Faculty of

Medicine
Medical Education-
Damietta
University

Level 1
Semester 1
Module 1B
 Nucleic Acids

Dr Raghdaa Shrief
Assistant Prof. Medical Microbiology & Immunology, Damietta Faculty of Medicine
 Instructor Information

• Contact: Medical Microbiology & Immunology Department.

• Official email: Ragnem@du.edu.eg
• Mobile (optional):
• Academic hours:
➢ Monday: 10:00-11:00 AM
➢ Wednesday: 10:00-11:00 AM
Lecture Outline
• Nucleotides Structures & Nomenclature.

• Function of Nucleotides.

• DNA Structure and Types.

• RNA Structure and Types.

Learning Outcomes
By the end of the lecture, the students will be able to:

1- Describe Nucleotides Structures & Nomenclature.

2- Define Function of Nucleotides.
3- Define DNA Structure and its Forms.
4- Recognize RNA Structure & Types.
5- Differentiate between DNA & RNA.
 Case Scenario
A 35 year Female, presented to the chest
clinic with a history of fever and upper
respiratory symptoms 3 days ago. She had a
history of contact with positive COVID-19
patients. On examination, she had sore throat
and cough and her body temperature is 38.5°C.
The doctor asked her to do complete blood
picture and COVID-19 PCR swab for nucleic acid
detection.

What is the type of nucleic acid and its

structure in her swab?
 Learning Outcome 1

Describe Nucleotides Structures &

Nomenclature.
 Nucleic Acids
• 2 types of nucleic acids:
deoxyribonucleic acid
(DNA) & ribonucleic
acid (RNA).

• Storage & expression

of genetic information.
 Nucleic Acids
• Long chains of repeated
subunits called nucleotides.

Nucleotides
• Building blocks of DNA & RNA.
• Present in body as poly-
nucleotide chain (DNA,RNA)
or free nucleotides.
 Nucleotides
1-Pentose sugar:
Ribose in RNA.
2-deoxy-ribose in DNA.

2-Nitrogenous base:
A-Purines: adenine, guanine,
hypoxanthine, xanthine.
B-Pyrimidine: cytosine , thymine,
uracil.

3-Phosphate group.
Nitrogenous bases are attached to the 1st carbon of
the sugar & N9 of a purine or N1 of a pyrimidine.
• Nitrogenous Base + a pentose sugar = nucleoside.

• Nucleoside + a phosphate group = nucleotide or nucleoside mono-

phosphate.

• Attachment of A 2nd phosphate group = nucleoside diphosphate.

• Attachment of A 3rd phosphate group = nucleoside triphosphate.

• DNA & RNA are polymers of nucleoside monophosphates.

 Nomenclature
Base Nucleoside Nucleotide
Adenine Adenosine, deoxy adenosine AMP, ADP,ATP, d.AMP, d.ADP, d.ATP

Guanine Guanosine, deoxy guanosine GMP, GDP, GTP, d.GMP, d.GDP , d.GTP

Cytosine Cytidine, deoxy-cytidine CMP, CDP, CTP ,d.CMP, d.CDP , d.CTP

Thymine Deoxy thymidine d.TMP, d.TDP , d.TTP
Uracil Uridine UMP,UDP,UTP
 Important Nucleotides
Phosphoadenosine-phospho-sulfate
Cyclic AMP (c.AMP) (PAPS)
A phosphodiester linkage may be
formed between the 3' and 5'
positions of ribose group.

S-adenosyl methionine
(SAM)
 Learning Outcome 2

Define Function of Nucleotides.

 Functions of nucleotides
1- Building blocks of RNA & DNA.

2- Source of energy: ATP, GTP act as source of Energy.

3- Mediate action of hormone: c.AMP & c.GMP are

second messenger.

4- Co-enzymes: NAD, FAD, Co-enzyme A.

 Functions of nucleotides
5- Activation of chemical compounds:
- UDP- glucose for synthesis of glycogen.
- CDP choline, CDP-ethanolamine for synthesis of
phospholipids.

6- Chemical group donors:

- PAPS is a sulfate donor for synthesis of sulfolipids.
- SAM is a methyl donor for transmethylation
reactions.
 Functions of nucleotides
7- Nucleotides Analogue: prepared by
altering the base ring or sugar part.

Anti-cancer: 5-flurouracil (pyrimidine

analogue):↓ DNA synthesis & ↓ growth
of cancer cells.
 Learning Outcome 3

Define DNA Structure and its Forms.

 DNA Structure
• DNA is a polynucleotide contains millions
of nucleotides.

• DNA is a polymer of deoxyribonucleoside

monophosphates (dNMPs).

• DNA is double stranded except in some

viruses.

• It has primary & secondary structure.

 1- Primary Structure
• DNA is 2 strands of polynucleotides;
d.AMP, d.GMP, d.TMP, d.CMP.

• The nucleotides are linked by 3`to 5`

phosphodiester bond between 3`(OH) of
sugar of one nucleotide & 5`(OH) of the
sugar of the adjacent nucleotide through a
phosphoryl group.
 1- Primary Structure
• Sugar-phosphate forms asymmetrical
backbone.

• Polarity: each strand has 2 ends; 5`end

with free phosphate & 3`end with free
(OH). DNA sequences are written in the
5` to 3` (5` GCA 3`).

• Two nitrogenous bases are inside the 2

stands at right angle.
 2- Secondary Structure
DNA has 3 structural forms:

• B-form: Described by
Watson & Crick in 1953; a
right-handed helix, 10 base
pairs per turn (or twist).
• A-form: a right handed
helix, 11 base pairs per turn.
• Z-form: a left handed helix.
 2- Secondary Structure
(B-form of DNA )
• Watson & Crick Model; DNA is a double
helix (B-form) (the common physiological
form);
• Right handed helix.
• Anti-parallel: one runs in 5` to
3`direction, the other strand
runs in 3` to 5` direction.
• Complementary base pairing:
through hydrogen bonds ) (A=T),
(GΞC).
 Learning Outcome 4

Recognize RNA Structure & Types.

 RNA Structure
• Single strand polymer of nucleotides; AMP,
GMP, CMP, UMP connected by phosphodiester
bonds.
• About 50% of cellular RNA is in the
ribosomes & endoplasmic reticulum, 25% in
cytoplasm, 15% in mitochondria & the rest
10% in nucleus.
• All RNA molecules are formed in the nucleus
then most of RNA is transported to
cytoplasm.
• RNA has 5 types.
 Types of RNA
1- Messenger RNA (m.RNA): 5 % of cellular RNA.

2-Transfer RNA (t.RNA): 15 % of cellular RNA.

3- Ribosomal RNA (r.RNA): 80 % of cellular RNA.

4-Small nuclear RNA (sn.RNA): less than 1 % of cellular RNA.

5- Micro-RNA (miRNA): They alter the function of mRNA.

 1- Messenger RNA
( m.RNA )
• 5% of cellular RNA.
• Carries message from DNA to ribosome where it directs synthesis of
specific protein.
• Each protein has specific m.RNA.
 1- Messenger RNA
( m.RNA )
Eukaryotic m.RNA is divided to 3 regions:
a) 5’ untranslated leading sequence: not translated , it ends by
cap 7-methyl-GTP.
b) Translated coding sequence: carries code for synthesis of
specific protein. Each 3 bases ( codon) will be translated for
specific amino acid .
c) 3’ untranslated tailing sequence: not translated, it ends by poly
(A) tail.
 2-Transfer RNA (t.RNA)
• 15 % of total cellular RNA.

• There is at least one specific tRNA molecule

for each of the 20 amino acids commonly
found in proteins.

• Clover-leaf appearance .

• Its structure is stabilized by hydrogen

bonds between complementary bases(A=U),
(GΞC).
 2-Transfer RNA (t.RNA)
• 4 arms with extensive base pairing.

1- D arm: contains dihydrouracil .

2- TΨC arm: it ends in loop contains sequence
thymine, pseudouridine & cytosine .
3- Anti-codon arm: it ends in loop that contain
7 bases, three in middle form the anti-codon.
4- Acceptor arm: not end in loop, ends in
sequence CCA which is the site of attachment
for amino acid carried by t.RNA.
5- Variable arm: in certain tRNAs.
 3-Ribosomal RNA ( r.RNA)
1- Forms about 80 % of total RNA.
2- It is associated with several proteins to form ribosome.
3- Responsible for Protein synthesis.
4- In the eukaryotic; 80S ribosome is formed of a-large subunit (60S)
& a small subunit (40S).
5- 60S subunit is composed of 50 proteins & 3 types of rRNA (5S,
5.8S, 28S).
6- 40 S subunit is composed of 30 proteins & 18S r.RNA.

• (“S” Svedberg unit for sedimentation rate)

 Learning Outcome 5

Differentiate between DNA & RNA.

 DNA RNA
1- Site Nucleus Cytoplasm

2- Functions Storage & transfer of Protein synthesis

genetic information
3- Bases A,G,C,T A,G,C,U

4- Sugar Deoxy-ribose Ribose

5- Strands 2 strands One strand only

6-Types One type but 3 forms 5 types; mRNA, tRNA,

(A,B,Z) rRNA, snRNA, miRNA

7- Shape Double helix Variable

 Case Discussion
A 35 year Female, presented to the chest
clinic with a history of fever and upper
respiratory symptoms 3 days ago. She had a
history of contact with positive COVID-19
patients. On examination, she had sore throat
and dry cough and her body temperature is
38.5°C. The doctor asked her to do complete
blood picture and COVID-19 PCR swab for
nucleic acid detection.

What is the type of nucleic acid and its

structure in her swab?
• DNA & RNA is a long chains of repeated
nucleotides formed of Pentose sugar,
Nitrogenous base & Phosphate group.

• Nucleotides act as a source of energy,

second messenger, …..

• DNA is a polymer of dNMPs form a right

handed double helix.

• RNA is a single strand & has 5 types.

 Questions 1

DNA is a polymer of ……………….. (1 Mark)

A.deoxyribonucleoside monophosphates.
B.deoxyribonucleoside diphosphates.
C.deoxyribonucleoside triphosphates.
D.deoxyribonucleoside tetraphosphates.
 Questions 2

In DNA helix, adenine base pairs with…… (1 Mark)

A.Uracil.
B.Guanine.
C.Thymine.
D.Cytosine.
 Questions 3

Mention 3 functions of free nucleotides. (3 Marks)

1- ……………………………………….
2- ……………………………………..
3- ………………………………………………..
Discussion & Feedback
 References

• DM Vasudevan,Textbook of Biochemistry for medical

students.

• Lippincott's Illustrated Reviews Biochemistry.

• Oraby's Illustrated Reviews of Biochemistry.