Chapter 2

Nucleic Acids
INTRODUCTION

Nucleic acids are key macromolecules in

the continuity of life; is an important class of
macromolecules found in all cells and viruses.
They carry the genetic blueprint of a cell and carry
instructions for the functioning of the cell. It direct
cellular activities such as cell division and protein
synthesis.
Nucleic acids are actually made of polymers
of strings of repeating units, and the two most
famous of the nucleic acids, that you've heard
about, are DNA and [Link] acid
(DNA) encodes the information the cell needs to
make proteins. A related type of nucleic acid,
called ribonucleic acid (RNA), comes in different Figure 1. DNA molecule
molecular forms that participate in protein
synthesis.
All life on Earth uses nucleic acids as their medium for recording hereditary
information – that is nucleic acids are the hard drives containing the essential blueprint or
“source code” for making cells.

OBJECTIVES

At the end of this module, the learner should be able to:

 Describe the basic structure and properties of nucleic acids

 Explain the structure and function of DNA and RNA
 Explain the central dogma of molecular biology
 Explain the process of DNA replication, transcription, and translation in the protein
synthesis.
 Explain the types of mutation
LEARNING CONTENTS

DEFINITION OF NUCLEIC ACIDS

Nucleic Acids
 Nucleic acids are polymers made of monomers called nucleotide; linked by
phosphodiester bond, therefore they are called polynucleotides.
 Two types of nucleic acids
- Deoxyribonucleic acid or DNA
- Ribonucleic acid or RNA
 DNA is present in nuclei and small amounts are also present in mitochondria,whereas
90% of the RNA is present in cell cytoplasm and 10% in the nucleolus.
 DNA directs RNA synthesis and, through RNA, controls protein synthesis, this entire
process is calle Gene Expression.

Nucleotide
Each nucleotide consists of three components:
a. Nitrogenous group
b. Pentose sugar
c. Phosphate group

a. Nitrogenous Bases of RNA and DNA

-Two classes of nitrogenous base are present in DNA and RNA namely purines and
pyrimidines.

 Purine Bases
- Purines are larger, with a six membered ring fused to five membered ring.
- The member of the purine family are Adenine (A) and Guanin (G).
 Figure 2. Structure of purine bases
 Pyrimidine Bases
- Pyrimidine has one six-membered ring of carbon and nitrogen atoms.
- The member of the pyrimidine family are Cytosine (C), Thymine (T),
and Uracil (U).
- Cytosine and uracil are found in RNAs andcytosine and Thymine in DNA.
- DNA contains thymine whereas RNA contains uracil.

Figure 3. Structure of pyrimidine bases

b. Pentose Sugars in RNA and DNA

- The pentose sugar is either D-

ribose or D-2-deoxyribose. DNA
contains D-2-deoxyribose and
RNA contains D-ribose.
 - A pentose sugar is linked to a base (purine & pyrimidine) via covalent N-glycosidic
bond. The combinationof sugar and base is known as nucleoside.
- If the sugar is ribose,
ribonucleoside is produced; if sugar Figure 4. Pentose sugars- Deoxy Ribose and Ribose
is 2-deoxyribose, a
deoxyribonucleoside is produced.

c. Phosphate group
-The third component of nucleic acids is phosphoric
acid.
- When this group forms a phosphate ester bond with a
nucleosside, the result is compound known as a
Figure 5. Phosphate group
nucleotide.

Structure of nucleotides
 Nucleotides are phosphorylated nucleosides. Nucleosides are nitrogen bases containing
pentose sugar.
 The phosphate group is attached to the nucleoside by an ester linkage to the hydroxyl
group of the pentose sugar.
Types of nucleotides
1. Deoxyribonucleotides: These nucleotides contain pentose sugar, deoxyribose and are
monomeric units of DNA.
2. Ribonucleotides: These nucleotides contain pentose sugar, D-ribose and are
monomeric units of RNA.
(pics of deoxyribonucleotide & ribonucleotide) (title: deoxyribonucleotide &
ribonucleotide)
 Figure 6. Structure of nucleotide

Biologically Important Nucleotides

 These are nucleotides involved in a various biochemical processes.
 Several nucleotides such as ATP, ADP, c-AMP, GTP, GDP, c-GMP, UDP, CTP, CDP,
etc. They participate in several biochemical and physiological functions.
ATP (Adenosine triphosphate)
 ATP serves as the main biological source of energy in the cell; is energy required as a
source of energy in several metabolic pathways, such as fatty acid synthesis,
glycolysis, gluconeogenesis, etc. and in physiologic function such as muscle
contraction, nerve impulses transmission, etc.
AMP (Adenosine monophosphate)
 AMP is the component of many coenzymes such as NAD+, NADP+, FAD, coenzyme
A, etc. These coenzymes are essential for the metabolism of carbohydrates, lipid, and
proteins.
C-AMP
 c-AMP is formed from ATP by the action of adenylate cyclase.
 c-AMP acts as a second messenger for many hormones, e.g. epinephrine, glucagon,
eth.
 It inhibits the aggregation of blood platelets.
GDP and GTP
 These guanosine nucleotides participate in the conversion of succinyl-CoA to
succinate, a reaction which is coupled to the substrate level phosphorylation of GDP to
GTP in citric acid cycle.
C-GMP (cyclic guanosine 3’ 5’-monophosphate)
 c-GMP is an intracellular signal or second messenger that can act antagonistically to c-
AMP.
UDP (Uridine diphosphate)
 UDP participates in glycogenesis.
 CTP (Cytidine triphosphate) and CDP (Cytidine diphosphate)
 CTP and CDP are required for the biosynthesis of some phospholipids. CDP-choline is
involved in the synthesis of sphingomyelin.

 DNA FUNCTION & STRUCTURE

 Deoxyribonucleic acid (DNA) serves as the genetic material for cells both prokaryotes
and eukaryotes. In eukaryotes, DNA is located in the nucleus separated from
cytoplasm by the nuclear membrane. Because prokaryotes lack internal membrane
systems, their DNA is not separated from the rest of the cellular contents. Eukaryotic
DNA is bound to proteins, forming a complex known as chromatin. DNA is also
present in mitochondria (less than 0.1% of the total DNA) and in chloroplast of plants.
Many viruses also contain DNA as their genetic material.

 FUNCTION OF DNA

 DNA is the store of genetic information. These genetic information is stored in the
DNA serves two functions.
1. It is the source of information for the synthesis of all protein molecules of the cell
and
2. It provides the information inherited by daughter cells or offspring.

 STRUCTURE OF DNA

 DNA is a very long, thread like macromolecules

made up of a large number of
deoxyribonucleotides. Deoxyribonucleotide is
composed of nitrogenous bas, a sugar and
phosphate group.
 The bases of DNA molecule carry genetic
information, whereas their sugar and
phosphate groups perform a structural role.
 The sugar in a deoxyribonucleotides is
deoxyribose.
  The purine bases in DNA are adenine (A), and guanine (G).
 Pyrimidine bases are thymine (T) and cytosine (C).
 DNA is composed of two strands of
nucleotides held together by hydrogen Figure 7. DNA structure
bonding. The strands each run from 5' to 3'
and run in antiparallel, or opposite, directions from one another.
Chargaff’s Rule
 Erwin Chargaff (1905-2002) showed that the quantity of
adenine (in moles) is always approximately
equal to the quantity of thymine, and the
quantity of guanine is always approximately
equal to the quantity of cytosine, although the
adenine/guanine ratio varies widely from species to Figure 8. Chargaff’s rule
species.
 Chargaff’s rule : The ratio of purine to pyrimidine bases in the DNA is always one,
i.e. G+A : T+C = 1.

Watson-Crick DNA Double Helical Structure

 The double helix originally proposed by
Watson & Crick is the most striking feature
of DNA structure.
 DNA molecules have
an antiparallel structure - that is, the two
strands of the helix run in opposite
directions of one another. Each strand has a
5' end and a 3' end.
 The two chains are held together by
hydrogen bonds between complementary
pairs of bases.
 The model proposed by Watson and Crick
(Figure 8) is a B form of DNA (B-DNA)
which is a right handed helix of 10 base
pairs per turn, containing grooves of Figure 8 Double helix DNA model by
alternate size, known as major and minor Watson and Crick
grooves.
  Major groove and minor groove arise because the two stands are not equally spaced
around the helix (Figure 7). Interactions of proteins and drugs with the major and
minor grooves of DNA serves as an active
area for research.
 The two strands are always complementary to
each other. In a double stranded DNA
molecule, the content of adenine equals to
that of thymine and the contents of guanine
equals to that of cytosine. The
complementary base pairing proves the
Chargaff’s rule.
 Adenine is always paired with
thymine by formation of two
hydrogen bonds. Guanine is
always paired with cytosine by
formation of tree hydrogen bonds (Figure 10).
Figure 10. Complementary Base Pairing showing
Hydrogen Bonding

 RNA FUNCTION AND STRUCTURE

 Ribonucleic acid (RNA) is an important biological macromolecule that is
present in all biological cells.
FUNCTION OF RNA

 It is principally involved in the synthesis of proteins, carrying the messenger

instructions from DNA, which itself contains the genetic instructions required for
the development and maintenance of life.

STRUCTURE OF RNA
 The RNAs are single stranded.
RNA is an unbranched linear
polymer of ribonucleotides
joined by 3’, 5’ phosphodiester
bonds. The phosphodiester bonds
join the 3’-OH group of ribose of
 one nucleotide unit to the 5’-OH group of ribose sugar of the next
nucleotide.

Figure 11. Structure of RNA

TYPES OF RNA
 Cell contain three major types of RNA; and are involved in the process of protein
biosynthesis. Each differs from the others by size and function.
1. Messenger RNA (mRNA)
2. Transfer RNA ( tRNA)
3. Ribosomal RNA (rRNA)
Messenger RNA (mRNA)
 mRNA molecules are produced in the process called transcription.
 mRNAs serve as template for protein biosynthesis and transfer genetic information
from DNA to protein synthesizing machinery.
Transfer RNA (tRNA)
 tRNA are relatively small molecules containing from 73-93 nucleotides per chain.
There are atleast one different tRNA molecule for each 20 amino acids from which the
body makes it protein.
 tRNA carries amino acids in an activated form to the ribosome for the protein
synthesis.
Ribosomal RNA (rRNA)
 rRNA are small spherical bodies located in the cells but outside the nuclei. They
consist of about 35% protein and 65% ribosomal RNA (rRNA).
 Necessary to maintain ribosomal structure and also participate in protein synthesis by
binding of mRNA to ribosome.
 Recent studies suggest that ribosomal RNAs may also provide some of the catalytic
activities and thus is an enzyme “a ribozyme”.
 Figure 12. Types of RNA

CENTRAL DOGMA OF MOLECULAR BIOLOGY

 The important role of DNA in transfer

of information in living cells,
formulated by Francis Crick, is called
the central dogma of molecular
biology (Figure 1.), which defines
three major steps in the processing of
genetic information.
Figure 13. The central dogma of molecular
1. The first is replication, the biology
copying of parent DNA to form daughter DNA molecules having nucleotide
sequences identical to those of the parent DNA.
2. The second step is transcription, the process in which the genetic message in
DNA are rewritten in the form of ribonucleic acid (RNA).
3. The third step is translation in which the genetic message coded by RNA is
translated by the ribosomes into the protein structure.
 In molecular biology, central dogma illustrates the flow of genetic information from
DNA to RNA to protein.

 DNA REPLICATION (DNA SYNTHESIS)

 DNA is a major store of genetic

information. To transfer this PARENT
DNA
 genetic information from a parent cell to a daughter cell during cellular
reproduction, the DNA must be duplicated.
 The duplication or synthesis of DNA is called replication. This method of DNA
replication results in semi conservative mechanism, in which each replicated
duplex daughter DNA molecule contains one parent strand and one newly
synthesized strand (Figure 2).

DNA REPLICATION PROCESS

Stages of Replication
The process of replication
can be divided into three
stages.
A. Initiation
B. Elongation
C. Termination

Figure 15. DNA replication in prokaryotes

A. Initiation
Steps involved in initiation
1. DNA replication begins at a particular site called the origin of replication.
2. Helicase then binds to this region and unwinds the parental DNA, and form a “Y”
where active synthesis occurs. This region is called the replicating fork (Figure 15).
3. The stress produced due to unwinding by helicase is released by topoisomerases by
cutting either one or both DNA strands.
4. The Single stranded binding proteins (SSBP’s) stabilizes the separated strands and
prevents their reassociation.
 5. To initiate the DNA synthesis by DNA polymerase III, it requires RNA primer. The
RNA primers are short pieces of RNA (some 5–50 nucleotides in length) formed by the
enzyme primase (RNA polymerase) using DNA as a template.

B. Elongation
1. Once RNA primer has been synthesized at each of the replicating forks, a DNA
polymerase III initiates the synthesis of new DNA strand by adding
deoxyribonucleotide to the 3' end of the RNA primer. Thus, DNA polymerase III
can synthesize a new chain only in the 5' to 3' direction. Both the DNA strands are
synthesized simultaneously but in opposite direction one is in direction towards the
replication fork, the other in a direction away from the replication fork.
2. The DNA chain which runs in the 3' → 5' direction is copied by polymerase III as a
continuous strand, requiring one primer. This new strand is known as the leading
strand.
3. The DNA chain which runs in the 5’ → 3' direction is copied by polymerase III as a
discontinuous manner because synthesis can only proceed in the 5' to 3' direction.
This new strand is known as the lagging strand. This requires numerous RNA
primers. As the replication fork moves, RNA primers are synthesized at specified
intervals. These RNA primers are extended by DNA polymerase III into short pices
of DNA called Okazaki fragments.
4. Upon completion of lagging strand synthesis, the RNA primers are removed from
fragments by DNA polymerase I. DNA Polymerase I also fills the gaps that are
produced by removal of the primer leaving only a nick.
It cannot join two polynucleotide chains together, an additional enzyme DNA ligase
is required to perform this function. This enzyme catalyzes the formation of a
phosphodiester bond to seal the Okazaki fragments.

C. Elongation
1. Termination sequences, e.g. “ter”, direct termination of replication. A specific
protein, ter binding protein, binds these sequences and prevents the helicase from
further unwinding of DNA and facilitates the termination of replication.

 Proofreading
• DNA is copied by DNA polymerase with high fidelity (accuracy). Incorrect
nucleotides are incorporated with a frequency of one in 108 –1012 bases, which
 could lead to mutation. But the error ratio during replication is kept at a very
low level by specific process. This process is known as proofreading.
• Mismatches, occur more frequently but do not lead to stable incorporations
because the all three DNA polymerases have 3' to 5' exonuclease activity
(proofreading activity).
• DNA polymerase I and II are known to excise mismatched nucleotides before
the introduction of the next nucleotide.

 TRANSCRIPTION (RNA SYNTHESIS)

 Is the process of making RNA strand from DNA strand.
 Stages of Transcription RNA synthesis involves (Figure 16):
1. Initiation
2. Elongation
3. Termination

Figure 16. DNA transcription

Initiation
 RNA polymerase attaches to the DNA molecule and moves along the DNA strand until
it recognises a promoter sequence. These are known as the transcription start sites. The
DNA double helix then unwinds and all the bases on each of the DNA strands are
exposed. This acts as a template for a new mRNA strand.

Elongation
  Ribonucleotides are added to the template strand that enables the growth of mRNA
growth.

Termination
 RNA polymerase encounters a terminator sequence and the transcription stops. RNA
polymerase then releases the DNA template.

 RNA Processing
 The transcribed RNA is
known as the pre-mRNA.
It is processed further to
convert it into mature
RNA. RNA processing
include:

 Capping
 Polyadenylation Figure 17. pre-mRNA strand that has not undergone processing (RNA splicing)

 Splicing

Capping
 A methylated guanine cap is added to protect the mRNA. It involves:

 Addition of methylated guanine.

 It occurs at 5′ end of mRNA transcript.
 It protects the mRNA from degradation

Polyadenylation
The poly-A tail also protects the mRNA from degradation. It involves:

 The endonucleases cleave the mRNA at a specific sequence.

 The enzyme polyA polymerase facilitates the addition of several adenine nucleotides.
 Splicing

 The non-coding sequences, i.e., the introns are removed by spliceosome excision.
 The coding sequences or the exons join together by ligation.
 Thus several proteins can be made from a single pre-mRNA. A mature mRNA is
obtained at the end of transcription.

 TRANSLATION (PROTEIN BIOSYNTHESIS)

- Translation is the process by

which ribosomes convert the
information carried by mRNA in
the form of genetic code to the
synthesis of new protein.
- As with mRNA synthesis, protein
synthesis can be divided into three
phases: initiation, elongation, and
termination. The process of
translation is similar in prokaryotes
and eukaryotes. Figure 18. Translation

INITIATION

 Protein synthesis begins with the formation of an initiation complex. This complex
involves the small 30S ribosome, the mRNA template, initiation factors and a
special initiator tRNA. The initiator tRNA interacts with the start codon AUG
(Met). Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts
as an energy source during translation—both at the start of elongation and during the
ribosome’s translocation.

 Once the appropriate AUG is identified, the 50S subunit binds to the complex of Met-
tRNAi, mRNA, and the 30S subunit. This step completes the initiation of translation.
ELONGATION

 The 50S ribosomal subunit of E. coli consists of three compartments:

the A (aminoacyl) site binds incoming charged aminoacyl tRNAs.
The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed
peptide bonds with the growing polypeptide chain but have not yet dissociated from
their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they
can be recharged with free amino acids. this creates an initiation complex with a free
A site ready to accept the tRNA corresponding to the first codon after the AUG.
 Elongation proceeds with charged tRNAs entering the A site and then shifting to the P
site followed by the E site with each single-codon “step” of the ribosome. Ribosomal
steps are induced by conformational changes that advance the ribosome by three bases
in the 3′ direction.

TERMINATION

 Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is

encountered. Upon aligning with the A site, these nonsense codons are recognized by
release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a
water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-
site amino acid to detach from its tRNA, and the newly made protein is released.

 The small and large ribosomal subunits dissociate from the mRNA and from each
other; they are recruited almost immediately into another translation initiation
complex. After many ribosomes have completed translation, the mRNA is degraded so
the nucleotides can be reused in another transcription reaction.

The Genetic Code

Characteristics of Genetic Code
• Number of codons: There are 64
possible codon sequences. Because
four nucleotide bases A, G, C and U
are used to produce the three base
codons, there are therefore 43 or 64
possible codon sequences (Figure 19).
• Stop or termination or nonsense
codons: Three of the 64 possible
nucleotide triplets, UAA, UAG and

Figure 19. The Genetic code

UGA do not code for any amino acids, they are called nonsense codons that normally signal
termination of polypeptide chains. These nonsense codons are arbitarily named amber, ochre
and opal.
• The code is degenerate but unambiguous: As there are 61 codons for 20 amino acids, one
amino acid has more than one codon and the code is referred to as degenerate, indicating that
there are redundancies. Although an amino acid may have more than one codon, each codon
specifies only one amino acid. Thus, the genetic code is unambiguous. Degeneracy
minimizes the deleterious effects of mutations.
• Codons that designate the same amino acid are called synonyms. Two amino acids
methionine (AUG) and tryptophan (UGC) each have only one codon. The remaining amino
acids have multiple codons, e.g. arginine is specified by six different codons (Figure 19).
• The code is almost universal: That is, the meaning of each codon is the same in almost all
known organisms. Exceptions to the universality of the genetic code are found in human
mitochondria, where the code: – UGA codes for tryptophan instead of serving as a stop
codon – AUA codes for methionine instead of isoleucine – CUA codes for threonine instead
of leucine.
• The code is non-overlapping and without punctuation: During translation, the code is read
sequentially, without spacer bases, from a fixed starting point, as a continuous sequence of
bases, taken 3 at a time, e.g. A U G C U A G A C U U U is read as: AUG / CUA / GAC /
UUU without “punctuation” between the codons.

MUTATION
 The term mutation refers to the
permanent changes in the DNA
sequence.
 Mutations in germ cells are
transmitted to the next progeny and
may give rise to inherited diseases.
 Mutations in somatic cells are not
transmitted to the progeny but are
important in the causation of cancers
and some congenital malfunctions.
 The effects of changes to the genetic
information of the cell are
Figure 20. Mutation
responsible for the huge diversity of genes found among organisms because mutations
are the ultimate source of new genes.
CAUSES OF MUTATIONS
Mutation arises by a number of different means:
• Errors in replication, If a mismatch base pair is not corrected during
proofreading and post replication repair system.
 Error due to recombination events.
• Spontaneous change in DNA, e.g. deamination of cytosine to uracil or
spontaneous depurination.
• Environmental factors like chemical mutagens and irradiations, e.g. UV light
or ionizing radiation can alter the structure of DNA.

TYPES OF MUTATIONS

A. BASE SUBSTITUTION OR POINT MUTATION

• Point mutation occurs when only one base in DNA is altered, which may be
transcribed into mRNA and therefore, may result in the translation of a protein with an
abnormal amino acid sequence. Single base change can be of transition type or
transversion type.
• Transition, in which one purine is replaced by another purine or one pyrimidine is
replaced by another pyrimidine.
• Transversion, in which a purine is replaced by a pyrimidine or a pyrimidine is
replaced by a purine.
• The point mutation can lead to:
1. Silent mutation
2. Missense mutation
3. Nonsense mutation

1. Silent mutation
Point mutations are said to be silent when there is no detectable effect. Silent
mutation leads to the formation of a codon synonym and no change in the amino acid
sequence of the protein occurs due to degeneracy of the codon, e.g. a codon change
from CGA to CGG does not affect the proteins because both of these codons specify
arginine.
 2. Missense mutation
Missense mutation will occur when a different amino acid is incorporated at the
corresponding site in the protein molecule. Depending upon the location of the
mistaken amino acid (missense) in the specific protein, missense mutation might be
acceptable, partially acceptable or unacceptable with respect to the function of that
protein.

 Acceptable missense mutations

For example, Hb-Hikari. This Hb has aspargine substituent for lysine at the 61
position in the β-globin chain. Hb-Hikari is a type of transversion mutation, in which
either AAA or AAG changed to either AAU or AAC. The replacement of the specific
lysine with aspargine does not alter the normal function of the β-chain in these
individuals and is therefore called acceptable missense mutation.

 Partially acceptable missense mutation

For example, HbS, sickle hemoglobin, in which the normal amino acid in
position 6 of the β-chain, glutamic acid has been replaced by valine. The
corresponding transversion might be either GGA or GAG of glutamic acid to GUA or
GUG of valine.

 Unacceptable missense mutation

For example, Hb M (Methemoglobin) in which normal amino acid in position 58
of α-chain, histidine has been replaced by tyrosine and nonfunctional Hb molecule is
generated which cannot transport oxygen.

3. Nonsense mutations
 Nonsense mutation leads to the conversion of an amino acid codon to a stop or
nonsense codon. Nonsense mutation causes the premature termination of a
polypeptide chain, which is usually nonfunctional, e.g. one type of thalassemia, in
which codon 17 of the β-chain is changed from UGG to UGA and results in the
conversion of a codon tryptophan to a nonsense codon.

B. FRAME SHIFT MUTATIONS

Frame shift mutation occurs when there is insertion or deletion of one or two
nucleotides in DNA, that generates altered mRNAs.
 a. Deletion frame shift mutation
• The deletion of a single nucleotide from the coding strand of a gene results in
an altered reading frame in the mRNA.
• Since there is no punctuation in the reading of codons, the translating
machinery does not recognize that a base was missing.
• Such frame shifts would result in the production of an entirely different protein
after transcription and translation or indeed, no protein, at all, if a stop codon is
encountered, as in cystic fibrosis of pancreas.

b. Insertion frame shift mutation

 Insertion may be of one or two nucleotides. As with deletions, insertions of
nucleotides into genes can lead to severe frame shift mutations, e.g. thalassemia.
If the number of nucleotides involved in deletion or insertion is three or
multiples of three, frame shift does not occur. Instead, an abnormal protein,
missing one or more amino acids, is synthesized. Such a mutation is likely to be
less severe than a frame shift mutation.

SUMMARY
NUCLEIC ACID
 The nucleic acids DNA and RNA are polynucleotides.
 In DNA and RNA, nucleotides are linked by 3'-5' phosphodiester bonds.
 Each nucleotide contains a nitrogenous base, a sugar and a phosphate.
 Nucleosides contain, D-ribose or D-2-deoxyribose, linked to N-1 of pyrimidines
or N-9 of purines, by a N-glycosidic bond.
 DNA contains the purine bases: adenine (A) and guanine (G) and pyrimidine
bases: cytosine (C) and thymine (T).
 RNA contains uracil (U) instead of thymine.
 Several synthetic analogues of purine and pyrimidine bases and their derivatives
are used chemotherapeutically as anticancer drugs.
 DNA is organized into two strands by the pairing of bases A to T and G to C, on
complementary strands. In contrast to DNA, RNA is single stranded structure.
 The three major types of RNA are mRNA, tRNA and rRNA, all are involved in
some aspects of protein synthesis.
CENTAL DOGMA
  Replication is the process of synthesis of DNA.
 DNA synthesis is semiconservative.
 The major enzyme involved in the replication of DNA is DNA polymerase.
 Synthesis of RNA from DNA template is called transcription.
 Transcription is catalyzed by enzymes known as RNA Polymerases.
 The direction of RNA synthesis is 5' → 3' direction as in DNA synthesis.
 In prokaryotes, a single RNA polymerase produces the precursors of mRNA,
tRNA and rRNA.
 Eukaryotic RNA is transcribed in the nucleus by three different RNA
polymerases; I, II, and III. Type I make rRNA, Type II mRNA and Type III
tRNA.
 Amino acids are coded by group of three bases called codons, present on
mRNA.
 Sixty-one out of the sixty-four codons specify particular amino acids, whereas
the other three codons (UAA, UAG, UGA) are signals for chain termination,
called nonsense or termination codons.
 The code is almost universal.
 The code is non-overlapping and without punctuation. The mRNA is read
continuously from a start codon AUG to a termination codon.
 Some tRNAs recognize more than one codon because of wobble in base pairing.
 Translation is the process by which ribosomes convert the information carried
by mRNA to the synthesis of protein.
MUTATION
 Mutations result when changes occur in the nucleotide sequence in DNA.
 Point mutations result from single base substitution. These may be transition or
transversion type. Types of point mutations are silent mutation, missense
mutation and nonsense mutation. Missense mutation might be acceptable or
unacceptable to the function of that protein molecule.
 Frame shift mutations result from deletion or insertion of nucleotides in DNA
that generates alterered mRNAs.
 An operon is a group of coordinately regulated genes. It consists of control sites
(an operator and promoter) and a set of structural genes.
 The rate of expression of prokaryotic genes is controlled mainly at the level of
transcription.
TEACHING AND LEARNING ACTIVITIES
Activity 1
Directions: Read each statement or question below carefully and fill in the blank(s) with the
correct answer.
1. The nitrogen bases are paired by ______________ bonds along the axis of the
molecules.
2. Purines have __________ring/s in their structure, and pyrimidines have _________
ring/s in their structure.
3. The two bases that are purines are ____________ and _____________. These bases
comprised of ____ rings.
4. The two bases that are pyrimidines ____________ and _____________. These bases
comprised of ____ rings.
5. A nucleotide is made up of three parts. These three parts are : ____________,
________________, _________________.
6. RNA stands for _____________________________________.
7. DNA stands for _______________________________________________.
8. DNA is located in the ________________ and _______________________.
9. Nucleic acids are polymers made of monomers called __________________.
10._________ serves as the main biological source of energy in the cell.
[Link] refers to the ____________________ in the DNA sequence.
[Link] of point mutations are ______________, _________________ and
___________________.
13.___________________is the process by which ribosomes convert the information
carried by mRNA to the synthesis of protein.
14.________________is the process of synthesis of DNA.
15. RNA contains _____________ instead of thymine.
Activity 2: Base Pairing
Direction: Write the complimentary DNA strand for each given strand of DNA.

1. C G T A C T G A C T G G G G G
_____________________________

2. A T T C C G T T A A U U G G C
____________________________

3. A C T A T A C G C T T T T T C
___________________________
4. C C C G G T A T A C A A C G
___________________________

5. G C C T T A A T C A T A C G
___________________________

Write the mRNA strand for the given DNA strand.

1. A T G T C G G T A A T C R
_________________________

2. G A A G G C T G A T C C C
_________________________

3. C C G C A T T C G A T C T
________________________

4. A C T A C G G T A G C T G
________________________

5. C A T C G G C T A A C C T
________________________

Translate the amino acid sequence for the given tRNA strand. Remember that codons are
3 base pair long.

1. AUG CAC UGU CCC AGG

________________________
 2. GCG CAA UGG ACG GCC
________________________

3. UUG UAC UAU GCU GCG

________________________

4. UAU UAC AAG GGC GGG

_______________________

5. GUU CCU UUU AUC GAA

_______________________
FLEXIBLE TEACHING LEARNING ACTIVITIES

Laboratory Exercise 1. DNA extraction from Fruit

Video Presentation 1: The Organic Chemistry Tutor (August 31, 2018). Nucleic Acids-RNA
& DNA Structure at [Link]
Video Presentation 2: Khan Academy (December 10, 2014). DNA Replication & RNA
transcription and Translation at [Link]

ASSESSMENTS
Direction: Choose the letter of the correct answer and write it on the space provided before
the number.
_____1. Which of the following enzyme joins Okazaki fragments?
a. DNA polymerase b. DNA ligase c. RNA polymerase d. Cardiolipins

_____2. Which of the following nucleotide base is not present in codons?

a. Adenine b. Thymine c. Guanine d. Cytosine

_____3. The toal number of codons are:

a. 64 b. 61 c. 63 d. 20

_____4. Termination of Protein biosynthesis requires presence of:

a. Termination sequence b. Rho factor c. Nonsense codons d. Sigma factor

_____5. Formation of Okazaki fragment occur in the process of:

 a. Reverse transcription b. Translation c. Transcription d. Replication

_____6. A nucleoside can be composed of, except:

a. Purine base b. Pentose sugar c. Phosphate group d. Pyrimidine base
_____7. The number of hydrogen bonds between guanosine and cytosine in DNA are:
a. One b. Two c. Three d. Four
_____8. Which of the following holds DNA strands together?
a. Phosphodiester bond b. Hydrogen bond c. Glycosidic bond d. Phosphate ester
9. DNA is present in:
a. Only nucleus b. Only mitochondria
[Link] nucleus and mitochondria d. Cytoplasm
10. RNA is present in:
a. Nucleus b. Only cytoplasm c. Mitochondria d. Cytoplasm and nucleolus

Direction:
[Link] the DNA sequence below into mRNA.
[Link] the mRNA code to create your tRNA code (anti codon).
[Link] the mRNA code and the Genetic Code to determine your amino acids.

1. DNA 5’ G G G A T T A G G T C G C A A A G A G A T T A C A T C G 3’

mRNA _______________________________________________________

ttRNA ________________________________________________________

Amino
Acid __________________________________________________________

Genetic code
REFERENCE
 Frederick A. Bettelheim and William H. Brown (2010) Organic and Biochemistry 7 th
edition pp. 396-421
 Jane B. Reece (2014) Campbell Biology 10th edition pp. 86-87; 333-359
 Mary K. Campbell and Shawn O. Farrel (2009) Biochemistry pp. 235-286
 Pankaja Naik (2012) Essentials of Biochemistry pp. 123-134 ; 313-333

 [Link]
 [Link]
%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/
02%3A_Structure_and_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids
 [Link]
 [Link]
 [Link]
%20acid%20(RNA)%20is%20an,development%20and%20maintenance%20of
%20life.
 [Link]
 [Link]
 [Link]
translation/

PHOTO REFERENCES
 [Link]
acid-nucleic-acid-structure-134634
 [Link]
 [Link]
 [Link]
 [Link]
 [Link]
dna-and-rna/[Link]
 [Link]
 [Link]
have-guanine-base-How-many-thymine-bases-are-present-in-this-segment-of-DNA
 [Link]
 [Link]
 [Link]
DNA
 [Link]
[Link]
strand-undergone-processing-rna-splicing--segments-labeled-looking-strand--
q47675231
 [Link]
transcri/[Link]
 [Link]
 [Link]