Concept of DNA

Dr. rer. nat. Anto Budiharjo, S.Si., M.Biotech\

Why study nucleic acids?

DNA is the focus of attention because of its role in carrying and expressing genetic information. The Human Genome Project where over 90% (99.9% accuracy) of the 3.2 billion nucleotides have been cloned and sequenced.

The information is hoped, will revolutionize the detection, prevention and treatment of conditions from cancer to depression to old age itself.

Important Scientists that determined DNAs Importance

Frederick Griffith : bacterial transformation Oswald Avery : DNA key to transformation Alfred Hershey & Martha Chase : Bacteriophage transformation experiment Erwin Chargaff : base-pairing rules

Important Scientists in the Race for the Double Helix

Maurice Wilkins & Rosalind Franklin
X-ray diffraction DNA must be a some type of spiral (helix) DNAs diameter is constant and stable

James Watson & Francis Crick

Created the first accurate model of DNA Won the Nobel Prize

The structure of nucleic acids

The chemistry of DNA has been studied since 1868 and by 1900 the basic chemistry of nucleic acids was worked out. By 1920, two forms of nucleic acids were differentiated: DNA & RNA

DNA & RNA

Both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are high-molecularweight polymeric compounds. The chain-like macromolecule is made up of strings of monomeric units called nucleotides.

Nucleotide

Nucleocide

Each nucleotide is composed of three components: MONOMERIC COMPONENTS

1. Pentose and Deoxypentose sugar: a cyclic 5 carbon sugar These sugars in polynucleotides occur in Either D-ribose in RNA or 2'-deoxyribose in DNA Ribose C2 = OH Deoxyribose C2 = H

Deoxyribose C2 = H

Ribose C2 = OH

2. The Nitrogenous bases, which is either Pyrimidine or a Purine derivative. The bases are planar, aromatic, heterocyclic molecules.

3. Phosphate group

A molecule of Phosphoric acid, PO43Nucleosides

When a purine or a pyrimidine base is linked to ribose or deoxyribose the resulting compound is known as a nucleoside.

The nucleosides from ribose = ribonucleosides

The nucleosides from deoxyribonucleosides 2-deoxyribose =

The Primary Structure of Nucleic Acids

In a nucleotide, a base is attached to a pentose sugar by N-glycosidic bonds to carbon # 1 of the sugar and a nitrogen atom of the base.

Sugar is attached at position N-1 of the pyrimidine base. Sugar is attached at position N-9 of the purine base.

The Primary Structure of Nucleic Acids

The phosphate is attached to the 5' carbon of the sugar by phosphodiester linkages. The phosphate is responsible for the strong negative charge of nucleic acids. Nucleic acids are polyanions.

Chemically, nucleic acids are composed of covalently linked chains of nucleotides.

Primary Structure of Nucleic Acids

Nucleotides are bound together to form nucleic acids.
The sequence of bases is like an instruction manual that can be read by the cell.

Genetic Diversity
Different arrangements of NUCLEOTIDES in a nucleic acid (DNA) provides the key to DIVERSITY among living organisms.

Secondary Structure of Nucleic Acids

DNA: The Double Helix
The vertical blue strand represents the sugar and phosphate group and the inner horizontal bands represent the nitrogenous bases

Secondary Structure of Nucleic Acids

DNA: The Double Helix
Complementary base pairs Helical

Secondary Structure of Nucleic Acids

RNA: Single stranded, but loopy in structure

DNA base composition

In 1952, Chargaff described fundamental features of DNA: The sum of purines is equal to the sum of pyrimidines. The sum of the amino bases is equal to the sum of keto bases.

This equivalence of A and T, and G and C are importance in relation to the formation of the DNA double helix.

 DNA isolated from different species reveals wide variations in the molar proportions of bases.

This is independent of the age of the organism, its nutritional state or any environmental factor. The ratio, A+T/G+C, called the base ratio may vary widely between species, and remains constant for any one species. These relationships are referred to as Chargaff's rule

Molar proportion of bases (as moles of base per 100 moles of phosphate) in DNAs from various sources.

Watson and Crick in 1953 proposed that the DNA molecule extended chain having a highly ordered structure and is composed of: two complementary polymeric chains twisted about each other.
the two stands run in opposite directions (antiparallel alpha-helices), and are of opposite polarity. the rails of the ladder run in opposite direction contain alternating units of deoxyribose sugar and phosphate. the polynucleotide chain, the sugar and phosphate groups are always linked together by 3 - 5 phosphodiester linkages.

 There are two reasons why the bases must pair in this specific way:
1. The purine, with a double ring are larger structures than pyrimidine, with a single ring. If two purine are paired their dimensions are too great to fit the constant diameter of the double helix (2 nm) while the dimensions of the two pyrimidine are too small.
2. The second determinant of specificity is the positions on the bases of the hydrogen atoms that can participate in bonding.

How to write DNA sequence

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DNA conformation
Wilkins and his colleagues demonstrated that, depending on the conditions chosen to produce the DNA fibres, they can have a variety of possible conformations (structures).

The major forms are the:

1. B-form, basically describes the Watson and Crick model, 2. A-form DNA, 3. Z-form DNA.

 B-form DNA is thought to represent the conformation of most DNA found in cells. The main features that distinguish B-form DNA from other forms are: the pitch, the angle of tilt that the base pairs make with the helical axis, and the distinct major and minor grooves. The B-DNA is long and thin.

DNA can either be linear or circular Most if not all bacterial chromosomes are circular. Certain phages or viruses have linear DNA e.g. Lamda phage, adenovirus, poxvirus. Some molecules that are linear when isolated from a virus particle are found as circular forms inside the host.

 DNA is naturally supercoiled and is biologically very important. Supercoiled refers to the twisting of the double helical DNA. DNA is naturally negatively supercoiled. DNA can be negatively suprecoiled (right handed) or positively supercoiled (left handed). Negative Supercoiling results from under-winding or unwinding, where as positive supercoiling results from tighter winding.

 DNA is always found complexed with specific DNA binding proteins to form compact molecules called chromatin. In eukaryotes, the most prominent DNA binding proteins are the histones. Histones are relatively small, positively charged arginine-lysine rich proteins that aggregate together, around which DNA supercoils. Bacteria contain histone-like DNA binding proteins.