Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning

of all known living organisms. The main role of DNA molecules is the long-term storage of information. DNA contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.

The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

 Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds.
Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication.

 Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus. In prokaryotic organisms such as bacteria DNA is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Structure of DNA

Four different deoxynucleotides, the structural units of DNA, are assembled into long polymers of DNA strands. Prior to assembly, they are in the form of nucleotide triphosphates similar to ATP and linked together by phosphodiester bond. Each nucleotide contains three parts: a phosphate group, the sugar deoxyribose and one of four nitrogen bases. The four bases of DNA, their designations and their triphosphate form are adenine (dATP), guanine (dGTP), thymine (dTTP), and cytosine (dCTP).

Nitrogenous bases of DNA molecule

Cytosine

Phosphate

Deoxyribose

DNA Deoxynucleotide

Three-dimension structure

Ribose

nucleotide nucleoside

Deoxyribose

deoxy nucleotide

 Chargaff developed the principle of base-pairing. He determined the relative amounts of A, T, C, and G in a variety of cells, proving that A = T and C = G and that there is exactly as much purine (adenine and guanine) in the nucleus as there is pyrimidine (thymine and cytosine). Through the use of X-ray crystallography, Wilkins and Franklin determined that DNA was double stranded and could form a helix.

Primary structure of DNA

Characteristics of the dsDNA

2 chains
purine opposite a pyrimidine
chains held together by H-bonds Guanine is paired with cytosine by three H-bonds Adenine is paired with thymine by two H-bonds anti-parallel orientation of the two chains 5'--------------->3 3'<---------------5' The molecule is stabilized by: 1- large number of H-bonds 2- hydrophobic bonding between the stacked bases

Forms of DNA
B-form DNA In this conformation, the backbone traces a right handed helix, each turn of which contains 10 nucleotides. This is the most popular double-helix conformation.

Z-form DNA

DNA is also capable of twisting to the left. In this form, the phosphate groups trace a zigzag pattern.

Thus the transition between the two forms might act like a gene switch

B-Form

Z-Form

Prokaryotic DNA
The main DNA in prokaryotes is a circular molecule attached to

the plasma membrane.

Some DNA is organized in smaller circles called plasmids. 90% of the genome consists of functional genes, i.e. genes coding for proteins involved in DNA replication and DNA transcription only.

Eukaryotic DNA In eukaryotes, DNA is associated with proteins to form a complex called chromatin, this structure allows numerous configurations of the DNA molecule.

Chromatin consists of:

1- Very long double-stranded DNA molecule

2- A nearly equal mass of: a- small basic proteins called histones b- non-histone proteins (acidic proteins and larger than histones), they include: enzymes involved in DNA replication such as DNA topoisomerase and proteins involved in transcription such as the RNA polymerase complex c- a small quantity of RNA

Non-histones are regulatory proteins, e.g. leucine zippers; zinc fingers.

DNA as Genetic Material

Frederick

Griffith found that Streptococcus pneumoniae bacterium had two forms when grown on agar plates, a smooth (S) and a rough (R) form.

The R bacteria were harmless, but the S bacteria were lethal when injected into mice. Heat-killed S cells were also harmless.

 Surprisingly when live R cells were mixed with killed S cells and injected into mice the mice died, and the bacteria rescued from the mice had been "transformed" into the S type. This experiment strongly implied that genetic material had been transferred from the dead (S) to the live cell (R).

The Discovery of DNA as the Genetic Material

Hershey and Chase determined that viral DNA, not protein shell, enters cell upon infection to produce more virus particles The Scientific Method

Observation: A kind of virus called T2 infects the bacterium Escherichia coli and essentially turns the bacterium into a T2factory by inserting viral genetic code into the bacterium.

Question: Since viruses are composed of DNA (some have RNA instead) in a protein coat/shell called a capsid, which of these two is the viral genetic material? Is the viral DNA or the protein inserted into the E. coli to direct the synthesis of more T2 virus?

Procedure
Step 1: Hershey and Chase grew two separate batches of T2 virus

(bacteriophage) and E. coli: one with radioactive sulfur and one with radioactive phosphorus

Radioactive Sulfur (in protein)

Radioactive Phosphorus (in DNA)

Step 2: The radioactive T2 were isolated from each of the containers and placed into separate, new batches of E. coli.

Step 3: Separately, each mixture was spun in a centrifuge to separate the heavy bacteria (with any viral parts that had gone into them) from the liquid solution they were in (including any viral parts that had not entered the bacteria).

Supernatant

Pellet

Radioactive Sulfur (in protein)

Radioactive Phosphorus (in DNA)

Result
In the batch of T2 that had been grown with radioactive sulfur, radioactivity was found in the supernatant but not the pellet, indicating that the viral protein did not go into the bacteria. In the batch of T2 that had been grown with radioactive phosphorus, radioactivity was found in the bacterial pellet but not the supernatant, indicating that the viral DNA did go into the bacteria.

Conclusion
It was concluded that the viral DNA is
the genetic code material

Role of DNA
It is now well established that, the bank of genetic information takes the form of a stable macromolecule, DNA. DNA serves as the carrier of genetic information in both prokaryotes and eukaryotes .

It is clear that the properties of cells are to a large extent determined by their constituent proteins. Many proteins serve as indispensable structural components of the cell. Other proteins, such as enzymes and certain hormones, are functional in character and determine most of the biochemical properties of the cell

As a result, the factor that controls the type and quantity of which protein a cell may synthesize is the same factor that determines the function of every living cell. DNA is relatively inert chemically. The information it contains is expressed indirectly via other molecules.

DNA directs the synthesis of specific RNA and protein molecules, which in turn determine the cell's chemical and physical properties. This role for DNA is called the Central dogma of molecular biology.

It is now well recognized that DNA is the macromolecule that controls every aspect of cell function.
This is done through protein synthesis as suggested by the following sequences:

DNA

Transcription

Translation mRNA Gene product (protein)

The transfer of information from DNA to protein

Also, DNA plays an important role in heredity, this is suggested by two facts: 1- DNA is a molecule of unusual capacity, that is able to encode a very large quantity of biologic information. 2- DNA is a replicon, a molecule that can undergo self replication.

It permits DNA to make copies of itself as a cell divides.

These copies are given to daughter cells which can thus inherit each and every property and characteristic of the original cell.

 Ribonucleic acid or RNA is a nucleic acid, consisting of many nucleotides that form a polymer.

Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate.

RNA is very similar to DNA, but differs in a few important structural details: - in the cell RNA is usually single stranded, while DNA is usually double stranded.

- RNA nucleotides contain ribose while DNA contains deoxyribose.

- In RNA the nucleotide uracil substitutes for thymine, which is present in DNA.

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil). However, there are numerous modified bases and sugars in mature RNAs: 1- Pseudouridine (), in which the linkage between uracil and ribose is changed from a CN bond to a CC bond. 2- Ribothymidine (T), are found in various places (most notably in the TC loop of tRNA). 3- Hypoxanthine, a deaminated guanine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code.

Types of RNA
1- Messenger RNA (mRNA) Is synthesized from a gene segment of DNA which ultimately contains the information on the primary sequence of amino acids in a protein to be synthesized. The genetic code as translated is for m-RNA not DNA. The messenger RNA carries the code into the cytoplasm where protein synthesis occurs.

 mRNA is heterogeneous in size and sequence. It always has a 5 ' cap composed of a 5' to 5' triphosphate linkage between two modified nucleotides: a 7-methylguanosine and a 2 ' O-methyl purine. This cap serves to identify this RNA molecule as an mRNA to the translational machinery. Most mRNA molecules contain a poly-adenosine tail at the 3' end. Both the 5' cap and the 3' tail are added after the RNA is transcribed and contribute to the stability of the mRNA in the cell.

mRNA

2- Transfer RNA (tRNA)

tRNA is the information adapter molecule.

It is the direct interface between amino-acid sequence of a protein and the information in DNA. Therefore it decodes the information in DNA. There are > 20 different tRNA molecules. All have between 75-95 nt. All tRNA's from all organisms have a similar structure, indeed a human tRNA can function in yeast cells.

tRNA

3- Ribosomal RNA (rRNA)

Ribosomal RNA (rRNA) is a component of the ribosomes, the protein synthetic factories in the cell.
Eukaryotic ribosomes contain four different rRNA molecules: 18 s, 5.8 s, 28 s, and 5 s rRNA (s stands for sedimentation coefficient). rRNA molecules are extremely abundant. They make up at least 80% of the RNA molecules found in a typical eukaryotic cell.

How is Information Stored?

One strand of the DNA double-helix (anti-sense strand) serves as a template for the construction of mRNA.

The sequence of nucleotides in this DNA strand is complimentary (opposite) the sequence in mRNA.
The sequence of nucleotides in mRNA determines the amino acids in the protein. For example GUG in mRNA (or CAC in DNA) codes for valine.

The strand of DNA that contains the genetic code is called the anti-sense. It is often referred to as the coding strand or the template strand.

The other strand (the sense strand) is not used. Notice that the sense strand has the same base sequence as mRNA except that mRNA has U instead of T.

The codes in DNA are copied to produce mRNA. Each three-letter code in mRNA (called a codon) codes for one amino acid.
The sequence of amino acids in proteins is therefore most directly determined by the sequence of codons in mRNA, which in turn, are determined by the sequence of bases in DNA.

There are four letters in the genetic alphabet (A, T, G, and C) and each codon contains three letters. It is therefore possible to have 64 different codons. Because there are only 20 different amino acids and 64 possible codons, some amino acids have several different codons. Terminators are codes that indicate the end of a genetic message (gene).

An initiator codon (usually AUG) indicates where the genetic information begins.

Second Base

U
UUU Phe U UUC Phe UUA Leu UUG Leu CUU Leu F i r s t B a s e C CUC Leu CUA Leu CUG Leu AUU Ile AUC Ile A AUA Ile AUG Met or Start GUU Val G GUC Val GUA Val GUG Val

C
UCU Ser UCC Ser UCA Ser UCG Ser CCU Pro CCC Pro CCA Pro CCG Pro ACU Thr ACC Thr ACA Thr ACG Thr GCU Ala GCC Ala GCA Ala GCG Ala

A
UAU Tyr UAC Try UAA Stop UAG Stop CAU His CAC His CAA Gln CAG Gln AAU Asn AAC Asn AAA Lys AAG Lys GAU Asp GAC Asp GAA Glu GAG Glu

G
UGU Cys UGC Cys UGA Stop UGG Trp CGU Arg CGC Arg CGA Arg CGG Arg AGU Ser AGC Ser AGA Arg AGG Arg GGU Gly GGC Gly GGA Gly GGG Gly U C A G U C A G U C A G U C A G T h i r d B a s e

Genetic codes