The document summarizes the structure of nucleic acids and nucleotides. It describes that nucleotides are the building blocks of nucleic acids like DNA and RNA, consisting of a phosphate group, a pentose sugar (ribose in RNA and deoxyribose in DNA), and a nitrogenous base. There are four main bases in DNA - adenine, thymine, guanine and cytosine. The document also describes the different forms DNA can take on like the A, B, C and Z forms, which differ in their structural parameters like base orientation and groove size. Watson and Crick first elucidated the double helix B-form structure of DNA in 1953 using X-ray crystallography data.

1. STRUCTURE OF
NUCLEIC ACID
AND NUCLEOTIDES
PRESENTED BY:
AJISHA S BABU
PRESENTED TO:
NISHA THOMAS MAM
HOD DEPARTMENT OF ZOOLOGY FMN COLLEGE KOLLAM

2. Content
1)Introduction
2) Bases
3)Sugar
4)The PhosphateGroup
5)The Ribose phosphateGroup
6)StructuralOrganization of DNA
7)Types of DNA
(¡)A form of DNA
(¡¡)B form of DNA
(¡¡¡)C form of DNA
(iv)Z form of DNA
8)Conclusion
9)Reference

3. INTRODUCTION
•Nucleic acids are biological important Polymers which are present in all living cells.
•Nucleic acids are important for the growth and development of all forms of life.
•They are responsible for the transfer of genetic information.
•The repeating units of a nucleic acid are called nucleotide.
• Nucleotide is a complex molecule made up of 1 unit of phosphate group, a pentose sugar
and a nitrogen containing heterocyclic base.
•Nucleic acids are linear Polymers of nucleotide units.
• A nucleotide comprises of (¡)a base and(¡¡) a sugar and (¡¡¡)a phosphate group.
•The hydrocyclic nitrogeneous base maybe any one of the two purines viz adenine and
guanine or three pyramidines viz thymine, cytosine and uracil.
•The sugar unit present in the nucleotide is either ribose or deoxyribose.
•The phosphate groups are responsible for the linkage in nucleic acid polymers.

5. Bases
• Nitrogeneous bases are organic molecules with the nitrogen atoms and that have the
chemical properties of a base.
•The basic properties of a nitrogen base are due to the lone pair of electrons of an nitrogen
atom.
•Nitrogenous bases are typically classified as the derivatives of two parent compounds,
pyrimidines and purines.
•They are nonpolar and planar compounds.
• Both pyrimidine and purines resemble pyridine .
• In the construction of DNA nucleotides, four different nitrogenous bases are used, which in
turn build up the nucleic acid, DNA. The nitrogenous bases are adenine(A), thymine(T),
guanine(G), and cytosine (C).
•In Rna, thymine is replaced by uracil . ie; the RNA contains the base adenine, guanine ,
cytosine and uracil.

7. SUGAR
• The pentose sugar is a 5 carbon sugar.
•The pentose sugar found in nucleic acids are of two types deoxyribose sugar
and ribose sugar.
• The sugar in nucleic acid are furanose: 5 membered ribose in RNAs and 2-
deoxyribose in DNAs.
• The five-membered furanose ring is puckered .
•It can be puckered in an envelope from with 4 atoms in a plane and the 5th
atom out of this plane; or it can be in a twist from with two adjacent atom of
the five- membered ring.

9. The Phosphate Group
• The phosphate group is not variable in the two kind of nucleic acids.
• It is the presence of phosphoric acid that is responsible for the acidic
nature of nucleic acids.
•The phosphate group is substituted to the sugar at that C5’ – position and a
nucleoside with the attachment of a phosphate group constitutes a
nucleotide four oxygen atoms are linked to the phosphorous atom by sp3
bonds and are tetrahedral.
•The orientation of the phosphate group relative to the sugar moiety is given
by the Torsion angle about the C5’- C4’ Bond.

11. The Ribose-phosphate Backbone
• The confirmation of the ribos-phosphate backbone of a nucleotide unit is
represented by six torsion angles.
•The rotation about C-O Bonds are restricted, largely due to the steric
hindrance between the phosphate group and the sugar moiety.
• In contrast, the rotations about the phosphoester bones are in the range g-.
• In summary, in the right handed double helical polynucleotides, all Torsion
angle are correlated so that structural changes follow a concerned motion and
the rotations are restricted to the range -.

13. STRUCTURAL ORGANISATION OF DNA
*The three dimensional structure of DNA was elucidated by James D Watson and Francis Crick in 1953.
*They proposed the structure on the basis of chemical and X-ray diffraction data.
Some essential features of the watson-crick model of DNA are summarised below :-
•The sugar phosphate backbone of each polynucleotide stand lies on the outside of double helix. The purine and
pyrimidine bases project inward at 90° to the axis of the Helix.
•DNA consist of two long helical polynucleotide chain coiled around a common axis in a right handed manner to form a
double helix. The two chains have opposite polarity and are anti parallel in nature. One running from the 5’ to the 3’ end
and other from 3’to5' end.
• The two strands of DNA molecules are held together by hydrogen bonding between base pairs. Base pairing is always
complementary. Adenine pairs with the thymine. Guanine always pairs with cytosine.
Chargaff's rule :-
a)[A]=[T]
b)[G]=[C]
c)[A]+[G]=[T]+[C]
It also states that one stand of DNA double helix must be complementary in base sequence to the other stand.

15. •Each base pair contains one two-ringed purine and one single-ringed pyramidine the dimensions of all the
base pairs are roughly the same so double helix has a constant diameter.
• Adenine pairs with thymine by two hydrogen bonds while guanine pairs with cytosine by three hydrogen bond.
GC bond is more stable than AT Bond. More GC base pairs in DNA, greater the energy needed to separate the
two strands.
* The DNA helix has 2 external helical grooves,a deep and wide major groove between the two consecutive
turns and a narrow minor groove, between two polynucleotide strands of the helix. The two groups are not
equal in size full size.
*The watson-crick model of DNA has thus the appearance of twisted ladder or spiral staircase. Vertical bar of
the ladder are formed of sugar phosphate Chain and the horizontal rungs of the ladder are formed of purines-
pyramidine base pair linked by hydrogen bonds.

17. Types of DNA
• In the Watson-crick model of the double-helical nucleic acid, some of the assumptions-
the coplanarity of the base-pairs, and the base-stacking perpendicular to the helix Axis
are not quite true.
•In reality, the base -pair are not coplanar, but have a propeller twist;and the bases are
not perpendicular to the helix Axis but are tilted and rolled.
•In addition, the Helix Axis does not pass through the centre of the base-pair in all the
forms and the base-pairs are dislocated from the Helix axis.
•Depending on relative humidity, uniqueness of the base sequences and the solvent and
salt concentration, nucleic acids exist in several structural forms and they can be
classified under A-,
B-, C-, and Z- families, based on structural features like base orientation based-pair
dislocation etc.
•Due to subtle variations in their structural parameters helical arrangements in different
families are microscopically different and distinct.

19. A form of DNA
• A form DNA was first identified from fibre-diffraction studies of DNA at ‘low'(75%)
relative relative humidity.
• More recently, crystal studies have identified specific sequence which can adopt A-dna
of structures.
•It contain 11 base pairs as compared to 10 base pairs of B-dna, which causes tilting from
the axis of helix by 20°.
•The helix axis is pushed into the major groove and the poly nucleotide chains wrap
around the Helix axis like a ribbon.
• As a consequence, there is a very deep and the narrow major groove , but a Shallow and
wide minor groove.
• The A-family has both the interstrand and intrastand base overlap.

21. B form of DNA
• B DNA is the Watson-Crick form of the double helix that most people are familiar with.
• It was first identified in fibres at 92% relative humidity. •Several sequences crystallized to
high resolution have been found to adopt the B- DNA confirmation.
•Under normal physiological conditions DNA always takes this classic B-type duplex.
•It is present in every cell at a very high relative humidity(92%).
•The B- form represents the general structure of DNA in the condition of the living cell.
•B DNA has some major groove and the minor groove. •However, it has been known for a
long time that DNA can exist in more than one form of double helical structure and under
certain conditions, duplex DNA can make a transition from the B- form to another form.
• Probably this effects rather a negligible portion of the DNA.
• The B- family has only intra- strand bases stacking.
•In B- DNA the helix axis passes through the centre of base-pairs. Therefore, the major and
minor grooves are of equal depth, but of unequal widths.

23. C form of DNA
•C-DNA belongs to the B-family and is an intermediate between A- and B-
forms.
•C-DNA is an isoform of DNA that occur under experimental conditions.
•It is found in relatively low humidity (66%) and in the presence of lithium and
magnesium ions.
•It is right handed duplex like a B form but less compact them the B-form.
• It has a diameter of 19 A°, smaller than that of A- and B- DNA.
•Previous x-ray diffraction studies have suggested that the C- form is poorly
favoured confirmation.
•C- form should be visualised as a family of related structures and suggested
that continuous smooth transitions occurs between the various members of the
C- family between B and C forms.

25. Z form of DNA
• Z is the only left-handed duplex.
•It has the most base pairs per turn and so the least twisted structure.
• It is skinny and derives its name from the zig-zag path followed by the sugar-phosphate backbone in its helical
winding.
• Z- DNA has only a single groove the minor groove.
• Z-DNA is believed to be formed in Vivo during transcription as a means of relieving torsional strain in DNA.
• Z-DNA is comparatively less stable than the other forms.
• Z-DNA is thought to play a role in the regulation of Gene expression, Z-DNA is also thought to be involved in
DNA processing events and genetic instability.
•Z- DNA usually forms when genes are transcribed and disappears through topoisomerase activity after the Gen
is no longer transcribed.
•Every time a stretch of z- DNA forms, two B- Z junctions are formed at either ends.
• Z- DNA or the left- handed DNA was first discovered by Robert Wells, during studies of repeating Polymer of
inosine-cytosine.

27. Conclusion
• DNA is the hereditary material in humans and almost all other organisms.
• Nucleic acids are biologically important Polymers which are present in all living cells.
• The repeating unit of a nucleic acid are called nucleotides. •A nucleotide is a complex molecule made up of 1 unit of
phosphate, a pentose sugar, nitrogen containing hetrocyclic base.
•The 3D structure of DNA was elucidated by Watson and Crick in 1953.
•Structure was proposed on the basis of chemical and x-ray diffraction data.
•The DNA helix has 2 external helical grooves. The two grooves are not equal in size.
•Thus the watson-crick model of DNA has the appearance of twisted ladder or spiral staircase.
•Depending on relative humidity, uniqueness of the base sequences and the solvent and salt concentration, nucleic acids
exist in several structural forms and they can be classified under A-,B-, C-, and Z-form.
• A-form of DNA is found that is 75% relative humidity. It is contains 11 base pairs. A- and B- are right handed duplex.
• B-form of DNA is found in almost all living cells. The double helix model of DNA proposed by Watson -Crick. B-DNA has a
major groove and minor groove.
• C-form of DNA occurs under experimental conditions. Found in relatively low humidity 66%. It is right handed duplex.
•Z- form of DNA is the only left handed duplex. It is the least twisted structure. Derives its name from the zigzag pathway
followed by sugar-phosphate backbone. Z- DNA has only single groove (minor groove) and these forms of DNA are less stable
than other forms.

28. References
1. Keshav Trehan, 1987,Biochemistry(second edition), Wiley eastern limited, new Delhi.
2. K. Vijayakumaran Nair, 2021, Cell and Molecular Biology, Academic PublicationsThiruvananthapuram.
3. Dr. M. Viswanathan, 2019, Principles Of Organic And Physical Chemistry Complementary Course,Jai Sai
Publications Kollam.
4. HR. Singh, 2017, Animal Physiology And Biochemistry Vishal Publishing CO Jalandhar.
5. Christopher K Matthews, 1999, Biochemistry (3rd edition) Person education Publications.
6. Reginald H. Garrett, 2006,Biochemistry(3rd edition )Brooks/cole publications.
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8. Http://en.m.wikipedia.org
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