Nucleic Acids

What Are Nucleic Acids?

Nucleic acids are macromolecules, similar to polysaccharides and polypeptides, and are
classified as biopolymers. They are present in all living organisms and are found in the cells
of every organism.

● Function:
○ Nucleic acids contain genetic material located within the nucleus.
○ They store hereditary information and are responsible for transferring genetic
information from one generation to another during cell division.

There are two types of nucleic acids:

1. DNA – Deoxyribonucleic Acid

2. RNA – Ribonucleic Acid

Structure of DNA
DNA is composed of three main components:

1. Sugar (Deoxyribose)
2. Nitrogenous Base
3. Phosphate Group

1. Sugar (Deoxyribose)

● DNA contains deoxyribose sugar, which is a modified form of ribose sugar.

● The term "deoxyribose" comes from the absence of oxygen on the 2' (two-prime)
carbon of the sugar molecule.

2. Nitrogenous Bases

● These are the information-carrying components of DNA.

● There are four nitrogenous bases in DNA:

○ Adenine (A)
○ Guanine (G)
○ Cytosine (C)
○ Thymine (T)

In RNA, thymine (T) is replaced by uracil (U).

Nitrogenous bases are divided into two groups:

 1. Purines:

○ Adenine (A) and Guanine (G)

○ Double-ring structure (larger and bulkier)
2. Pyrimidines:

○ Cytosine (C) and Thymine (T) (or Uracil (U) in RNA)

○ Single-ring structure (smaller and less bulky)

3. Phosphate Group

● The phosphate group is attached to the 5' (five-prime) carbon of the sugar.
● This group is responsible for linking nucleotides together to form a nucleic acid chain.

Structure of RNA
RNA is similar to DNA but has a few key differences:

1. The sugar in RNA is ribose, not deoxyribose.

2. RNA contains uracil (U) instead of thymine (T).
3. RNA is single-stranded, while DNA is double-stranded.

Nucleotide: The Basic Unit of Nucleic Acids

The nucleotide is the structural and functional unit of nucleic acids. Each nucleotide is
composed of three components:

1. Sugar (Deoxyribose in DNA, Ribose in RNA)

2. Nitrogenous Base (Adenine, Guanine, Cytosine, Thymine/Uracil)
3. Phosphate Group

Energy Currency of the Cell: ATP

● ATP (Adenosine Triphosphate) is a nucleotide that serves as the primary energy
carrier in the cell.
● Adenosine refers to a combination of:
○ Sugar (Ribose)
○ Nitrogenous Base (Adenine)
○ Three Phosphate Groups

Other energy-carrying nucleotides include:

● GTP – Guanosine Triphosphate

● CTP – Cytidine Triphosphate
 ● TTP – Thymidine Triphosphate

These nucleotides are involved in various biochemical processes, including energy transfer
and cell signaling.

Nucleotide and Nucleoside

1. Nucleotide
A nucleotide is the basic structural unit of nucleic acids (DNA and RNA). It is composed of
three components:

1. Sugar (Deoxyribose in DNA, Ribose in RNA)

2. Nitrogenous Base (Adenine, Guanine, Cytosine, Thymine/Uracil)
3. Phosphate Group

2. Nucleoside
A nucleoside is similar to a nucleotide but lacks the phosphate group. It consists of:

1. Sugar (Ribose or Deoxyribose)

2. Nitrogenous Base

Key Difference:

● Nucleotide = Sugar + Nitrogenous Base + Phosphate

● Nucleoside = Sugar + Nitrogenous Base (No Phosphate)

Structure of RNA
The other type of nucleic acid besides DNA is RNA (Ribonucleic Acid).

● Sugar: RNA contains ribose, which has a hydroxyl group (-OH) at the 2' (two-prime)
carbon.
● Nitrogenous Base: In RNA, uracil (U) replaces thymine (T).
● Strand Type: RNA is usually single-stranded, unlike the double-stranded structure of
DNA.

Definition of Nucleic Acids

Nucleic acids are linear, unbranched macromolecules made up of monomeric units called
nucleotides.
 ● Nucleotides are linked together by phosphodiester bonds, forming a nucleic acid
chain.
● When one nucleotide joins with another, the 5' (five-prime) end of one nucleotide
binds to the 3' (three-prime) end of the next nucleotide.

Phosphodiester Bond
A phosphodiester bond is a type of ester linkage that connects two nucleotides.

● Diester means the bond is formed on both sides through ester linkages.
● This bond forms the backbone of nucleic acids.

Structure of the Nucleic Acid Backbone:

● 5' End: Phosphate group is free.

● 3' End: Hydroxyl group (-OH) is free.

Role of Nucleases
Nucleases are enzymes responsible for breaking down nucleic acids.

● They degrade phosphodiester bonds and split both DNA and RNA molecules.
● Types of Nucleases:
○ Exonuclease: Removes nucleotides from the ends of the DNA/RNA strand.
○ Endonuclease: Cuts nucleotides within the strand.

Watson and Crick's Discovery

● James Watson and Francis Crick were scientists working at the Cavendish
Laboratory in Cambridge.
● They discovered the double-helix structure of DNA.

Key Features of the Double-Helix Structure:

1. Two strands of DNA run in opposite directions (antiparallel).

2. The strands are held together by hydrogen bonds between complementary nitrogenous
bases:
○ Adenine (A) pairs with Thymine (T).
○ Guanine (G) pairs with Cytosine (C).

Complementary Base Pairing in DNA

In DNA, purines always pair with pyrimidines to maintain a consistent structure.
 1. Adenine (A) pairs with Thymine (T) through two hydrogen bonds.

○ Why? Purines are double-ringed structures, while pyrimidines are single-

ringed. The pairing of adenine (a purine) with thymine (a pyrimidine) ensures
a stable and uniform double helix.
2. Guanine (G) pairs with Cytosine (C) through three hydrogen bonds.

Stability of AT vs. GC Bonds

● A-T bonds are easier to break because they have two hydrogen bonds.
● G-C bonds are harder to break due to their three hydrogen bonds.

In primer design, the GC content is carefully considered:

● 40% to 60% GC content is optimal for stable and efficient DNA amplification.
● Higher GC content increases stability, while lower GC content makes it easier to
separate strands during processes like PCR (Polymerase Chain Reaction).

Three Forms of DNA

DNA exists in three structural forms based on environmental conditions:

1. A-Form DNA
● Condition: Exists in high salt concentrations or dehydrated environments.
● Helix Type: Right-handed double helix.
● Helix Width per Turn: 2.4 nm (or 24.6 Å).
● Distance Between Bases: 0.24 nm (or 2.4 Å).
● Bases per Turn: 11.

2. B-Form DNA
● Condition: Found under normal physiological conditions (e.g., in human cells).
● Helix Type: Right-handed double helix.
● Helix Width per Turn: 3.32 nm (or 33.2 Å).
● Distance Between Bases: 0.34 nm (or 3.4 Å).
● Bases per Turn: 10.
● Significance: This is the most common form of DNA in living organisms, including
humans.
3. Z-Form DNA
● Condition: Appears in harsh conditions or in regions with alternating purines and
pyrimidines.
● Helix Type: Left-handed double helix (unusual).
● Helix Width per Turn: 4.56 nm (or 45.6 Å).
● Distance Between Bases: 0.37 nm (or 3.7 Å).
● Bases per Turn: 12.
● Significance: Less common, Z-DNA may play roles in gene regulation and stress
responses.

Structure of RNA
● Single-stranded molecule.
● Nitrogenous base: Uracil (U) replaces Thymine (T) found in DNA.
● Ribose sugar: Contains a hydroxyl group (-OH) at the 2' position, unlike
deoxyribose in DNA.

Types of RNA
There are three main types of RNA:

1. Messenger RNA (mRNA)

2. Transfer RNA (tRNA)
3. Ribosomal RNA (rRNA)

1. Messenger RNA (mRNA)

● Synthesis:

○ mRNA is synthesized in the nucleus through a process called transcription.

○ It then moves to the cytoplasm, where it plays a key role in protein synthesis.
● Function:

○ mRNA acts as a direct copy or blueprint of DNA.

○ During transcription, DNA is transcribed into mRNA, which carries the genetic
information required to make proteins.
○ The information present in DNA is transferred as-is into mRNA.
● Coding and Non-Coding Regions:

○ Exons: Coding regions of DNA that are transcribed into mRNA and used for
protein synthesis.
○ Introns: Non-coding regions of DNA that are not translated into proteins.
2. Transfer RNA (tRNA)
● Function:

○ tRNA helps in the transport of specific amino acids during translation (the
process where proteins are assembled).
○ It delivers amino acids to the ribosome, where they are linked together to form
a protein.
● Process of Translation:

○ mRNA attaches to the ribosome.

○ tRNA brings specific amino acids to the ribosome, where they are assembled
into a polypeptide chain.
○ This process forms proteins.

3. Ribosomal RNA (rRNA)

● Function:

○ rRNA combines with proteins to form ribosomes, which are the sites of protein
synthesis.
○ It plays a structural and catalytic role, facilitating the assembly of amino acids
into proteins.
● Role in Ribosomes:

○ rRNA is an essential part of the ribosome structure.

○ Ribosomes act as factories or machinery for protein synthesis by translating
the information in mRNA into a polypeptide chain.