Nucleic Acids

The genetic materials

 Eukaryotic cells Prokaryotic cells
with a nucleus without a nucleus

• Nucleus • Cytoplasm
• Mitochondria • Ribosomes
• Chloroplast • Nuclear Zone
• Ribosomes • DNA
• RER • Plasmid
• SER • Cell Membrane
• Golgi body • Mesosome
• Cytoplasm • Cell Wall
• Vacuoles • Capsule (or slime layer)
• Flagellum
 Macromolecules
Protein

Nucleic acids

Olygosaccharides

Lipids

Complex macromolecules
 DNA
• DNA is often called
the blueprint of life.
• In simple terms,
DNA contains the
instructions for
making proteins
within the cell.
DNA is the genetic material
• Composed of 4 nucleotide
bases, 5 carbon sugar and
phosphate.

• Base pair = rungs of a

ladder.

• Edges = sugar-phosphate
backbone.

• Double Helix

• Anti-Parallel
 Basics: the primary structure

3’ end
5’ end
pApGpCpT

A G C T

P 3’ end
P P P
5’ end OH
5’
 A, G, C or T A, G, C or U
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

O Base O Base
O P O CH2 O P O CH2
5′ O 5′ O
O
– 4′ 1′ O– 4′ 1′
H H H H
H H H H
Phosphate 3′ 2′
Phosphate 3′ 2′
OH H OH OH
Deoxyribose Ribose

(a) Repeating unit of (b) Repeating unit of

deoxyribonucleic ribonucleic acid (RNA)
acid (DNA)

The structure of nucleotides found in (a) DNA and (b) RNA

 Base + sugar  nucleoside
 Example
 Adenine + ribose = Adenosine

 Adenine + deoxyribose = Deoxyadenosine

 Base + sugar + phosphate(s)  nucleotide

 Example
 Adenosine monophosphate (AMP)

 Adenosine diphosphate (ADP)

 Adenosine triphosphate (ATP)

 Nucleotides are covalently linked together by
phosphodiester bonds
 A phosphate connects the 5’ carbon of one nucleotide to
the 3’ carbon of another
 Therefore the strand has directionality
 5’ to 3’
 In a strand, all sugar molecules are oriented in the same
direction

 The phosphates and sugar molecules form the

backbone of the nucleic acid strand
 The bases project from the backbone
The de-oxynucleotide triphosphate and the
phospho diester bond
 Two Kinds of Bases in DNA

N
• Pyrimidines are N C

single ring bases.. O C C

N C

• Purines are double N

ring bases. N C
C C
N
N C
N C
 N
O
N N C
C

O C C
O C C
C
N C
N C
thymine cytosine

N O

N C N C

C C N C C
N N

N C N C
C
Adenine N C Guanine N
 The ladder of two strands

• DNA has two

strands that fit
together
something like a
zipper.
• The teeth are the
nitrogenous bases
but why do they
stick together?

14
 N
guanine
• The bases attract each
other because of hydrogen

C
N
bonds.

N
• Hydrogen bonds are weak

C
but there are many of them

C
O

N
in a single molecule of DNA.

N
• The bonds between

C
N
cytosine and guanine are C N
shown here with dotted
lines C C O
cytosine
C N
 O
• When making N C
hydrogen bonds,
O C C C
cytosine always N
pairs up with N C
C
guanine N
C N
C
• Adenine is bonded N
C C
N
to thymine here
 Chargraff’s Rule:
• Adenine and Thymine always
join together
• A T
• Cytosine and Guanine always
join together
• C G
The DNA structure
 2 nm

5 P 3

S P
P
A S
P S 5 end 3 end
S G C P CH 3 H H HO
P
S H N
NH 2 T N H H H
S G C P O - N
O -
H O
O P O CH2 N A
P S
N H O CH 2 O P O
O
O - N O
C P S H H
S H H H

P S H
P N
H NH2 O H H
S P
S O
A T S H C N H N G N
H H H
P O P O CH 2 N N O -
O
S O - O H2N H O
CH 2 O P O
C G H H
S P H H O
P T A S H
H CH 3
S P
G C P N T H2N N H H
S O
N
P S O P O CH 2 O H N A N
H H H
P O-
O
N
O -
O
P H
H H
H H
H
CH 2 O P O
P S
One complete G S H O
P S
turn 3.4 nm C G
S P H N H2N H
P T A
O
S O P O CH 2 N G N H N C H
H
S G C P O
O- N N H H H
P S One nucleotide H
H H
H
NH 2 O O -
O
A T H
CH2 O P O
S P S 0.34 nm OH H
O -
P S
PS
P 3 end 5 end
S C G
S P
C G S
S 5
P
3
 Types of DNA structures

1. 3 types: A, B, and Z

2. Not in equilibrium
3. Transition depends on humidity, temperature
and DNA binding proteins
The B-DNA

Major

Minor
B-DNA (Watson-Crick)
1. Two Antiparallel polynucleotide strands
2. Sugar phosphates on periphery

3. Helix approximately 20 Angstroms in diameter

4. 10.5 base pairs per turn, ~36 degrees per base pa
5. Bases flat, perpendicular to axis
6. Major and minor grooves readily apparent
A-DNA: Right handed helix, 11 base-pairs per turn. The helix
diameter is 26 angstroms instead of 20. The major groove is
narrow.
Z-DNA: Left handed helix, 18 Angstroms diameter
 3 meter DNA/cell
1013 cells/human
3 x 1013 meters of DNA/human
3.8 x 108 meters from Earth to moon
How is the DNA packaged?
DNA can be denatured
 Melting Point of DNA
Lower G + C

Higher G + C
A260

Temperature oC
50 70 90

Hyperchromicity Tm (melting temperature)

 Thermodynamics of DNA

Melting temperature: Primer Melting Temperature (Tm) by definition

is the temperature at which one half of the DNA duplex will
dissociate to become single stranded and indicates the duplex
stability. Primers with melting temperatures in the range of 52-58 o
C generally produce the best results.

For DNA of length upto 15 bases, the melting temperature can be

calculated by the formula:
Tm = 2*(nA+nT) + 4*(nG+nC)

This formula holds only for primers upto 15 bases length because it
doesnot take into account for the thermodymamic considerations for
the neighboring base pairs.
Coiling and supercoiling of DNA
Linking Number: Understanding Supercoiling
Understanding DNA supercoiling
Twist and Writhe
Visualizing DNA supercoils
 Rosalind Franklin’s X-Ray Photo Showing Regular
Repeating Patterns in DNA Structure

Cross Pattern
indicates Helix

Helical rise
3.4 nm

Layer line spacing

1/10 from center
to spot
(10 base pairs per repeat)

Wet DNA Fibers

 Deductions from X-Ray and Other Data

• Cross pattern indicates helix

• Density data indicates two DNA strands
• Two stand helix stabilized by H-bonding
if bases were paired in a particular way:
– A-T and G-C, i.e., purine to pyrimidine to
allow regular diameter (not possible with
purine to purine or pyrimidine to pyrimidine)
• For self- complementary oligonucleotide duplexes, the TM is
calculated from the predicted H° and S° and the total
oligonucleotide strand concentration CT, by using the equation:

Where the H° and S° are calculated as sum of H° and S°
predicted for the NN dimers eg. AC/TG

G0 = G0(CG/GC) + G0(GT/CA) + G0(TT/AA) + G0(TG/AC) +

G0(GA/CT)

The G0 values for each NN pair are calculated theoretically and are