Reproduction

In a general sense reproduction is one of the most important concepts in biology: it means
making a copy, a likeness, and thereby providing for the continued existence of species.
Although reproduction is often considered solely in terms of the production of offspring in
animals and plants, the more general meaning has far greater significance to living organisms.
To appreciate this fact, the origin of life and the evolution of organisms must be considered. One
of the first characteristics of life that emerged in primeval times must have been the ability of
some primitive chemical system to make copies of itself.

At its lowest level, therefore, reproduction is chemical replication. As evolution progressed, cells
of successively higher levels of complexity must have arisen, and it was absolutely essential
that they had the ability to make likenesses of themselves. In unicellular organisms, the ability of
one cell to reproduce itself means the reproduction of a new individual; in multicellular
organisms, however, it means growth and regeneration. Multicellular organisms also reproduce
in the strict sense of the term—that is, they make copies of themselves in the form of
offspring—but they do so in a variety of ways, many involving complex organs and elaborate
hormonal mechanisms.

Interphase

Interphase is the longest stage in the eukaryote cell cycle. During interphase, the cell acquires
nutrients, creates and uses proteins and other molecules, and starts the process of cell division
by replicating the DNA. Interphase is divided into three distinct stages, Gap 1, Synthesis, and
Gap 2, which are discussed below. The purpose of interphase in all cell types is to prepare for
cell division, which happens in a different stage of the cell cycle.

Depending on which species of organism is dividing, the functions of the cell during interphase
can vary widely. Some cell, like neurons, do not replicate their DNA during interphase, but enter
resting phase or quiescence instead. This stage can be seen in the graphic below as the G0
stage. In this state the cell will exist without dividing until the cell dies. Other cells, like skin cells,
divide a lot. Each time, they must pass through interphase (I) to accumulate resources to
structure the new cells and replicate the DNA. The unique proteins produce by skin cells help
them bond together after they die, creating a solid surface of skin cells that protects your body.

Mitotic Phase

The cell cycle of eukaryotes is a cyclical series of biological events that certain asexual cells go
through. In essence, the cell cycle is highlighted by a sequence of events such as the
duplication of DNA via DNA replication, in preparation to cell division wherein the parent cell
divides and gives rise to two genetically identical daughter cells. The cell cycle is comprised of
these fundamental events: (1) resting phase (Gap 0), (2) interphase (Gap 1, S phase, Gap 2),
and (3) cell division (i.e. mitotic phase and cytokinesis). The interphase is the period prior to cell
division. Thus, it would entail two major events, particularly cell growth (during gap phases) and
DNA replication (during S phase). During G2 phase of the interphase, apart from growing further
in cell size, the cell readies itself for cell division. It has a control mechanism called G2-M DNA
damage checkpoint that ensures the cell is ready for cell division. Following Gap 2, the cell
enters the mitotic phase. The mitotic phase is the phase in the cell cycle that is highlighted by
chromosomal separation resulting into two identical sets in two nuclei. During the mitotic phase,
there are four series of events that gave rise to four major phases: (1) prophase, (2) metaphase,
(3) anaphase, and (4) telophase.

Adenine

Adenine (A) is one of four chemical bases in

DNA, with the other three being cytosine (C),
guanine (G), and thymine (T). Within the DNA
molecule, adenine bases located on one strand
form chemical bonds with thymine bases on the
opposite strand. The sequence of four DNA
bases encodes the cell's genetic instructions. A
form of adenine called adenosine triphosphate
(ATP) serves as an energy storage molecule and
is used to power many chemical reactions within
the cell.
Adenine is one of the four building blocks of DNA. It's the A of the A, C, G, and T that's in DNA.
Adenine has the property that, when it's in the double helix, it is always found opposite of
thymine, so adenine and thymine pair one on each strand. Adenine is also used elsewhere in
the cell, not just in DNA and RNA, but it's part of the molecule adenosine triphosphate, which is
the energy source for the cell. So adenine plays a dual role in the cell: it's used for building DNA
and RNA, but it's also used at storing energy in the cell.

Thymine

Thymine (T) is one of four chemical bases in DNA, the

other three being adenine (A), cytosine (C), and guanine
(G). Within the DNA molecule, thymine bases located on
one strand form chemical bonds with adenine bases on the
opposite strand. The sequence of four DNA bases encodes
the cell's genetic instructions.
Thymine is one of the building blocks of DNA. It's one of
the four nucleotides that are strung together to make the
long sequence that you find in DNA, of C, A, Gs, and Ts.
It's the T of the C, A, Gs, and Ts. And in the double helix,
thymine pairs with adenine, or the A nucleotide.
Guanine

Guanine, an organic compound belonging to the purine group, a class of compounds with a
characteristic two-ringed structure, composed of carbon and nitrogen atoms, and occurring free
or combined in such diverse natural sources as guano (the accumulated excrement and dead
bodies of birds, bats, and seals), sugar beets, yeast, and fish scales. It is a component of
nucleic acids, the cell constituents that store and transmit hereditary traits.
Guanine was first discovered in guano in 1846 and was isolated in 1891 from nucleic acids from
which it is readily prepared.
More complex compounds obtainable from nucleic acids include the nucleosides guanosine and
deoxyguanosine, in which guanine is combined with the sugars ribose and deoxyribose and the
nucleotides guanylic acid and deoxyguanylic acid, which are phosphoric acid esters of
guanosine and deoxyguanosine. Nucleotides are molecules that constitute the fundamental
structural units of nucleic acids; nucleosides are smaller subunits lacking in phosphoric acid.
Guanosine triphosphate (GTP) is used by the body to form the guanylic acid units in ribonucleic
acids (RNA’s).

Cytosine

Cytosine is one of the four building blocks of DNA and RNA. So it's one of the four nucleotides
that's present both in DNA, RNA, and each cytosine makes up part of the code. Cytosine has
the unique property in that it binds in the double helix opposite a guanine, one of the other
nucleotides. Cytosine has one other interesting property that none of the other nucleotides
have, is that very often in the cell, cytosine can have an extra chemical attached to them, a
methyl group. And this DNA methylation at cytosines is thought helps regulate genes try to help
turn them on and off.

Helicases

Helicases are conserved enzymes that hydrolyze adenosine triphosphate (ATP) in the presence
of nucleic acids. These enzymes are able to translocate along double-stranded DNA and/or
RNA molecules in a specific direction and to separate (unwind) the complementary strands of
the duplex by dissociating the hydrogen bonds between the bases. Multiple helicases exist in all
organisms, and their activities facilitate virtually all transactions in nucleic acid metabolism. They
have diverse functions in the cell and their substrate specificity varies. Malfunction is often
associated with genetic human diseases or syndromes.
Helicases are highly versatile molecules and every genotype and phenotype is associated with
a helicase. They take part in a wide range of cellular processes ranging from replication to
translation, and genome maintenance; hence these are the lifeline of the cell. They have
importance in proliferation, differentiation, and embryogenesis and are also involved in
metabolic and signaling pathways. Both high expression and low expression of helicases can be
fatal for cells. Ded1 helicases are essentially required for RNA metabolism. The studies of Ded1
family helicases in humans have shown that they participate in a variety of functions and are
vital for cells to survive. Further studies are required to understand the biochemical and
functional roles of Ded1 family members of helicases of P. falciparum. Helicases are essential
for cell survival and, thus, can be used as potent drug targets.

Pyrimidine

Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine.[3] One of the three
diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has the nitrogen
atoms at positions 1 and 3 in the ring.[4]:250 The other diazines are pyrazine (nitrogen atoms at
the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2 positions). In nucleic acids,
three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U).
Pyrimidine 5′-nucleotidase type-I (P5N-1) is also called cytosolic 5′-nucleotidase III (cNIII) or
uridine monophosphate hydrolase type I (UMPH-1) and is a 34kDa monomeric protein
preferentially catalyzing the dephosphorylation of UMP and CMP to their corresponding
nucleosides and it is inactive toward purine nucleotides. The activity is dependent on the
presence of magnesium ions and it is readily inhibited by heavy metals. Consequently, subjects
with chronic low-level lead poisoning may develop severe acquired deficiency of P5N-1, which
also results in anemia and basophilic stippling. Clearing of lead returns the nucleotidase activity
to normal and resolves the anemia. P5N-1 also displays phosphotransferase activity specific for
pyrimidine nucleosides, suggesting an additional role in nucleotide metabolism.

Cytoplasmic

The cytoplasmic of the cell is all the material outside of the nucleus. On occasion, it is necessary
to distinguish between the cytosol and the cytoplasm. The cytosol is defined as all the material
in the cytoplasm, excluding the contents of the various membranous organelles. The cytosol,
therefore, does include the cytoskeleton, the ribosomes, and the centrosome, together with all
the other macromolecules and solutes outside the nucleus and also outside the lumen of the
various cytoplasmic membranous organelles

Chemical Structure of Genes

Sequencing and other molecular analyses have revealed that a very large fraction of all
vertebrate genomes, perhaps well over 90 percent, does not encode precursors to mRNAs or
any other RNAs. In multicellular organisms, this noncoding DNA contains many regions that are
similar but not identical. Variations within some stretches of this repetitious DNA are so great
that each single person can be distinguished by a DNA “fingerprint” based on these sequence
variations. Moreover, some repetitious DNA sequences are not found in constant positions in
the DNA of individuals of the same species. Such “mobile” DNA segments, which are present in
both prokaryotic and eukaryotic organisms, can cause mutations when they move to new sites
in the genome. These mobile segments probably have played an important role in evolution,
even though they generally have no function in the life cycle of an individual organism.
In higher eukaryotes, DNA regions encoding proteins — that is, genes — lie amidst this expanse
of nonfunctional DNA. In addition to the apparently nonfunctional DNA between genes,
noncoding introns are common within genes of multicellular plants and animals. Introns are less
common, but sometimes present, in single-celled eukaryotes and very rare in bacteria.
Sequencing of the same protein-coding gene in a variety of eukaryotic species has shown that
evolutionary pressure selects for maintenance of relatively similar sequences in the coding
regions, or exons. In contrast, wide sequence variation, even including total loss, occurs among
introns, suggesting that most of the sequence of introns is nonfunctional. Cloning and
sequencing have also confirmed the widespread existence of “families” of similar genes
encoding proteins with related, but distinct, specialized functions.

The sheer length of cellular DNA is a significant problem with which cells must contend. The
DNA in a typical bacterial cell, which is about 103 times longer than the length of the cell, is
folded and organized to fit within the cell. The total length of the DNA in eukaryotic cells is even
longer compared with the cell diameter. Specialized eukaryotic proteins associated with nuclear
DNA organize it into the structures of DNA and protein visualized as individual chromosomes
during mitosis. Mitochondria and chloroplasts also contain DNA, probably evolutionary remnants
of their origins, that encodes essential components of these vital organelles.

In this chapter we first present a molecular definition of genes and then discuss the main
classes of eukaryotic DNA and the special properties of mobile DNA. Next we describe several
examples of functional rearrangements of chromosomal DNA, including the process for
generating functional antibody genes. We also consider the packaging of DNA and proteins into
compact complexes, the large-scale structure of chromosomes, and the functional elements
required for chromosome duplication and segregation. In the final section, we discuss organelle
DNA.