Nucleic Acids: DNA and RNA

(seminar paper)













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Contents:


1. Introduction .........................................................................................................3
2.1.History of Nucleic Acids .....................................................................................4
2.2. Structure of Nucleic Acids..................................................................................6
2.2.1. Structure of DNA ....................................................................................6
2.2.2. Structure of RNA ....................................................................................7
2.3.Uses in technology ...............................................................................................8
2.3.1. Genetic engineering ..................................................................................8
2.3.2. Bioinformatics ..........................................................................................8
2.3.3. Forensics ...................................................................................................9
2.3.4. History and anthropology .........................................................................9
3. Conclusion ..................................................................................................................10
4. Summary .....................................................................................................................10
5. References .................................................................................................................. 12











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1. Introduction
Nucleic acids are polymeric macromolecules, or large biological molecules, essential for all
known forms of life. There are two types of nucleic acids: deoxyribonucleic acid, better
known as DNA and ribonucleic acid, better known as RNA. They are composed of nucleotide
monomers. Nucleotides have three parts - a nitrogenous base, a five-carbon sugar and a
phosphate group. Nucleic acids allow organisms to transfer genetic information from one
generation to the next. When a cell divides, its DNA is copied and passed from one cell
generation to the next generation. DNA contains the "programmatic instructions" for cellular
activities. When organisms produce offspring, these instructions, in the form of DNA, are
passed down. RNA is involved in the synthesis of proteins. "Information" is typically passed
from DNA to RNA to the resulting proteins.
Nucleic acids were discovered by Friedrich Miescher in 1869. Experimental studies of nucleic
acids constitute a major part of modern biological and medical research, and form a
foundation for genome and forensic science, as well as the biotechnology and pharmaceutical
industries.
Together with proteins, nucleic acids are the most important biological macromolecules; each
is found in abundance in all living things, where they function in encoding, transmitting and
expressing genetic informationin other words, information is conveyed through the nucleic
acid sequence, or the order of nucleotides within a DNA or RNA molecule. Strings of
nucleotides strung together in a specific sequence are the mechanism for storing and
transmitting hereditary or genetic, information via protein synthesis.






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2.1. History of Nucleic Acids
For many years, the role of nucleic acids in living systems was unknown. In the winter of
1868/9 the young Swiss doctor Friedrich Miescher, while working in the laboratory,
performed experiments on the chemical composition of leukocytes that lead to the discovery
of DNA. In his experiments, Miescher noticed a precipitate of an unknown substance. Its
properties during the isolation procedure and its resistance to protease digestion indicated that
the novel substance was not a protein or lipid. Analyses of its elementary composition
revealed that, unlike proteins, it contained large amounts of phosphorous and, as Miescher
confirmed later, lacked sulphur. Miescher recognised that he had discovered a novel
molecule. Since he had isolated it from the cells' nuclei he named it nuclein, a name preserved
in today's designation deoxyribonucleic acid. In subsequent work Miescher showed that
nuclein was a characteristic component of all nuclei and hypothesised that it would prove to
be inextricably linked to the function of this organelle. But even though it was Miescher who
discovered DNA, his name is not usually associated with this molecule today. Also, it wasnt
strictly DNA that was discovered, but globally there were both DNA and RNA included as
nucleid acids.

In 1919, Phoebus Levene identified the base, sugar and phosphate nucleotide unit. It
happened to be a very important discovery because with those facts he could characterize the
different forms of nucleic acids, and those were DNA and RNA. In 1905, Levene was
appointed as head of the biochemical laboratory at the Rockefeller Institute of Medical
Research. He spent the rest of his career at this institute, and it was there that he identified the
components of DNA.

In 1944 Oswald Avery presented evidence that nucleic acids were involved in the storage and
transfer of the genetic information needed for the synthesis of proteins. This suggestion was
actively opposed by many of his contemporaries, who believed that the structure of the
nucleic acids was too regular and therefore too dull to carry the information that codes
for the thousands of different proteins a cell needs to survive.
In retrospect, the first clue about how nucleic acids function was obtained by Erwin Chargaff,
who found that DNA always contains the same amounts of certain pairs of bases. There is
always just as much adenine as thymine, for example, and just as much guanine as cytosine.
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In 1953, James Watson and Francis Crick suggested what is now accepted as the first correct
double-helix model of DNA structure in the journal Nature. Their double-helix, molecular
model of DNA was then based on a single X-ray diffraction image taken by Rosalind
Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases
are paired also obtained through private communications from Erwin Chargaff in the
previous years. Chargaff's rules played a very important role in establishing double-helix
configurations for different types of DNA. Although it was Rosalind Franklin who discovered
the DNA structure through the X-ray crystallographic method, her colleague Maurice
Wilkins, as so as Watson and Crick were those whose names famous for building its structure.
In 1962 James Watson, Francis Crick, and Maurice Wilkins jointly received the Nobel Prize
in physiology or medicine for their 1953 determination of the structure of deoxyribonucleic
acid (DNA). Wilkinss colleague Rosalind Franklin, who died of cancer at the age of 37, was
not so honored because the Nobel Prize can only be shared by three scientists.
















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2.2. Structure of Nucleic Acids
The nucleic acidsDNA and RNAare the principal informational molecules of the cell.
DNA and RNA are polymers of nucleotides, which consist of purine and pyrimidine bases
linked to phosphorylated sugars. DNA contains two purines (adenine and guanine) and two
pyrimidines (cytosine and thymine). Adenine, guanine, and cytosine are also present in RNA,
but RNA contains uracil in place of thymine. The bases are linked to sugars (2-
deoxyribose in DNA, or ribose in RNA) to form nucleosides. Nucleotides additionally contain
one or more phosphate groups linked to the 5 carbon of nucleoside sugars.

2.2.1. STRUCTURE OF DNA
Deoxyribonucleic acid (DNA) has a unique role as the genetic material, which in eukaryotic
cells is located in the nucleus. The DNA segments carrying this genetic information are called
genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating
the use of this genetic information. Along with RNA and proteins, DNA is one of the three
major macromolecules that are essential for all known forms of life. DNA consists of two
long polymers of simple units called nucleotides, with backbones made of sugars and
phosphate groups joined by ester bonds. These two strands run in opposite directions to each
other and are, therefore, anti-parallel. The polymerization of nucleotides to
form nucleic acids involves the formation of phosphodiester bonds between the 5 phosphate
of one nucleotide and the 3 hydroxyl of another. Oligonucleotides are small polymers
containing only a few nucleotides; the large polynucleotides that make up
cellular RNA and DNA may contain thousands or millions of nucleotides, respectively. It is
important to note that a polynucleotide chain has a sense of direction, with one end of the
chain terminating in a 5 phosphate group and the other in a 3 hydroxyl group.
Polynucleotides are always synthesized in the 5 to 3 direction, with a free nucleotide being
added to the 3 OH group of a growing chain. By convention, the sequence of bases in DNA
or RNA is also written in the 5 to 3 direction.


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Within cells DNA is organized into long structures called chromosomes. During cell division
these chromosomes are duplicated in the process of DNA replication, providing each cell its
own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists)
store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as
mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA
only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact
and organize DNA.

2.2.2. STRUCTURE OF RNA
Different types of ribonucleic acid (RNA) participate in a number of cellular
activities. Messenger RNA (mRNA) carries information from DNA to the ribosomes, where it
serves as a template for protein synthesis. Two other types of RNA (ribosomal
RNA and transfer RNA) are involved in protein synthesis. Still other kinds of RNAs are
involved in the processing and transport of both RNAs and proteins. In addition to acting as
an informational molecule, RNA is also capable of catalyzing a number of chemical reactions.
In present-day cells, these include reactions involved in both protein synthesis and RNA
processing.

Nucleotides are not only important as the building blocks of nucleic acids. They also play
critical roles in other cell processes. Perhaps the most prominent example is adenosine 5-
triphosphate (ATP), which is the principal form of chemical energy within cells. Other
nucleotides similarly function as carriers of either energy or reactive chemical groups in a
wide variety of metabolic reactions. In addition, some nucleotides are important signaling
molecules within cells.






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2.3. Uses in technology

2.3.1. GENETIC ENGINEERING
Methods have been developed to purify DNA from organisms, and to manipulate it in the
laboratory. Modern biology and biochemistry make intensive use of these techniques in
recombinant DNA technology. Recombinant DNA is a man-made DNA sequence that has
been assembled from other DNA sequences. They can be transformed into organisms in the
form of plasmids or in some other appropriate format. The genetically modified organisms
produced can be used to produce products such as recombinant proteins, used in medical
research, or be grown in agriculture.


2.3.2. BIONFORMATICS
Bioinformatics is an interdisciplinary scientific field that develops methods for storing,
retrieving, organizing and analyzing biological data. A major activity in bioinformatics is to
develop software tools to generate useful biological knowledge. Bioinformatics is a distinct
science from biological computation, the latter being a computer science and computer
engineering subfield using bioengineering and biology to build biological computers, whereas
bioinformatics simply uses computers to better understand biology.
Bioinformatics involves the manipulation, searching, and data mining of biological data, and
this includes DNA sequence data. The development of techniques to store and search DNA
sequences have led to widely applied advances in computer science, especially string
searching algorithms, machine learning and database theory. String searching or matching
algorithms, which find an occurrence of a sequence of letters inside a larger sequence of
letters, were developed to search for specific sequences of nucleotides. The DNA sequence
may be aligned with other DNA sequences to identify homologous sequences and locate the
specific mutations that make them distinct. These techniques, especially multiple sequence
alignment, are used in studying phylogenetic relationships and protein function.


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2.3.3. FORENSICS
Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a crime
scene to identify a matching DNA of an individual, such as a perpetrator. This process is
formally termed DNA profiling, but may also be called "genetic fingerprinting". In DNA
profiling, the lengths of variable sections of repetitive DNA, such asshort tandem
repeats and minisatellites, are compared between people. This method is usually an
extremely reliable technique for identifying a matching DNA. However, identification can
be complicated if the scene is contaminated with DNA from several people. DNA
profiling was developed in 1984 by British geneticist Sir Alec Jeffreys, and first used in
forensic science to convict Colin Pitchfork in the 1988 Enderby murders case.
DNA profiling is also used to identify victims of mass casualty incidents. As well as
positively identifying bodies or body parts in serious accidents, DNA profiling is being
successfully used to identify individual victims in mass war graves matching to family
members.


2.3.4. HISTORY AND ANTROPOLOGY
Because DNA collects mutations over time, which are then inherited, it contains historical
information, and, by comparing DNA sequences, geneticists can infer the evolutionary history
of organisms, their phylogeny. This field of phylogenetics is a powerful tool in evolutionary
biology. If DNA sequences within a species are compared, population geneticists can learn
the history of particular populations. This can be used in studies ranging from ecological
genetics to anthropology.
DNA has also been used to look at modern family relationships, such as establishing family
relationships between the descendants. This usage is closely related to the use of DNA in
criminal investigations detailed above. Indeed, some criminal investigations have been solved
when DNA from crime scenes has matched relatives of the guilty individual.



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3. Conclusion
DNA contains the genetic information that allows all modern living things to function, grow
and reproduce. However, it is unclear how long in the 4-billion-year history of life DNA has
performed this function, as it has been proposed that the earliest forms of life may have used
RNA as their genetic material. RNA may have acted as the central part of early cell
metabolism as it can both transmit genetic information and carry out catalysis as part
of ribozymes. This ancient RNA world where nucleic acid would have been used for both
catalysis and genetics may have influenced the evolution of the current genetic code based on
four nucleotide bases.
Although there are many researches of nucleic acids, and many known facts, field of DNA
analyzes is still widely unknown if it goes back in time, as so as there are many more facts
that could be revealed and discovered.
Also, one DNA or RNA molecule differs from another primarily in the sequence of
nucleotides. Nucleotide sequences are of great importance in biology since they carry the
ultimate instructions that encode all biological molecules, molecular assemblies, subcellular
and cellular structures, organs and organisms, and directly enable cognition, memory and
behavior. Enormous efforts have gone into the development of experimental methods to
determine the nucleotide sequence of biological DNA and RNA molecules, and today
hundreds of millions of nucleotides are sequenced daily at genome centers and smaller
laboratories worldwide.

4. Summary
Living organisms are complex systems. Hundreds of thousands of proteins exist inside each
one of us to help carry out our daily functions. These proteins are produced locally, assembled
piece-by-piece to exact specifications. An enormous amount of information is required to
manage this complex system correctly. This information, detailing the specific structure of the
proteins inside of our bodies, is stored in a set of molecules called nucleic acids.
The nucleic acids are very large molecules that have two main parts. The backbone of
a nucleic acid is made of alternating sugar and phosphate molecules bonded together in a long
chain. Though only four different nucleotide bases can occur in a nucleic acid, each nucleic
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acid contains millions of bases bonded to it. The order in which these nucleotide bases appear
in the nucleic acid is the coding for the information carried in the molecule. In other words,
the nucleotide bases serve as a sort of genetic alphabet on which the structure of
each protein in our bodies is encoded. In most living organisms (except for viruses), genetic
information is stored in the molecule deoxyribonucleic acid, or DNA. DNA is made and
resides in the nucleus of living cells. DNA gets its name from the sugar molecule contained in
its backbone (deoxyribose); however, it gets its significance from its unique structure. Four
different nucleotide bases occur in DNA: adenine (A), cytosine (C), guanine (G), and thymine
(T). The versatility of DNA comes from the fact that the molecule is actually double-stranded.
The nucleotide bases of the DNA molecule form complementary pairs: The
nucleotides hydrogen bond to another nucleotide base in a strand of DNA opposite to the
original. In the early 1950s, four scientists, James Watson and Francis Crick at Cambridge
University and Maurice Wilkins and Rosalind Franklin at King's College, determined the true
structure of DNA from data and X-ray pictures of the molecule that Franklin had taken. In
1953, Watson and Crick published a paper in the scientific journal Nature describing this
research. Watson, Crick, Wilkins and Franklin had shown that not only is the DNA molecule
double-stranded, but the two strands wrap around each other forming a coil, or helix. The true
structure of the DNA molecule is a double helix, as shown at right.
The double-stranded DNA molecule has the unique ability that it can make exact copies of
itself, or self-replicate. When more DNA is required by an organism (such as during
reproduction or cell growth) the hydrogen bonds between the nucleotide bases break and the
two single strands of DNA separate. New complementary bases are brought in by the cell and
paired up with each of the two separate strands, thus forming two new, identical, double-
stranded DNA molecules.






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References

Cooper. The Cell: A Molecular Approach. 2nd edition. Available at
http://www.ncbi.nlm.nih.gov/books/NBK9879/

Nucleic Acids. About.com. Available at
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Nucleic Acid. Wikipedia, the free encyclopedia. Available at
http://en.wikipedia.org/wiki/Nucleic_acid

Nucleic Acids. Chemical Heritage Foundation. Available at
http://www.chemheritage.org/discover/online-resources/chemistry-in-
history/themes/biomolecules/dna/watson-crick-wilkins-franklin.aspx

DNA. Wikpedia, the Free Encyclopedia. Available at
http://en.wikipedia.org/wiki/DNA