Natural Science Forum / Biology / Biology / January 2008

On Jan 25, 11:39 am, b...@cs.toronto.no-uce.edu wrote:

DNA Process Model

Developmental Biology - DNA Process Details

                                Deoxyribonucleic acid DNA

                       Deoxyribonucleic acid DNA 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 longterm 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.

Chemically, DNA is a long polymer of simple units called nucleotides,
with a backbone made of sugars and phosphate groups joined by ester
bonds. Attached to each sugar is one of four types of molecules called
bases. It is the sequence of these four bases along the backbone that
encodes information. This information is read using the genetic code,
which specifies the sequence of the amino acids within proteins. The
code is read by copying stretches of DNA into the related nucleic acid
RNA, in a process called transcription. Most of these RNA molecules
are used to synthesize proteins, but others are used directly in
structures such as ribosomes and spliceosomes.Within cells, DNA is
organized into structures called chromosomes and the set of
chromosomes within a cell make up a genome. These chromosomes are
duplicated before cells divide, in a process called DNA replication.
Eukaryotic organisms such as animals, plants, and fungi store their
DNA inside the cell nucleus, while in prokaryotes such as bacteria it
is found in the cells cytoplasm. Within the chromosomes, chromatin
proteins such as histones compact and organize DNA, which helps
control its interactions with other proteins and thereby control which
genes are transcribed.

                                Nucleic acid
                       A nucleic acid is a macromolecule composed of
nucleotide chains. In biochemistry these molecules carry genetic
information or form structures within cells. The most common nucleic
acids are deoxyribonucleic acid DNA and ribonucleic acid RNA. Nucleic
acids are universal in living things, as they are found in all cells.
They are also found in viruses.Artificial nucleic acids include
peptide nucleic acid PNA, Morpholino and locked nucleic acid LNA, as
well as glycol nucleic acid GNA and threose nucleic acid TNA. Each of
these is distinguished from naturallyoccurring DNA or RNA by changes
to the backbone of the molecule.The definition of the term
macromolecule implies large molecule. In the context of science and
engineering, the term may be applied to conventional polymers and
biopolymers such as DNA as well as nonpolymeric molecules with large
molecular mass such as lipids or macrocycles. However, other large
networks of atoms, such as metallic covalent networks or fullerenes,
are not generally described as macromolecules. The term macromolecule
was coined by Nobel laureate Hermann Staudinger in the 1920s.A
nucleotide is a chemical compound that consists of 3 portions a
heterocyclic base, a sugar, and one or more phosphate groups. In the
most common nucleotides the base is a derivative of purine or
pyrimidine, and the sugar is the pentose fivecarbon sugar deoxyribose
or ribose. Nucleotides are the monomers of nucleic acids, with three
or more bonding together in order to form a nucleic acid.Nucleotides
are the structural units of RNA, DNA, and several cofactors CoA,
flavin adenine dinucleotide, flavin mononucleotide, adenosine
triphosphate and nicotinamide adenine dinucleotide phosphate. In the
cell they have important roles in metabolism and signaling.

                                Developmental biology
                       Developmental biology is the study of the
process by which organisms grow and develop. Modern developmental
biology studies the genetic control of cell growth, differentiation
and morphogenesis, which is the process that gives rise to tissues,
organs and anatomy.The term cell growth is used in two different ways
in biology. When used in the context of reproduction of living cells
the phrase cell growth is shorthand for the idea of growth in cell
populations by means of cell reproduction. During cell reproduction
one cell the mother cell divides to produce two daughter
cells.Cellular differentiation is a concept from developmental biology
describing the process by which cells acquire a type. The morphology
of a cell may change dramatically during differentiation, but the
genetic material remains the same, with few exceptions.A cell that is
able to differentiate into many cell types is known as pluripotent.
These cells are called stem cells in animals and meristematic cells in
higher plants. A cell that is able to differentiate into all cell
types is known as totipotent.
In mammals, only the zygote and early embryonic cells are totipotent,
while in plants, many differentiated cells can become totipotent with
simple laboratory techniques.Biological tissue is a collection of
interconnected cells that perform a similar function within an
organism.The study of tissue is known as histology, or, in connection
with disease, histopathology.The classical tools for studying the
tissues are the wax block, the tissue stain, and the optical
microscope, though developments in electron microscopy,
immunofluorescence, and frozen sections have all added to the sum of
knowledge in the last couple of decades.With these tools, the
classical appearances of the tissues can be examined in health and
disease, enabling considerable refinement of clinical diagnosis and
prognosis. There are four basic types of tissue in the body of all
animals, including the human body and lower multicellular organisms
such as insects. These compose all the organs, structures and other
contents.

                                Molecule
                       In chemistry, a molecule is defined as a
sufficiently stable electrically neutral group of at least two atoms
in a definite arrangement held together by strong chemical bonds.In
organic chemistry and biochemistry, the term molecule is used less
strictly and also is applied to charged organic molecules and
biomolecules. Molecules are distinguished from polyatomic ions in the
strict sense.This definition has evolved as knowledge of the structure
of molecules has increased. Earlier definitions were less precise
defining molecules as the smallest particles of pure chemical
substances that still retain their composition and chemical
properties.This definition often breaks down since many substances in
ordinary experience, such as rocks, salts, and metals, are composed of
atoms or ions, but are not made of molecules.In the kinetic theory of
gases the term molecule is often used for any gaseous particle
regardless of their composition.According to this definition noble
gases would also be considered molecules despite the fact that they
are composed of a single nonbonded atom.

                                             Organic chemistry is a
specific discipline within chemistry which involves the scientific
study of the structure, properties, composition, reactions, and
preparation by synthesis or by other means of chemical compounds
consisting primarily of carbon and hydrogen, which may contain any
number of other elements, including nitrogen, oxygen, halogens as well
as phosphorus, silicon and sulfur.The original definition of organic
chemistry came from the misperception that organic compounds were
always related to life processes. Not all organic compounds support
life on Earth, but life as we know it also depends heavily on
inorganic chemistry for example, many enzymes rely on transition
metals such as iron and copper and materials such as shells, teeth and
bones are part organic, part inorganic in composition. Apart from
elemental carbon, inorganic chemistry deals only with simple carbon
compounds, with molecular structures which do not contain carbon to
carbon connections its oxides, acids, carbonates, carbides, and
minerals. This does not mean that singlecarbon organic compounds do
not exist viz. methane and its simple derivatives. Biochemistry mainly
deals with the chemistry of proteins and other large biomolecules.

                                Biochemistry
                       Biochemistry from Greek ß???, bios, life and
Egyptian keme, earth1 is the study of the chemical processes in living
organisms. It deals with the structure and function of cellular
components, such as proteins, carbohydrates, lipids, nucleic acids,
and other biomolecules. Chemical biology aims to answer many questions
arising from biochemistry by using tools developed within chemical
synthesis.Although there are a vast number of different biomolecules,
many are complex and large molecules called polymers that are composed
of similar repeating subunits called monomers. Each class of polymeric
biomolecule has a different set of subunit types. For example, a
protein is a polymer made up of 20 or more amino acids. Biochemistry
studies the chemical properties of important biological molecules,
like proteins, in particular the chemistry of enzymecatalyzed
reactions.The biochemistry of cell metabolism and the endocrine system
has been extensively described. Other areas of biochemistry include
the genetic code DNA, RNA, protein synthesis, cell membrane transport,
and signal transduction.This article only discusses terrestrial
biochemistry carbon and waterbased, as all the life forms we know are
on Earth. Since life forms alive today are hypothesized by most to
have descended from the same common ancestor, they have similar
biochemistries, even for matters that seem to be essentially
arbitrary, such as handedness of various biomolecules. It is unknown
whether alternative biochemistries are possible or practical.zIn
biology and ecology, an organism in Greek organon = instrument is a
living complex adaptive system of organs that influence each other in
such a way that they function in some way as a stable whole. The
origin of life on Earth and the relationships between its major
lineages are controversial. Two main grades may be distinguished, the
prokaryotes and eukaryotes. The prokaryotes are generally considered
to represent two separate domains, called the Bacteria and Archaea,
which are not closer to one another than to the eukaryotes. The gap
between prokaryotes and eukaryotes is widely considered a major
missing link in evolutionary history. Two eukaryotic organelles,
namely mitochondria and chloroplasts, are generally considered to be
derived from endosymbiotic bacteria. A similar symbiogenesis
hypothesis has been proposed involving the origins of the cell
nucleus, it is described as viral eukaryogenesis. Fungi, animals and
plants are examples of species that are eukaryote.

                                Organic compound
                       An organic compound is any member of a large
class of chemical compounds whose molecules contain carbon. For
historical reasons discussed below, a few types of compounds such as
carbonates, carbon oxides and cyanides, as well as elemental carbon
are considered inorganic. The study of organic compounds is termed
organic chemistry, and since it is a vast collection of chemicals over
half of all known chemical compounds, systems have been devised to
classify organic compounds. HI yall.A few of the compound classes
based on socalled functional groups they carry are alcohols,
aldehydes, alkenes and amines. A large group of organic compounds
belong to the aromatic compounds because they share a common benzene
ring somewhere in their structure. Organometallic compounds are a
special group of organic compounds that incorporate a metal atom which
make them a hybrid between organic and inorganic chemistry.

Many polymers, including all plastics are organic compounds as
well.Many organic compounds are also of prime importance in
biochemistry antigens, carbohydrates and sugars, enzymes, hormones,
lipids and fatty acids, neurotransmitters, nucleic acids, proteins,
peptides and amino acids, vitamins and fats and oils to name just a
few.The name organic is a historical name, dating back to 19th
century, when it was believed that organic compounds could only be
synthesised in living organisms through vis vitalis the lifeforce. The
theory that organic compounds were fundamentally different from those
that were inorganic, that is, not synthesized through a lifeforce, was
disproved with the synthesis of urea, an organic compound by
definition of its known occurrence only in the urine of living
organisms, from potassium cyanate and ammonium sulfate by Friedrich
Wöhler in the Wöhler synthesis. The kinds of carbon compounds that are
still traditionally considered inorganic are those that were
considered inorganic before Wöhlers time that is, those which came
from inorganic i.e., lifeless sources such as minerals.Most pure
organic compounds today are artificially produced, although an
important subset are still extracted from natural sources because they
would be far too expensive to produce artificially. Examples include
most sugars, some alkaloids and terpenoids, certain nutrients such as
vitamin B12, and in general, those natural products with large or
stereoisometrically complicated molecules which are present in
reasonable concentrations in living organisms.

                                Biomolecule
                       A biomolecule is a molecule that naturally
occurs in living organisms. Biomolecules consist primarily of carbon
and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur.
Other elements sometimes are incorporated but are much less common.All
known forms of life are comprised solely of biomolecules. For example,
humans possess skin and hair. The main component of hair is keratin,
an agglomeration of proteins which are themselves polymers built from
amino acids. Amino acids are some of the most important building
blocks used, in nature, to construct larger molecules. Another type of
building block is the nucleotides, each of which consists of three
components either a purine or pyrimidine base, a pentose sugar and a
phosphate group. These nucleotides, mainly, form the nucleic acids.
Besides the polymeric biomolecules, numerous organic molecules are
absorbed by living systems.Nucleosides are molecules formed by
attaching a nucleobase to a ribose ring. Examples of these include
cytidine, uridine, adenosine, guanosine, thymidine and
inosine.Monosaccharides are carbohydrates in the form of simple
sugars. Examples of monosaccharides are the hexoses glucose, fructose,
and galactose and pentoses, ribose, and deoxyriboseDisaccharides are
formed from two monosaccharides joined together. Examples of
disaccharides include sucrose, maltose, and lactoseMonosaccharides and
disaccharides are sweet, water soluble, and
crystalline.Polysaccharides are polymerized monosaccharides, complex,
unsweet carbohydrates. Examples are starch, cellulose, and glycogen.
They are generally large and often have a complex, branched,
connectivity. They are insoluble in water and do not form crystals.
Shorter polysaccharides, with 215 monomers, are sometimes known as
oligosaccharides.Nucleosides can be phosphorylated by specific kinases
in the cell, producing nucleotides, which are the molecular building
blocks of DNA deoxyribonucleic acid and RNA ribonucleic acid. was up
bit.

                                Kinetic theory
                       Kinetic theory or kinetic theory of gases
attempts to explain macroscopic properties of gases, such as pressure,
temperature, or volume, by considering their molecular composition and
motion. Essentially, the theory posits that pressure is due not to
static repulsion between molecules, as was Isaac Newtons conjecture,
but due to collisions between molecules moving at different
velocities. Kinetic theory is also known as kineticmolecular theory or
collision theory.In 1738, Dutch born Swiss physicist and mathematician
Daniel Bernoulli published Hydrodynamica, which laid the basis for the
kinetic theory of gases. In this work, Bernoulli positioned the
argument, still used to this day, that gases consist of great numbers
of molecules moving in all directions, that their impact on a surface
causes the gas pressure that we feel, and that what we experience as
heat is simply the kinetic energy of their motion. The theory was not
immediately accepted, in part because conservation of energy had not
yet been established, and it was not obvious to physicists how the
collisions between molecules could be perfectly elastic. Other
pioneers of the kinetic theory were Mikhail Lomonosov 1745,
GeorgesLouis Le Sage 1818, John Herapath 1820 and John James Waterston
1843, which connected their research with the development of
mechanical explanations of gravitation. However, those scientists were
neglected by their contemporaries. For example, Herapath, considered
how a system of colliding particles could give rise to action at a
distance. In this direction, when thinking about the effect of the
high temperatures near the Sun on his gravific particles he was led to
a relationship between temperature and particle velocity. Herapath
postulated that the momentum of a particle in a gas is a measure of
the absolute temperature of the gas. He used momentum, rather than the
kinetic energy on which the later established theory is based, as it
seemed to him to avoid some difficulties around whether elastic
collisions were possible between indivisible atoms.

                                Noble gas
                       The noble gases are the elements in group 18
also sometimes Group 0 IUPAC Style, or Group 8 of the periodic table.
It is also called helium family or neon family. Chemically, they are
very stable due to having the maximum number of valence electrons
their outer shell can hold. A thorough explanation requires an
understanding of electronic configuration, with references to quantum
mechanics. Noble gases rarely react with other elements since they are
already stable. Under normal conditions, they occur as odorless,
colorless, monatomic gases. Each of them has its melting and boiling
point close together, so that only a small temperature range exists
for each noble gas in which it is a liquid. Noble gases have numerous
important applications in lighting, welding and space technology.Noble
gas is the translation of the German Edelgas, which was in use as
early as 18981. The term edelgas is literally translated as immaculate
gas. This refers to the extremely low level of reactivity under normal
conditions.

                                             The noble gases have
also been referred to as inert gases, but these terms are not strictly
accurate because several of them do take part in chemical reactions.
Another old term is rare gases, although in fact argon forms a
considerable part 0.93% by volume, 1.29% by mass of the Earths
atmosphere.2 The noble gases are the elements in group 18 also
sometimes Group 0 IUPAC Style, or Group 8 of the periodic table. It is
also called helium family or neon family. Chemically, they are very
stable due to having the maximum number of valence electrons their
outer shell can hold. A thorough explanation requires an understanding
of electronic configuration, with references to quantum mechanics.
Noble gases rarely react with other elements since they are already
stable. Under normal conditions, they occur as odorless, colorless,
monatomic gases. Each of them has its melting and boiling point close
together, so that only a small temperature range exists for each noble
gas in which it is a liquid. Noble gases have numerous important
applications in lighting, welding and space technology.
DNA Process Model

Developmental Biology - DNA Process Details
1