA forming the mature mRNA which now only contains the
o These extra arms help identify a specific tRNA Exons

Central Dogma of Life

• Transfer amino acids from the cytoplasm into the ribosome for
the translation of the information in the sequence of
nucleotides in the mRNA into specific amino acid sequence
• There are at least 20 species of tRNA in every cell, at lease one
corresponding to each of the 20 amino acids required of protein
synthesis
• The synthesis of proteins is directed by the sequence of the
nucleotide present in the DNA molecules
• The DNA establishes the similarities between and a parent and
its offspring that we regard as Hereditary Characteristics
• The overall process of Protein Synthesis is shown in the diagram
referred to as the Central Dogma

• rRNA are transcribed from the DNA in the nucleus and are
assembled with proteins to form Ribosome Subunits
• Ribosomes
o 2 subunits (large and small)
o These subunits are composed of rRNAs

• Involves the following processes:

1. Replication
2. Transcription
3. Translation

REPLICATION
• Involved in rRNA and mRNA processing (splicing) and gene In which a DNA is being replicated to form a new DNA with the
regulation enzyme DNA Polymerase
• U1, U2, U3, U4, U5, and U6 – involved in intron removal and ↓
processing of pre-mRNA into mRNA TRANSCRIPTION
• U7 – involved in production of correct 3’ ends of histone mRNA The synthesis of an RNA out of a DNA molecule by the enzyme
RNA Polymerase
↓
TRANSLATION
Process of forming a polypeptide chain using the sequence of
codons present in the mRNA

• Both the Replication and Transcription happen in the nucleus

while the Translation happens in the ribosome

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 o These RNA Primers are extended by DNA Polymerase to
(Highlighted in Green) form the Okazaki Fragments
After the RNA Primers are replaced by DNA by another DNA
Polymerase, the Okazaki Fragments are joined together by the
enzyme DNA Ligase.
After that, there will be the reconstitution of the chromatin
structure

• Reverse Transcription
o A DNA is formed from an RNA
• RNA Replication
o A new RNA is being synthesized from an RNA molecule

• DNA Polymerase – deoxynucleotide polymerization

• Helicase – unwinding of dsDNA (ATP driven)
• Topoisomerase – relieves torsional strain produced from the
unwinding of dsDNA
• DNA Primase – initiates the synthesis of RNA primers From Harper’s
• Single-Stranded Binding Proteins (SSBs) – prevent premature
reannealing ssDNA strands to form dsDNA
• DNA Ligase – seals the single-strands nick between the nascent
chain and Okazaki fragments in the lagging strand 1. Initiation
2. Elongation
3. Termination with 5’ → 3’ Polarity

The DNA serves as the Template Strand with the enzyme DNA-
Dependent RNA Polymerase synthesizing the RNA Product

1. Identification of the origin of replication In the picture…

2. Removal of nucleosome and unwinding of dsDNA
3. Formation of replication fork; RNA Primer Synthesis • One strand of DNA, which is the Template Strand, is being
4. Initiation of DNA synthesis and elongation copied starting from the Initiation Point, which has the
5. Formation of replication bubbles with ligation of the newly sequence TATAAA
synthesized DNA segments • An mRNA is synthesized using complementary base pairing
6. Reconstitution of the chromatin structure with Uracil, replacing Thymine
• The newly formed mRNA moves out of the nucleus into the
DNA replication begins with helicase unwinding the double ribosomes in the cytoplasm and the DNA rewinds
stranded DNA forming 2 single stranded DNAs that serves as
templates for the synthesis of 2 new DNA molecules.
There are single strand binding proteins that stabilize these
single stranded DNAs that prevent them from premature
reannealing.
o One DNA, which is called the Leading Strand, is
synthesized continuously in a 5’ to 3’ direction by DNA
polymerase by pairing bases complementary to the
bases present on the template strand.
o The other strand, which is called the Lagging Strand, is
synthesized discontinuously, needing an RNA Primer that
is synthesized by a Primase
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• Initiation occurs when mRNA attaches to the ribosome
• On the mRNA, the start codon AUG binds to the tRNA with
anticodon UAC and carries Methionine
• The second codon attaches to a tRNA carrying the next amino
acid
• A peptide bond forms between 2 adjacent amino acids
• The first tRNA detaches from the ribosome and the ribosome
shifts to the next codon on the mRNA (Translocation)
• A third codon can now attach where the second codon was
before the Translocation
• The Translation continuous with the succeeding codons present
on the mRNA and a Stop Codon will terminate Translation and
a Protein Product is formed
General Properties of Nucleic Acids
• Acidity
o Amphiphilic molecules, normally acidic because of
phosphate
• Viscosity
o Insoluble in organic solvents, can be precipitated by ethanol
• Optical Absorption
o Capable of UV absorption due to aromatic groups
• Thermal Stability
o Disassociation with extremes of temperature
• Dissociation of the different bonds (hydrogen bonds, glycosidic
bonds, phosphodiester bonds)
• The temperature at which 50% of the double helix is being
unwound
• Greatly influenced by the number of hydrogen bonds in between
base pairs
The more hydrogen bonds, the greater the Tm
• When DNA was heated to its Tm, the light absorption would
increase, which indicates that the double strand helix DNA was
separated into single strands
• When cooling down (annealing) the denatured DNA solution, the
single DNA can reform a double strand helix to recover its
biological function
Mutations
• Alterations in DNA structure that produce permanent changes
in the genetic information encoded
• Mutation is a change in the sequence of the bases present in a
gene that is being formed during DNA Replication
• Such errors alter the genetic information that is passed on
during transcription
• Different factors including chemicals, viruses, ionizing
radiation, and UV lights increase the rate of mutation
• When one base is exchanged for another
• It may be a Transition or a Transversion
• Transition
o Happens when a given pyrimidine is substituted by another
pyrimidine base
o A purine is substituted by another purine
• Transversion
o Happens when a pyrimidine is substituted by a purine
o A purine is substituted by pyrimidine
• Consequence of Substitution
1. Missense Mutation – encodes a different amino acid and
causes a small change in protein product
2. Silent Mutation – encodes the same amino acid and
causes no change in the protein product
3. Nonsense Mutation – substitution results to a stop codon
causing the production of an incomplete protein
• Extra bases are inserted into a DNA sequence
• Insertion of a nucleotide into a sequence of nucleotides in an
mRNA results in a shift in the reading frame upon the process
of Translation changes all the succeeding codons and causing
the incorrect amino acids to be placed in the synthesis of a
protein product
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• A section of the DNA sequence is deleted
• Occurs when a portion or segment of a chromosome or a
sequence of DNA is lost during DNA Replication
• The protein product does not contain the corresponding the
amino acids encoded by the missing sequence of codons

Key Points
• Nucleic acids serve as molecular storage of genetic information
• There are 2 types of nucleic acids: the double stranded DNA and
the single stranded RNA
o These are polymers of nucleotide units and each of the
nucleotide unit is composed of a base, sugar, and a
phosphate group
• The nucleic acids play a role in the different processes involved
in the Central Dogma of Life, Replication, Transcription, and
Translation
• The DNA molecules are complexed with other proteins for its
organization to form Chromosomes in order for the DNA
material to fit into the nucleus
• Mutations are alteration in the DNA structure that produce
permanent changes in the genetic information encoded

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