Bicol University

College of Nursing
Legazpi City 2015-2016

Research in lecture
All about Nucleic Acid

Submitted to: Dr. Noemi R. Madrid

Submitted by: Phoebe Gillian N. Magpayo

Nucleic Acids
Nucleic acids are large organic compounds found in the chromosomes of living cells and viruses.
They are strong acids found in the nucleus of the cells. The nucleic acid polymers are with
high molecular weights as high as 100,000,000 grams per mole. With proteins, nucleic acids are
most important biological macromolecules. They are found in abundance in all living cells.

Nucleic Acid Definition

Nucleic acids are essential large biological molecules for all forms of life. The nucleic acids include
the DNA and the RNA. They are the hereditary determinants of living organisms. They are present
in most living cells either in free state or bound to proteins as nucleoproteins. The nucleic acids are
biopolymers with mononucleotides ad their repeating units. The monomers are known as
nucleotides, they are made up of three units: a sugar, an amine and a phosphate group.

Types of Nucleic Acids

Nucleic acids are of two types DNA and RNA

DNA (deoxyribonucleic acid)

DNA is one of the macromolecules, they are essential to all living forms.
Deoxyribonucleic acid contains the genetic information, it is used in the development and
functioning of all living organisms.
The DNA segments carry genetic information are called the genes.
Other DNA segments have structural functions or regulate the genetic information.
DNA are made of two chains made of polymer units of nucleotides.

The backbones of DNA are made of sugar and phosphate groups which are joined by ester
bonds.

The two strands of DNA are anti-parallel, they run in opposite directions.
Each sugar molecule is attached to one of the four nucleobases.

 The nucleobases encode genetic information, that is read using the genetic code.
Inside the cell, the DNA are arranged in long structures called chromosomes.
The chromosomes are duplicated in the process of DNA replication, during cell division.

Each cell has its own one complete set of chromosomes.

In eukaryotic organisms, most DNA is stored in the nucleus of the cell, and also some of it in
cellular organelles like mitochondria or chloroplast.
The prokaryotes store the DNA in the cytoplasm.

Chromatin proteins like histones compact and organize the DNA

RNA (ribonucleic acid)

The functions of ribonucleic acid is to convert genetic information from genes into amino
acid sequences of protein.
In some viruses, RNA contains the genetic information.
RNA is of three types, they are tRNA (transfer RNA), mRNA (messenger RNA) and rRNA
(ribosomal RNA).
Messenger RNA, as the name suggests acts a messenger. It carries genetic information
sequences between DNA and ribosomes, and it also directs protein synthesis.
rRNA is a major component of the ribososmes, they catalyze the formation of peptide bond.
The tRNA act as a carrier molecule for the amino acids that are used in protein synthesis. The
tRNA are also responsible for decoding the mRNA

Sugars in Nucleic Acid

The Deoxyribose Sugar
The deoxyribose sugar in DNA is a pentose, a five-carbon sugar. Four carbons and an oxygen
make up the five-membered ring; the other carbon branches off the ring. Similar to the

numbering of the purine and pyrimidine rings (seen in ), the carbon constituents of the sugar
ring are numbered 1'-4' (pronounced "one-prime carbon"), starting with the carbon to the right
of the oxygen going clockwise (). The fifth carbon (5') branches from the 4' carbon.

It is from this numbering system of the sugar group that DNA gets its
polarity. The linkages between nucleotides occur between the 5' and 3' positions on the sugar
group. One end has a free 5' end and the other has a free 3' end.
Attached to the remaining free carbons at the 1', 3' and 5' positions is an oxygen-containing
hydroxyl group (-OH). The DNA sugar is called adeoxyribose because it is lacking a hydroxyl
group at the 2' position. Instead there is just a hydrogen (see ).

Nitrogen base in NUCLEIC Acid

A nitrogenous base, or nitrogen-containing base, is an organic molecule with a nitrogen atom that
has the chemical properties of a base. The main biological function of a nitrogenous base is
to bond nucleic acids together. A nitrogenous base owes its basic properties to the lone
pair of electrons of a nitrogen atom.

Nitrogenous bases are typically classified as the derivatives of two parent

compounds, pyrimidine and purine.[1] They are non-polar and due to their aromaticity,planar. Both
pyrimidines and purines resemble pyridine and are thus weak bases and relatively unreactive
towards electrophilic aromatic substitution.[2]

Role in nucleic acids[

Main article: Nucleobase

In the biological sciences, nitrogenous bases are increasingly termed nucleobases because of their
role in nucleic acids - their flat shape is particularly important when considering their roles as the
building blocks of DNA and RNA. A set of five nitrogenous bases is used in the construction
of nucleotides, which in turn build up the nucleic acids like DNA and RNA. These nitrogenous bases
are adenine (A), uracil (U), guanine (G), thymine (T), and cytosine (C). These nitrogenous
bases hydrogen bond between opposing DNA strands to form the rungs of the "twisted ladder"
or double helix of DNA or a biological catalyst that is found in thenucleotides. Adenine is always
paired with thymine, and guanine is always paired with cytosine. These are known as base pairs.
Uracil is only present in RNA, replacing thymine. Pyrimidines include uracil, thymine, cytosine. They
have a single ring structure. Purines include adenine and guanine. They have a double ring structure.
[3]

nitrogenous bases accounts for the DNA absorbance peak at

260nm.

II Structural formula of Nucleic Acid

Structure of nucleic acids DNA and RNA are similar. The structure is divided into four different
levels, primary, secondary, tertiary and quaternary.

Primary Structure
Primary structure of nucleic acids is a linear sequence of nucleotides, which are linked to each
other by phosphodiester linkages. Nucleotides are made up of three components - Nitrogenous
base, 5-carbon sugar and phosphate groups.
Nitrogenous base are purines(adenine, guanine) and pyrimidines {cytosine, thymine (present in
DNA only), uracil (present in RNA only)}. The 5-carbon sugar is deoxyribose for DNA and and
ribose sugar in RNA. The purine bases, form glycosidic bond between their 9' nitrogen and the 9' OH group of the sugar molecule. The pyrimidine bases, they form glycosidic bond between 1'
nitrogen and the 9' -OH of the deoxyribose. In both purine and pyrimidine bases the phosphate
group forms a bond with the sugar molecule between one of its negatively charged oxygen groups
and the 5' -OH of the sugar. Nucleotides forms phosphodiester linkages between the 5' and 3'
carbon atoms, these form the nucleic acids. Nucleotides sequences are complementary to
one another.
Example of complementary sequence AGCT is TCGA.

Secondary Structure
Secondary structure is the interaction between the bases. This structure shows parts of which
strands are bound to each other. The two strands of DNA in the double helix of the DNA are bound
to each other by hydrogen bounds. The nucleotides on one strand base pairs with the nucleotides of
the other strand. The secondary structure of the DNA is predominantly the base pairing of the two
polynucleotide strands forming a double helix.

Tertiary Structure
Tertiary structure is the three dimensional shape into which the entire chain is folded. Tertiary
structure arrangement differs in four structural forms:
1. Left or right handedness.
2. Length of the turn of the helix.

3. Number of base pairs per turn.

4. The difference in size between major and the minor groove.
Quaternary Structure
Quaternary structure is the higher-level of organization of the nucleic acids. This structure refers to
the interactions of the nucleic acids with the other molecules. The most commonly seen
organization is the form of chromatin which shows interaction with small proteins histones.

Biofunctions of Nucleic acid

The main functions is store and transfer genetic information.
To use the genetic information to direct the synthesis of new protein.
The deoxyribonucleic acid is the storage for place for genetic information in the cell.
DNA controls the synthesis of RNA in the cell.
The genetic information is transmitted from DNA to the protein synthesizers in the cell.
RNA also directs the production of new protein by transmitting genetic information to the
protein building structures.
The function of the nitrogenous base sequences in the DNA backbone determines the
proteins being synthesized.
The function of the double helix of the DNA is that no disorders occur in the genetic
information if it is lost or damaged.
RNA directs synthesis of proteins.
m-RNA takes genetic message from RNA.
t-RNA transfers activated amino acid, to the site of protein synthesis.
r-RNA are mostly present in the ribosomes, and responsible for stability of m-RNA.

Denaturation of Nucleic acid

When a DNA solution is heated enough, The double-stranded DNA unwinds, and the Hydrogen bonds that hold the
two strands together weaken and finally break. The process of breaking a double-stranded DNA into single strands
is known as DNA denaturation, or DNA melting. The temperature at which the DNA strands are half denatured,
meaning half double-stranded, half single-stranded, is called the melting temperature(Tm). The amount of strand
separation, or melting, is measured by the absorbance of the DNA solution at 260nm. Nucleic acids absorb light at
this wavelength because of the electronic structure in their bases, but when two strands of DNA come together, the
close proximity of the bases in the two strands quenches some of this absorbance. When the two strands separate,
this quenching disappears and the absorbance rises 30%-40%.This is called Hyperchromicity. The Hypochromic
effect is the effect of stacked bases in a double helix absorbing less ultra-violet light.

Applications of DNA denaturationt

Sequence differences between two different DNA sequences can also be detected by using DNA denaturation. DNA
is heated and denatured into single-stranded state, and the mixture is cooled to permit strands to rehybridize. Hybrid
molecules are formed between similar sequences and any differences between those sequences will give a
disruption of the base-pairing

What determines the Melting Temperature (Tm)?

While the ratio of G to C and A to T in an organism's DNA is fixed, the GC content (percentage of G +C) can vary
considerably from one DNA to another. The percentage of GC content of DNA has a significant effect on its Tm.
Because G-C pairs form three hydrogen bonds, while A-T pairs form only two, the higher the percentage of GC
content, the higher its Tm. Thus, A double-stranded DNA riches in G and C needs more energy to be broken than
one that is riches in A and T, meaning higher melting temperature(Tm). Above the Tm, DNA denaturaizes, below it,
DNA anneals. Annealing is the reverse of denaturation.
One aspect of thermal denaturation is never discussed. The heat supplied to effect such denaturation has no
preferred direction and is therefore a scalar quantity. However, unwinding a double helix involves unwinding and this
has direction and is therefore a vector. The issue is this: how does a scalar change induce a vector change ?

Other methods to denature DNA

Heating is not the only way to denature DNA. Organic solvents such as dimethyl sulfoxide and formamide, or high
pH, could break the hydrogen bonding between DNA strands too. Low salt concentration could also denature DNA
double-strands by removing ions that stabilize the negative charges on the two strands from each other.
The central difficulty with denaturation of the double helix remains. How would two strands, typically consisting of
many turns, and often many hundreds of turns, actually effect strand separation after the hydrogen bonds have
been severed ?
A further, major difficulty lies in the fact that the application of heat to a suspension of nucleic acids amounts to the
application of a scalar quantity because the heat applied in this way has no direction. However, unwinding the
strands requires an angular force and this is a vector as it has a preferred direction. It has never been explained
how a scalar quantity (heat) can effect a vector change (rotation) in a solution.
A solution to these problems is offered by the side-by-side models in which there is no net winding of strands around
each other.

Mutations of Nucleic Acids

Description
Mutations can involve the duplication of large sections of DNA, usually through genetic recombination.[5]
These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes
duplicated in animal genomes every million years.[6] Most genes belong to larger gene families of shared
ancestry, known as homology.[7] Novel genes are produced by several methods, commonly through the
duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new
combinations with new functions.[8][9]
Here, protein domains act as modules, each with a particular and independent function, that can be mixed
together to produce genes encoding new proteins with novel properties.[10] For example, the human eye uses
four genes to make structures that sense light: three for cone cell or color vision and one for rod cell or night
vision; all four arose from a single ancestral gene.[11] Another advantage of duplicating a gene (or even an
entire genome) is that this increases engineering redundancy; this allows one gene in the pair to acquire a new
function while the other copy performs the original function.[12][13] Other types of mutation occasionally
create new genes from previously noncoding DNA.[14][15]
Changes in chromosome number may involve even larger mutations, where segments of the DNA within
chromosomes break and then rearrange. For example, in theHomininae, two chromosomes fused to produce
human chromosome 2; this fusion did not occur in the lineage of the other apes, and they retain these separate
chromosomes.[16] In evolution, the most important role of such chromosomal rearrangements may be to
accelerate the divergence of a population into new species by making populations less likely to interbreed,
thereby preserving genetic differences between these populations.[17]
Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the
genetic material of plants and animals, and may have been important in the evolution of genomes.[18] For
example, more than a million copies of the Alu sequence are present in the human genome, and these sequences
have now been recruited to perform functions such as regulating gene expression.[19] Another effect of these
mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and
thereby produce genetic diversity.[2]
Nonlethal mutations accumulate within the gene pool and increase the amount of genetic variation.[20] The
abundance of some genetic changes within the gene pool can be reduced by natural selection, while other "more
favorable" mutations may accumulate and result in adaptive changes.
Prodryas persephone, a LateEocene butterfly
For example, a butterfly may produce offspring with new mutations. The majority of these mutations will have
no effect; but one might change the color of one of the butterfly's offspring, making it harder (or easier) for
predators to see. If this color change is advantageous, the chance of this butterfly's surviving and producing its
own offspring are a little better, and over time the number of butterflies with this mutation may form a larger
percentage of the population.
Neutral mutations are defined as mutations whose effects do not influence the fitness of an individual. These
can accumulate over time due to genetic drift. It is believed that the overwhelming majority of mutations have
no significant effect on an organism's fitness.[citation needed] Also, DNA repair mechanisms are able to mend

most changes before they become permanent mutations, and many organisms have mechanisms for eliminating
otherwise-permanently mutated somatic cells.Beneficial mutations can improve reproductive success

FACTORS OF MUTATION
Four classes of mutations are (1) spontaneous mutations (molecular decay), (2) mutations due to errorprone replication bypass of naturally occurring DNA damage (also called error-prone translesion
synthesis), (3) errors introduced during DNA repair, and (4) induced mutations caused by mutagens.
Scientists may also deliberately introduce mutant sequences through DNA manipulation for the sake of
scientific experimentation.
Spontaneous mutation
Spontaneous mutations on the molecular level can be caused by:[21]
Tautomerism A base is changed by the repositioning of a 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 atypical base containing a keto group in place
of the original amine group. Examples include C U and A HX (hypoxanthine), which can be
corrected by DNA repair mechanisms; and 5MeC (5-methylcytosine) T, which is less likely to be
detected as a mutation because thymine is a normal DNA base.
Slipped strand mispairing Denaturation of the new strand from the template during replication,
followed by renaturation in a different spot ("slipping"). This can lead to insertions or deletion

Types of Mutation

By effect on structure

Illustrations of five types of chromosomal mutations.

Selection of disease-causing mutations, in a standard table of the genetic code of amino acids.[29]

The sequence of a gene can be altered in a number of ways. Gene mutations have varying
effects on health depending on where they occur and whether they alter the function of essential
proteins. Mutations in the structure of genes can be classified as:

Small-scale mutations, such as those affecting a small gene in one or a few nucleotides,
including:

Point mutations, often caused by chemicals or malfunction of DNA replication,

exchange a single nucleotide for another.[30] These changes are classified as transitions or
transversions.[31] Most common is the transition that exchanges a purine for a purine (A
G) or a pyrimidine for a pyrimidine, (C T). A transition can be caused by nitrous acid,
base mis-pairing, or mutagenic base analogs such as BrdU. Less common is a
transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T
A/G). An example of a transversion is the conversion of adenine (A) into a cytosine (C).
A point mutation can be reversed by another point mutation, in which the nucleotide is
changed back to its original state (true reversion) or by second-site reversion (a
complementary mutation elsewhere that results in regained gene functionality). Point
mutations that occur within the protein coding region of a gene may be classified into three
kinds, depending upon what the erroneous codon codes for:

Silent mutations, which code for the same (or a sufficiently similar) amino
acid.

Missense mutations, which code for a different amino acid.

Nonsense mutations, which code for a stop codon and can truncate the
protein.

Insertions add one or more extra nucleotides into the DNA. They are usually
caused by transposable elements, or errors during replication of repeating elements.
Insertions in the coding region of a gene may alter splicing of themRNA (splice site
mutation), or cause a shift in the reading frame (frameshift), both of which can significantly
alter thegene product. Insertions can be reversed by excision of the transposable element.

Deletions remove one or more nucleotides from the DNA. Like insertions, these
mutations can alter the reading frame of the gene. In general, they are irreversible: Though
exactly the same sequence might in theory be restored by an insertion, transposable
elements able to revert a very short deletion (say 12 bases) in any location either are
highly unlikely to exist or do not exist at all.

Large-scale mutations in chromosomal structure, including:

Amplifications (or gene duplications) leading to multiple copies of all chromosomal

regions, increasing the dosage of the genes located within them.

Deletions of large chromosomal regions, leading to loss of the genes within those
regions.

Mutations whose effect is to juxtapose previously separate pieces of DNA,

potentially bringing together separate genes to form functionally distinct fusion
genes (e.g., bcr-abl). These include:

Chromosomal translocations: interchange of genetic parts from

nonhomologous chromosomes.

Interstitial deletions: an intra-chromosomal deletion that removes a segment

of DNA from a single chromosome, thereby apposing previously distant genes. For
example, cells isolated from a human astrocytoma, a type of brain tumor, were found to
have a chromosomal deletion removing sequences between the Fused in Glioblastoma
(FIG) gene and the receptor tyrosine kinase (ROS), producing a fusion protein (FIGROS). The abnormal FIG-ROS fusion protein has constitutively active kinase activity
that causes oncogenic transformation (a transformation from normal cells to cancer
cells).

Chromosomal inversions: reversing the orientation of a chromosomal

segment.

Loss of heterozygosity: loss of one allele, either by a deletion or a genetic

recombination event, in an organism that previously had two different alleles.

By effect on function

Loss-of-function mutations, also called inactivating mutations, result in the gene

product having less or no function (being partially or wholly inactivated). When the allele has a
complete loss of function (null allele), it is often called an amorphic mutation in the Muller's
morphs schema. Phenotypes associated with such mutations are most often recessive.
Exceptions are when the organism is haploid, or when the reduced dosage of a normal gene
product is not enough for a normal phenotype (this is calledhaploinsufficiency).

Gain-of-function mutations, also called activating mutations, change the gene product
such that its effect gets stronger (enhanced activation) or even is superseded by a different
and abnormal function. When the new allele is created, a heterozygote containing the newly
created allele as well as the original will express the new allele; genetically this defines the
mutations as dominant phenotypes. Often called a neomorphic mutation.[32]

Dominant negative mutations (also called antimorphic mutations) have an altered

gene product that acts antagonistically to the wild-type allele. These mutations usually result
in an altered molecular function (often inactive) and are characterized by a dominant or semidominant phenotype. In humans, dominant negative mutations have been implicated in
cancer (e.g., mutations in genes p53,[33] ATM,[34] CEBPA[35] and PPARgamma[36]). Marfan
syndrome is caused by mutations in the FBN1 gene, located onchromosome 15, which
encodes fibrillin-1, a glycoprotein component of the extracellular matrix.[37] Marfan syndrome is
also an example of dominant negative mutation and haploinsufficiency.[38][39]

Lethal mutations are mutations that lead to the death of the organisms that carry the
mutations.

A back mutation or reversion is a point mutation that restores the original sequence and
hence the original phenotype.[40]

By effect on fitness
In applied genetics, it is usual to speak of mutations as either harmful or beneficial.

A harmful, or deleterious, mutation decreases the fitness of the organism.

A beneficial, or advantageous mutation increases the fitness of the organism. Mutations

that promotes traits that are desirable, are also called beneficial. In theoretical population
genetics, it is more usual to speak of mutations as deleterious or advantageous than harmful
or beneficial.

A neutral mutation has no harmful or beneficial effect on the organism. Such mutations
occur at a steady rate, forming the basis for the molecular clock. In the neutral theory of
molecular evolution, neutral mutations provide genetic drift as the basis for most variation at
the molecular level.

A nearly neutral mutation is a mutation that may be slightly deleterious or advantageous,

although most nearly neutral mutations are slightly deleterious.

Distribution of fitness effects

Attempts have been made to infer the distribution of fitness effects (DFE)
using mutagenesis experiments and theoretical models applied to molecular sequence data.
DFE, as used to determine the relative abundance of different types of mutations (i.e., strongly
deleterious, nearly neutral or advantageous), is relevant to many evolutionary questions, such as
the maintenance of genetic variation,[41] the rate of genomic decay,[42] the maintenance of
outcrossing sexual reproduction as opposed to inbreeding[43] and the evolution of sex and genetic
recombination.[44] In summary, the DFE plays an important role in predicting evolutionary
dynamics.[45][46] A variety of approaches have been used to study the DFE, including theoretical,
experimental and analytical methods.

Mutagenesis experiment: The direct method to investigate the DFE is to induce

mutations and then measure the mutational fitness effects, which has already been done in
viruses, bacteria, yeast, and Drosophila. For example, most studies of the DFE in viruses
used site-directed mutagenesis to create point mutations and measure relative fitness of
each mutant.[47][48][49][50] In Escherichia coli, one study used transposon mutagenesis to directly
measure the fitness of a random insertion of a derivative of Tn10.[51]In yeast, a combined

mutagenesis and deep sequencing approach has been developed to generate high-quality
systematic mutant libraries and measure fitness in high throughput. [52] However, given that
many mutations have effects too small to be detected [53] and that mutagenesis experiments
can detect only mutations of moderately large effect; DNA sequence data analysis can
provide valuable information about these mutations.

The distribution of fitness effects (DFE) of mutations invesicular stomatitis virus. In this experiment, random
mutations were introduced into the virus by site-directed mutagenesis, and the fitness of each mutant was
compared with the ancestral type. A fitness of zero, less than one, one, more than one, respectively, indicates
that mutations are lethal, deleterious, neutral, and advantageous.[47]

Molecular sequence analysis: With rapid development of DNA sequencing technology,

an enormous amount of DNA sequence data is available and even more is forthcoming in the
future. Various methods have been developed to infer the DFE from DNA sequence data. [54][55]
[56][57]

By examining DNA sequence differences within and between species, we are able to infer

various characteristics of the DFE for neutral, deleterious and advantageous mutations. [20] To
be specific, the DNA sequence analysis approach allows us to estimate the effects of
mutations with very small effects, which are hardly detectable through mutagenesis
experiments.
One of the earliest theoretical studies of the distribution of fitness effects was done by Motoo
Kimura, an influential theoretical population geneticist. His neutral theory of molecular evolution
proposes that most novel mutations will be highly deleterious, with a small fraction being neutral.
[58][59]

Hiroshi Akashi more recently proposed a bimodalmodel for the DFE, with modes centered

around highly deleterious and neutral mutations. [60] Both theories agree that the vast majority of
novel mutations are neutral or deleterious and that advantageous mutations are rare, which has
been supported by experimental results. One example is a study done on the DFE of random
mutations invesicular stomatitis virus.[47] Out of all mutations, 39.6% were lethal, 31.2% were nonlethal deleterious, and 27.1% were neutral. Another example comes from a high throughput

mutagenesis experiment with yeast.[52] In this experiment it was shown that the overall DFE is
bimodal, with a cluster of neutral mutations, and a broad distribution of deleterious mutations.
Though relatively few mutations are advantageous, those that are play an important role in
evolutionary changes.[61]Like neutral mutations, weakly selected advantageous mutations can be
lost due to random genetic drift, but strongly selected advantageous mutations are more likely to
be fixed. Knowing the DFE of advantageous mutations may lead to increased ability to predict the
evolutionary dynamics. Theoretical work on the DFE for advantageous mutations has been done
by John H. Gillespie[62] and H. Allen Orr.[63] They proposed that the distribution for advantageous
mutations should be exponential under a wide range of conditions, which, in general, has been
supported by experimental studies, at least for strongly selected advantageous mutations. [64][65][66]
In general, it is accepted that the majority of mutations are neutral or deleterious, with rare
mutations being advantageous; however, the proportion of types of mutations varies between
species. This indicates two important points: first, the proportion of effectively neutral mutations is
likely to vary between species, resulting from dependence on effective population size; second,
the average effect of deleterious mutations varies dramatically between species. [20] In addition, the
DFE also differs between coding regions andnoncoding regions, with the DFE of noncoding DNA
containing more weakly selected mutations.[20]

By impact on protein sequence[edit]

A frameshift mutation is a mutation caused by insertion or deletion of a number of

nucleotides that is not evenly divisible by three from a DNA sequence. Due to the triplet nature
of gene expression by codons, the insertion or deletion can disrupt the reading frame, or the
grouping of the codons, resulting in a completely different translation from the original.[67] The
earlier in the sequence the deletion or insertion occurs, the more altered the protein produced
is.
In contrast, any insertion or deletion that is evenly divisible by three is termed an in-frame
mutation
A nonsense mutation is a point mutation in a sequence of DNA that results in a
premature stop codon, or a nonsense codon in the transcribed mRNA, and possibly a
truncated, and often nonfunctional protein product. (See Stop codon.)

 Missense mutations or nonsynonymous mutations are types of point mutations where a

single nucleotide is changed to cause substitution of a different amino acid. This in turn
can render the resulting protein nonfunctional. Such mutations are responsible for
diseases such as Epidermolysis bullosa, sickle-cell disease, and SOD1-mediatedALS.[68]
A neutral mutation is a mutation that occurs in an amino acid codon that results in the use
of a different, but chemically similar, amino acid. The similarity between the two is enough
that little or no change is often rendered in the protein. For example, a change from AAA to
AGA will encode arginine, a chemically similar molecule to the intendedlysine.
Silent mutations are mutations that do not result in a change to the amino acid sequence
of a protein, unless the changed amino acid is sufficiently similar to the original. They may
occur in a region that does not code for a protein, or they may occur within a codon in a
manner that does not alter the final amino acid sequence. The phrasesilent mutation is
often used interchangeably with the phrase synonymous mutation; however, synonymous
mutations are a subcategory of the former, occurring only within exons (and necessarily
exactly preserving the amino acid sequence of the protein). Synonymous mutations occur
due to the degenerate nature of the genetic code.

By inheritance

A mutation has caused this gardenmoss rose to produce flowers of different colors. This is
a somaticmutation that may also be passed on in the germline.

In multicellular organisms with dedicated reproductive cells, mutations can be subdivided

into germline mutations, which can be passed on to descendants through their reproductive
cells, and somatic mutations (also called acquired mutations),[69] which involve cells outside
the dedicated reproductive group and which are not usually transmitted to descendants.

A germline mutation gives rise to a constitutional mutation in the offspring, that is, a mutation
that is present in every cell. A constitutional mutation can also occur very soon
after fertilisation, or continue from a previous constitutional mutation in a parent. [70]
The distinction between germline and somatic mutations is important in animals that have a
dedicated germline to produce reproductive cells. However, it is of little value in understanding
the effects of mutations in plants, which lack dedicated germline. The distinction is also
blurred in those animals that reproduce asexually through mechanisms such as budding,
because the cells that give rise to the daughter organisms also give rise to that organism's
germline. A new mutation that was not inherited from either parent is called a de
novomutation.
Diploid organisms (e.g., humans) contain two copies of each genea paternal and a maternal
allele. Based on the occurrence of mutation on each chromosome, we may classify mutations
into three types.
A heterozygous mutation is a mutation of only one allele.
A homozygous mutation is an identical mutation of both the paternal and maternal
alleles.
Compound heterozygous mutations or a genetic compound comprises two different
mutations in the paternal and maternal alleles. [71]
A wild type or homozygous non-mutated organism is one in which neither allele is mutated.

Repair mechanisms
DNA repair is a collection of processes by which a cell identifies and corrects damage to
the DNA molecules that encode itsgenome. In human cells, both normal metabolic activities and
environmental factors such as UV light and radiation can cause DNA damage, resulting in as
many as 1 million individual molecular lesions per cell per day.[1] Many of these lesions cause
structural damage to the DNA molecule and can alter or eliminate the cell's ability
to transcribe the gene that the affected DNA encodes. Other lesions induce potentially
harmful mutations in the cell's genome, which affect the survival of its daughter cells after it
undergoesmitosis. As a consequence, the DNA repair process is constantly active as it responds

to damage in the DNA structure. When normal repair processes fail, and when
cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand
breaks and DNA crosslinkages (interstrand crosslinks or ICLs). [2][3]
The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell,
and the extracellular environment. A cell that has accumulated a large amount of DNA damage, or
one that no longer effectively repairs damage incurred to its DNA, can enter one of three possible
states:
1. an irreversible state of dormancy, known as senescence
2. cell suicide, also known as apoptosis or programmed cell death
3. unregulated cell division, which can lead to the formation of a tumor that is cancerous
The DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal
functionality of that organism. Many genes that were initially shown to influence life span have
turned out to be involved in DNA damage repair and protection. [4]

Paul Modrich

The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich, and Aziz
Sancar for their work on the molecular mechanisms of DNA repair processes. [5][6]
DNA damage

DNA damage, due to environmental factors and normal metabolic processes inside the cell,
occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day.[1] While this constitutes
only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs),
unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability
to carry out its function and appreciably increase the likelihood of tumor formation and contribute
to tumour heterogeneity.
The vast majority of DNA damage affects the primary structure of the double helix; that is, the
bases themselves are chemically modified. These modifications can in turn disrupt the molecules'
regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit

in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and
therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and
wound around "packaging" proteins calledhistones (in eukaryotes), and both superstructures are
vulnerable to the effects of DNA damage.

Sources of damage[edit]
DNA damage can be subdivided into two main types:
1. endogenous damage such as attack by reactive oxygen species produced from normal
metabolic byproducts (spontaneous mutation), especially the process of oxidative
deamination
1. also includes replication errors
2. exogenous damage caused by external agents such as
1. ultraviolet [UV 200-400 nm] radiation from the sun
2. other radiation frequencies, including x-rays and gamma rays
3. hydrolysis or thermal disruption
4. certain plant toxins
5. human-made mutagenic chemicals, especially aromatic compounds that act as
DNA intercalating agents
6. viruses[7]
The replication of damaged DNA before cell division can lead to the incorporation of wrong bases
opposite damaged ones. Daughter cells that inherit these wrong bases carry mutations from
which the original DNA sequence is unrecoverable (except in the rare case of a back mutation, for
example, through gene conversion).

Types of damage
There are several types of damage to DNA due to endogenous cellular processes:

1. oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine (8-oxoG)] and generation of DNA strand

interruptions from reactive oxygen species,
2. alkylation of bases (usually methylation), such as formation of 7-methylguanosine, 1methyladenine, 6-O-Methylguanine
3. hydrolysis of bases, such as deamination, depurination, and depyrimidination.
4. "bulky adduct formation" (i.e., benzo[a]pyrene diol epoxide-dG adduct, aristolactam I-dA
adduct)
5. mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is
stitched into place in a newly forming DNA strand, or a DNA base is skipped over or
mistakenly inserted.
6. Monoadduct damage cause by change in single nitrogenous base of DNA
7. Diadduct damage
Damage caused by exogenous agents comes in many forms. Some examples are:
1. UV-B light causes crosslinking between adjacent cytosine and thymine bases
creating pyrimidine dimers. This is called direct DNA damage.
2. UV-A light creates mostly free radicals. The damage caused by free radicals is
called indirect DNA damage.
3. Ionizing radiation such as that created by radioactive decay or in cosmic rays causes
breaks in DNA strands. Intermediate-level ionizing radiation may induce irreparable DNA
damage (leading to replicational and transcriptional errors needed for neoplasia or may
trigger viral interactions) leading to pre-mature aging and cancer.
4. Thermal disruption at elevated temperature increases the rate of depurination (loss
of purine bases from the DNA backbone) and single-strand breaks. For example,
hydrolytic depurination is seen in the thermophilic bacteria, which grow in hot springs at
40-80 C.[8][9] The rate of depurination (300 purine residues per genome per generation) is
too high in these species to be repaired by normal repair machinery, hence a possibility of
an adaptive response cannot be ruled out.

5. Industrial chemicals such as vinyl chloride and hydrogen peroxide, and environmental
chemicals such as polycyclic aromatic hydrocarbons found in smoke, soot and tar create a
huge diversity of DNA adducts- ethenobases, oxidized bases, alkylated phosphotriesters
and crosslinking of DNA, just to name a few.
UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of
induced damage. Spontaneous damage can include the loss of a base, deamination, sugar ring
puckering and tautomeric shift.

Nuclear versus mitochondrial DNA damage

In human cells, and eukaryotic cells in general, DNA is found in two cellular locations inside
the nucleus and inside the mitochondria. Nuclear DNA (nDNA) exists as chromatinduring nonreplicative stages of the cell cycle and is condensed into aggregate structures known
as chromosomes during cell division. In either state the DNA is highly compacted and wound up
around bead-like proteins called histones. Whenever a cell needs to express the genetic
information encoded in its nDNA the required chromosomal region is unravelled, genes located
therein are expressed, and then the region is condensed back to its resting conformation.
Mitochondrial DNA (mtDNA) is located inside mitochondriaorganelles, exists in multiple copies,
and is also tightly associated with a number of proteins to form a complex known as the nucleoid.
Inside mitochondria, reactive oxygen species (ROS), or free radicals, byproducts of the constant
production of adenosine triphosphate (ATP) via oxidative phosphorylation, create a highly
oxidative environment that is known to damage mtDNA. A critical enzyme in counteracting the
toxicity of these species is superoxide dismutase, which is present in both the mitochondria
and cytoplasm of eukaryotic cells.

Senescence and apoptosis[edit]

Senescence, an irreversible process in which the cell no longer divides, is a protective response
to the shortening of the chromosome ends. The telomeres are long regions of
repetitive noncoding DNA that cap chromosomes and undergo partial degradation each time a
cell undergoes division (see Hayflick limit).[10] In contrast, quiescence is a reversible state of
cellular dormancy that is unrelated to genome damage (see cell cycle). Senescence in cells may
serve as a functional alternative to apoptosis in cases where the physical presence of a cell for
spatial reasons is required by the organism,[11] which serves as a "last resort" mechanism to
prevent a cell with damaged DNA from replicating inappropriately in the absence of pro-

growth cellular signaling. Unregulated cell division can lead to the formation of a tumor
(see cancer), which is potentially lethal to an organism. Therefore, the induction of senescence
and apoptosis is considered to be part of a strategy of protection against cancer.[12]

Essential and nonessential Amino Acids

Amino acids
(essential and non-essential)

essential amino acids

acids

______ non-essential amino

Histadine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

Arginine
Alanine
Asparagine
Aspartate
Cysteine

Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine

These are the 20 biologically active amino acids in humans. In nature, there are more
than 100 different types of amino acids to be found.
However, the human uses only 20 of them. Because the human uses only 20 different
amino acids out of the many types found in nature, we refer to them as 'biologically
active'.
They are 'biologically active' simply because if we consume other types of amino acids,
they will not be incorporated into proteins, and are deemed useless or 'non-biologically
active'. Consuming some amino acids are are not biologically active can also be harmful
(Download)
Amino acids are the building blocks of proteins. An amino acid can chemically bond with
another amino acid and so forth, eventually forming a chain. When two or more amino
acids are connected they are referred to as a protein. Some proteins are very short in
legth. Some are very long. See below.
The sweetener known as Aspartame, is a protein with a length of only two amino acids.
Since this protein has only two amino acids, we conveniently call it a di-peptide (di,
meaning '2' and peptide, meaning 'bond for proteins'). This is how we make things easier
to chat about in the laboratory or hospital while we are drinking lots of coffee (with
Aspartame sometimes!)Although Aspartame is a small protein, it fools the human

tongue, causing the brain believe it's a sugar. Aspartame is up to 180 times as
sweet as sugar, but minus the calories!
This is but one example of how powerful and useful amino acids and thus,
proteins are, even the small ones. It's the small ones you have to watch out
for! And that's not an exaggeration. Read how some proteins can 'sneak into'
the body and cause serious health problems. (download)
Amino acids and proteins can be both useful and equally harmful.
We looked at how short in legth proteins can be when as little as two combine.
But how many amino acids can combine in length to make longer and larger
proteins?
Human Growth Hormone is a protein which is 192 amino acids in length. It is
produced in the pituitary gland of the brain and control growth, metabolism
and other functions. Imagine cells in our body, such as those of the pituitary
gland having the chemical instructions and power to actually bond (link) amino
acids together in order to make proteins such as growth hormone and many
others.

Cells that link amino acids together to form proteins must perform perfectly
each time they produce a protein. If the cell places even 1 amino acid out of
sequence during protein synthesis, unpredictable function of the protein will
result.
Reference
://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/DNA_Denaturationhttps
://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/DNA_Denaturationhttps
_://nutriology.comhttp /aaessnoness.html
http://nutriology.com/aaessnoness.html

https://en.wikipedia.org/wiki/DNA_repair
https://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/DNA_Denaturation