DNA Ekstrakromosomal,

Sifat, dan Kegunaannya

Soraya Rahmanisa
Pengertian
 DNA ekstrakromosomal : DNA lain yang
terdapat dalam sel di luar nukleus, yaitu :
 - DNA mitokondria, DNA kloroplas, DNA
plasmid
The Genome Defines the Program of
Multicellular Development
 The cells in an individual animal or plant are extraordinarily varied. Fat cells,
skin cells, bone cells, nervecells—they seem as dissimilar as any cells could be.Yet all
these cell types are generated during embryonic development from a single fertilized egg
cell, and all (with minor exceptions) contain identical copies of thegenome of the
species.
 The explanation lies in the way in which these cells make selective use of their genetic
instructions according to the cues they get from their surroundings. The DNA is not just
a shopping list specifying the molecules that every cell must have, and the cell is not an
assembly of all the items on the list. Rather, the cell behaves as a multipurpose machine,
with sensors to receive environmental signals and highly developed abilities to call
different sets of genes into action according to the sequences of signals to which the cell
has been exposed. A large fraction of the genes in the eucaryotic genome code for
proteins that serve to regulate the activities of other genes. Most of these gene regulatory
proteins act by binding, directly or indirectly, to the regulatory DNA adjacent to the genes
that are to be controlled (Figure 1-40), or by interfering with the abilities of other
proteins to do so. The expanded genome of eucaryotes therefore serves not only to
specify the hardware of the cell, but also to store the software that controls how that
hardware is used.
Eucaryotic Genomes Are Rich in
Regulatory DNA

Much of our noncoding DNA is almost certainly dispensable

junk, retained like a mass of old papers because, when there
is little pressure to keep an archive small, it is easier to retain
everything than to sort out the valuable information and
discard the rest. Certain exceptional eucaryotic species, such
as the puffer fish (Figure 1-39), bear witness to the profligacy
of their relatives; they have somehow managed either to rid
themselves of large quantities of noncoding DNA, or to have
avoided acquiring it in the first place.Yet they appear similar
in structure, behavior, and fitness to related species that have
vastly more such DNA.
DNA
- inheritance blueprint
- consist the genes (functional units)
- covered into chromosome
Chromosomal aberration 􀃆
include the genes (multi genes)
Chromosome Abnormalities
 The puffer fish (Fugu rubripes).. This organism has
a genome size of 400 million nucleotide pairs—about one-
quarter as much as a zebrafish, for example, even though the
two species of fish have similar numbers of genes. (From a
woodcut by Hiroshige,
Even in compact eucaryotic genomes such as that of puffer fish,
there is more noncoding DNA than coding DNA, and at least
some of the noncoding DNA certainly has important functions. In
particular, it serves to regulate the expression of adjacent genes.
With this regulatory DNA, eucaryotes have evolved distinctive
ways of controlling when and where a gene is brought into play.
This sophisticated gene regulation is crucial for the formation of
complex multicellular organisms.
In a developing multicellular organism, each cell is governed by the
same control system, but with different consequences depending
on the signals the cell exchanges with its neighbors. The outcome,
astonishingly, is a precisely patterned array of cells in different
states, each displaying a character appropriate to its position in the
multicellular structure. The genome in each cell is big enough to
accommodate the information that specifies an entire multicellular
organism, but in any individual cell only part of that information is
used
The Mouse Serves as a Model for
Mammals
 Mammals have typically three or four times as many genes as Drosophila, a genome that is 20 times larger, and
millions or billions of times as many cells in their adult bodies. In terms of genome size and function, cell
biology, and molecular mechanisms, mammals are nevertheless a highly uniform group of organisms. Even
anatomically, the differences among mammals are chiefly a matter of size and proportions; it is hard to think of a
human body part that does not have a counterpart in elephants and mice, and vice versa. Evolution plays freely
with quantitative features, but it does not readily change the logic of the structure.
 To get a more exact measure of how closely mammalian species resemble one another genetically, we can compare
the nucleotide sequences of corresponding (orthologous) genes, or the amino acid sequences of the proteins that
these genes encode. The results for individual genes and proteins vary widely. But typically, if we line up the amino
acid sequence of a human protein with that of the orthologous protein from, say, an elephant, about 85% of the
amino acids are identical. A similar comparison between human and bird shows an amino acid identity of about
70%—twice as many differences, because the bird and the mammalian lineages have had twice as long to diverge
as those of the elephant and the human
Human and mouse:
similar genes and similar
development. The
human baby and the
mouse shown here have
similar white patches on
their foreheads because
both have mutations in
the same gene
(called kit),required for
the development and
maintenance of pigment

Source : Molecular
Biology of the Cell. 4th
edition.
Alberts B, Johnson A,
Lewis J, et al.
New York: Garland
Science; 2002.
Eucaryotic cells, by definition, keep their DNA in a separate membrane-bounded compartment, the nucleus. They have, in addition, a
cytoskeleton for movement, elaborate intracellular compartments for digestion and secretion, the capacity (in many species) to
engulf other cells, and a metabolism that depends on the oxidation of organic molecules by mitochondria. These properties suggest
that eucaryotes originated as predators on other cells. Mitochondria—and, in plants, chloroplasts—contain their own genetic
material, and evidently evolved from bacteria that were taken up into the cytoplasm of the eucaryotic cell and survived as symbionts.
Eucaryotic cells have typically 3–30 times as many genes as procaryotes, and often thousands of times more noncoding DNA. The
noncoding DNA allows for complex regulation of gene expression, as required for the construction of complex multicellular
organisms. Many eucaryotes are, however, unicellular, among them the yeast Saccharomyces cerevisiae, which serves as a simple model
organism for eucaryotic cell biology, revealing the molecular basis of conserved fundamental processes such as the eucaryotic cell
division cycle. A small number of other organisms have been chosen as primary models for multicellular plants and animals, and the
sequencing of their entire genomes has opened the way to systematic and comprehensive analysis of gene functions, gene
regulation, and genetic diversity. As a result of gene duplications during vertebrate evolution, vertebrate genomes contain multiple
closely related homologs of most genes. This genetic redundancy has allowed diversification and specialization of genes for new
purposes, but it also makes gene functions harder to decipher. There is less genetic redundancy in the nematode Caenorhabditis
elegans and the fly Drosophila melanogaster, which have thus played a key part in revealing universal genetic mechanisms of animal
development.
Eucaryotic DNA Is Packaged into a Set of
Chromosomes
 In eucaryotes, the DNA in the nucleus is divided between a set of different chromosomes. For example, the human genome—approximately 3.2 ×
109 nucleotides—is distributed over 24 different chromosomes. Eachchromosome consists of a single, enormously long linear DNA molecule associated with
proteins that fold and pack the fine DNA thread into a more compact structure. The complex of DNA and protein is called chromatin(from the Greek chroma,
“color,” because of its staining properties). In addition to the proteins involved in packaging the DNA, chromosomes are also associated with many proteins
required for the processes of geneexpression, DNA replication, and DNA repair.
 Bacteria carry their genes on a single DNA molecule, which is usually circular (see Figure 1-30). This DNA is associated with proteins that package and
condense the DNA, but they are different from the proteins that perform these functions in eucaryotes. Although often called the bacterial “chromosome,” it
does not have the same structure as eucaryotic chromosomes, and less is known about how the bacterial DNA is packaged. Even less is known about how DNA
is compacted in archaea. Therefore, our discussion of chromosome structure will focus almost entirely on eucaryotic chromosomes.
 With the exception of the germ cells, and a few highly specialized cell types that cannot multiply and lack DNAaltogether (for example, red blood cells), each
human cell contains two copies of each chromosome, one inherited from the mother and one from the father. The maternal and paternal chromosomes of a
pair are calledhomologous chromosomes (homologs). The only nonhomologous chromosome pairs are the sex chromosomes in males, where a Y
chromosome is inherited from the father and an X chromosome from the mother. Thus, each human cell contains a total of 46 chromosomes—22 pairs common to
both males and females, plus two so-called sex chromosomes (X and Y in males, two Xs in females). DNA hybridization(described in detail in Chapter 8) can be
used to distinguish these human chromosomes by “painting” each one a different color (Figure 4-10). Chromosome painting is typically done at the stage in the
cell cycle when chromosomes are especially compacted and easy to visualize
Nucleosomes Are the Basic Unit of
Eucaryotic Chromosome Structure

 The proteins that bind to the DNA to form eucaryotic chromosomes are traditionally divided into
two general classes: the histones and the nonhistone chromosomal proteins. The complex of both classes
of protein with the nuclear DNA of eucaryotic cells is known as chromatin. Histones are present in
such enormous quantities in the cell (about 60 million molecules of each type per human cell) that
their total mass in chromatin is about equal to that of the DNA.
 Histones are responsible for the first and most basic level of chromosome organization,
the nucleosome, which was discovered in 1974. When interphase nuclei are broken open very
gently and their contents examined under the electron microscope, most of the chromatin is in the
form of a fiber with a diameter of about 30 nm(Figure 4-23A). If this chromatin is subjected to
treatments that cause it to unfold partially, it can be seen under the electron microscope as a series
of “beads on a string” (Figure 4-23B). The string is DNA, and each bead is a “nucleosome core
particle” that consists of DNA wound around a protein core formed from histones. The beads on a
string represent the first level of chromosomal DNA packing.
Structural
organization of the
nucleosome. A
nucleosome contains
a protein core made
of eight histone
molecules. As
indicated, the
nucleosome core
particle is released
from chromatin by
digestion of the
linker DNA with a
nuclease, an enzyme
that breaks
Each nucleosome core particle is separated from the next by a region of
linker DNA, which can vary in length from a few nucleotide pairs up to about
80. (The term nucleosome technically refers to a nucleosome core particle plus
one of its adjacent DNA linkers, but it is often used synonymously with
nucleosome core particle.) On average, therefore, nucleosomes repeat at
intervals of about 200 nucleotide pairs. For example, a diploidhuman cell with
6.4 × 109 nucleotide pairs contains approximately 30 million nucleosomes. The
formation of nucleosomes converts a DNA molecule into a chromatin thread
about one-third of its initial length, and this provides the first level of DNA
packing.
The Structure of DNA Provides a
Mechanism for Heredity
 Genes carry biological information that must be copied accurately for transmission to the next generation each time a cell divides to form two daughter cells.
Two central biological questions arise from these requirements: how can the information for specifying an organism be carried in chemical form, and how is it
accurately copied? The discovery of the structure of the DNA double helix was a landmark in twentieth-century biology because it immediately suggested
answers to both questions, thereby resolving at the molecular level the problem of heredity. We discuss briefly the answers to these questions in this section,
and we shall examine them in more detail in subsequent chapters.
 DNA encodes information through the order, or sequence, of the nucleotides along each strand. Each base—A, C, T, or G—can be considered as a letter in a
four-letter alphabet that spells out biological messages in the chemical structure of the DNA. As we saw in Chapter 1, organisms differ from one another
because their respective DNA molecules have different nucleotide sequences and, consequently, carry different biological messages. But how is the nucleotide
alphabet used to make messages, and what do they spell out?
 As discussed above, it was known well before the structure of DNA was determined that genes contain the instructions for producing proteins.
The DNA messages must therefore somehow encode proteins (Figure 4-6). This relationship immediately makes the problem easier to understand, because of
the chemical character of proteins. As discussed in Chapter 3, the properties of a protein, which are responsible for its biologicalfunction, are determined by
its three-dimensional structure, and its structure is determined in turn by the linear sequence of the amino acids of which it is composed. The linear
sequence of nucleotides in a gene must therefore somehow spell out the linear sequence of amino acids in a protein. The exact correspondence between the
four-letter nucleotide alphabet of DNA and the twenty-letter amino acid alphabet of proteins—thegenetic code—is not obvious from the DNA structure,
and it took over a decade after the discovery of thedouble helix before it was worked out. In Chapter 6 we describe this code in detail in the course of
elaborating the process, known as gene expression, through which a cell translates the nucleotide sequence of a gene into the amino acid sequence of a protein.
The complete set of information in an organism's DNA is called its genome, and it
carries the information for all the proteins the organism will ever synthesize.
(The term genome is also used to describe the DNA that carries this
information.) The amount of information contained in genomes is staggering:
for example, a typical human cell contains 2 meters of DNA. Written out in the
four-letter nucleotide alphabet, the nucleotide sequence of a very small
human gene occupies a quarter of a page of text (Figure 4-7), while the
complete sequence of nucleotides in the human genome would fill more than a
thousand books the size of this one. In addition to other critical information, it
carries the instructions for about 30,000 distinct proteins.
In Eucaryotes, DNA Is Enclosed in a
Cell Nucleus

 Nearly all the DNA in a eucaryotic cell is sequestered in a nucleus, which

occupies about 10% of the total cell volume. This compartment is delimited by
a nuclear envelope formed by two concentric lipid bilayer membranes that are
punctured at intervals by large nuclear pores, which transport molecules
between the nucleus and thecytosol. The nuclear envelope is directly connected
to the extensive membranes of the endoplasmic reticulum. It is mechanically
supported by two networks of intermediate filaments: one, called the nuclear
lamina, forms a thin sheetlike meshwork inside the nucleus, just beneath
the inner nuclear membrane; the other surrounds theouter nuclear
membrane and is less regularly organized