Introduction to Nucleic Acids

Assoc. Prof. Dr. Atif Amin Baig ,

Faculty of Medical Sciences,
University Sultan Zainal Abidin.
atifamin@unisza.edu.my
 Recalls
1. structure of amino acids
2. concept of zwitter ion and its clinical importance.
3. Basis of classifications of amino acids
4. Classification of amino acids based on structure.
5. Polarity of amino acids and its importance
6. R-group and types of amino acids
7. Nutritional and non nutritional amino acids
8. Non-standard amino acids.
9. metabolic fate of amino acids
10. Illustrate the formation of a peptide bond
11. What are Proteins?
12. Classification of proteins based on chemical nature and functions?
13. Describe various types of protein structures and their importance?
14. Some examples of protein involved in diseases.
 Learning Outcomes
1. Introduction to the nucleic acids
2. Nucleotides and nucleosides
3. Nitrogenous bases and their forms
4. Sugars in nucleic acids
5. Phosphate backbone in nucleic acids
6. Properties of nucleic acids
7. Classifications of nucleic acids
8. DNA IDs and future
9. IUPAC and Nomenclature of nucleic acids as per DNA Sequencing
10. Concept of genome, Transcriptome and proteome
11. Structural conformations of nucleic acids
12. Types of RNA
13. Differences between RNA and DNA
DNA ID ?
 NUCLEIC ACIDS
• Macro biomolecules
• Polymers of Nucleotides
• Are produced by two pathways (CLA)
• Polyprotic acids
• Location?
 Mitochondrial DNA
Nucleus and chromosomes
Plasmids
Human chromosomes and their sizes
 Central Dogma

Genome

Transcriptome

Proteome
Genome Vs Nucleic Acids Vs Body Complexity
 Structure of Nucleotides
Nucleic Acid = Nucleotide + Nucleotide + ……… (n)

Nucleotide = Nucleoside + Phosphate Group

Nucleoside for DNA = Deoxyribose + Nitrogenous base

Nucleoside for RNA = Ribose + Nitrogenous base

Phosphate

Nitrogenous Base

Ribose or
Deoxyribose Sugar

Nucleoside

Nucleotide
 Nitrogenous Bases
• There are two classes/groups of nitrogenous
bases:

1. Pyrimidines
2. Purines

?
Main Differences
 Pyrimidines

• Pyrimidines includes
three different
nitrogenous bases

1. Cytosine (DNA, RNA)

1. Uracil (RNA)
1. Thymine (DNA)
 Purines
• Purines includes two different nitrogenous
bases

1. Adenine (DNA, RNA)

1. Guanine (DNA, RNA)
 Pentoses of Nucleic Acids
• D-ribose (in RNA)

• 2-deoxy-D-ribose (in DNA)

• The difference - 2'-OH vs 2'-H

• This difference affects secondary structure and

stability
 Chemical Bonding of Nucleoside
How a Nitrogenous Base is Linked to a Pentose sugar?

• Base is linked via a glycosidic bond

• The carbon of the glycosidic bond is anomeric
• Sugars make nucleosides more water-soluble than free bases
• Could have a syn or anti isomeric (conformation)
Nucleotides
 Functions of Nucleotides

1. Provides recognition sequence for amino acids

2. Involved in cell signaling
3. Involves in cell division and metabolism
4. ATP is central to energy metabolism
5. GTP drives protein synthesis
6. CTP drives lipid synthesis
7. UTP drives carbohydrate metabolism
 Polynucleotides
5’ 3’
N C
5’ Sense/ Leading/ Direct/ +/ Coding 3’
3’ Anti sense/ Lading/ Indirect/ -/ Template 5’
 Base Pairing and DNA Double Helix
• Similar Sequence

• Complementary Sequence

• "Base pairs" arise from hydrogen bonds

• Erwin Chargaff had the pairing data, but didn't understand its implications

• Rosalind Franklin's X-ray fiber diffraction data was crucial

• Francis Crick knew it was a helix

• James Watson figured out the H-bonds

 DNA Sequencing & IUPAC
• International Union of Pure and Applied Chemistry
• International council for Science

• IUPAC nomenclature and DNA Sequence

 Classification of Nucleic Acids
• Based on number of strands
• Based on Types of ribose sugar
• Based on Location
• Based on conformation
 Classification based on strands
• Double stranded are called Deoxyribonucleic Acids
• Single stranded are called Ribose Nucleic Acids
Classification Based on Type of Ribose
1. Ribose sugar containing nucleic acids are
called Ribonucleic acids (RNA)

2. Deoxyribose sugar containing nucleic acids

are called Deoxyribose nucleic acids (DNA)
 Classification based on Location
1. Nuclear DNA
2. Mitochondrial DNA
3. Plastids and chloroplast DNA
4. Plasmids

* We are not adding the synthetic/artificial DNA

Classification based on conformation

Importance in the body? (CLA)

 Properties of Nucleic Acids
1. Keto-enol tautomerism
2. Acid/base dissociations
3. Strong absorbance of UV light
Optical Absorbance of Nucleotides
 Acid Base Dissociations

• RNA is resistant to dilute acid

• DNA is depurinated by dilute acid
• DNA is not susceptible to base
• RNA is hydrolyzed by dilute base
 Quantification of Nucleic Acids
1. Semi quantification of nucleic acids
Using Electrophoresis (Agarose Gel)

2. Quantification of nucleic acids

Using spectrophotometer: at UV 260 nm

Concentration (μg/ml) = A260 – A320 x Dilution Factor x 50 μg/ml

(A260 of 1.0 = 50 μg/ml pure ds DNA)

 Quality of Nucleic Acids
Quality in terms of:

1. Concentration of nucleic acids

2. Purity

Concentration can be checked by semi

quantitative method
 Purity of Nucleic Acids
What are the impurities in the extracted Nucleic Acids?

Assignment to read only

What does it means?

So how to check the purity of Nucleic Acids?

Purity of DNA (A260/A280) = (A260 – A320) / (A280 – A320)

Ideal = 1.5A or greater

 Types of RNA
• mRNA
• tRNA
• rRNA
• Many other types
 Differences Between DNA and RNA

1. Thymine and Uracil?

Cytosine can deaminate to form Uracil but the repair system

recognize the normal Uracil from Mutated Uracil ?

5- methyl Uracil = Thymine

 Differences Between DNA and RNA
2. Why DNA is having Deoxy
ribose?

DNA is more stable

OR

RNA is more stable?

Thank you