DNA chemistry

1. Nucleic acid chemistry
&DNA structure
Presented by
Dr/Shymaa Ahmed Maher
Lecturer of medical biochemistry and molecular biology

2. Nucleic
Acid
• Nucleic acids are required for the storage
and expression of genetic information.
• There are two chemically distinct types
of nucleic acids:
A. RNA (ribonucleic acid) is a polymer of
Ribonucleotide
B. DNA (deoxyribonucleic acid) is a
polymer of deoxyribonucleotides

3. Central dogma
of life

4. Nucleic acids structure
Nucleic acids are biopolymers, or large
biomolecules, essential for all known forms of life.
Nucleic acids, which include DNA (deoxyribonucleic
acid) and RNA (ribonucleic acid), are made from
monomers known as nucleotides.
Nucleotides are composed of a nitrogenous base, a
five-carbon sugar (ribose or deoxyribose), and at
least one phosphate group.

5. Nucleotide
s
• Monomers for nucleic acid polymers
• Each nucleotide consists of:
1. Pentose sugar
2. Nitrogenous base
3. Phosphate group

6. 1-Sugars
Pentoses (5-C sugars)
Numbering of sugars is
“primed”

7. 2-Nitrogenous Bases
• Purines • Pyrimidines

8. 3-
Phospha
te
Groups
Phosphates can be bonded to either C3 or
C5atoms of the sugar.
The second and third phosphates are each
connected to the nucleotide by a "high energy
"bond. But first phosphate is connected to the
sugar by ester bond (low energy bond)
The phosphate groups are responsible for the
negative charges associated with nucleotides ,and
cause DNA and RNA to be referred to as "nucleic
acids

9. 3-Phosphate Groups

10. Nucleosides
Result from linking one of the
sugars with a purine or Pyrimidine
base through an N-glycosidic
linkage
Purines bond at their N9 atoms to
the C1’ carbon of the sugar
Pyrimidines bond at their N1 atoms
to the C1’ carbon of the sugar

11. Nucleotides
• Result from linking one or more
phosphates with a nucleoside onto
the 5’ end of the molecule through
esterification

12. Nucleic acid structure

13. Difference
s between
DNA &
RNA
-
1 They contain different sugars
DNA contains deoxyribose
RNA contains ribose
-
2 Nitrogenous bases
 DNA contains A, G, T, & C
RNA contains A, G, U, & C
Uracil (U) replaces thymine (T) in RNA, thus A pairs
with U when DNA is used as a template to make RNA
-
3 Form
 DNA – most stable as double helix
 RNA most often exists as a single strand of nucleotides

14. DNA Vs RNA

15. Differences
between
DNA & RNA
• Size
DNA molecules are larger
RNAs are smaller
• Mobility
DNAs are basically immobile
RNAs are highly mobile
• Life span
DNAs are long-lived
RNAs are broken down soon after their
job is done

16. Deoxyribonucleic acid (DNA)
DNA is a polymer of deoxyribonucleoside
monophosphates (dNMPs) covalently linked
by 3′→5′ phosphodiester bonds.
DNA exists as a double-stranded molecule, in
which the two strands wind around each
other,
forming a double helix.
In eukaryotic cells, DNA is found associated
with proteins ( as nucleoprotein) present in
the nucleus, whereas in prokaryotes, the
protein-DNA – RNA complex is present in the
nucleoid.

17. Nucleotide

18. Structure
of DNA
A- Phosphodiester bonds = 1ry structure
of DNA
1- Phosphodiester bonds join the 5'-hydroxyl group of
the phosphate of one nucleotide to the 3'-hydroxyl
group of the deoxypentose of an adjacent nucleotide .
2- Polarity of DNA: with both a 5'-end (the end with
the free phosphate) and a 3'-end (the end with the free
hydroxyl) that are not attached to other nucleotides.
3- The bases located along the resulting
deoxyribosephosphate backbone are, written in
sequence from the 5'-end of the chain to the 3'-end.
For example " (5'-TACG-3').

20. Structure
of DNA
B- The Double Helix Structure of DNA =
2ry structure of DNA (B-form= Watson
& Crick 1953)
1-The double helix, the two chains are coiled
around a common axis called the axis of
symmetry.
-
2 The chains are paired in an antiparallel
manner, that is, the 5'-end of one strand is
paired with the 3'-end of the other strand.
-
3 In the DNA helix, the hydrophilic
deoxyribosephosphate backbone of each chain
is on the outside of the molecule, whereas the
hydrophobic bases are stacked inside.

21. Structure
of DNA
 The spatial relationship between the two strands
in the helix creates a major (wide) groove and a
minor(narrow) groove.
 These grooves provide access for the binding of
regulatory proteins to their specific recognition
sequences along the DNA chain.
 Factors stabilize the structure of the double
helix:
A-Hydrogen bonds between bases.
B- The hydrophobic interactions between the
stacked bases

23. Structure
of
DNA(The
Double
Helix DNA)
 Chargaff's Rule(base pairing):
 DNA has equal numbers of adenine and
thymine residues (A=T) and equal
numbers of cytosine and guanine residues
(G=C)
 the total amount of purines equals the total amount of pyrimidines.
The base pairs are held together by
hydrogen bonds: two between A and T
(A=T) and three between G and C (G = C).
Each base will only bond with one other specific base.
 Adenine (A)& Thymine (T)
 Cytosine (C)&Guanine (G)
Because of this complementary base pairing, the order of the bases in one strand
determines the order of the bases in the other strand.

24. Structure of DNA(The Double Helix DNA)
Denaturation &renaturation &melting
temperature (effect of PH
&TEMPERATURE).
Structural forms of the double helix
:There are three major structural forms
of DNA: the B form (described by
Watson and Crick in 1953), the A form,
and the Z form.

25. DNA
Organizatio
n:
• DNA in a single human cell, if stretched to
its full length is about two meters.
• Eukaryotic DNA is associated with tightly
bound basic proteins, called histones to
form nucleosomes which appear as beads
on strings, which then further organized
to form chromosomes.

26. Nucleosomes
• There are 5 classes of histones,
designated H1, H2A, H2B, H3,
andH4.
• These small proteins are positively
charged at physiologic pH as a
result of their high content of
lysine and arginine.

27. Nucleosome
s
1-Two molecules each of H2A, H2B, H3, and H4 form
the structural core of the individual nucleosome
“beads.” = octamer = 8
2-Around this core, a segment of the DNA double helix
is wound nearly twice, forming a negatively charged
super-twisted helix .
3-Neighboring nucleosomes are joined by “linker” DNA
approximately 50 base pairs long.
4-Histone H1 is not found in the nucleosome core, but
instead binds to the linker DNA chain between the
nucleosome beads

28. Higher
levels of
organizatio
n
1-Nucleosomes can be packed more tightly to
form a polynucleosome (6-7 Nucleosomes per
turn) to form 30nm fiber also called
nucleofilament (SOLENOID).
2-The fiber is organized into loops that are
anchored by a nuclear scaffold containing several
proteins(LOOPED DOMAIN)
3-Choromatid
4- Additional levels of organization lead to the
final chromosomal structure

33. Messenger RNA (mRNA )
• mRNA comprises only about 5% of the RNA in
the cell yet is by far the most heterogeneous
type of RNA in size and base sequence.
• Carries codon specifying amino acid sequence in
protein.
• Act as a templet for protein synthesis .

37. Ribosomal
RNA
• rRNAs are found in association with
several proteins as components of the
ribosomes the sites for protein
synthesis.
• In prokaryotic cells there are three
distinct size species of rRNA (23S, 16S,
and 5S).
• In the eukaryotic cytosol, there are four
rRNA species (28S, 18S, 5.8S, and 5S.
• “S” is the Svedberg unit for
sedimentation rate, which is
determined by the size and shape of
the particle.)
• rRNAs make up about 80% of the total
RNA in the cell.

39. THANK YOU