Seventh lecture
DNA &Chromosome
Chromatin, Chromosomes, and the Cell Nucleus
Every organism is defined by a blueprint consisting of
information stored in its chromosomes. With the exception of a few
viruses, these chromosomes are composed of enormously long
circular or linear molecules of DNA. (Those few viruses use RNA
instead.) Chromosomes have fascinated biologists ever since it was
realized that they contain the genetic information that defines each
organism-its genome. After Watson and Crick's proposal of a
structure for DNA in 1953, it was realized that the DNA is a linear
sequence of A, T, G, and C bases that can be thought of as a code to
describe the physical attributes for every organism
Originally, this code was thought to be impossibly complex, but
recent technological advances have permitted scientists to determine
the complete sequence of large DNA molecules. Between 1996 and
2006, investigators determined the sequences of the DNA molecules
that make up the genomes of over 300 prokaryotes and 20
eukaryotes, including several fungi, the nematode worm
Caenorhabditis elegans, 12 species of fruit flies (including Drosophila
melanogaster), the plant Arabidopsis thaliana, chickens, mice, rats,
and humans. These genome sequences not only reveal much about
the biology of living organisms but also are the most important
source of information about the evolution of life on earth (see
Chapter 2).
Body_ID: P012002
This does not mean that we understand everything about
chromosomes, however. Far from it. We still know very little about
how chromosomal DNA molecules are packaged so that they not only
fit into cells but also allow access to the library of genetic information
that they contain. In prokaryotes, the single chromosome is
concentrated in a specialized region of the cytoplasm called the
nucleoid. In eukaryotes, the chromosomes are packaged in a
specialized membrane-bounded compartment known as the nucleus.
This difference in organization has important consequences for the
regulation of gene expression.
Every species has a characteristic number of chromosomes that
occupy distinct territories within the nucleus and can be visualized as
separate entities only during cell division. For example, humans have
46 chromosomes that contain, in total, about 6.2 × 109 base pairs of
DNA.
Analysis of the human genome sequence revealed that the genes that
encode proteins and RNAs are often surrounded by huge noncoding
deserts. In fact, the vast majority of the chromosomal DNA in
humans has no coding function and might instead serve a structural
role. Two specific DNA structures are essential for the maintenance
of a constant chromosome complement in a given species:
centromeres and telomeres. Centromeres consist of DNA sequences
that, together with 60 or more proteins (Chapter 13), direct the
segregation of chromosomes during cell division. Telomeres are
specialized
structures that protect the ends of chromosomes and permit
complete replication of the chromosomal DNA.
Body_ID: P012005
Given the spacing of 3.4 Å per base pair in B-form DNA, each human
cell contains more than 2 m of DNA packaged into a nucleus only 5 to
20 × 10-6 m in diameter! Chapter 13 explains how DNA is extensively
folded to fit into the nucleus. The first levels of packaging shorten the
DNA about 40-fold by wrapping it around histone proteins to form
nucleosomes and then twisting the nucleosomes into 30-nm fibers.
Higher levels of packaging of the chromatin fiber are still poorly
understood.
Body_ID: P012006
The complex of DNA with its packaging proteins is called chromatin.
Nuclei contain two broad classes of chromatin: heterochromatin,
which is highly condensed throughout the cell cycle and is generally
inactive in transcription, and euchromatin, which is less condensed
and contains actively transcribed genes. Different types of chromatin
are defined by complex patterns of posttranslational modifications of
the histone proteins. This "histone code" directs the binding of other
proteins that induce the chromatin to adopt either a more compact or
more open and active structure.
Body_ID: P012007
Chapter 14 discusses the structure and physiology of the nucleus. The
boundary of the nucleus is a nuclear envelope composed of inner and
outer nuclear membranes, separated by a perinuclear space that is
continuous with the lumen of the endoplasmic reticulum. The inner
nuclear membrane is supported by a protein layer called the nuclear
lamina. Mutations in the lamina and other nuclear envelope proteins
cause a wide spectrum of inherited human diseases, with mutations
in the lamin A gene alone causing over a dozen different diseases.
Body_ID: P012008
Traffic into and out of the nucleus moves through nuclear pore
complexes that span the two membrane bilayers of the nuclear
envelope. Newly processed RNAs head out to the cytoplasm. So do
the ribosomal subunits that will translate them into proteins, some of
which then wend their way back into the nucleus. Proteins that are
destined for transport across the nuclear envelope (either alone or
associated with RNA molecules) typically contain short stretches of
amino acids , called nuclear localization sequences or nuclear export
sequences, that bind to specific adapter and receptor proteins to
facilitate transport across the nuclear pore. A small guanosine
triphosphatase (GTPase) called Ran regulates the directionality of
this transport, because it is present primarily in its GTP-bound form
in the nucleus and its GDP-bound form in the cytoplasm. Ran-GTP
in the nucleus causes imported cargos to fall off their transporters
and cargos destined for export to bind to their carriers.
Body_ID: P012009
The nucleus contains a number of substructures. The most
prominent of these is the nucleolus, a versatile factory for
transcription of ribosomal RNA (rRNA) from a tandem array of
genes and processing of rRNA and other noncoding RNAs, as well as
ribosome assembly. Nuclei also contain several other specialized
regions. Although in many cases, their functions are not known, the
presence of these specialized subdomains suggests that
compartmentalization of the nucleus contributes to the regulation of
nuclear functions.
PACKAGING OF DNA MOLECULES INTO CHROMOSOMES
G in one strand will always be paired with a C in the other.
Similarly an A will always pair with a T. The two strands are
therefore said to be complementary.
Erwin Chargaff’s Puzzling Data
In a key discovery of the 1950s, Erwin Chargaff analyzed the
purine and pyrimidine content of DNA isolated from many different
organisms and found that the amounts of A and T were always the
same, as were the amounts of G and C. Such an identity was
inexplicable at the time, but helped James Watson and Francis Crick
build their double-helix model in which every A on one strand of the
DNA helix has a matching T on the other strand, and every G on one
strand has a matching C on the other. Different Forms of DNA The
original Watson–Crick model of DNA is now called the B-form. In
this form, the two strands of DNA form a right-handed helix. If
viewed from either end, it turns in a clockwise direction. B-DNA is
the predominant form in which DNA is found. Our genome, however,
also contains several variations of the B-form double helix. One of
these, Z-DNA, so-called because its backbone has a zig-zag shape,
forms a left-handed helix and occurs when the DNA sequence is
made of alternating purines and pyrimidines. Thus the structure
adopted by DNA is a function of its base sequence.
DNA AS THE GENETIC MATERIAL
Deoxyribonucleic acid carries the genetic information encoded in
the sequence of the four bases—adenine, guanine, cytosine, and
thymine. The information in DNA is transferred to its daughter
molecules through replication (the duplication of DNA molecules)
and subsequent cell division. DNA directs the synthesis of proteins
through the intermediary molecule RNA.
The DNA code is transferred to RNA by a process
known as transcription The RNA code is then
translated into a sequence of amino acids during
protein synthesis. This is the central dogma of
molecular biology: DNA makes RNA makes protein.
Retroviruses such as human immunodeficiency virus, the cause of
AIDS, are an exception to this rule. As their name suggests, they
reverse the normal order of data transfer. Inside the virus coat is a
molecule of RNA plus an enzyme that can make DNA from an
RNA template by the process known as reverse transcription.
PACKAGING OF DNA MOLECULES INTO CHROMOSOMES
Eukaryotic Chromosomes and Chromatin Structure A human
cell contains 46 chromosomes (23 pairs), each of which is a single
DNA molecule bundled up with various proteins. On average, each
human chromosome contains about 1.3 × 108 base pairs (bp) of DNA.
DNA has to be highly compacted in order to fit into the cell 1400 nm
Histone octamer 30nm solenoid 30nm nucleosomes ("beads on a
string") so the 46 chromosomes in all represent about 2 m of DNA.
The nucleus in which this DNA must be contained has a
diameter of only about 10μm, so large amounts ofDNAmust be
packaged into a small space. This represents a formidable problem
that is dealt with by binding the DNA to proteins to form chromatin.
the DNA double helix is packaged at both small and larger scales. In
the first stage, shown on the right of the figure, the DNA double helix
with a diameter of 2 nm is bound to proteins known as histones.
Histones are positively charged because they contain high amounts of
the amino acids arginine and lysine and bind tightly to the negatively
charged phosphates on DNA. DNA is wound around a protein
complex composed of two molecules each of four different histones—
H2A, H2B, H3, and H4—to form a nucleosome. Because each
nucleosome is separated from its neighbor by about 50 bp of linker
DNA, this unfolded chromatin state looks like beads on a string when
viewed in an electron microscope. Nucleosomes undergo further
packaging. A fifth type of histone, H1, binds to the linker DNA and
pulls the nucleosomes together helping to further coil the DNA into
chromatin fibers 30 nm in diameter, which are referred to as 30-nm
solenoids. The fibers then form loops with the help of a class of
proteins known as nonhistones, and this further condenses the DNA
into a higher order set of coils in a process called supercoiling. In a
normal interphase cell about 10% of the chromatin is highly
compacted and visible under the light microscope This form of
chromatin is called heterochromatin and is the portion of the genome
where noRNAsynthesis is occurring. The remaining interphase
chromatin is less compacted and is known as euchromatin.
Chromatin is in its most compacted form when the cell is preparing
for mitosis,.. The chromatin folds and condenses further to form the
1400-nm-wide chromosomes we see under the light microscope.
Because the cell is to divide, the DNA has been replicated, so that
each chromosome is now formed by two chromatids, each one a DNA
double helix. This means the progeny cell, produced by division of
the progenitor cell, will receive a full set of 46 chromosomes.
Prokaryotic Chromosomes
The chromosome of the bacterium E. coli is a single circular DNA
molecule of about 4.5 × 106 base pairs. It has a circumference of 1
mm, yet must fit into the 1-μm cell, so like eukaryotic chromosomes it
is coiled, supercoiled, and packaged with basic proteins that are
similar to eukaryotic histones. However, an ordered nucleosome
structure similar to the “beads on a string” seen in eukaryotic cells is
not observed in prokaryotes. Prokaryotes do not have nuclear
envelopes so the condensed chromosome together with its associated
proteins lies free in the cytoplasm, forming a mass that is called the
nucleoid to emphasize its functional equivalence to the eukaryotic
nucleus.
Plasmids
Plasmids are small circular minichromosomes found in bacteria
and some eukaryotes. They are several thousand base pairs long and
are probably tightly coiled and supercoiled inside the cell. Plasmids
often code for proteins that confer resistance to a particular
antibiotic. plasmids are used by scientists and genetic engineers to
artificially introduce foreign DNA molecules into bacterial cells.