Lecture 3 - DNA Structure PDF

MOLECULAR BIOLOGY
For Second Year
PART 1 MOLECULAR BIOLOGY
The double-helical structure of DNA
provides an explanation for the
transmission of genetic information
from generation to generation over
billions of years.
DNA Structure
Lecture Contents
3.1 Nucleic Acid Chemistry
Nucleoside and Nucleotide Chemistry
3.2 The Watson–Crick Model
Double-Helical form of DNA
3.3 Alternative Forms of DNA Exist

Right and Left-handed Helices
3.4 Summary
3.5 Study Questions
3.1 Nucleic Acid Chemistry
DNA is a nucleic acid, and nucleotides are the building blocks of all nucleic
acid molecules.
Nucleotide Structure:
1. nitrogenous base
2. pentose sugar (a five carbon sugar), and
3. phosphate group.
There are two kinds of nitrogenous bases:
purines double ring
pyrimidines Single ring
purines Of two type.... adenine “A” and guanine “G”
Whereas
Pyrimidine ...... thymine “T” , cytosine “C” and uracil “U”
Purines in DNA and RNA are “A” and “G”

But
Pyrimidines of DNA are “T” and “C”
Whereas
Pyrimidines of RNA are “C” and “U”
RNA ( A G U C ) , DNA ( A G T C )
Sugar of DNA Sugar of RNA
So the question here, what’s the difference between these two sugar ?
The answer is, looks back again to the chemical structures above !
3.1.1Nucleoside and Nucleotide

3.1.2 Linkage and Phosphodiester bond
Nucleotides bonded to one another by 3′–5′ phosphodiester bonds.
Note
phosphodiester bond link two nucleotides in the same strand
3.1.3 Nitrogenous Base-Composition
On the basis of Chargaff data, the following conclusions may be drawn:
1. The amount of adenine residues is proportional to the amount of thymine

residues in DNA. Also, the amount of guanine residues is proportional to the
amount of cytosine residues.
ex. 5′-GTTCCTAATTATCCG-3′
3′-CAAGGATTAATAGGC-5′
In the example above, we see numbers of adenine is “9” which equals(proportional
) the numbers of thymine.
*Try to check the proportional of guanine and cytosine in the same example!
2. Based on this proportionality, the sum of the purines (A + G) equals the sum of
the pyrimidines (C + T).
*Let’s prove that (A + G) =(C + T) in the example above:
No. Of adenine = no. Of thymine = 9
No. Of guanine = no. Of cytosine =6
So (A+G) (9+6)=15
And (C+T) (6+9)=15
(A + G) = (C + T)
3. The percentage of (G + C) does not necessarily equal the percentage of (A + T).
Instead, this ratio varies greatly between different organisms.
Homework: prove that (G + C) = (A + T) in the example above.
3.2 The Watson–Crick Model
This model has the following major features:

1. Two long polynucleotide chains are coiled around a central axis, forming a
right-handed double helix.
2. The two chains are antiparallel.
3. The nitrogenous bases of opposite chains are paired as the result of hydrogen
bonds; A=T and G≡C pairs
4. In any segment of the molecule, alternating larger major grooves and smaller
minor grooves.
5. The double helix measures 20 Å
(2.0 nm) in diameter.
6. Each complete turn of the helix is
34 Å (3.4 nm) long; thus, 10 bases
exist per turn in each chain.
3.3 Alternative Forms of DNA Exist
A-DNA B-DNA Z-DNA

Right-handed Helix Right-handed Helix Left-handed Helix
(75%) relative humidity 92% relative humidity
11 bp per turn 10 bp per turn 12 bp per turn
Regular shape regular shape Irregular and zigzag shape
Short and wide long and narrow narrower than the A-and B
3.4 Summary
A nucleotide is a DNA building block. It consists of a deoxyribose, a phosphate,

and a nitrogenous base. The rungs of the DNA double helix consist of hydrogen-
bonded complementary base pairs (A with T, and C with G). The rails are chains
of alternating sugars and phosphates that run antiparallel to each other. DNA is
highly coiled. DNA can be A, B or Z helices.
3.5 Study Questions
1. What are the structural differences between (a) purines and pyrimidines, and
(b) ribose and deoxyribose sugars?
2. Describe the various characteristics of the Watson–Crick double helix model for
DNA.
3. If the GC content of a DNA molecule is 60%, what are the molar percentages of
the four bases (G, C, T, A)?

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MOLECULAR BIOLOGY

For Second Year

PART 1 MOLECULAR BIOLOGY

The double-helical structure of DNA

provides an explanation for the

transmission of genetic information

from generation to generation over

3.1 Nucleic Acid Chemistry

Nucleoside and Nucleotide Chemistry

3.2 The Watson–Crick Model

Double-Helical form of DNA

3.3 Alternative Forms of DNA Exist

3.1 Nucleic Acid Chemistry

There are two kinds of nitrogenous bases:

purines double ring

pyrimidines Single ring

purines Of two type.... adenine “A” and guanine “G”

Purines in DNA and RNA are “A” and “G”

Sugar of DNA Sugar of RNA

3.1.1Nucleoside and Nucleotide

Nucleotides bonded to one another by 3′–5′ phosphodiester bonds.

3.1.3 Nitrogenous Base-Composition

On the basis of Chargaff data, the following conclusions may be drawn:

1. The amount of adenine residues is proportional to the amount of thymine

3.2 The Watson–Crick Model

This model has the following major features:

A-DNA B-DNA Z-DNA

(75%) relative humidity 92% relative humidity

11 bp per turn 10 bp per turn 12 bp per turn

Regular shape regular shape Irregular and zigzag shape

A nucleotide is a DNA building block. It consists of a deoxyribose, a phosphate,

3.5 Study Questions

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