DNA Structure

Nucleic acids are required for the storage and expression of genetic information.
There are two chemically distinct types of nucleic acids: deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA).
DNA, the storehouse of genetic information, is present not only in chromosomes in
the nucleus of eukaryotic organisms, but also in mitochondria and the chloroplasts
of plants. Prokaryotic cells, which lack nuclei, have a single chromosome, but may
also contain non chromosomal DNA in the form of plasmids.

STRUCTURE OF DNA

DNA is a polydeoxyribonucleotide that contains many monodeoxyribonucleotides

covalently linked by 3'-5'-phosphodiester bonds. DNA exists as a double-stranded
molecule, in which the two strands wind around each other, forming a double
helix.
A. 3'-5'-Phosphodiester bonds

Phosphodiester bonds join the 5'-hydroxyl group of the deoxypentose of one

nucleotide to the 3'-hydroxyl group of the deoxypentose of an adjacent nucleotide
through a phosphate group. Phosphodiester linkages between nucleotides (in DNA
or RNA) can be cleaved hydrolytically by chemicals, or hydrolyzed enzymatically by
a family of nucleases: deoxyribonucleases for DNA and ribonucleases for RNA.

B. Double helix
In the double helix, the two chains are coiled around a common axis called the axis
of symmetry. The chains are paired in an antiparallel manner, that is, the 5'-end of
one strand is paired with the3'-end of the other strand (Figure 29.3).
1. Base pairing: The bases of one strand of DNA are paired with the bases of the
second strand, so that an adenine is always paired with a thymine and a cytosine is
always paired with a guanine. One polynucleotide chain of the DNA double helix is
always the complement of the other. Given the sequence of bases on one chain,
the sequence of bases on the complementary chain can be determined (Figure
29.4).

[Note: The specific base pairing in DNA leads to Chargaff's Rules: In any sample of
double-stranded DNA, the amount of adenine equals the amount of thymine, the
amount of guanine equals the amount of cytosine, and the total amount of purines
equals the total amount of pyrimidines.]

The base pairs are held together by hydrogen bonds: two between A and T and
three between G and C (Figure 29.5).These hydrogen bonds, plus the hydrophobic
interactions between the stacked bases, stabilize the structure of the double helix.
STRUCTURE OF RNA
There are three major types of RNA that participate in the process of protein
synthesis ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA
(mRNA). However, they differ as a group from DNA in several ways, for example,
they are considerably smaller than DNA, and they contain ribose instead of
deoxyribose and uracil instead of thymine. Unlike DNA, most RNAs exist as single
strands that are capable of folding into complex structures. The three major types
of RNA also differ from each other in size, function, and special structural
modifications.

Protein synthesis and the genetic code

The genetic code

The genetic code is a dictionary that identifies the correspondence between a
sequence of nucleotide bases and a sequence of amino acids. Each individual word
in the code is composed of three nucleotide bases. These genetic words are called
codons.

Codons
codon consists from three nucleotides (triplet) and provides informations for the
sequence of amino acids in the protein synthesis.
Because of codon is degenerated each amino acid has more than one codon e.g.
valine has three codons: GUC, GUA, and GUU, in addition to that, there are amino
acids like methionine and tryptophan have single codon.

Main step in protein synthesis

1/ Replication
2/ transcription
3/ translation
1/ Replication: this process is the production of two double strand DNA molecules
that are identical in every way to the parent DNA. Each daughter DNA contains one
strand of parent DNA and one synthesized daughter strand.

2/ Transcription: This process lead to the synthesis of RNA, with a sequence that is
complementary to that of the DNA template. RNA polymerases (RNAPs) catalyze
transcription, in eukaryotes there are four types of (RNAPs) enzymes each one
responsible for the synthesis of certain RNA type.

The informations in DNA are transcribed as mRNA, therefore mRNA acts as a

template, and transports the genetic code from the nucleus into cytoplasm and
there are four steps to the occurrence of transcription :
a/ Binding: RNAP binds to DNA to begin transcription.

b/ Initiation: Involves the formation of the first phosphodiester bond.

c/ Elongation.

d/ termination.

3/ translation (protein synthesis).

This involves the polymerization of amino acids in a precise sequence directed by

the sequence of bases in mRNA. Protein synthesis occurs in the following steps:

(1) Activation of amino acids: the enzyme aminoacyl-tRNA synthetase link

amino acids to their specific tRNA to form aminoacyl-tRNA (fig. 10-10). Each
aminoacyl-tRNA synthetase joins specific amino acid to the 3-terminal OH of
a specific tRNA.
(2) Initiation of polypeptide chain formation: this step needs for: a.a.tRNA,
mRNA, rRNA (ribosome), GTP, and initiating factors (eIF1,eIF2, and eIF3),
eukaryotic initiating factors. One large (60s) and one small (40s) sub unit
make up each ribosome. The activation of ribosome begins by its association
into two parts 60s and 40s. mRNA, small ribosomal subunit (40s), eukaryotic
initiation factor (eIF), GTP, and methionyl tRNA form 40s initiation complex,
which binds to 60s to form 80s initiation complex (fig. 1)
(3) Elongation: elongation occurs in a three steps, cycle that repeat each time an
amino acid is added. (a) the incoming of aa-tRNA binds to the aminoacyl site
of the large 80s ribosomal subunit. This requires several protein elongation
factors (EFS) and the hydrolysis of GTP (fig. 2). (b) the formation of peptide
bonds: peptidyl transferase catalyzes the transfer of amino acid or peptide
from P site to the aa-tRNA on the A site with the formation of peptide
bbond. The uncharged tRNA dissociate from the complex (fig. 3).
(c) translocation: the new peptidyl-tRNA moves to the p site instead of the
discharged tRNA, which requires EF2 and GTP hydrolysis (fig. 4).
(4) Termination: the termination begins by the termination of all mRNA codons
after the addition of last amino acid, and the releasing of peptide chain
begins from the ribosome. This process requires three factors R1, R2, and R3
which bind to ribosome and transport peptidyl tRNA from A site to P site.
Then (R1,R2,R3), peptide chain, mRNA, and tRNA are separated from
ribosome to stay inactive alone and ready for the activation again.
Mutations
Mutations are change in the DNA of cell and are caused by radiation, viruses, and
mutagenic chemicals, as well as errors that occur during meiosis and DNA
replication.

Classification of mutations
A gene is essentially a sentence made up of the bases A, T, G, and C that describes
how to make a protein. Any changes to those instructions can alter the genes
meaning and change the protein that is made, or how or when a cell makes that
protein. There are many different ways to alter a gene. In the following examples
of some types of mutations, we use the sentence '' the fat cat ate the wee rat'' as
a sample gene.

Point mutation

A point mutation is a simple change in one base of the gene sequence. This is
equivalent to changing one letter in a sentence, such as this example, where we
change the 'c' in cat to an 'h' :

Original the fat cat ate the wee rat.

Point mutation the fat hat ate the wee rat.

Frame shift mutation

In a frame shift mutation, one or more bases are inserted or deleted, the
equivalent of adding or removing letters in a sentence. This type of mutation can
make the DNA meaningless and often results in a shortened protein. An example of
frame shift mutation using our sample sentence is when the 't' from cat is
removed, but we keep the original letter spacing:

Original the fat cat ate the wee rat.

Frame shift the fat caa tet hew eer at.

Deletion

Mutations that results in missing DNA are called deletions. These can be small,
such as the removal of just one "word", or longer deletions that affect a large
numbers of genes on the chromosome. Deletion can also cause frame shift
mutation. In this example, the deletion eliminated the word cat.

Original the fat cat ate the wee rat.

Deletion the fat ate the wee rat.

Insertion

Mutations that result in the addition of extra DNA are called insertions. Insertions
can also cause frame shift mutations, and general result in a nonfunctional protein.

Original the fat cat ate the wee rat.

Insertion the fat cat xlw ate the wee rat.

Inversion

In an inversion mutation, an entire section of DNA is reversed. A small inversion

may involve only a few bases within a gene, while longer inversions involve large
regions of a chromosome containing several genes.

Original the fat cat ate the wee rat.

Inversion the fat tar eew eht eta tac.

 The structure of genetic code tends to minimize the effects of mutation.

 Changes in the third codon base often do not change the biological function
of produced protein. This type of mutation called silent mutation.
 Suppressor mutation: sometimes mutation canceling occurs by the
occurrence of another mutation in the same gene, the second mutation
suppresses the first mutation.
Causes of mutation
Two classes of mutations are spontaneous mutations (molecular decay), and
induced mutations caused by mutagens.

Spontaneous mutations on the molecular level include:

 Tautomerism: a base is changed by the repositioning of hydrogen atom,

altering the hydrogen bonding pattern of that base resulting in incorrect
base pairing during replication.
 Depurination: loss of a purine base (A or G) to form an apurinic site (AP
site).
 Deamination: hydrolysis changes a normal base to an a typical base
containing a keto group in place of the original amino group.
 Transition: a purine changes to another purine, or pyrimidine to another
pyrimidine.
 Transversion: a purine becomes a pyrimidine, or vice versa.

Induced mutations on the molecular level can be caused by:

 Chemicals: like nitrous acid which converts amine groups on A and C to diazo
groups, altering their hydrogen bonding patterns which leads to incorrect
base pairing during replication.
 Radiation: like ultraviolet radiation and ionizing radiation.
 Viral infection.
Harmful mutations

Changes in DNA caused mutation can cause errors in protein sequence, creating
partially or completely non-functional proteins, if a mutation does change a
protein, this will probably be harmful, for example certain mutations can cause the
cell to become malignant, and thus cause cancer.

Beneficial mutations

Although most mutations that change protein sequences are harmful, some
mutations have a positive effect on an organism. In this case, the mutation may
enable the mutant organism to withstand particular environment stresses, or
reproduce more quickly.

Example: a sickle cell anemia is an inherited disease, caused by mutation

(substitution of valine instead of glutamic acid); in this case strange type of
hemoglobin appears, consisting of normal and mutant strand. This mutation
decreases the solubility of deoxyhemoglobin so that makes fibrous precipitate,
changing the erythrocytes to a sickle shape. The human infected with sickle cell
anemia are protected from the lethal malaria infection.
DNA repair

The maintenance of integrity of the information in DNA molecules is of utmost

importance to the survival of a particular organism as well as to survival of the
species.

The detective region in one strand can be returned to its original form by relying on
the complementary information stored in the unaffected strand.

(1)Mismatch repair

Mismatch repair correct errors made when DNA is copied, for example a C could
be inserted apposite to an A

Mechanism of mismatch

The template strand is methylated and the newly synthesized strand is not. This
difference allows the repair enzymes to identify the strand that contains the errant
nucleotide which requires replacement.

If mismatch is found, a GATC endonuclease cuts the strand bearing the mutation.
An exonuclease (an enzyme responsible for repairing) then digests the strand, thus
removing the faulty DNA. The defect is then filled in by normal cellular enzymes
according to base pairing rules. The following figure illustrates mismatch repair.
(2) Base excision repair

The depurination of DNA, which happens spontaneously owing to the thermal

liability of the purine N-glycosidic bond, Specific enzymes recognize a depurinated
site and replace the appropriate purine directly without interruption of the
phosphodiester backbone.

Mechanism of base excision repair

Specific n-glycosylases recognize and remove the abnormal bases from the DNA
(nuclease excise the abnormal base). The proper base is then replaced by a repair
DNA polymerase, and ligase returns the DNA to its original state. This series of
events is called base excision repair. The following figure explains this repair.
(3) Nucleotide excision repair

This mechanism is used to replace regions of damaged DNA up to 30 bases in

length. Common causes such DNA damage includes ultraviolet light, ionizing
radiation, smoking, and variety of chemicals. These are repaired by a process called
nucleotide excision repair as shown below.