Nucleic acids

definition
The nucleic acids are the compounds that are responsible for the storage and
transmission
of the genetic information that controls the growth, function and reproduction of all
types
of cells.

Classification
They are classified into two general types:

 the deoxyribonucleic acids (DNA)whose structures contain the sugar residue

b-D-deoxyribose;
 the ribonucleic acids (RNA) whose structures contain the sugar residue b-D-
ribose.

Both types of nucleic acids are polymers based on a repeating structural unit
known as a
nucleotide.
These nucleotides form long single-chain polymer molecules in both DNA and
RNA.
Each nucleotide consists of a purine or pyrimidine base bonded to a sugar
residue by a glycosidic link and a phosphate group.

Deoxyribonucleic acid (DNA)

 DNA occurs in the nuclei of cells in the form of a very compact DNA–protein
complex called chromatin.
 The protein in chromatin consists mainly of histones
 The DNA is coiled twice around an octomer of histone molecules with a ninth
histone molecule attached to the exterior of these mini coils to form a structure
like a row of beads spaced along a string.
 This ‘string of beads’ is coiled and twisted into compact structures which form
the basis of the structures of chromosomes.
 Chromosomes are the structures that form duplicates during cell division in order
to transfer the genetic information of the old cell to the two new cells.

Structure
 DNA molecules are large with relative molecular masses up to one trillion (10 12).

 The principal bases found in their structures are adenine (A), thymine (T),
guanine (G) and cytosine (C),

 experimental observations led Crick and Watson in 1953 to propose that the
three dimensional
structure of DNA consisted of two single-molecule polymer chains held together
in the form of a double helix by hydrogen bonding between the same pairs of
bases, namely: adenine to thymine (A–T) and cytosine to guanine (C–G).
functions of DNA
The DNA found in the nuclei of cells has three functions:
1. To act as a repository for the genetic information required by a cell to
reproduce that cell.
2. To reproduce itself in order to maintain the genetic pool when cells divide.
3. To supply the information that the cell requires to manufacture specific
proteins.

Genes
 Each species has its own internal and external characteristics.
 These characteristics are determined by the information stored and supplied by
the DNA in the nuclei of its cells.
 This information is carried in the form of a code based on the consecutive
sequences of bases found in sections of the DNA structure.
 This code controls the production of the peptides and proteins required by the
body.
 The sequence of bases that act as the code for the production of one specific
peptide or protein
molecule is known as a gene.
 Genes can normally contain from several hundred to 2000 bases.
 Changing the sequence of the bases in a gene by adding, subtracting or
changing one or more bases may cause a change in the structure of the protein
whose production is controlled by the gene.
 In simple organisms, such as bacteria, genetic information is usually stored in a
continuous sequence of DNA bases.
 in higher organisms the bases forming a particular gene may occur in a number
of separate sections known as exons separated by sections of DNA that do not
appear to be a code for any process. These non-coding sections are referred to
as introns.
 The complete set of genes that contain all the hereditary information of a
particular species is called a genome.

Replication
 The reproduction of DNA is known as replication.

 It is believed to start with the unwinding of a section of the double helix.

  Unwinding may start at the end or more commonly in a central section of the
DNA helix.

 The separated strands of the DNA act as templates for the formation of a new
daughter strand.

 Individual nucleotides bind by hydrogen bonding between the bases to the

complementary parent nucleotides.

 This hydrogen bonding is specific in that only the complementary base pairs can
hydrogen bond ie the hydrogen bonding can only be between either thymine and
adenine or cytosine and guanine.

 This means that the new daughter strand is an exact replica of the original DNA
strand bound to the parent strand.

 Consequently replication will produce two identical DNA molecules.

 This means that the growth of the daughter strand that starts at the 3 0 end of the
parent strand can continue smoothly as the DNA helix continues to unwind. This
strand is known as the leading strand.

 However, this smooth growth is not possible for the daughter strand that started
from the 50 end of the parent strand. This strand, known as the lagging strand.

 unwinding continues in both directions until the complete molecule is duplicated.

Ribonucleic acid (RNA)

 Ribonucleic acid is found in both the nucleus and the cytoplasm.
 In the cytoplasm RNA is located mainly in small spherical organelles known as
ribosomes.
 These consist of about 65per cent RNA and 35 per cent protein.
  Ribonucleic acids are classified according to their general role in protein
synthesis:
1. messenger RNA (mRNA)
2. transfer RNA (tRNA)
3. ribosomal RNA (rRNA).

Messenger RNA informs the ribosome as to what amino acids are required and their
order in the protein, that is, they carry the genetic information necessary to produce a
specific protein.
This type of RNA is synthesised as required and once its message has been delivered it
is decomposed.

Transfer RNA transports the required amino acids in the correct order to the ribosome.

ribosomal RNA controls the synthesis of the required protein.

 The structures of RNA molecules consist of a single polymer chain of nucleotides

with the same bases as DNA with the exception of thymine, which is replaced by
uracil.

 All types of RNA are formed from DNA by a process known as transcription, which
occurs in the nucleus.

 It is thought that the DNA unwinds and the RNA molecule is formed in the 5 0 to 30
direction.

 This bonding is catalysed by enzymes known as RNA polymerases.

 Since only complementary base pairs can hydrogen bond, the order of bases in
the new RNA strand is determined by the sequence of bases in the parent DNA
strand.

 In this way DNA controls the genetic information being transcribed into the RNA
molecule.

 The strands of DNA also contain start and stop signals, which control the size of
the RNA molecule produced.

Messenger RNA (mRNA)

 mRNA carries the genetic message from the DNA in the nucleus to a ribosome.
 This message instructs the ribosome to synthesise a specific protein
 mRNA is believed to be produced in the nucleus by removal of the introns and
the splicing together of
the remaining exons into a continuous genetic message,
 the process being catalysed by specialised enzymes.
 The net result is a smaller mRNA molecule with a continuous sequence of bases
that are complementary to the gene’s exons.
 This mRNA now leaves the nucleus and carries its message in the form of a code
to a ribosome.
 each naturally occurring amino acid had a DNA code that consisted of a
sequence of three consecutive bases known as a codon and that an amino acid
could have several different codons.
  In addition, three of the codons are stop signals, which instruct the ribosome to
stop protein synthesis. Furthermore, the codon that initiates the synthesis is
always AUG, which is also the codon for methionine.
 Consequently, all protein synthesis starts with methionine.
 The mRNA’s codon code is known as the genetic code
 Its use is universal, with all living matter using the same genetic code for protein
synthesis. This suggests that all living matter must have originated from the
same source and is strong evidence for Darwin’s theory of evolution.

Transfer RNA (tRNA)

 tRNA is also believed to be formed in the nucleus.
 tRNA molecules are relatively small and usually contain 73–94 nucleotides in a
single strand.
 The strand of tRNA is usually folded into a three-dimensional L shape.
 This structure, which consists of several loops, is held in this shape by hydrogen
bonding between complementary base pairs
 the structures of most tRNAs are represented as a cloverleaf.
 tRNA molecules carry amino acid residues from the cell’s amino acid pool to the
mRNA attached to the ribosome.
 The tRNA recognises the point on the mRNA where it has to deliver its amino acid
through
the use of a group of three bases known as an anticodon.
 This anticodon is a sequence of three bases found on one of the loops of the
tRNA.
 The anticodon can only form base pairs with the complementary codon in the
mRNA

Ribosomal RNA (rRNA)

  Ribosomes contains about 35 per cent protein and 65 per cent rRNA.
 Their structures are complex and have not yet been fully elucidated.
 they have been found to consist of two sections, which are referred to as the
large and small subunits.

Protein synthesis
Protein synthesis starts from the N-terminal of the protein. It proceeds in the 5 0 to 30
direction along the mRNA and may be divided into four major stages: activation;
initiation;
elongation; and termination.
Elongation is the formation of the protein, whilst termination is the ending of the protein
synthesis and its release from the ribosome.

1 Activation
 Activation is the formation of the tRNA–amino acid complex.
 It is believed that an amino acid from the cellular pool reacts with the tRNA
specific for the amino acid to form an aminoacyl–tRNA complex.
 the reaction being catalysed by a synthase that is specific for that amino acid.

2. Initiation
 Initiation is the binding of mRNA to the ribosome and activation of the ribosome.
 Initiation is thought to start with the two subunits of the ribosome separating and
the
binding of the mRNA to the smaller subunit.
 Protein synthesis then starts by the attachment of a methionine–tRNA complex to
the
mRNA, so that it forms the N-terminal of the new protein.
 Methionine is always the first amino acid in all protein synthesis because its tRNA
anticodon is also the signal for the ribosome system to start protein synthesis.
 As soon as the methionine–tRNA has bound to the mRNA the larger ribosomal
subunit is believed to bind to the smaller subunit so that the mRNA is sandwiched
between the two subunits.

 3. Elongation
Elongation is the formation of the peptide chain of the protein by a stepwise repetitive
process. A great deal is known about the nature of this process but its exact mechanism
is
still not fully understood.

 4 .Termination
 The elongation process continues until a stop codon is reached.
 This codon cannot accept an amino acid–tRNA complex and so the synthesis
stops.
 The stop codon of the mRNA is recognized by proteins known as release factors,
which promote the release of the protein from the ribosome.

Recombinant DNA technology (genetic engineering)

  The body requires a constant supply of certain peptides and proteins if it is to
remain
healthy and function normally.
 Many of these peptides and proteins are only produced in very small quantities.
 They will only be produced if the correct genes are present in the cell.
 Consequently, if a gene is missing or defective an essential protein will
not be produced, which can lead to a diseased state. For example, cystic fibrosis
is caused
by a defective gene
 Several thousand hereditary diseases found in humans are known to be caused
by faulty
genes.
 Recombinant DNA (rDNA) technology (genetic engineering) offers a new way of
combating these hereditary diseases by either replacing the faulty genes or
producing the
missing peptides and proteins so that they can be given as a medicine.

Gene cloning
 Bacteria are frequently used as host cells for gene cloning.
 This is because they normally use the same genetic code as humans to make
peptides and proteins.
 However, in bacteria the mechanism for peptide and protein formation is
somewhat different.
 It is not restricted to the chromosomes but can also occur in extra nuclear
particles called plasmids.
 Plasmids are large circular supercoiled DNA molecules whose structure contains
at least one gene and a start site for replication.
 It is possible to isolate the plasmids of bacterial cells.
 The isolated DNA molecules can be broken open by cleaving the phosphate
bonds between specific pairs of bases by the action enzymes known as
restriction enzymes or endonucleases
 Cutting the strand can result in either blunt ends, where the endonuclease cuts
across both chains of the DNA at the same points, or cohesive ends (sticky ends),
where the cut is staggered from one chain to the other.
  Mixing the foreign DNA and the linearised DNA in a suitable medium results in
the
formation of extended plasmid loops when their ends come into contact. This
contact is converted into a permanent bond by the catalytic action of an enzyme
called
DNA ligase.
 The new DNA of the modified plasmid is known as recombinant DNA (rDNA).
 The new plasmids are reinserted into the bacteria by a process known as
transformation.
 Bacteria are mixed with the new plasmids in a medium containing calcium
chloride. This
medium makes the bacterial membrane permeable to the plasmid.
 These modified bacteria are allowed to replicate and, in doing so, produce many
copies of the modified plasmid.
 Under favourable conditions one modified bacterial cell can produce over 200
copies of the new
plasmid.
 The gene in these modified plasmids will use the bacteria’s internal machinery to
automatically produce the appropriate peptide or protein.
 Since many bacteria replicate at a very rapid rate this technique offers a
relatively quick way of producing large quantities of essential naturally occurring
compounds that cannot be produced by other means.
 Plasmids are not the only vectors that can be used to transport DNA into a
bacterial host cell.
 Foreign DNA can also be inserted into bacteriophages and cosmids by similar
 techniques.
 Bacteriophages (phage) are viruses that specifically infect bacteria whilst a
 cosmid is a hybrid between a phage and a plasmid that has been especially
synthesised for
use in gene cloning.
 small fraction will increase to a significant level as the cell replicates.

Medical applications
The main uses of gene cloning in the medical field are:
 to correct genetic faults and absences;
 to manufacture rare essential natural compounds.