STRUCTURE OF DNA

1. primary structure2. secondary structure

3. tertiary structure

PRIMARY STRUCTURE OF DNA

James Watson Francis Crick

1962 Nobel Prize

http://www.sciencemag.org/cgi/content/full/300/5617/255http://www.lecb.ncifcrf.gov/~toms/icons/Watson.Crick.Nature.jpg

Polynucletide chain of DNA(primary/covalent structure)

N

NH

N

N

NH2

O G uan ine

OCH2OH

O

OCH2

O

PO

O

O

PO O

O

N

N

NH2

O

C ytos ine

OCH2

OH

PO

O

O

NH

NH

O

O

CH3

Thym ine

3' end

5' end

• The polynucleotide chain of DNA consist of nucleotides joined together by 3’,5’ phosphodiester bonds.

• Phosphodiester bonds link the 3’- and 5’-sugar carbons of adiacent monomer.

• Polynucleotides are directional macromolecules: each end of a polymer is distinct.

• 3’ –end is one with a free 3’-hydroxyl.

• 5’ –end is one with a free or phosphorilated 5’-hydroxyl.

• Polynucleotides bear a negative charge at physiological pH

3’linkage

5’linkage

1’

N

NH

N

N

NH2

O G uan ine

OCH2OH

O

OCH2

O

PO

O

O

PO O

O

N

N

NH2

O

C ytos ine

OCH2

OH

PO

O

O

NH

NH

O

O

CH3

Thym ine

3' end

5' end

P

P

P

G

C

T

OH

OH

Simplified representation of DNA chain

5’

5’

5’

3’3’

3’

Sugar: horisontal line

Base: single letter

Phosphodiester bond:

oblique line with P

N

NH

N

N

NH2

O G uan ine

OCH2OH

O

OCH2

O

PO

O

O

PO O

O

N

N

NH2

O

C ytos ine

OCH2

OH

PO

O

O

NH

NH

O

O

CH3

Thym ine

3' end

5' end

Simplified representation of DNA chain

Convention dictates that a single-stranded DNA sequence is written in the 5’ to 3’ direction.

e.g. GCT means 5’GCT 3’

Quick Quiz

Question :

• Identify which is the 3’end of this oligonucleotide?

• Write the simplified representation of this oligonucleotide.

SECONDARY STRUCTURE OF DNA

Double helix of DNA

• Watson and Crick discovered the secondary structure of DNA: a double helix – two sugar phosphate chains wrapping round each other, with the phosphate groups sticking out – the nucleotide from strand 1 meets the nucleotide from strand 2 in the middle. These pairs of nucleotides are complementary – where one strand has a C, the other has a G and vice versa; where one strand has an A the other has a T and vice versa.

• Human DNA consists of approximately 3 x 109 such “base pairs”.

1. DNA is double stranded: each molecule of DNA is composed of two polynucleotide chain that are joined together by formation of hydrogen bonds between the bases.

2. DNA strands are twisted to form a double helix.

3. DNA strands are antiparallel (one strand runs in the 5’ to 3’ direction and the other in the 3’ to 5’ direction, analogous to two street lanes carrying traffic in opposite direction).

The DNA double helix(secondary structure)

3. G-C pairs have 3 hydrogen bonds

A-T pairs have 2 hydrogen bonds

4. One strand is the complement of the other, as they are formed by complementary bases (G is complementary to C, while A is complementary to T).

5. The concentration of deoxyadenosine (A) nucleotides equals that of thymidine (T) nucleotides (A=T), while the concentration of deoxyguanosine (G) nucleotides equals that of deoxycytidine (C) nucleotides (G=C)

The DNA double helix(secondary structure)

Quick Quiz Question

1. Write the complementary strand of the following DNA strand: ATTTTAAGCTAAGGCCCTTT

2. Calculate the number of the hydrogen bonds existing beteen the complementary strands

3. Specify which base is at the 3’end of this strand and which base is at the 3’ end of its complementary strand.

6. The B form of DNA described by Watson and Crick is right handed.

7. The distance spanned by one complete turn of the B-DNA double helix is 34 Å.

8. One turn of B-DNA includes 10 base pairs.

9. Oter forms of DNA include:- A-DNA which is more compact than B-DNA- Z-DNA is left handed and its bases are positioned more toward the periphery of the helix.

The DNA double helix(secondary structure)

Quick Quiz Question

• DNA1. Is composed of nucleosides joined by

phosphodiester bonds2. Contains negatively charged phosphate groups3. Contains base pairs A/T and G/C4. Consists of two strands which run in the same

direction.

What are the hydrogen bonds inside the DNA double helix?

• Hydrogen bonds represent non-covalent (relatively weak) intermolecular bonds which are caused by the polarity of H-O bond.

“TERTIARY” STRUCTURE OF DNA:

the polynucleosome

From DNA to Chromosomes

• In eukaryotes, the DNA is stored in the nucleus. Since there is not much space and DNA molecules are extremely large (the length of DNA from one singlehuman cell is 2m!!!), the DNA must be highly organised.

• There are five levels of DNA compaction (or packing) that result in a 10.000 –fold decrease in DNA length.

Levels of packing of DNA in the nucleus

-the first level-

r • The DNA double helix is wrapped around protein complexes called histones- each unit of DNA wrapped round a histone complex is called a nucleosome.

• Histones are small proteins, rich in basic aminoacids (Arg, Lys).

Levels of packing of DNA in the nucleus

- the first level-

r • Nucleosome contains an octameric core formed by two molecules of each histones H2A, H2B, H3, H4, around which 140 base pairs of DNA are wrapped.

• The nucleosomes are separated by a small distance (DNA linker formed by 30 base paires). H1 histones interact with DNA linker.

• The polynuceosome structure of DNA are similar to the “beads on a string” (=10nm fibrils of chromatin).

Amethyst Beads on a String

r

“Beads on a string” appearance of DNA

Levels of packing of DNA in the nucleus-the second level-

• The polynucleosome chain is further compacted to form solenoid structures.

• Solenoid structure has 6-7 nucleosomes pe turn.

• Solenoid structure form the 30 nm fiber of chromatin.

r

Levels of packing of DNA in the nucleus

-the third, fourth and fifth levels-

r- The chromatin fibres fold together to form large looped domains.

- These looped domains are then supercoiled and organised into distinct structures called chromosomes.

- The human nuclear DNA ( genome) consists of 23 pairs of chromosomes.

The difference between diploid and haploid cells

• Many eukaryotic cells contain pairs of chromosomes and are hence called diploid.

• Other cells contain single chromosomes and are called haploid.

The chromosomes of the human genome

1

DNA stands for deoxyribose nucleic acid

This chemical substance is present in the nucleusof all cells in all living organisms

DNA controls all the chemical changes which take place in cells

The kind of cell which is formed, (muscle, blood,nerve etc) is controlled by DNA

The kind of organism which is produced (buttercup,giraffe, herring, human etc) is controlled by DNA

DNA 2

DNA is a very large molecule made up of a long chain of sub-units

The sub-units are called nucleotides

Each nucleotide is made up of

a sugar called deoxyribose

a phosphate group -PO4 and

an organic base

DNA molecule 3

Ribose is a sugar, like glucose, but with only fivecarbon atoms in its molecule

Deoxyribose is almost the same but lacks one oxygen atom

Both molecules may be represented by the symbol

Ribose & deoxyribose 4

The most common organic bases are

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

The bases 5

The deoxyribose, the phosphate and one of the bases

adenine

deoxyribose

PO4

Combine to form a nucleotide

Nucleotides 6

A molecule of DNA is formed by millions of nucleotides joined together in a long chain

PO4

PO4

PO4

PO4

sugar-phosphate backbone

+ bases

Joined nucleotides 7

In fact, the DNA usually consists of a double strand of nucleotides

The sugar-phosphate chains are on the outsideand the strands are held together by chemical bonds between the bases

8

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

2-stranded DNA 9

The bases always pair up in the same way

Adenine forms a bond with Thymine

and Cytosine bonds with Guanine

Bonding 1 10

Adenine Thymine

Cytosine Guanine

PO4

PO4

PO4

thymine

PO4

PO4

PO4

PO4

adenine

cytosine

PO4

guanine

Bonding 2 11

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

Pairing up 12

The paired strands are coiled into a spiral called

A DOUBLE HELIX

13

sugar-phosphatechain

bases

THE DOUBLE HELIX

14

A DIY model ofpart of a DNA molecule

15

During a cell divides, the DNA strands unwind and separate

Each strand makes a new partner by addingthe appropriate nucleotides

The result is that there are now two double-stranded DNA molecules in the nucleus

So that when the cell divides, each nucleus contains identical DNA

This process is called replication

replication 16

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

The strands separate

17

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

Each strand builds up its partner by adding the appropriate nucleotides

18

The sequence of bases in DNA forms the Genetic Code

A group of three bases (a triplet) controlsthe production of a particular amino acid in the cytoplasm of the cell

The different amino acids and the order in which they are joined up determines the sort of protein being produced

Genetic code 1 19

Ser-Cyst-Val-Gly-Ser-Cyst Ala Val Val-Cyst-Ser-Ala-Ser-Cyst-Gly

Val- Cyst-Ala-Ala-Ser-Gly

This is a small, imaginary protein molecule showing how a sequence of 5 different amino acids could determine the shape and identity of the molecule

Each amino acid (Serine, Cysteine, Valine, Glycine and Alanine) is coded for by a particular triplet of bases

Genetic code 2 20

For example

Cytosine

Adenine Codes for Valine

Cytosine (C)

Guanine (G)

Adenine (A)

Codes for Alanine

Thymine

Coding 21

This is known as the triplet code

Each triplet codes for a specific amino acid

CGA - CAA - CCA - CCA - GCT - GGG - GAG - CCA -

Ala Val Gly Gly Arg Pro Leu Gly

Ala Val Gly Gly Arg Pro Leu Gly

The amino acids are joined together in the correct sequence to make part of a protein

Triplet code 22

The proteins build the cell structures

They also make enzymes

The DNA controls which enzymes are made andthe enzymes determine what reactions take place

The structures and reactions in the cell determinewhat sort of a cell it is and what its function is

So DNA exerts its control through the enzymes

DNA and enzymes 23

A sequence of triplets in the DNA molecule may code for a complete protein

Such a sequence forms a gene

There may be a thousand or more bases in one gene

Genes 24

Question 1

Which of the following are components of nucleotides?

(a) deoxyribose

(b) amino acids

(c) phosphate

(d) enzymes

(e) organic bases

Question 2

Which of the following represent a correct pairing of bases?

(a) adenine with thymine

(b) adenine with guanine

(c) thymine with adenine

(d) guanine with cytosine

(e) thymine with thymine

Question 3

DNA molecules are formed from

(a) organic bases

(b) amino acids

(c) deoxyribose

(d) nucleotides

Question 4

Which of the following are organic bases?

(a) Valine

(b) Guanine

(c) Thymine

(d) Serine

Question 5

Replication of DNA occurs

(a) During cell division

(b) before cell division

(c) at any time

Question 6

A nucleotide triplet codes for

(a) a protein

(b) an amino acid

(c) an enzyme

(d) an organic base

Answer

CORRECT

Answer

INCORRECT

PerbedaanPerbedaan DNA RNA

Letak Sebagian besar di nukleus, sedikit di mitochondria dan kloroplast

Dalam sitoplasma, nucleolus dan kromosom

Pyrimidine bases CytosineThymine

CytosineUrasil

Purine bases AdenineGuanine

AdenineGuanine

Pentose deoxyribose ribose

Hydrolizing enzyme Deoxyribonuclease (DNase)

Ribonuclease (RNase)

Peranan Genetic information Synthesis of proteins