Nucleic acid

Yahyea Baktiar Laskar
ZOOHCC-303: Fundamentals of Biochemistry (U3)
NUCLEIC ACID
Assistant Professor
Department of Zoology
Ramanuj Gupta Degree College
yahyea92@gmail.com
yahyeabaktiar.laskar@aus.ac.in

Nucleic Acids
General Introduction:
▪ Nucleic acids are long-chain polymeric molecules.
▪ The monomer or the repeating unit is known as the nucleotides and hence sometimes
nucleic acids are referred to as polynucleotides.
▪ It plays a key factor in transferring genetic information from one generation to the next.
▪ In the nucleus, nucleotide monomers are linked together comprising of distinct components
namely a Phosphate Group, Nitrogenous Bases and Ribose or Deoxyribose sugar.
▪ Based on the sugar group, nucleic acids are of two types— DNA-deoxyribonucleic acid and
RNA-ribonucleic acid.
▪ Pyrimidines (Cytosine and Thymine) and Purines (Guanine and Adenine) are two types of
nitrogenous bases in DNA.
▪ Thymine is replaced by Uracil in RNA.

Nucleic Acids

Nucleic Acids
Structure of Purines and Pyrimidines:
Purines:
▪ Purine is a heterocyclic aromatic organic compound composed of a pyrimidine ring fused with imidazole ring.
▪ It consists of two hydrogen-carbon rings and four nitrogen atoms. The melting point of purine is 214°C.
▪ Catabolism results in the production of uric acid.
Pyrimidines:
▪ Pyrimidine is a heterocyclic aromatic organic
compound that is composed of carbon and
hydrogen.
▪ It consists of one hydrogen-carbon ring and two
nitrogen atoms.
▪ The melting point of pyrimidine is 20-22°C.
▪ Catabolism produces carbon dioxide, beta-amino
acids and ammonia

Nucleic Acids
Structure of Nucleosides and Nucleotides:
Nucleosides:
▪ Nucleoside has only a nitrogenous base and a five-carbon sugar.
▪ The base is bound to either ribose or deoxyribose via a β-glycosidic linkage at
1’ position.
▪ Nucleosides are named as Adenosine, Guanosine, Thymidine, Cytidine,
Uridine.
Nucleotides:
▪ Nucleotide is composed of a nucleobase, a five-carbon sugar, and one or
more phosphate groups.
▪ In DNA (double helix) there are two antiparallel strands of polynucleotides
that are linked together by hydrogen bonds between nitrogenous bases.
▪ Phosphate group interlinks the sugar molecules of two nucleotides forming a
chain.
▪ Sugar phosphate chain forms the backbone of a polynucleotide chain.

Nucleic Acids
Structure of Nucleosides and Nucleotides:
Properties of Nucleotides:
▪ Sparingly soluble in water.
▪ Absorb light in UV region at 260 nm. (for detection & quantitation of
nucleotides).
▪ Capable of forming hydrogen bond.
▪ Aromatic base atoms numbered 1 to 9 (1 to 6 for pyrimidine).
▪ Purine ring is formed by fusion of pyrimidine ring with imidazole ring.
▪ Numbering is anticlockwise.
Functions of Nucleotides:
▪ They are the building blocks of nucleic acids.
▪ They are the energy currency (ATP) in metabolic transactions.
▪ Act as essential chemical links (cAMP) in the response of cells to hormones
and other extracellular stimuli.
▪ Forming a portion of several important coenzymes such as NAD+, NADP+,
FAD and coenzyme A.

Deoxyribonucleic acid or DNA
Structure of DNA:
▪ DNA stands for Deoxyribonucleic Acid, which is a molecule that contains the instructions an organism
needs to develop, live and reproduce.
▪ DNA is found in the nucleus, with a small amount of DNA also present in mitochondria and
chloroplast in the eukaryotes.
▪ In 1953, James Watson and Francis Crick discovered the structure of DNA.
▪ The works of Rosalind Franklin lead to Watson and Crick’s discovery.
▪ DNA has a double helix structure and looks like a twisted ladder.
▪ Each strand has a 5′end (with a phosphate group) and a 3′end (with a hydroxyl group).
▪ The strands are antiparallel, meaning that one strand runs in a 5′→ 3′direction, while the
other strand runs in a 3′ → 5′ direction.
▪ The sides of the ladder are made of alternating sugar (deoxyribose) and phosphate molecules while the steps of the ladder
are made up of a pair of nitrogen bases.
▪ The amount of adenine equals the amount of thymine; the amount of guanine equals the amount of cytosine. The pairs are
held together by hydrogen bonds.

Structure of DNA:
▪ The deoxyribonucleotides are linked together by 3′ → 5′phosphodiester
bonds.
▪ The shape of the helix is stabilized by hydrogen bonding and hydrophobic
interactions between bases.
▪ The diameter of double helix is 2 nm and the double helical structure
repeats at an interval of 3.4 nm which corresponds to ten base pairs.
▪ As a result of the double helical nature of DNA, the molecule has two
asymmetric grooves.
▪ This asymmetry is a result of the geometrical configuration of the bonds
between the phosphate, sugar, and base groups that forces the base groups
to attach at 120° angles instead of 180°.
▪ The larger groove is called the major groove, occurs when the backbones
are far apart; while the smaller one is called the minor groove, occurs when
they are close together.

Base Pairing:
▪ There are 4 types of nitrogen bases—Adenine (A) Thymine (T) Guanine (G) Cytosine
(C) in DNA.
▪ The nitrogen bases have a specific pairing pattern.
▪ This pairing pattern occurs because the amount of adenine equals the amount of
thymine; the amount of guanine equals the amount of cytosine.
▪ The pairs are held together by hydrogen bonds.
▪ The base adenine always interacts with a thymine (A-T) on the opposite strand via
two hydrogen bonds and cytosine always interacts with guanine (C-G) via three
hydrogen bonds on the opposite strand.
Chargaff’s Rule
Erwin Chargaff, a biochemist, discovered that the number of nitrogenous bases in the DNA was present in equal quantities. The
amount of A is equal to T, whereas the amount of C is equal to G.
A=T; C=G
In other words, the DNA of any cell from any organism should have a 1:1 ratio of purine and pyrimidine bases.

Biological Importance of DNA:
There are mainly three different DNA types:
▪ Hereditary material—The genetic information contained in the nucleotide sequence of DNA aids in the production of certain
proteins or polypeptides and is transmitted to daughter cells or progeny.
▪ Autocatalytic role— During the S phase of the cell cycle, each DNA strand of a double helix might serve as a template for
daughter strand synthesis.
▪ Hetero-catalytic role—During transcription, any one DNA strand serves as a template for RNA production.
▪ Variations—During meiosis, DNA undergoes recombination and the occasional mutation (changes in nucleotide sequences),
which generates diversity in the population and ultimately leads to evolution.
▪ DNA finger printing—Each individual possesses mini-satellites or VNTRs, which are small nucleotide repeats (Variable Number
of Tandem Repeats). VNTRs are vary between individuals and provide the basis of DNA fingerprinting. This method is used to
identify criminals, determine paternity, and verify immigrants, among other purposes.
▪ Recombinant DNA technology (Genetic engineering)—Recombinant DNA is the result of the artificial cleaving and rejoining of
DNA sequences from two or more organisms. Utilized for the manufacture of genetically modified organisms (GMOs),
genetically modified foods (GMFs), vaccines, hormones, enzymes, clones, etc.

Forms of DNA:
There are mainly three different DNA types:
▪ A-DNA: It is a right-handed double helix similar to the
B-DNA form. Dehydrated DNA takes an A form that
protects the DNA during extreme conditions such as
desiccation. Protein binding also removes the solvent
from DNA, and the DNA takes an A form.
▪ B-DNA: This is the most common DNA conformation and is a right-handed helix. The majority of DNA has a B type
conformation under normal physiological conditions.
▪ Z-DNA: Z-DNA is a left-handed DNA where the double helix winds to the left in a zig-zag pattern. It was discovered by Andres
Wang and Alexander Rich. It is found ahead of the start site of a gene and hence, is believed to play some role in gene
regulation.
▪ D-DNA: Rare variant with 8 base pairs per helical turn, form in structure devoid of guanine.
▪ C-DNA: Formed at 66% relative humidity and in presence of Li+ and Mg2+ ions.
▪ E- DNA: Extended or eccentric DNA.

Complementarity of DNA:
▪ Complementarity describes a relationship between two structures each following the
lock-and-key principle.
▪ Complementarity is the base principle of DNA replication and transcription.
▪ It is a property shared between two DNA or RNA sequences, such that when they are
aligned antiparallel to each other, the nucleotide bases at each position in the
sequences will be complementary, much like looking in the mirror and seeing the
reverse of things.
▪ This complementary base pairing allows cells to copy information from one generation
to another and even find and repair damage to the information stored in the sequences.
▪ The degree of complementarity between two nucleic acid strands may vary, and
determines the stability of the sequences to be together.
▪ Complementarity is achieved by distinct interactions between nucleobases: adenine,
thymine (uracil in RNA), guanine and cytosine.
▪ All other configurations between nucleobases would hinder double helix formation.

Self-Complementarity and hairpin loop:
▪ A sequence of RNA that has internal complementarity which results in it folding into a hairpin.
▪ Self-complementarity refers to the fact that a sequence of DNA or RNA may fold back on itself, creating a double strand like
structure.
▪ Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin
loops, junctions, bulges or internal loops.
▪ RNA is more likely to form these kinds of structures due to base pair binding not seen in DNA, such as guanine binding with
uracil.

Denaturation and Renaturation of DNA:
▪ DNA denaturation and renaturation processes are used for genetic research and studies.
▪ In the process of denaturation, an unwinding of DNA double-strand takes place, resulting in two separate single strands on
applying high temperature, extreme pH, etc.
▪ Separate single strands rewind on cooling and the process is known as renaturation.

Denaturation of DNA double helix takes place by the following denaturation agents:
▪ Temperature— If a DNA solution is heated to approximately 90°C or above, it will denature the DNA completely causing it to
separate into single strands. If several samples of DNA are melted, it is found that the Tm is highest for those DNAs that
contain the highest proportion of G—C.
▪ Chemical Agents—Denaturation can also be brought about by certain chemical agents such as urea and formamide as they
enhance the aqueous solubility of the purine and pyrimidine groups.
▪ pH—Denaturation also occurs at acidic (pH= 2-3) and alkaline (pH=12) solutions in which ionic changes of the purine and
pyrimidine bases can occur.
Denaturation involves the following changes of the properties of DNA:
▪ Increase in absorption of UV-Light at 260 nm.
▪ Double-stranded DNA shows a strong positive rotation which highly decreases with denaturation.
▪ Denaturation causes a marked decrease in viscosity.

▪ Renaturation is also known as annealing.
▪ When the temperature and pH return to optimum biological
level, the unwound strand of DNA rewind and give back the
dsDNA.
▪ Renaturation occurs when the denatured DNAs are cooled in
suitable conditions.
▪ Renaturation also depends on temperature, pH, length and
constituents of the DNA structure.
▪ The renaturation rate is directly proportional to the number of
complementary sequences present.
▪ With renaturation, absorption of UV (260nm) decreases and
viscosity increases again.

Ribonucleic acid or RNA
Types of Ribonucleic acid or RNA:
▪ It is a single-stranded nucleic acid similar to DNA but having ribose sugar rather than deoxyribose sugar and uracil instead of
thymine as one of the nucleotide bases.
▪ RNA polymerase synthesizes RNA from DNA that is functionally for protein-coding (messenger RNA, mRNA) or non-coding
(RNA genes). Because of these functions, RNA molecules are of following types:
❖ messenger RNA (mRNA)– It is the RNA that carries information from DNA to the ribosomes (site of protein synthesis) in
the cell. The mRNA code sequences determine the amino acid sequence in the protein that is produced.
❖ ribosomal RNA (rRNA)– It incorporates into the ribosomes.
❖ transfer RNA (tRNA)– It is used to transfer specific amino acids to growing polypeptide chains at the ribosomal site of
protein synthesis during translation.
❖ small nuclear RNA (snRNA)—snRNA has different genes in multiple copies, which play different roles in the synthesis of
other RNA classes, such as, snRNA which is part of the spliceosomes that help in the conversion of pre-messenger RNA
(hnRNA) into mRNA by excising the introns and splicing the exons.
❖ microRNA (miRNA)– They are used to regulate gene activity; They are tiny (~22 nucleotides) RNA molecules that
regulate the expression of mRNA molecules.

Ribonucleic acid or RNA
Types of Ribonucleic acid or RNA:
❖ small nucleolar RNA (snoRNA)—They are small RNAs of about
60-300 nucleotides found in the cell nucleolus. They play a role in
the synthesis of ribosomes, by cutting the large RNA precursor of
the 28S, 18S, and 5.8S. They also help in the splicing of pre-mRNA
to different forms of mature mRNA. One type of snoRNA serves
as a template for the synthesis of the telomeres.
❖ long non-coding RNA (lncRNA)—This is a heterogeneous group of
non-coding transcript RNA that are 200 nucleotides in size. Major
functions of lncRNA are still unknowns, however, some scientific
evidence indicates its role in gene regulation and physiological
mechanism involvements.
❖ catalytic RNA (ribozymes)— which functions as an enzymatically
active RNA molecule.

Disclaimer: The information/images in this study material has been adapted from various sources including but not limited to books, journals, websites, and
related materials openly available in the internet. This will be purely utilized for academic purpose only, by college students. The author has no intension of
using these information/images/other materials that may be copyrighted and included in this study material for commercial benefit.

Nucleic acid

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