The document provides a comprehensive overview of nucleic acids, detailing their structure, function, and various types, including DNA and RNA. It discusses the roles of nucleotides, the process of DNA replication, transcription, and translation, as well as the significance of mutations and the central dogma of molecular biology. Additionally, it addresses genetic engineering applications, forensic identification, and the enzymatic processes involved in DNA and RNA synthesis.

1. Nucleic Acids
Md. Saiful Islam
B.Pharm, M.Pharm (PCP)
North South University
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2. Adenine Guanine
Cytosine UracilThymine
Purines
Pyrimidines
Nitrogenous Bases: Two types

3. Nucleosides: The addition of pentose sugar to a base produces
a nucleoside, if the sugar is ribose, a riboncleoside is produced,
if the sugar is 2-deoxyribose, a deoxyribonucleoside is produced.
Adenosine
Guanosine
Deoxyadenosine
Deoxyguanosine

4. Cytidine Uridine
Deoxycytidine Thymidine (Deoxythymidine)

5. Nucleotides are phosphate esters of nucleosides. Most commonly, the
phosphoryl group is attached to the oxygen of the 5'-hydroxyl group
In nucleic acids, the 5'
phosporyl is esterified to
the 3' OH of the next
sugar, forming a sugar
phosphate backbone, from
which the purine and
pyrimidine bases extend.
Nucleotides:

6. G - C
A - T
Crucial property: Nitrogenous bases form pairs between purine and
pyrimidine, Adenine must pair with Thymine, and Guanine must pair
with Cytosine. The bases form weak hydrogen bonds.
• In a body or somatic cell:
A = 30.3%
T = 30.3%
G = 19.5%
C = 19.9%

7. Structure of DNA and RNA
“Legs of ladder”
Phosphate &
Sugar Backbone
Nitrogenous
Base (A,T,G or C)
“Rungs of ladder”

9. DNA: DNA is a double helical strand consists of nucleotides that
contains the genetic information used in the development and
functioning of all known living organisms with the exception of some
viruses where RNA carries the genetic information. The main role of
DNA molecule is storage of information in the long term.
The DNA segment that caries this information are called genes (in
other Word the structural and functional unit of DNA is gene), but
other part of DNA sequences have structural purposes or are
involved in regulating the use of this genetic information.
DNA consists of two long polymers of simple units called nucleotides
with backbones of sugars and phosphate group joined by ester bonds.
These two strands ran in opposite directions to each other and are
therefore antiparallel (one is 5’ – 3’ and the other one is 3’ – 5’).

10. Organization of DNA:
Within cells, DNA is organized into long structures called
chromosomes, these chromosomes are duplicated before cell division in
a process called DNA replication. The largest human chromosome is
chromosome number 1 and is about 220million base pairs long. Human
genome has approximately 3 billion base pairs of DNA arranged into 46
chromosomes. Eukaryotic organisms store most of their DNA inside
the cell nucleus and some of their DNA locates in mitochondria or
chloroplast. In contrast prokaryotes store their DNA only in the
cytoplasm.
In eukaryotic cells, DNA is packaged with proteins to form chromatin
fibers that make up chromosomes. This organization allows eukaryotic
DNA to be accurately replicated and sorted into daughter cells
without much error during cell division. Prokaryotic cells usually contain
circular DNA molecules called plasmids, which are stored within the
cell's cytoplasm. Eukaryotic chromosomes, on the other hand, have
several levels of organization.

11. Eukaryotic DNA coil around histone
proteins to form histone-DNA
complexes called nucleosomes, which
are organized into large, coiled loops
held together by scaffolding proteins.
Nucleosomes are octamer with 2
copies of each of H2A, H2B, H3 and
H4 histones. About 147 bp of DNA
wrapped around histone core particle.
Linker DNA between core particles
gives total of about 200 bp per
nucleosome. Histone H1 is works as
linker between octamers. Humans have
about 25 million nucleosomes/cell.

14. Use of DNA:
Genetic Engineering: The genetically modified organisms can be used
to produce products such as recombinant protein, used in medical
research, or be grown in agriculture.
Forensics / Criminal identification: DNA in blood, skin, saliva or hair
found in crime scene can be used for criminal identification. The
method is called DNA profiling or genetic finger printing.
Parental identification: there are some segments in the DNA which
are identical with DNA of parents
Medical diagnosis: genetic disease diagnosis
History / Anthropology:

15. Genetic Code:
Only one of the two strands of DNA codes for proteins, so scientists
write the genetic code as a sequence of bases. The genetic code is
read in groups of three bases / nucleotides, each group representing
one amino acid. Each trinucleotide sequence is called a codon. A gene
includes a series of codons that is read sequentially from a starting
point at one end to a termination point at the other end (5’ – 3’
direction). There are 64 codons, each of these codons has a specific
meaning in protein synthesis. 61 codons represents amino acids, three
codons cause the termination of protein synthesis.
Phe: UUU UUC; Leu: UUA, UUG, CUU, CUC, CUA, CUG;
Met: AUG
Stop codon: UAA, UAG, UGA; when one of these codons appears in an
mRNA, it stops transcription.

17. Mutations: Alterations in the DNA sequence called mutations.
Silent mutation: Changed base may code for the same amino
acid.
Missense mutation: changed base code for different amino
acid.
Non sense mutation: Changed base may become a termination
codon.
Frameshift mutation: If one or two nucleotides are either
deleted or added to the coding region of a sequence.
Transition mutation: substitution of one pyrimidine by the
other, G-C to A-T
Transversion mutation: Substitution of purine by pyrimidine
or vice versa: A-T to T-A or C-G

18. Central dogma: The flow of information from DNA to RNA to protein is
termed as the central dogma of molecular biology and is descriptive of all
organisms with the exception of some viruses that have RNA as the
repository of their genetic information. Central dogma includes replication,
transcription and translation.
Replication: A double-stranded nucleic acid is duplicated to give identical
copies during cell division.
Transcription: Generation of single-stranded RNA which is identical in
sequence with one of the strands of the duplex DNA. There are three types
of RNA: messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA
(rRNA).
Translation: Its a process through which converts the nucleotide sequence
of RNA into the sequence of amino acids comprising a protein. An mRNA is
translated into a protein sequence. The entire length of an mRNA is not
translated, but each mRNA contains at least one coding region (exon) that is
related to protein sequence, the non-coding sequence of the mRNA is known
as intron.

19. DNA replication is
semiconservative:
The genetic material is
reproduced accurately. The
parental duplex is replicated to
form two daughter duplexes,
each of which consists of one
parental strand and one newly
synthesized daughter strand.
This behaviour is called
semiconservative replication.

20. E coli were grown in a
medium containing 15N heavy
isotope of nitrogen in
ammonium chloride (NH4Cl).
Thus all the nitrogenous
components in cells including
bases in their DNA became
highly enriched in heavy
nitrogen. The DNA isolated
from such cells have a
density 1% greater than
that of normal DNA and can
be separated by
centrifugation in cesium
chloride solution. DNA
duplexes at lower position
are heavy, normal duplexes
are at upper position and
mixed duplexes are at
middle position.

21. DNA Replication:
Replication of DNA is a complex system which involves in the stages of
initiation, elongation and termination.
Initiation involves recognition of an origin by a complex of proteins.
Before DNA synthesis begins, the parental strands must be separated
and stabilized in the single stranded state. Then synthesis of daughter
strands can be initiated at the replication fork. Initiation in E. Coli is
accomplished by a protein complex called the primosome.
Elongation is undertaken by another complex of proteins called replisome
and assembled from its components at the onset of replication. As the
replisome moves along DNA, the parental strand unwind and daughter
strands are synthesized with the help of DNA Polymerase.
Termination: At the end of replicon, joining and or termination reactions
are necessary. Following termination, the duplicate chromosomes must be
separated from one another.

22. Mammalian DNA Polymeases:
DNA pol I ----- Priming
DNA pol III -------DNA synthesis
DNA pol II ------- Repair
DNA pol  ------ Repair
DNA pol γ -----Replication (mitochondrial)
DNA Polymerases:
An enzyme that can synthesize a new DNA strand on a template
strand is called a DNA polymerase. Both prokaryotic and eukaryotic
cells contain multiple DNA polymerases.

23. DNA synthesis is semidiscontinuous:
The antiparallel structure of the two strand of duplex DNA poses a problem
for replication. As the replication fork advances, daughter strand must be
synthesized on both the exposed parental single strands. The fork moves in
the direction from 5’ – 3’ on one strand, and in the direction from 3’ – 5’ on
the other strand. Nucleic acids are synthesized only from a 5’ end toward a
3’ end.
Two of the newly synthesized strands have different properties:
Leading strand: On the leading strand DNA synthesis can proceed
continuously in the 5’ to 3’ direction as the parental duplex is unwound.
Lagging strand: On the lagging strand a stretch of single stranded parental
DNA must be exposed, and then a segment is synthesized in the reverse
direction. A series of these fragments are synthesized, each 5’ to 3’, then
they are joined together to create an intact lagging strand. These
fragments are also known as Okazaki fragments. Thus the lagging strand is
synthesized discontinuously and the leading strand is synthesized
continuously. This mode of synthesis is called semidiscontinuous replication.

24. DNA polymerase can not initiate a DNA chain, a priming activity is
required to provide 3’-OH ends to start the DNA chain on both the
leading and lagging strand. The leading strand requires only one
primer at the origin but there must be a series of initiation events
on the lagging strand, since each Okazaki fragments require its own
start. Each Okazaki fragment starts with a primer of ~10 bases of
RNA. At the end, RNA has been removed and replaced, Okazaki
fragments are then linked with the enzyme DNA ligase.
Helicase: A helicase is an enzyme that separates
the strands of DNA, usually using the hydrolysis of
ATP to provide the necessary energy.
Replication
Fork
Parental DNA Molecule
3’
5’
3’
5’

25. • The Leading Strand is synthesized as a single strand from the
point of origin toward the opening replication fork
• The Lagging Strand is synthesized discontinuously against overall
direction of replication
• This strand is made in many short segments It is replicated from
the replication fork toward the origin
RNA Primer
Leading Strand
DNA Polymerase
5
’
5’
3’
3’
Lagging Strand
5’
5’
3’
3’

26. • Okazaki Fragments - series of short segments on the lagging strand
• Must be joined together by an enzyme, ligase.
Lagging Strand
RNA
Primer
DNA
Polymerase
3’
3’
5’
5’
Okazaki Fragment

27. Proofreading New DNA
• DNA polymerase initially makes about 1 in 10,000 base pairing
errors
• Enzymes proofread and correct these mistakes
• The new error rate for DNA that has been proofread is 1 in
1 billion base pairing errors
DNA Damage & Repair
• Chemicals & ultraviolet radiation damage the DNA in our
body cells
• Cells must continuously repair damaged DNA
• Excision repair occurs when any of over 50 repair enzymes
remove damaged parts of DNA
• DNA polymerase and DNA ligase replace and bind the new
nucleotides together

28. RNA: RNA contain ribose instead of deoxyribose in DNA, and
uracil instead of thymine. RNA exists as single strand and are
capable of folding into complex structures.
RNA is the working copies of DNA, the copying process during which
a DNA strand serves as a template for the synthesis of RNA is
called transcription. The synthesis of RNA molecules using DNA
strands as the templates so that the genetic information can be
transferred from DNA to RNA.
There are three types of RNA:
i) Ribosomal RNA (rRNA): rRNA make up about 80% of the total
RNA in the cell, rRNA associates with ribosomes and serves as the
sites for protein synthesis.

29. ii) Transfer RNA (tRNA): tRNA make up about 15% of the total
RNA in the cell. There is at least one specific type of tRNA for
each of the 20 amino acids found in proteins. Each tRNA serves
as an adaptor molecule at the 3’ end that carries its specific
amino acid. It recognizes the genetic code on an mRNA.
iii) Messenger RNA (mRNA): mRNA comprises only about 5% of
the total RNA in the cell. It is most heterogenous type of RNA
in size and base sequence. The mRNA carries genetic information
from the nuclear DNA to the cytosol where it used for protein
synthesis.

30. • Both processes use DNA as the template.
• Phosphodiester bonds are formed in both cases.
• Both synthesis directions are from 5´ to 3´.
Similarity between replication and transcription
Replication Transcription
template double strands single strand
substrate dNTP NTP
primer yes no
Enzyme DNA polymerase RNA polymerase
product dsDNA ssRNA
Differences between replication and transcription

31. • The whole genome of DNA needs to be replicated, but only small
portion of genome is transcribed in response to the development
requirement, physiological need and environmental changes.
• DNA regions that can be transcribed into any RNA or protein product
other than regulatory factor or proteins are called structural genes.
The template strand is the strand from which the RNA is actually
transcribed or new strand of DNA is synthesized during replication.
It is also termed as antisense strand.
The coding strand is the strand whose base sequence specifies the
sequence of RNA or amino acid sequence of the encoded protein.
Therefore, it is also called as sense strand.
G C A G T A C A T G T C5' 3'
3' C G T C A T G T A C A G 5' template
strand
coding
strand
transcription
RNAG C A G U A C A U G U C5' 3'

32. Transcription of prokaryotic genes:
In bacteria one type of RNA polymerase synthesizes all of the RNA
except for the short RNA primers which needs primase.
RNA polymerase is a multisubunit enzyme:
a) Core enzyme: consists of four peptide subunits, 2, 1 and 1
/
and are
responsible for 5’ to 3’ RNA polymerase activity.
b) Holoenzyme: the sigma (σ) subunit recognize the promoter region on the
DNA. The sigma (σ) subunit plus the core enzyme make up the holoenzyme.
subunit MW function
 36512 Determine the DNA to be transcribed
 150618 Catalyze polymerization
 155613 Bind & open DNA template
 70263
Recognize the promoter
for synthesis initiation

33. Steps in the RNA synthesis:
Initiation, Elongation, Termination,
Initiation: RNA polymerase holoenzyme binds to the promoter region
of the DNA and starts transcription, the prokaryotic promoter
contains characteristic consensus sequences; pribnow box (six
nucleotides) at ~-10 position, and a special sequence at -35 region.
• Each transcriptable region is called operon.
• One operon includes several structural genes and upstream
regulatory sequences (or regulatory regions).
• The promoter is the DNA sequence where RNA-polymerase
can bind. It is the key point for the transcription control.
Promoter exists in the upstream region of each gene.

34. 5'
3'
3'
5'
-50 -40 -30 -20 -10 1 10
start-10
region
T A T A A T
A T A T T A
(Pribnow box)
-35
region
T T G A C A
A A C T G T
Prokaryotic promoter

35. Elongation: Once the promoter region has been recognized by RNA Pol,
local unwinding of the DNA occurs and begins to synthesize a transcript
of the DNA sequence.The elongation phase is said to begin when the
tanscript exceeds 10 nucleotides in length. Sigma factor is then
released and the core enzyme is able to move and synthesize RNA using
NTP as substrate. RNA polymerase does not require a primer and has
no proofreading activity.
Termination: Termination factor requiers for termination, eg, ρ (Rho)
factor for E coli. Elongation continues until a termination signal is
reached. Termination may be spontaneous or dependent on ρ (Rho)
factor.

36. Transcription of Eukaryotic genes:
Three types of RNA polymerase:
i) RNA Polymerase I: Synthesizes rRNA
ii) RNA Polymerase II: Synthesizes mRNA,
iii) RNA polymerase III: Produces tRNA and other small RNAs
structural gene
GCGC CAAT TATA
intronexon exon
CAAT box
GC box
TATA box (Hogness box)
Promoter Region of Eukaryotic genes:
(~-25bp position)
(~-70 - 80bp position)
(~-90bp position)

37. Initiation: Transcription initiation needs promoter and upstream
regulatory regions. RNA-pol does not bind the promoter directly.
RNA-pol II associates with six transcription factors, TFII A, TFIIB,
TFIID, TFIIE, TFIIF and TFII H to make a pre-initiation complex
and then starts transcription.
Elongation: Elongation is similar to that of prokaryotes and continues
up to termination codon.
Pre-initiation complex
(PIC)RNA pol II
TF II F
TATA
DNA
TF II
A
TF II
B
TF II E
TF II H
TFIID

38. Posttranscriptional
modification includes:
Capping (GpppGp)
at the 5- end ,
Tailing at the 3-
end,
mRNA splicing,
RNA edition

39. Exon and intron:
Exons are the coding sequences that appear on split genes
and primary transcripts, and found in matured mRNA.
Introns are the non-coding sequences that are transcript
into primary mRNAs, and will be spliced out in the later
cleavage process.

40. mRNA splicing