Introduction to the DNA

The aim of this article, aims to inform you the difference between DNA, genes and chromosomes. To identify and understand the structure of the DNA molecule. To understand the differences between the DNA in eukaryotic and prokaryotic cells. This is needed to be clarified before my upcoming article about DNA damage and its link to cancer in sha Allah

In the human body, we have millions of eukaryotic cells. Amongst the organelles in the cell is the nucleus that contains the genetic information in the form of deoxyribonucleic acid (DNA) to control the cell. It is important to note that there are other types of eukaryotic cells besides the animal cell. These are plants, fungi and protists. The structure of a eukaryotic cell is shown below:

The relationship between genes, chromosomes and DNA
The nucleus consists of chromosomes. Chromosomes are synthesised from long DNA molecules. A gene is a short section of DNA. A gene occupies a fixed position, called a locus, on a particular DNA molecule. Each gene codes for a polypeptide (protein) by stating the order of the amino acids sequence. A polypeptide are lots of amino acids monomers bind together via peptide bonds to form protein polymers. This is done via a condensation reaction where water is also produced as a by-product. Therefore, the function of DNA is to produce proteins.
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What is DNA?
It is a nucleic acid polymer that consists of monomers called nucleotides that are bound together via a condensation reaction. Water is also formed in the reaction as a by-product.
 
A nucleotide is composed of the following elements:

The structure of the nucleotide
 
A nucleotide consists of three components:
A)   a phosphate group
B)   a sugar
C)   a nitrogenous base.

Phosphate molecule
The phosphate group is negatively charged and this provides the nucleic acid with acidic properties. It is attached to the 5’ carbon of the sugar molecule
Sugar molecule
It is a 5-carbon sugar called a pentose. There are two types of pentose sugars: ribose and deoxyribose. Deoxyribose means that the ribose has lost an oxygen atom ‘de-oxy’.

Nitrogenous base
There are four nucleobases: cytosine ( C), Guanine (G), Thymine (T) and Adenine (A). These are attached in the position where the hydroxyl group (-OH) is located in the sugar molecule which is 1’ carbon.
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The bases are known by their first letters. Because there are four different bases, the nucleotide is named based on the type of base as shown below:

However, this is not to say that more phosphate groups cannot be added to the nucleotide. For instance, Adenosine Triphosphate (ATP) has three phosphate groups and plays a role in respiration as energy is provided as ATP.
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Nucleotide polymerisation
Nucleotides polymerisation does not involve the bases and is conducted by producing phosphodiester bonds between carbon 3' of the ribose sugar and an oxygen atom of the phosphate group. This is a form of a condensation reaction.
 
Two nucleotides: dinucleotides
Three nucleotides: trinucleotides
Few nucleotides: oligonucleotides.
Many nucleotides: polynucleotides
 
A polynucleotide has a free phosphate group at one end, called the 5' end. This is because the phosphate group is bound to carbon 5' of the ribose sugar. This forms the sugar phosphate backbone. There is a 3’ end because there is a hydroxyl (-OH) group on carbon 3’ of the ribose sugar.

Two scientists,Watson and Crick in 1953, investigated the 3D DNA structure more closely and discovered that the DNA molecule has the following:

• Double stranded as there are two nucleotide strands wounded together to form a double helix.

• The strands are wounded together by hydrogen bonding between the bases. This form of bonding provides stability and protection from damage.

• The bases form specific pairs: Adenine can only associate with Thymine whereas Cytosine can only associate with Guanine.This is known as complementary base pairing. This structure allows DNA to be adapted to its function as storying and expressing genetic material.

• These strands are anti-parallel, in other words they run opposite direction.

• The strands are complementary which provides a copy of genetic information. This is beneficial for repair, copy and checking errors.

 
Purines and Pyrimidines.
There are two forms of nitrogenous bases: purines and pyrimidines. Purines are double-ringed structures whereas pyrimidines have one ring.

• Adenine (A) - a purine
• Thymine (T) - a pyrimidine
• Cytosine(C) - a pyrimidine
• Guanine (G) - a purine

The Genetic Code    
The genetic code is universal, non-overlapping and degenerate. There are 20 different amino acids and 4 different bases. Therefore, bases are read in groups of 3 called a triplet. Consequently, this provides 64 combinations that is more than sufficient enough to code for the 20 amino acids. A sequence of three DNA bases that code for an amino acid is called a codon. The 64 codons form the genetic code. Some codons symbolise the start of a gene whereas other codons symbolise the end of the gene.

However, it is important to note that approximately 2% of all DNA molecules situated in eukaryotic cells do not code for polypeptides. The remaining DNA molecules are called non-coding DNA and they do not produce genes. There are two types of non-coding DNA and is dependent on where it is situated:

• In a gene:  non-coding DNA are called introns whereas the coding DNA molecules are called exons. All eukaryotic genes contain introns and their length is longer than exons. Introns are utilized for interruption sequences whereas eukaryotic genes are needed for expressed sequences.
• Between genes: non-coding DNA are called satellite DNA and are composed of simple repetitive DNA sequences that function in various means: DNA replication, gene regulation, aiding in coiling DNA into chromosomes, and some non-coding DNA are pseudogenes. Pseudogenes are untouched gene copies.

The differences between the DNA in Prokaryotic and Eukaryotic cells

Prokaryotic cells have a simple structure and a cell size of 1-10um and have a large surface area to volume. This increases their metabolic and growth rates providing a shorter generation time in comparison to eukaryotic cells. Examples of Prokaryotes are bacteria and archae. They do not have a nuclear membrane around its DNA nor contains any membrane-bound organelles. Majority of prokaryotes are unicellular (one cell), however some prokaryotic cells are multicellular (more than one cell) such as cyanobacteria.
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Alternatively, eukaryotic cells have a complex structure and it has a membrane bound nuclei. Examples of eukaryotic cells are plants and animal cells. The size of eukaryotes is 10-100um.

Key Points to Remember

• Gene --> DNA --> Chromosomes.
• Adenosine always binds with Thymine
• Guanine always binds with Cysteine.

• Prokaryotes have DNA molecules are short, circular and not associated with histone proteins. On the other hand, eukaryotes DNA are long, linear and associated with histone proteins.
• Mitochondria and Chloroplasts contain DNA and are similar to prokaryotic DNA as they are short, circular and not linked with histone proteins.
• Most eukaryotic nuclear DNA do not code for polypeptides (proteins).
• Exons in a gene code for amino acids and are separated by non-coding sequences called introns.