Nucleic acid

Nucleic acids are biological molecules essential for life, and include DNA (deoxyribonucleic

acid) and RNA (ribonucleic acid). Together with proteins, nucleic acids make up the most
important macromolecules; each is found in abundance in all living things. Nucleic acids were first
discovered by Friedrich Miescher in 1871.[1] 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

Types of nucleic acids

Deoxyribonucleic acid
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the
development and functioning of all known living organisms. The main role of DNA molecules is the
long-term storage of information and DNA is often compared to a set of blueprints, since it contains
the instructions needed to construct other components of cells, such as proteins and RNA
molecules. The DNA segments that carry this genetic information are called genes, but other DNA
sequences have structural purposes, or are involved in regulating the use of this genetic
information.
Ribonucleic acid
Ribonucleic acid (RNA) functions in converting genetic information from genes into the
amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA),
messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic
sequence information between DNA and ribosomes, directing protein synthesis. Ribosomal RNA is
a major component of the ribosome, and catalyzes peptide bond formation. Transfer RNA serves as
the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding
the mRNA. In addition, many other classes of RNA are now known.

Artificial nucleic acid analogs

Artificial nucleic acid analogs have been designed and synthesized by chemists, and
include peptide nucleic acid, morpholino- and locked nucleic acid, as well as glycol nucleic
acid and threose nucleic acid. Each of these is distinguished from naturally-occurring DNA or RNA
by changes to the backbone of the molecule.
Classification of Bases
1) Purine bases have nine ring atoms numbered from one to nine, which lie in the same plane.
Of the nine ring atoms, five are carbon atoms and four are nitrogen atoms.
2) . Pyrimidine bases have six ring atoms numbered from one to six, which lie in the same
plane. Of the six ring atoms, four are carbon atoms and two are nitrogen atoms.

 RNA contains ribose pentose sugar. There are two types of nitrogen bases in RNA.
1) Purine bases such as Adenine (A) and
2) Guanine (G) and
3) Pyrimidine such as Cytosine (C)
4) and Uracil (U).
RNA consists of only one polynucleotide chain.

 The four nucleotides have the abbreviations A, G, C and T, which are their initials. A is for for
adenine, G is for guanine, C stands for cytosine and T stands for thymine. There are two
types of nitrogenous bases called purine bases and pyrimidine bases. Purine bases are the
larger of the two types of nitrogenous bases found in DNA.
1) Adenine (A) and
2) guanine(G) are purine bases.
3) Cytosine (C) and
4) thymine (T) are pyrimidine bases
Types of Sugar
The human body needs to maintain a definite percentage of carbohydrates intake for a
healthy constitution. The World Health Organization recommends that about 55-75% of energy
requirements of an adult should be met from carbohydrate intake. A body needs to maintain this
level of intake, failing which, there can be complications like muscle cramps, fatigue, poor mental
functions and decreased resistance to diseases and ailments. There are two main types
of carbohydrates, simple and complex.

Simple Carbohydrates

These are made up of a single basic sugar. Simple carbohydrates provide the sweet taste in our
food. Fruit sugar, table sugar or corn sugar are all types of simple sugars. On consumption, these
sugars are directly absorbed in the blood as glucose requirements of the body. Glucose provides
instant energy as it reaches different parts of the body via blood. Simple sugars are occur in plenty
in natural foods like fruits, vegetables, milk and milk products. In addition to these, honey, molasses
brown sugar, corn syrup and maple syrup are rich sources of simple sugars.

Complex Carbohydrates
Complex carbohydrates, as the name suggests, are a combination of different types of sugars. These
take a longer time for break down into their elementary form and hence, require more time for
digestion. The slow break down process, supplies us with constant energy for a longer duration.
Since these carbohydrates require more time for conversion, they are constantly used up by the
body. Therefore, sugar converted to fat is not stored in a large quantity unlike the simple
carbohydrates. Simple carbohydrates provide instant energy because these are broken down in
lesser time as compared to complex carbohydrates. This increases the storage of broken down fats,
which if not burned or used up, may lead to health issues.

Complex carbohydrates are abundantly found in foods like cereals, bread, pasta, whole grains,
fruits, vegetables, nuts and seeds.

Carbohydrates can also be classified on the basis of their chemical composition. These are the most
easily available and the largest set of compounds on the Earth. Based on the complexity of their
structures, there are five major classes of carbohydrates. These are described in brief as follows.

Monosaccharides

These are the basic compounds with a cyclic structure consisting of carbon, hydrogen and oxygen in
the ratio 1:2:1. 'Mono' refers to single and saccharides means sugar. Glucose, fructose and galactose
are types of monosaccharides.

Disaccharides

These carbohydrates mean 'two sugars', which refer to the commonly available types such as
sucrose, maltose and lactose. When two monosaccharides bond together by a condensation
reaction, they release one molecule of water and a disaccharide is formed. This bond is called a
glycosidic bond.

Oligosaccharides

These are carbohydrates with more than two basic types of sugar molecules, usually between three
and ten basic units. Their main function in the body is the storage of glucose. Raffinose and
stachyose are the main types of oligosaccharides which consist of repetitive chains of fructose,
galactose and glucose.

Polysaccharides

These are also called monomers and are composed of thousands of molecules of the basic units of
glucose. Carbohydrates stored in the form of starch contain these type of compounds. Amylose,
which is a straight chain compound and amylopectin, which is a branched compound, are the most
common types of polysaccharides.

Nucleotides

It is another complex carbohydrate which contains many molecules of cyclic sugar.

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are complex five sided sugars classified
under this category. The difference between RNA and DNA is that the former has one extra
hydroxyl group.
Biological functions of RNA
 Immunity
RNA interference is a vital part of the immune response to viruses and other foreign genetic
material, especially in plants where it may also prevent self-propagation bytransposons.[62] Plants
such as Arabidopsis thaliana express multiple dicer homologs that are specialized to react
differently when the plant is exposed to different types of viruses. [63] Even before the RNAi pathway
was fully understood, it was known that induced gene silencing in plants could spread throughout
the plant in a systemic effect, and could be transferred from stock to scion plants via grafting.
[64]
 This phenomenon has since been recognized as a feature of the plant adaptive immune system,
and allows the entire plant to respond to a virus after an initial localized encounter. [65] In response,
many plant viruses have evolved elaborate mechanisms that suppress the RNAi response in plant
cells.[66] These include viral proteins that bind short double-stranded RNA fragments with single-
stranded overhang ends, such as those produced by the action of dicer. [67] Some plant genomes also
express endogenous siRNAs in response to infection by specific types of bacteria.[68] These effects
may be part of a generalized response to pathogens that downregulates any metabolic processes in
the host that aid the infection process.[69]
Although animals generally express fewer variants of the dicer enzyme than plants, RNAi in some
animals has also been shown to produce an antiviral response. In both juvenile and
adult Drosophila, RNA interference is important in antiviral innate immunity and is active against
pathogens such as Drosophila X virus.[70][71] A similar role in immunity may operate in C. elegans, as
argonaute proteins are upregulated in response to viruses and worms that overexpress
components of the RNAi pathway are resistant to viral infection. [72][73]
The role of RNA interference in mammalian innate immunity is poorly understood, and relatively
little data is available. However, the existence of viruses that encode genes able to suppress the
RNAi response in mammalian cells may be evidence in favour of an RNAi-dependent mammalian
immune response.[74][75] However, this hypothesis of RNAi-mediated immunity in mammals has
been challenged as poorly substantiated.[76] Alternative functions for RNAi in mammalian viruses
also exist, such as miRNAs expressed by the herpes virus that may act
as heterochromatin organization triggers to mediate viral latency.[42]
 Downregulation of genes
Endogenously expressed miRNAs, including both intronic and intergenic miRNAs, are most
important in translational repression[52] and in the regulation of development, especially on the
timing of morphogenesis and the maintenance of undifferentiated or incompletely differentiated
cell types such as stem cells.[77] The role of endogenously expressed miRNA in downregulating gene
expression was first described in C. elegans in 1993.[78] In plants this function was discovered when
the "JAW microRNA" ofArabidopsis was shown to be involved in the regulation of several genes that
control plant shape.[79] In plants, the majority of genes regulated by miRNAs are transcription
factors;[80] thus miRNA activity is particularly wide-ranging and regulates entire gene
networks during development by modulating the expression of key regulatory genes, including
transcription factors as well as F-box proteins.[81] In many organisms, including humans, miRNAs
have also been linked to the formation of tumors and dysregulation of the cell cycle. Here, miRNAs
can function as both oncogenes and tumor suppressors.[82]
 Upregulation of genes
RNA sequences (siRNA and miRNA) that are complementary to parts of a promoter can increase
gene transcription, a phenomenon dubbed RNA activation. Part of the mechanism for how these
RNA upregulate genes is known: dicer and argonaute are involved, and there is histone
demethylation.[83][84]
• Information decoding (mRNA)
• Information transfer (tRNA)
• Structural molecule (rRNA)
• Catalytic function (ribozymes)
• Regulatory function

Biological functions of DNA

Genes and genomes
Genomic DNA is tightly and orderly packed in the process called DNA condensation to fit the small
available volumes of the cell. In eukaryotes, DNA is located in the cell nucleus, as well as small
amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly
shaped body in the cytoplasm called the nucleoid.[67] The genetic information in a genome is held
within genes, and the complete set of this information in an organism is called its genotype. A gene
is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism.
Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such
aspromoters and enhancers, which control the transcription of the open reading frame.
In many species, only a small fraction of the total sequence of the genome encodes protein. For
example, only about 1.5% of the human genome consists of protein-codingexons, with over 50% of
human DNA consisting of non-coding repetitive sequences.[68] The reasons for the presence of so
much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size,
or C-value, among species represent a long-standing puzzle known as the "C-value enigma".
[69]
 However, DNA sequences that do not code protein may still encode functional non-coding
RNA molecules, which are involved in the regulation of gene expression.[70]

T7 RNA polymerase (blue) producing a mRNA

(green) from a DNA template (orange).[71]
Some non-coding DNA sequences play structural
roles in
chromosomes. Telomeres and centromeres typical
ly contain few genes, but are important for the
function and stability of chromosomes.[44][72] An
abundant form of non-coding DNA in humans
are pseudogenes, which are copies of genes that
have been disabled by mutation.[73] These
sequences are usually just molecular fossils,
although they can occasionally serve as raw genetic material for the creation of new genes through
the process of gene duplication and divergence.[74]
Transcription and translation
A gene is a sequence of DNA that contains genetic information and can influence the phenotype of
an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger
RNA sequence, which then defines one or more protein sequences. The relationship between the
nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules
of translation, known collectively as the genetic code. The genetic code consists of three-letter
'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).
In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA
copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger
RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations,
there are 64 possible codons (43 combinations). These encode the twenty standard amino acids,
giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense'
codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.

DNA replication. The double helix is unwound by a helicase and topoisomerase. Next, one DNA

polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand.
This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins
them together.
Replication
Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA
in its genome so that the two daughter cells have the same genetic information as their parent. The
double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two
strands are separated and then each strand's complementary DNAsequence is recreated by
an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the
correct base through complementary base pairing, and bonding it onto the original strand. As DNA
polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to
copy the antiparallel strands of the double helix.[75] In this way, the base on the old strand dictates
which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.
Central Dogma
The central dogma of molecular biology was first articulated by Francis Crick in 1958 and
re-stated in a Nature paper published in 1970:
Information flow in biological systems
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of
sequential information. It states that information cannot be transferred back from protein to
either protein or nucleic acid.

Table of the 3 classes of information transfer suggested by the

dogma

General Special Unknown

DNA → DNA RNA → DNA protein → DNA

DNA → RNA RNA → RNA protein → RNA

RNA → protein DNA → protein protein → protein

DNA Replication
As the final step in the Central Dogma, to transmit the genetic information between parents
and progeny, the DNA must be replicated faithfully. Replication is carried out by a complex group of
proteins that unwind the superhelix, unwind the double-stranded DNA helix, and, using DNA
polymeraseand its associated proteins, copy or replicate the master template itself so the cycle can
repeat DNA → RNA → protein in a new generation of cells or organisms.

Reference:
http://www.buzzle.com/articles/types-of-carbohydrates.html
http://en.wikipedia.org/wiki/RNA_interference
http://www.blurtit.com/q378621.html
http://dna.microbiologyguide.com/
http://search.yahoo.com
http://www.news-medical.net/health/DNA-Biological-Functions.aspx
http://www.google.com/imgres?imgurl=http://www.hort.purdue.edu/hort/courses/HORT250/pict.gif
%2520images/l4%2520central%2520dogma
%2520pict.gif&imgrefurl=http://usmlemd.wordpress.com/2007/07/31/the-central-dogma-of-molecular-
biology/&h=233&w=431&sz=5&tbnid=Zk8MyHc_SEVU_M:&tbnh=68&tbnw=126&prev=/images%3Fq
%3Dcentral
%2Bdogma&zoom=1&q=central+dogma&hl=fil&usg=__sE3CN69X2ZM9Dv2LVzG82onftFM=&sa=X&ei=of
X6TPShGYfOrQe8n-mGCA&ved=0CDQQ9QEwBQ

Republic of the Philippines

Bicol University
College of Nursing
SY 2010-2011

Biochemistry

Raymond Basilonia
BSN I-B

Prof. Noemi Madrid

Biochemistry