Chemistry of nucleic acid

& DNA structure

Chromosome & DNA

Basic of cell structures:

• Nucleus
• Cell Membrane
• Cytoplasm with organelles
Genetic code in
DNA
Cell > Chromosome > Gene
 Chemistry of nucleic acid
• DNA is made up of nucleic acids found in the nuclei of living cells
- act as vehicles of genetic inheritance.
• Nucleotides: molecules that form the building blocks of nucleic acid.
• TWO nucleotides that bound to each other called dinucleotide

• TWO or many polynucleotide chains will form DNA

A nucleotide

Polynucleotide
 Nucleotide structure
➢ 3 types of chemicals make up the building blocks
for individual nucleotide :
i) phosphate
ii) nitrogen base
iii) 5-carbon sugar called
deoxyribose
 Base→Nucleosides→Nucleotides
Nucleoside = N containing base (purine or
pyrimidine) linked to a pentose sugar

Nucleotide = a nucleoside and one or more

phosphate groups.

Thus, nucleosides can be phosphorylated (by

specific kinases present in the cell), on the sugar's primary
alcohol group (-CH2-OH) to produce
nucleotides.
Nucleotide
NUCLEOTIDE STRUCTURE

NUCLEOTIDE
Phosphodiester bond
Hydrogen bonds
 How the nucleotides bound to each other ?

• Ribose sugar is a pentose (5-carbon atom)

• Deoxyribose : almost the same but lacks 1 oxygen atom P

C P
5 O
C P
C
4 1
P
C C
3 2
P

• Sugar --- phosphate bind together: called the P

sugar-phosphate backbone C3
- linked by 3’,5’-phosphodiester bond/bridge
- The phosphate group joins the 3rd Carbon of one C5
sugar to the 5th Carbon of the next in line.
 Phosphodiester bond
➢ Individual nucleotides are linked
together/connected to each other by the formation
of phosphate-ester bonds to form a long chain

➢ Phosphodiester bond:
• Strong covalent bond
• formed between the phosphate group of one
nucleotide and the 3’ –OH of the next nucleotide
 Nitrogen bases bind with
sugar-phosphate backbone
• The nitrogen-bases are attached to the 1st carbon P
G
• The order of BASES in a nucleotide contain
information necessary to produce the correct amino
P
acid sequence in cell’s protein C

P
C

P
A

P
T

P
T
2 types of nitrogenous-bases (also called nucleobases)

i) Pyrimidine bases :
• Contains: 1 carbon-nitrogen ring
and 2 nitrogen, which are
- cytosine (C)
- thymine (T)
ii) Purine bases :
• Contains: 2 carbon-nitrogen ring
and 4 nitrogen, which are:
-adenine (A)
- guanine (T)
 Structure of DNA
✓ DNA is made of TWO strands of Hydrogen bonds
polynucleotides P
G C
P
✓ It is composed of sugar-phosphate
P
backbone and attached nitrogen bases C G
P
✓ connected to complementary strand by P
hydrogen bond C G
P
✓ Hydrogen bond P
A T
• non-covalent, weak: can easily break and
P
form again
• determine the alignment & stabilize the P
T A
double helix structure
P
P
T A
P
 Exploring the Nucleotide

DNA chain..
1. The sugar in the backbone

2. Attaching the phosphate group

by phosphodiester bond

3. Attaching the bases and form

nucleotide

4. Joining the nucleotides

into a DNA chain by hydrogen bond

5. Joining the 2 DNA chains

>> form DNA double helix
➢ DNA : deoxyribonucleic acid
➢ Carry genetic information or genetic material >> code for protein
➢ Self-duplication & inheritance
➢ Chromosomal DNA consist very long DNA molecules
(~1 metre long)
➢ Where is DNA can be found ?
-present in every nucleated cells, mostly are located in the nucleus
▪blood
▪skin cells
▪hair, bones
▪teeth
▪saliva
 Levels of structure in DNA

DNA structure is also described in terms of :

• Primary structure : refers to polynucleotide sequence
• Secondary structure : refers to hydrogen bonding between A-T and
G-C base pairs
• Tertiary structure : twisting/supercoiling of DNA molecule
 Secondary structure of DNA: The double helix
➢ Many polynucleotides will form DNA

➢ The sugar-phosphate backbone is the

outerpart of the helix.
The strands run in ANTIPARALLEL direction,
(opposite direction) which; one 3’to 5’ and
one 5’to 3’.
➢ The two strands of DNA linked by
hydrogen bonds that occur between
complementary nucleotide base
pairs.
i) Adenine pairs with Thymine
(2 H bonds)
ii) Cytosine pairs with Guanine
(3 H bonds)
 PO4
PO4
adenine thymine

PO4
PO4
cytosine guanine

PO4
PO4

PO4
polynucleotides polynucleotides

2 polynucleotides will form DNA strand

 Tertiary structure of DNA
• The paired strands are coiled into a spiral
called the double helix

• Double helix structural of DNA : found by

Dawson & Crick in 1953

• It is important to compact the DNA structure

>> because DNA length is very long

• the length of nucleotides can be thousands of

times that of a cell; supercoiling of DNA
reduces the space and allows for much more
DNA to be packaged

➢ The double helix:

TWISTING and COILING
❑ individual nucleotide structure ?
❑ sugar-phosphate backbone ?
❑ phosphodiester bond ?
❑ hydrogen bond ?
❑ bases complimentary ?
❑base pairing rules
❑ double helix structure ?
❑ What stabilizes DNA structure?
❑ backbone ?
❑ bonding (H and phosphodiester)
❑ How the formation of phosphodiester
bond?
❑ nucleoside ?
❑ end product of purine catabolism
DNA & RNA
 There are 3 types of RNA
- tRNA
- mRNA
- rRNA
They differ in their structure and
functions
 RNA STRUCTURE
• The basic components of RNA are the same
than for DNA with two major differences.
• The pyrimidyne base uracil replace thymine
and ribose replace deoxyribose
• Adenine and Uracil for a base pair formed by
two hydrogen bonds.
Structure of t-RNA