NUCLEIC ACID CHEMISTRY – DR.

VILIRAN

NUCLEIC ACID CHEMISTRY HISTONES = Important in the packaging/condensation of DNA

Dr. Dolores V. Viliran BASIC (Positively Charged) Composed of Basic Amino Acids
Compatible with the ACIDIC nature of DNA
DNA coils around the histones Makes the DNA in its condensed
4 IMPORTANT MACROMOLECULES: form
1. Carbohydrates Chromosomes are not pure DNA, it is associated with proteins.
2. Lipids NAKED DNA = without proteins
3. Proteins
4. Nucleic Acids -----------------------------------------------------------------------------------------------
REVIEW (COMPLEMENTARY BASE PAIRS – Watson-Crick Base Pairs):
Among the 4 macromolecules, NUCLEIC ACIDS are the most important Adenine – Thymine
– WHY? It is the chemical basis of heredity DNA Cystosine – Guanine

BIOMEDICAL IMPORTANCE OBJECTIVES

What is the chemical basis of heredity? DNA is the fundamental units of Functions of Nucleic Acids
genetic information. Structure of Nucleic Acids
Difference Between DNA and RNA
DNA (Deoxyribonucleic Acid)
Cellular Location of Nucleic Acids
Chemical basis of heredity
Central Dogma of Life: Replication, Transcription, Translation
Polymeric molecule
Composed of 4 monomeric unit that build up the DNA
FUNCTION OF NUCLEIC ACIDS
Adenine, Guanine, Cytosine, Thymine
Nucleic Acid = An informational molecule
What is the genetic basis of disease? DNA Alteration/Mutation NUCLEIC ACIDS Informational molecule Stores genetic
information (Both DNA and RNA can store genetic information)
If DNA will be changed or altered DNA Alteration/Mutation
Disease Two Kinds of Nucleic Acids:
1. DNA (Deoxyribonucleic Acid)
Why differences in physical appearance and metabolism occurs in each
Blueprint of living organisms
individual? DNA Polymorphisms
Contains genetic information for the synthesis of proteins
Primary function of DNA: Storage of genetic material
Differences in physical appearance and metabolism Each
2. RNA (Ribonucleic Acid)
individual have different set of genes
Machinery for the expression of the coded information in DNA to
proteins
mRNA = Carrier of genetic information encoded in the DNA

Final end-product of gene expression = PROTEINS

Without DNA, there will be no proteins
DNA Very important molecule Inside the cell, there is
another compartment that will protect the cell = NUCLEUS
Genetic information should be relayed:
DNA RNA = Transcription
RNA Proteins = Translation
Translation (Protein Synthesis) occurs in the RIBOSOME, which
is located in the CYTPLASM
DNA from nucleus to cytoplasm Very prone to
alterations/mutations Need another molecule to transmit
the information = RNA (mRNA)

CENTRAL DOGMA OF LIFE

(Picture Above) CHROMOSOMES AND NUCLEIC ACIDS Central Dogma of LIFE: Flow of genetic material
DNA = found inside the nucleus CHROMOSOMES
In humans, we have 46 chromosomes which are usually in pairs.
2 Types of Chromosomes:
1. Autosomes = Chromosome 1-22
- If you have a problem from chromosome 1-22, the genetic
disorder can be classified as:
AUTOSOMAL DOMINANT (if it is expressed with a single (Picture Above) CENTRAL DOGMA OF LIFE
gene) First, before the cell divides, during the S Phase of the Cell Cycle,
AUTOSOMAL RECESSIVE (in which you need two recessive DNA Synthesis or DNA Replication occurs.
genes for the condition to be expressed) Replication = “Replica” Produce identical DNA
2. Sex Chromosome = Chromosome 23 Before the cell divides, from 46 chromosomes, it will be doubled
- If you have a problem with the sex chromosome, it could be to 92 chromosomes Each daughter cell will get the same
classified as: number of chromosomes, which is 46
X-LINKED (XX for female and XY for males) Replication is followed by Transcription, which is the conversion of
Y-LINKED DNA to mRNA.
Chromosomes are condensed form of DNA Transcription = “Transcribe” Writing something in a different
HISTONES = Important in the packaging/condensation of DNA way
BASIC (Positively Charged) Composed of Basic Amino Acids LEA THERESE R. PACIS 1
Compatible with the ACIDIC nature of DNA
Chromosomes are not pure DNA, it is also composed of proteins.
NAKED DNA = without proteins
 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

- Pyrimidines = Cytosine (C), Uracil (U), Thymine(T)

way
Our DNA is composed of Adenine, Guanine, Cytosine, and
HETEROCYCLIC RING = In the ring, aside from Carbon and
Thymine (A, G, C, and T) and RNA is composed of Adenine,
Hydrogen, you also have Nitrogen.
Guanine, Cytosine, and Urasil (A, G, C, U)
Classified into 2 Types:
They called it transcription because it deals with the same
1. Purine = Adenine, Guanine
language – Nucleic Acids. The only difference is the letter and
2. Pyrimidine = Cytosine, Thymine (DNA), Uracil (RNA)
the sugar.
mRNA is converted to protein by the process called Translation.
b. A PENTOSE SUGAR, ribose or deoxyribose, in a furanose ring form
Translation = “Translate” Change one language to another
- DNA = deoxyribose
language
- RNA = ribose
Two language: Nucleic Acid language translated to Amino Acid
- Sugar hold the base on one side and the phosphate on the other
language (4 letters translated to 20 letters)
side. Thus, sugar hold the components of the nucleotide
Translation = Protein Synthesis
together
c. A PHOSPHATE GROUP esterified to the sugar
TEMPLATE PRODUCT
DNA Replication DNA DNA
Transcription DNA RNA A NUCLEOSIDE contains only a base and a sugar
Translation mRNA Protein When you phosphorylate a nucleoside Becomes a
*TAKE NOTE: Product of Transcription is RNA. mRNA is not the only NUCLEOTIDE Contains a base, a sugar, and a phosphate
RNA produced during transcription. You could also produced rRNA group
and tRNA. But the template for Translation should be mRNA. TAKE NOTE: In the middle, we have the SUGAR group, on one
side, we have the BASE, and on the other side, we have the
Present Concept of the Central Dogma PHOSPHATE group.
Specific transfer of information from RNA to RNA has been observed in
viral systems NUCLEOSIDE = coupling of a base and a sugar
Specific transfer of information from RNA to DNA has been observed in NUCLEOTIDE = when a nucleoside becomes phosphorylated
viral systems and tumor.

Aside from the transfer from DNA to RNA to Proteins, you can also
have RNA to DNA or RNA to RNA. This is true in certain viruses and
tumors. An example would be HIV, which has the enzyme REVERSE
TRANSCRIPTASE (converts RNA genome to a viral DNA).

How does DNA and RNA perform these various functions?

Structure is intimately related to function
Change the structure and the function may be lost
Thus we need to know the structure in order to understand the function
(Picture Above) STRUCTURE OF A NUCLEOTIDE
According to Mr. Francis Crick, structure is intimately related to
function. BASE Contains Nitrogen
4 letters spells our DNA If you change the sequence of letter PHOSPHATE GROUP Contains Phosphate (Obviously. HAHA)
(even if you change just one letter, the meaning will change) SUGAR Furan Ring (Furanose = Pentose Sugar) = RIBOSE
The function will change If the C2 prime has an OH, it is RIBOSE and if there is no
Example: The fat cat ate the rat. If you change C to R and R to oxygen, it is DEOXYRIBOSE. In the example above, it is an
C The fat rat ate the cat. (You now have a very different example of an RNA
meaning.)
This also applies to our DNA molecule. If you change one of the The linkage between the sugar and the base is called the
4 letters in the sequence and it might result to one of the genetic GLYCOSIDIC BOND. In this example, it is N-Glycosidic Bond
disorders. because it is attached to a Nitrogen.
The linkage between the sugar and the phosphate group is
called the PHOSPHOESTER BOND.
COVALENT STRUCTURE OF NUCLEIC ACIDS
Genetic information is encoded in DNA and carried by mRNA as sequence Nucleotides in DNA
or a chain of nucleotides 1. ADENINE-2-deoxyRIBOSE-PHOSPHATE
2. GUANINE-2-deoxyRIBOSE-PHOSPHATE
I. Composed of polymers of nucleoside monophosphates (Nucleotide- 3. CYTOSINE-2-deoxyRIBOSE-PHOSPHATE
Nucleotide-Nucleotide) 4. THYMINE-2-deoxyRIBOSE-PHOSPHATE
Monomeric units consist of: NUCLEOTIDE Nucleotides in RNA
1. ADENINE-RIBOSE-PHOSPHATE
NUCLEOTIDES 2. GUANINE-RIBOSE-PHOSPHATE
Monomeric unit of DNA molecule 3. CYTOSINE-RIBOSE-PHOSPHATE
Composed of base, sugar, and a phosphate 4. URACIL-RIBOSE-PHOSPHATE
- BASE: Nitrogenous Base Contains nitrogenous
- SUGAR: Deoxyribose (DNA), Ribose (RNA) Abbreviation if it is a triphosphate (DNA) Deoxynucleoside
- PHOSPHATE Reason why the DNA is negatively charged Triphosphate (DNTP) = This is the substrate for DNA Synthesis
For RNA Synthesis, you just remove “deoxy” Nucleoside
Base-Sugar-Phosphate (BSP) Triphosphate (NTP)
a. NITROGENOUS BASE which may be a purine or a pyrimidine
- Purines = adenine(A), Guanine (G)

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

Chemical Structure of Nitrogenous Bases NUCLEOSIDES

To convert the base into a nucleoside You add purine + sugar

to the base. The linkage is an N-Glycoside.
For Purines --> The connection is between C-1 of sugar ribose
and N-9 of Purines
For Pyrimidines The connection is between N-1 and C-1

Purines = N9-C1 glycosidic bond

Pyrimidines = N1-C1 glycosidic bond
Purine Has 2 rings Addition of pentose sugar to a base produces a nucleoside.
Pyrimidine Has only 1 ring - Adenine Adenosine
TAKE NOTE: Each carbon and nitrogen atom has amphibolic - Guanine Guanosine
sources intermediates We can synthesize nucleotides in our - Cytosine Cytidine
body. - Thymine Thymidine
- Uracil Uridine
Substitutions -- OXYGEN, AMINO GROUPS, METHYL GROUPS
Most of the nucleosides for PURINE ends with “-sine,” while
How do you generate the different type of bases? Through nucleosides with PYRIMIDINE ends with “-dine.”
substation of the oxygen, amino group, and the methyl group If is you attach DEOXYRIBOSE:
The ones noted below are the chemical names of each Deoxy-Adenosine, Deoxy-Guanosine, Deoxy-Cytidine, and
nucleotide. so on. Without the “deoxy” word, you have RIBOSE.

PURINES NUCLEOTIDES
- ADENINE = 6-aminopurine
- GUANINE = 2-amino,6-oxypurine To convert Nucleoside to a Nucleotide Add Phosphate

Nucleotides can have one, two or three phosphates:

(Picture Above) CHEMICAL NAMES OF PURINES

ADENINE = 6-aminopurine On the 6th carbon atom of
purine, you have the amino group
GUANINE = 2-amino,6-oxypurine You have an amino
group on the 2nd carbon, and an oxygen on the 6th carbon

PYRIMIDINES
- CYTOSINE = 2-oxy,4-amino pyrimidine
- URACIL = 2,4-dioxypyrimidine
- THYMINE = 2,4-dioxy,5-methylpyrimidine

(Picture Above) CHEMICAL NAMES OF PYRIMIDINES

URACIL = 2,4-dioxypyrimidine You have 2 oxygen located (Picture Above) STRUCTURE OF ATP
on the 2nd and 4th carbon Function of ATP = Energy currency of the cell
THYMINE = 2,4-dioxy,5-methylpyrimidine Same as uracil, When you cleave phosphate, 7 calories can generated per each bond
you have 2 oxygen located on the 2nd and 4th carbon, but this (When ATP is converted to ADP, energy is released)
time you have a methyl group on the 5th carbon
CYTOSINE = 2-oxy,4-amino pyrimidine You have an oxygen
on the 2nd carbon and an amino group on the 4th carbon

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

II. NUCLEOTIDES - are linked together by phosphodiester bonds between the

3’ hydroxyl on the sugar of one nucleotide and the 5’- phosphate on the
sugar of another nucleotide
1. Trinucleotides - addition of another nucleotide at the 3’ hydroxyl of the
sugar
2. These compounds have polarity of direction- 5’ – 3’
3. Characteristically nucleotides are acidic by virtue of their phosphate
groups

How are you going to connect the different nucleotides? Through
the phosphodiester bond. A phosphodiester bond will be created
between the 3’ hydroxyl on the sugar of one nucleotide, and to the
5’ phosphate on the sugar of another nucleotide.
So when you cut the DNA molecule into 2 fragments, you destroy
the phosphodiester bond using the enzyme phosphodiesterase.
It is important to know the direction. For polynucleotides, you need
to indicate the direction – from 5’ to 3’.
The net charge of nucleotides are negative (acidic) Primarily
because of the phosphate group.
(Picture Above) STRUCTURE OF CYCLIC AMP (cAMP) AND S-
ADENOSYLMETHIONE (SAM)
cAMP = a 2nd messenger
Where is it from? From the structure of ATP, you remove the
diphosphate Become AMP It forms a ring, thus cAMP
Adenylyl Cyclase = Enzyme that converts ATP to cAMP
S-Adenosylmethionine (SAM) = a methyl donor/source of methyl
group for methylation reactions

(Picture on the Left)

TWO NUCLEOTIDES
REACTING TO FORM A
DINUCLEOTIDE
One nucleotide + One
nucleotide Forms
3’ hydroxyl group and
5’ phosphate group +
Phosphodiester
Linkage (Yellow)

(Picture Above) OTHER FUNCTIONS OF NUCLEOTIDES – Functions as

Coenzymes

(Picture Above) UNCOMMON NATURALLY OCCURING PYRIMIDINE AND

PURINES + STRUCTURE OF HYPOXANTINE, XANTHINE, AND URIC ACID
Figure 32-7: Uncommon Naturally Occurring Pyrimidine and Purines
(Not discussed)
Figure 32-8: Structures of Hypoxanthine, Xanthine, and Uric Acid
We need to know the structure of URIC ACID because we always
encounter it in the clinical setting.
Purine is degraded to Uric Acid. (Hypoxanthine and Xanthine are its
intermediates – Hypoxanthine Xanthine Uric Acid) (Picture Above) SYNTHETIC PYRIMIDINE AND PURINE ANALOGS
Allopurinol = Drug for Gout
Structure is almost similar with Xanthine and Hypoxanthine
Being structural analogs, it inhibits the enzyme that converts
(Picture on the Left) CAFFEINE – A Xanthine and Hypoxanthine to Uric Acid (Xanthine Oxidase)
Trymethylxanthine Uric Acid
5-Iodo-2-Deoxyuridine, 5-Fluorouracil, etc = Anti-Cancer Drugs
Trimethylxanthine Caffeine As an analog They can be incorporated as one of the
THEOBROMINE nucleotides Process of replication in the cancer cell will not
(Dimethylyxanthine) Chocolate proceed If there is no replication, cancer cell will die.
THEOPHYLLINE Being a structural analog It will inhibit the enzyme for DNA
(Dimethylxanthine) Tea replication (Polymerase Enzyme)

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

NOMENCLATURE OF NUCLEIC ACIDS

DNA Denaturation:
A. Polynucleotides
If you want to separate the two strand Destroy/Cut the
B. Polyribonucleotides – Polynucleotides containing ribose as opposed to
Hydrogen Bonds = DNA Denaturation
deoxyribose
When you denature the DNA, hydrogen bonding is destroyed.
1. Naturally occuring are called RNA
(You denature the DNA from a double stranded to a single
2. Bases found in RNA’s (w/ a few exception) = Guanine, Cytosine, Adenine,
stranded DNA)
and Uracil
C. Differences Between the Primary Structure of DNA and RNA
1. DNA has a 2’-deoxyribose as its sugar moiety rather than ribose CHARGAFF’S RULE:
2. DNA has one different base-thymine (5-methyl-uracil) Content of A = Content of T
3. RNA has one different base-uracil Content of G = Content of C

Ways of Presenting the Structure of a Polynucleotide (Abbreviated Form) This means that in the lab, you can predict the base composition of
A. 5’ p-T-A-C-G-G-G-C-G-A-T-T-T-G-G-GOH³’ a particular DNA by just examining one base.
B. 5’ pTpApCpGpGpGpCpGpApTpTpTpGpGOH³ For example, the percentage composition of A is 20%.
- Percentage composition of T is also 20%.
DNA - Percentage composition of C and G is 30%.
*100 = 20 (Percentage Composition of A) + 20 (Percentage
DNA – THE GENETIC MATERIAL
Composition of T) + 2x (Percentage Composition of C and G)
BASIC STRUCTURAL CHARACTERISTICS: A Double Helical Structure as
x = 30
proposed by Watson and Crick (1953)

NICE TO KNOW: Watson is the teacher of Crick. 4. The helix is 2 nm in diameter.

1. TWO ANTI – PARALLEL POLYDEOXY RIBONUCLEOTIDE CHAINS – Wound Bases are separated by 3.4 A° along the helix axis, and each base is
around each other with the bases inside of the helix sugar and PO4 – rotated 36° in relation to the previous base.
outside The helical structure repeats at intervals of 34 A° (every 10 base –
pairs)
Primary Structure of DNA: Sequence of nucleotides connected In solution, the helical structure of DNA probably does not repeat
by phosphodiester linkage every 10-base pairs but nearer to every 11 with the bases inclined 20°
Secondary Structure of DNA: Composed of two polynucleotides from the horizontal
wound around each other HELIX (Right Handed Double Helix) GENETIC INFORMATION IS STORED AS THE SEQUENCE OF BASES
Take Note: Bases are sandwiched on the inside, while the ALONG THE CHAIN
sugar phosphate backbone are on the outside.
(Picture on the Right)
2. STACKING OF THE HYDROHOBIC RINGS – Result when the planes of the DIAGRAMMATIC REPRESENTATION
OF THE WATSON AND CRICK
MODEL OF THE DOUBLE HELICAL
Hydrophobic Rings --> Refers to the nitrogenous space STRUCTURE OF THE B FORM OF
DNA
bases are perpendicular to the axis of the helix What is the significance of the
3. HYDROGEN Bonding – between one bases on one stand pairing w/ MAJOR and MINOR GROOVE?
another base on the anti-parallel strand Based on their analysis, it is the
site where the transcription
Two stands are connected by Hydrogen Bonding factors interact.

(Picture on the Left) DNA

REPLICATION -- The double-
stranded structure of DNA and the
template function of each old strand
(orange) on which a new
complementary strand (blue) is
synthesized)
The DNA strand unwinds to give
way for DNA replication and
producing another daughter DNA.
Helicase Enzyme removes the
Hydrogen Bonds. Each template
strand will act as a pattern for the
(Picture Above) BASIC STRUCTURAL CHARACTERISTICS OF DNA synthesis of new daughter strand,
As described by Mr. Watson and Crick: to produce one DNA molecule.
DNA is composed of two polynucleotides, anti-parallel with each
other (One strand runs from 5’ to 3’, while the other strand runs
from 3’ to 5’) = Opposite Direction
On the outside = Sugar-Phosphate Backbone
On the inside = Hydrophobic Bases For a DNA to be replicated, it must be denatured/separated
The two strands are connected by Hydrogen Bonding between Become single stranded
base pairs (Watson-Crick Base Pairs): Substrate for DNA replication = DNTPs (Deoxynucleoside
- Adenine – Thymine = 2 Hydrogen Bonds (Easier to separate) Triphosphate)
- Cytosine – Guanine = 3 Hydrogen Bonds (Harder to separate)

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

A, B, Z Forms of DNA (Picture on the Right)

SUPERCOILING IN EUKARYOTIC
DNA
DNA coils around the Histone
Octomer Can be compare
to a TOP (Turumpo – The nail
is the Histone Octomer, and
the rope is the DNA)
Why is there an interaction?
Because histones are BASIC
and DNA is ACIDIC There is
electrostatic attraction.
There are 3 different forms of DNA:
Supercoiling together with
A Form
histone is needed to package
B Form
the DNA inside the nucleus.
Z Form
NUCLEOSOME = Histone +
The normal form of DNA = B DNA (Right Handed Helix)
Supercoil

DENATURATION OF DNA
The double helix is disrupted during DNA replication, transcription, repair
and recombination
Therefore the forces that hold the two strands together are adequate for
providing stability and yet weak enough to allow easy strand separation

Dissociation and Reassociation of the Double Helical Chains of DNA

Double helical chains of DNA have a remarkable ability to dissociate from
one another and to reassociate again. This behavior is essential to the
processes of REPLICATION and TRANSCRIPTION

A. DENATURATION – rupture of the hydrogen bonds between the bases,

resulting from increasing temperature or the alteration of the H +
concentration, which causes the two strands to come apart.
1. Increasing pH – deprotonates ring nitrogens of guanine and thymine;
decreasing pH protonates ring nitrogens of adenine and cytosine

pH = Alkaline Metal Add Aluminum Hydroxide to the tube

(Picture Above) A, B, AND Z DNA of DNA sample Can cause DNA Denaturation ( pH can
Z DNA = Most condensed destroy the bases)
Change from B to A DNA = When you lack hydration
Dark-Stained = More condensed 2. Increasing acidity – can cause rupture of purine glycosidic bonds, and
Among the 3 forms of DNA, B DNA is better expressed 10 base at high temperatures phosphodiester bonds may be broken.
pair only (Unlike A DNA, which has 11 and Z DNA, which has 12) Alkali – method of choice for DNA denaturation
3. Increasing temperature – the double helical chain dissociates at a
definite temperature known as Melting Temperature (Tm)
Tertiary Structure of DNA – Supercoiling
Extract DNA in the tube Boiling water bath DNA
RECALL: Denaturation
Primary Structure of DNA = Nucleotides Melting Temperature (Tm) – Temperature at which 50% of
Secondary Structure of DNA = Double Helix (Right-Handed) the DNA is already separated
Melting causes unstacking of the base pairs Result to
Tertiary Structure of DNA = You just twist the double helix further absorbance/Hyperchromic Effect
SUPERCOILING Needed for the formation of CHROMATINS - In a DNA structure, when it is double stranded, the
bases are inside, and when it is single stranded
Supercoiling in Prokaryotic DNA (denatured), the bases are exposed. Bases absorb light.
- Positive supercoils When you denature the DNA and the bases are
- Negative supercoils exposed, it absorbs light HYPERCHROMIC EFFECT
Supercoiling in Eukaryotic DNA when you denature DNA
- Formation of chromatin
Electrostatic attraction between the negatively charged phosphate a. Tm is the temp. at which 50% of the double helix is unwound
groups on the DNA and the positively charged groups on the b. Melting causes “unstacking of the base pairs” which results in
protein increased absorbance (Hyperchromic Effect)
c. Tm is strongly influenced by the base composition of the DNA
- DNA rich GC pairs has a higher Tm than DNA with a higher
proportion of AT pairs
- Mammalian DNA, which is about 40% GC pairs has a Tm of about
87oC

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

B. RENATURATION (Annealing)
Annealing Temperature
20oC to 25oC below the Tm
Basis of PCR
- The amount of DNA per cell increases as the complexity of the cellular
function increases
DNA Renaturation Humans have bigger DNA as compared to the DNA of bacteria
because humans are more complex than bacteria.

1. If the temperature of melted (dissociated) duplex DNA is rapidly - The DNA in the cell is packaged as 46 chromatin fibers
reduced, the original double helical structure does not reform (anneal) - Metaphase = Condensed state the largest chromosome is about 10µm
2. If, however, the temperature is held at a value of about 20oC to 25oC If stretched out is about 8 cm long
below the Tm, the original double helical structure reforms.

(Picture Above) GENUM SIZE IN DIFFERENT CELLS

Plasmids = Circular DNA found in bacteria (This is different from
(Picture Above) DENATURATION-RENATURATION its genomic DNA.)
Intact Double Helix Heat the sample reaching the Tm 50% In humans, circular DNA is present in the mitochondria.
Separated, 50% Intact High than 87-940C From a Double Genomic DNA is present in the nucleus
Stranded DNA becomes a Single Stranded DNA You lower the Plasmids, Viruses, and Bacteria ranges from 103 to a million base
temperature – Annealing Temperature (From 940C to 600C) pairs – Very little as compared to humans, which has
Renaturation approximately 3 billion base pairs, which is cut into
Chromosome 1 to 23
Take Note of BEANS: Has almost 40 billion base pairs This is
Nucleotides Absorb Ultraviolet Light
the reason why when you are suffering from gouty arthritis, you
CLINICAL SIGNIFICANCE: Basis of SKIN CANCER are not allowed to eat BEAN, NUTS, SOYA (TAHO!)
Nucleotides absorb ultraviolet light (Bases can absorb light) Beans increases URIC ACID LEVELS

The conjugated double bonds of purine and pyrimidine derivatives Techniques of Determining DNA Size
absorb light a. Equilibrium Centrifugation: Cesium Chloride
The mutagenic effect of UV light is due to its absorption by nucleotides
in DNA resulting in chemical modifications (UV-light induced thymine- It is a very tedious procedure Takes a long time to centrifuge
thymine (pyrimidine) dimer the DNA See levelling in the test tube
At pH 7.0 all nucleotides absorb light at wavelength 260 nm Reagent used: Cesium Chloride

b. Electron Microscopy
Secrets of Lasting Relationship c. Electrophoresis
Mark Goulston,M.D.
Gel Electrophoresis
Six Pillars of Lasting Love: (C-R-E-A-T-E) Principle: It is the migration of molecules based on charges –
1. Chemistry depending on the charges, one will move from one region to
2. Respect another.
3. Enjoyment Cathode = Negatively charged because it attracts CATIONS
4. Acceptance Anode = Positively charged because it attracts ANIONS
5. Trust Net Charge of DNA = NEGATIVE
6. Empathy Movement: Cathode to Anode

Like DNAs, it can DENATURE = hiwalay and RENATURE = magbalikan…

so it is like a relationship. HAHA! :))

TYPES OF DNA STRUCTURE

Usually, the unit of expression for DNA is the number of base pairs or
the length.
Size of DNA is Highly Variable
- DNA size can be expressed as number of base pairs, molecular mass, the
length of the strands and actual mass of DNA
- DNA of molecular weight 1 x 106
- Contains 1500 base pairs (or 1.5 kilobase pair) and is 0.5 nm long
Which will travel faster – a 5kb DNA or a 50kb DNA? 5kb
The bigger the DNA, the slower; the smaller the DNA, the
faster.
Which will travel faster – linear DNA or circular DNA? Circular
Circular travels faster than linear DNA.

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

DNA may be Linear or Circular

Inverted Repeat: The strand on top is the same as the strand
Nuclear DNA = LINEAR below when it is inverted.
Strand on Top (5’ to 3’): GGAATCGATCT
Mitochondria DNA = CIRCULAR
Strand Below (5’ to 3’): GGAATCGATCT
Which contains ENDS? Nuclear DNA or Mitochondrial DNA? Mirror Repeat: “Parang nakaharap daw sa mirror” (Facing the
Nuclear DNA contains ENDS TELOMERES mirror)
CENTER = CENTROMERE Strand on Top (5’ to 3’): GGAATCGATCTT
Strand on Top (3’ to 5’): GGAATCGATCTT
AGING PROCESS Can be explained by the shortening of the Strand Below (3’ to 5’): CCTTAGCTAGAA
DNAs, specially shortening of the ends of the DNAs TELOMERIC Strand Below (5’ to 3’): CCTTAGCTAGAA
SHORTENING Direct Repeat: In the same strand, the sequence is repeated.
To avoid Telomeric Shortening, we have a an enzyme called Strand on Top (5’ to 3’): GGAATCGATCTT -- GGAATCGATCTT
TELEMERASE Strand Below (3’ to 5’): CCTTAGCTAGAA -- CCTTAGCTAGAA

Triple-Stranded DNA
How are Triple-Stranded DNA formed?
You have a double-stranded DNA
a. Double-Stranded Circles Another strand attaches to it
b. Single-Stranded DNA
c. Circular DNA is a Superhelix
Formed in DNA regions with continuous
SHAPE OF DNA MOLECULES: string of of purine bases, that is homopurine-
1. Chromosomal DNA may be linear or circular. homopyrimidine regions
2. DNA is complexed with histones in the eukaryotic chromosome, which Generated by the hydrogen bonding of a
profoundly influence the structure of the chromosome. third strand into the major groove of B-DNA
3. Supercoiling-essential for stage of replication, transcription and The third strand forms hydrogen bonds with
recombination it occurs only when there is restraint upon the rotation of another surface of the double helix thru
the ends of the DNA chains, such as occurs in circular DNA or in linear Hoogsteen Pairs
DNA when the ends are too far apart to allow rapid spinning Limited to only four triplet bases:
- TAT
- CGC
Alternative DNA Conformations
- GGC
DNA Bending
- AAT
- NA sequences with runs of 4 to 6 Adenine bases phased by 10-bp
Polypurine-polypyrimidine regions
spacers produce bend conformations
have potential biological roles:
- Important in the interaction between DNA sequences and proteins
- Transcription control
that catalyze replication, transcription and site-specific recombination
- Initiation of replication
- Replication terminators
Cruciform DNA
- Initiators of genetic
Dos DNA (Defined Ordered Sequence DNA)
recombination
- Inverted Repeat (Palindromes)
- Enhancers of stability of
- Mirror Repeats
telomeres
- Direct Repeats
Present within noncoding DNA regions INTRONS
TAKE NOTE: The ends (telomeres) must be stable.
FUNCTION: Inverted repeats may function as a molecular switches for
What will happen if the ends are no stable?
replication and transcription
It is like a rope Pag walang ends Makakalas Cause
abnormality in the DNA

INTRAMOLECULAR TRIPLE
HELICES – Polypurine-
polypyrimidine regions of DNA
with a mirror repeat symmetry
can form an intramolecular triple
helix in which the third strand lays
in the major groove whereas its
complementary strand acquires a
(Picture Above) SYMMETRY ELEMENTS OF DNA SEQUENCES – single-stranded conformation.
Three types of symmetry elements for double-stranded DNA
sequences are shown. Arrows illustrate the special relationship of One of the disease that can be
these elements in one of these sequence. In INVERTED REPEATS, explained by formation of a triple
also referred to as PALINDROMES, each single DNA strand is self- stranded DNA is known as HEREDITARY
complementary within the inverted region that contains the PERSISTENCE OF FETAL HEMOGLOBIN
symmetry elements. A MIRROR REPEAT is characterized by the Composition of a Fetal Hemoglobin:
presence of identical base pairs equidistant from a center of Alpha and Gamma Globulin
symmetry within the DNA segment. DIRECT REPEATS are regions In terms of Oxygen Release: Adult
of DNA in which a particular sequence is repeated. The repeats Hemoglobin
need not be adjacent to one another. Persistence of Fetal Hemoglobin
afterHeabdnormal because

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

Histones are small proteins that carry a considerable (+) charge devided
after birth is not good Oxygen should be released
into 5 classes H1;H2A;H2B, H3 and H4
What happens is that you have a triple-stranded formation
Expression of Gamma Chain was not changed to Beta Sometimes, histones are called HISTONE OCTAMER:
Chain
2 Pairs of H2A
Four-Stranded DNA (Quadruplex) 2 Pairs of H2B
May form during DNA recombination 2 Pairs of H3
Contains repeated motifs high in guanine content (G-quartet DNA) 2 Pairs of H4
Form at telomeres NO H1 In the book, H1 are labelled as the linker histone
It is not included in the histone octamer.
(Picture on the Left) PARALLEL
QUADRUPLEX DNA
Quadruplex structures in CHROMOSOMAL ORGANIZATION
which all four strands are • If the DNA of all 46 chromosomes were lined up in the B-DNA conformation
parallel can form from four it would be more than 2 meters long
single-strand tracts of • DNA needs to fit within a cell nucleus with a diameter of approximately 5
polyguanine. These µm
quadruplexes, referred to as • Packaging of DNA:
G-quartets, are associated by Beads-on-a-string: DNA association with histones
Hoogsteen base pairs. 10 nm fiber
30 nm fiber (solenoid)
Slipped DNA
The DNA of all 46 chromosomes will be 2 meters long if it is lined
During replication up + The nucleus has a diameter of 5 µm How can you
There is a loop formation accommodate that long DNA molecule in a very small nucleus?
Mispairing BY PROPER PACKAGING with the aid of HISTONES.
Basis of FRAMESHIFT How are DNA Packaged? Formation of “beads-on-a-string,”
MUTAGENEIS wherein DNA is associated with histones Further Coiling = 10 nm
fiber; 30 nm fiber
Slipped, mispaired DNA (SMP-
DNA) (Picture on the Right) POSTULATED
Formation involves the STRUCTURES FOR THE
unwinding of the double helix NUCLEOSOME AND
and realignment and CHROMATOSOME – The
subsequent pairing of one NUCLEOSOME consists of
copy of the direct repeat with approximately146 bp of DNA
an adjacent copy on the other strand- generating a single-stranded loop corresponding to 1¾ superhelical
turns wound around a histone
octamer. The CHROMATOSOME
(two-turn particle) consists of about
166 bp of DNA (two superhelical
turns). The H1 subunit is retained by
this particle and may be associated
with it. Chromosomes containing les
that 166 bp do not bind with the H1
subunit.
Histone octamer at the center;
DNA coiling around Supercoil
(Tertiary Structure)
Without H1 Nucleosome
With H1 Chromatosome

(Picture Above) FRAMESHIFT MUTAGENESIS BY DNA SLIPPAGE –

DNA Replication within a run of a single base can produce a single
base frameshift. In the example shown here, a run of five A’s is
replicated and, depending on whether a slippage occurs in the
progeny strand or the template strand, a T may be added or
deleted from the DNA.

Nucleotide moves whenever you insert or deleted 1 nucleotide.

EUKARYOTIC DNA
1. DNA is packaged into unit structures called CHROMOSOMES.
2. Combined with proteins called CHROMATIN. Chromatin contains about
equal amounts (by weight) of DNA and protein.
3. DNA is associated with basic proteins called histones and with nonhistones
chromosomal proteins. These are non-covalent associations.

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

(Last Picture from the Previous Page) ORGANIZATION OF

POLYNUCLEOSOMES INTO CHROMOSOMES – A speculative
drawing showing the condensation of polynucleosomes into the
30-mm fiber as the subsequent packaging of this fiber into a
twisted, looped structure within the chromosome.
(1) Naked DNA = No histones yet (2) Histones are needed for
packaging of DNA “Beads-on-a-String” (3) Further coiling
until you have the condensed chromosome

CYTOPLASMIC DNA IN EUKARYOTIC ORGANELLES:

Mitochondria and chloroplasts of eukaryotic cells contain DNA that differs
from nuclear DNA
1. Neither mitochondrial nor chloroplasts DNA is associated with histones
2. Mitochondrial DNA of animal cells is:

Mitochondrial DNA is just 1% of the cellular DNA

a. Double – stranded
b. Circular
c. About 15,000 base-pairs in length
3. Mitochondrial DNA sequences code for only about 5% of the protein
components of mitochondrial structure and function. The bulk of
information for mitochondrial protein synthesis is stored in nuclear DNA
(Picture Above) CENTRAL DOGMA OF LIFE – DNA Replication is not
Most of the pathways happens in the mitochondria Enzymes
shown here
inside the mitochondria are still encoded by nuclear DNA
Products of Transcription rRNA (Ribosomal), mRNA (Messenger),
and tRNA (Transfer)
Will all of these become a protein? NO. rRNA and tRNA will not
RNA become a protein – only mRNA.
CHEMICAL NATURE OF RNA All of the will be needed to produce proteins:
1. Sugar moiety is ribose rather than 2’ deoxyribose of DNA - rRNA Part of ribosomes Ribosomes are the site where you
2. Pyrimidine component is URACIL ribonucleotide produce proteins
3. Exists as a single strand - tRNA Transports amino acids to the site of protein synthesis
- mRNA Template that directs the synthesis of proteins
Will be degraded after protein synthesis = Has the most rapid
turn-over (Mabilis masira/Easily destroyed)

MESSENGER RNA (mRNA)

Characteristics:
Most frequently synthesized and with most rapid turnover among the
RNA’s
To distinguish an mRNA It has a cap and a tail
Synthesized in transcription
You need a cap To protect the RNA because it will travel from
Carries the genetic information from the DNA (codons- triplet nucleotide)
the nucleus to the cytoplasm
and is used as the template for protein synthesis
You need a tail For transport because It will travel; Also for
stability because you extended the end
Carries the genetic information from the DNA as a CODON
After you synthesize an RNA through transcription, this will undergo
A codon has 3 nucleotides – WHY 3 nucleotides in a codon?
Post-Transcriptional Processing
We have 4 nucleotides A, G, C, and U
If it is 41 = 4
If it is 42 = 16
If it is 43 = 64
If it is 44 = 256
Translation = Translate Nucleic Acid language Amino Acid
language (You translate these 4 letters into 20 letters)
- You have 20 amino acids that will be added during protein
synthesis
- Among these combination:
If it is 41 = 4 Not Enough
If it is 42 = 16 Not Enough
If it is 43 = 64 More than Enough Most ideal
combination to produce the 20 Amino Acids

Genetic Code = Dictionary for the translation of nucleic acids

Single stranded
What is the smallest RNA? tRNA Read and translated 5’ to 3’
Has methylguanosine cap at the 5’ end and a polyadenine tail

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

Acceptor Arm = Part where amino acids attaches

Anti-Codon Arm = Attach to the codon in your mRNA
Also known as a bilingual molecule You have nucleotides and
amino acids in the structure

RIBOSOMAL RNA (rRNA)

Characteristics:
Intimately associated with ribosomes
Most abundant of all RNA’s
Least characterized among all RNA’s and is synthesized during
transcription

(Picture Above) THE CAP STRUCTURE ATTACHED TO THE 5’ TERMINAL

OF MOST EUKARYOTIC MESSENGER RNA – A 7-methylguanosine
triphosphate (black) is attached at the 5’ terminal of the mRNA (shown
in color), which usually also contains a 2’-O-methylpurine nucleotide.
These modifications (the cap and methyl group are added after mRNA is
transcribed from RNA.
Methylguamosine Cup Found in the 5’ region of mRNA
Poly-A-Tail Found at the 3’ end (Not shown) Assume a hairpin
look formation One way to terminate the process of
TRANSCRIPTION
(Picture on the Left) DIADRAMMATIC
REPRESENTATION OF THE
SECONDARY STRUCTURE OF A SINGLE
STRANDED RNA MOLECULE IN WHICH
A STEM LOOP, OR “HAIRPIN,” HAS
BEEN FORMED. Formation of this
structure is dependent upon the
indicated intramolecular base pairing
(horizontal lines between bases). Note
that A forms hydrogen bonds with U in
RNA
Odd and Even Number = Depends sa
first digit 70s = 70 is an even
number; Just look at the first digit
7 = ODD NUMBER Prokaryotes
S Stands for SVEDBURG UNIT
(Ayeshaaa!!!! :)) HAHA.)
Ribosomal RNAs:
30s Small Subunit 16S rRNA
Site where mRNA attaches to the
small subunit (Interaction
between mRNA and 16s rRNA)
50s Large Subunit 23S rRNA
An RNA but can function as an
enzyme = RIBOZYME
True or False: All enzymes are
protein in nature? FALSE – Why?
Because 23s rRNA functions as an
enzyme but it is not a protein.

TRANSFER RNA (tRNA)

Characteristics:
With the lowest molecular weight
Synthesized during transcription
With about 60 different types, with atleast one tRNA for every AA some
amino acids have 2 or more corresponding tRNA’s
Transfers amino acids from the cytoplasm to the ribosomes
“Adaptor” molecule that carries specific amino acid to the site of protein
synthesis. There, if recognizes the genetic code word that specifies the
addition of its amino acid to the growing peptide chain. (Picture Above) SCHEMATIC PRESENTATION OF A EUKARYOTIC GENE
Contains the anti-codon – The top horizontal line represents a part of the DNA genome of a
Single stranded but assumes a cloverleaf structure (secondary level) eukaryote; the bottom line represents the mRNA produced by it. In
Contains unusual/rare bases like ribothymine, pseudouracil and this hypothetical example, the DNA consists of two introns and three
dihydroxyuracil exons. The intron sequences are transcribed as hnRNA (precursor
Amino acid is always attached to the 3’ end and the 3’ end always end in mRNA) but are not present if mature mRNA.
CCA sequence
When you transcribe the DNA, you produce a heterogenous nuclear
tRNA Acceptor Arm (Part of the RNA Precursor of mRNA
tRNA which always ends with a Before you convert the heterogenous nuclear RNA to mature
CCA sequence at the 3’ End) mRNA, there are 3 post-transcriptional events:
Part where amino acids attaches 1. Capping To become stable
2. Addition of Poly-A-Tail
Amino acid is attached to the tRNA 3. Splicing Removal of introns and joining of exons
during the activation stage of translation Introns = Non-coding Regions
Exons = Coding Regions
Mature mRNA = Contains only EXONS
(Picture on the Right) SECONDARY hnRNA is longer than mature mRNA because mature mature mRNA
STRUCTURE OF tRNA – Cloverleaf is INTRON-LESS.
Appearance

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

(Picture Above) THE RELATIONSHIP BETWEEN THE SEQUENCES OF AN

RNA TRANSCRIPT AND ITS GENE, IN WHICH THE CODING AND (Picture Above) MAMMALIAN RIBOSOMES
TEMPLATE STRANDS ARE SHOWN WITH THEIR POLARITIES – The RNA Mammalian Ribosomes are EVEN NUMBERS = 40s and 60s
transcript with a 5’ to 3’ polarity is complementary to the template strand
with its 3’ to 5’ polarity. Note that the sequence is the same as that in the
coding strand, except that the U of the transcript replaces the T of the
gene; the initiating nucleotide of RNAs contain a terminal 5’-triphosphate
(ie. pppA)

Before you transcribe the DNA, DNA should be denatured first so that
one strand will act as the template.
Take Note: In a DNA strand, one is labelled as the Coding Strand (also
called Sense Strand), and the other is labelled as the Template Strand
(Anti-Sense Strand)
Direction of Template is 3’ to 5’ Direction of the mRNA should be
5’ to 3’
RNA Polymerase adds “U”:
A–U
C–G
T–A
G–C
RNA is complementary with the Template Strand.
The sequence of the Coding Strand is the same with the RNA, except
for URACIL.

(Picture Above) SUMMARY

Aside from the rRNA, nRNA, and tRNA, we have what we call SMALL-
STABLE RNAs.
U RNAs are needed when you splice. They help identify where to cut
the introns.
(Picture Above) THE EXPRESSION OF GENETIC INFORMATION IN DNA
INTO THE FORM OF AN mRNA TRANSCRIPT WITH 5’ TO 3’ POLARITY
SHOWN.
The small subunit interacts with the mRNA through the 16s rRNA.
Fate of mRNA Destroyed by Ribonuclease
Take Note: mRNA can be easily translated by ribosomes into specific
protein molecule
5’ of mRNA Corresponds to the N-Terminal of the polypeptide
Genetic information is usually stored as DNA, but may be RNA.
RNA and DNA is a polynucleotide (polymer) Made up of nucleotides
(monomer)
Nucleotides contains:
Sugar
- DNA = Deoxyribose
- RNA = Ribose
Bases
- Purine Bases for DNA and RNA: Adenine, Guanine
- Pyrimidine Bases for DNA = Cytosine, Thymine
- Pyrimidine Bases for RNA = Cytosine, Uracil
Phosphate Gives off Negative Charge to the DNA and RNA
Central Dogma of Life
For cell division to occur DNA REPLICATION should occur during
the S Phase of Mitoses
Genes are expressed through TRANSCRIPTION and TRANSLATION
- Products of TRANSCRIPTION: rRNA, tRNA, mRA (Not all the
products of transcription are translated to a protein, only mRNA
becomes a protein)
rRNA = associated with ribosomes
tRNA = transfers amino acids to the site of protein synthesis
mRNA = directs amino acid sequence, messenger of genetic
information; acts a template for translation
Structure of DNA
Secondary Structure of DNA: Double-Stranded Helix Anti-
Parallel (5’-3’, 3’-5’)
Exists in Different Forms: B-DNA (Normal Form of DNA); A-DNA
(Lacks water)
Stabilized by HYDROGEN BONDS between A-T (2 Hydrogen Bonds),
C-

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 NUCLEIC ACID CHEMISTRY – DR. VILIRAN

C-G (3 Hydrogen Bonds)

Can become Single Stranded through DENATURATION Destroy
HYDROGEN BONDS
If you cut the DNA (From 1 fragment to 2 fragments Destroy
PHOSPHODIESTER BOND
If you cut the sugar from the base Destroy N-C GLYCOSIDIC
BOND
If you remove the Phosphate Destroy PHOSPHOESTER BOND
Structural Hierarchy
Primary Structure: Nucleotides
- DNA: DNTPs Remove 2 Phosphates DNMPs
- RNA: NTPs Remove 2 Phosphates DNMPs
Secondary Structure:
- DNA: Right Handed Double Helix
- RNA: Cloverleaf (tRNA); Hairpin Look (mRNA)
Tertiary Structure (True only for DNA): Supercoiling
Tertiary Structure together with Histones Important for packaging
of DNA as condensed chromosome called CHROMATIDS

Konting push nalang, Christmas break na!

MERRY CHRISTMAS Batch 2013 – Love Lea <3

LEA THERESE R. PACIS 13