Sixth Lecture
Nucleus
The nucleus is the center for the genetically determined
information in every eukaryotic cell. The nucleus also serves as a
command or logistics center for the regulation of cell functions. There
is a correlation between the geometry of the nucleus and the cell
dimensions, which offers important diagnostic clues. The nucleus is
usually round in polygonal and isoprismatic (cuboid) cells and
ellipsoid in pseudostratified columnar cells; it has the form of a
spindle in smooth muscle cells and is flattened in flat epithelial cells.
In granulocytes, the nucleus has several segments. The fibrocyte in
this figure is from subcutaneous connective tissue. Its elongated,
irregularly lobed nucleus shows indentations and deep dells.
The structural components of a nucleus are the nuclear
membrane, the nuclear lamina, the nucleoplasm, and the
chromosomes with the chromatin and the nucleolus. The chromatin is
finely granular (euchromatin), but more dense near the inner nuclear
membrane (heterochromatin). The small electron-dense patches are
heterochromatin structures as well. The DNA is packaged in a much
denser form in heterochromatin than in euchromatin, and
heterochromatin therefore appears more heavily stained in light
microscopy preparations.
The nucleus is centrally located and spherical cellular
component which controls all the vital activities of the cytoplasm and
carries the hereditary material the DNA in it. The nucleus consists of
the following three structures :
1. Chromatin. Nucleus being the heart of every type of eukaryotic
cell, contains the genes, the hereditary units. Genes are located on the
chromosomes which exist as chromatin network in the non- dividing
cell, i.e., during interphase. The chromatin has two forms :
1. Euchromatin is the well-dispersed form of chromatin which takes
lighter DNA-stain and is genetically active, i.e., it is involved in gene
duplication, gene transcription (DNA- dependent RNA synthesis) and
phenogenesis or phenotypic expression of a gene through some type
of protein synthesis.
2. Heterochromatin is the highly condensed form of chromatin which
takes dark DNA-stain and is genetically inert. Such type of
chromatin exists both in the region of centromere (called constitutive
heterochromatin) and in the sex chromatin (called facultative
heterochromatin) and is latereplicating one.
The chromatin contains a single DNA molecule, equal amount of five
basic types of histone proteins, some RNA molecules and variable
amount of different types of acidic proteins. In fact, the chromatin
has its unit structures in the form of nucleosomes. The chromatin
binds strongly to the inner part of nuclear lamina, a 50 to 80 nm
thick fibrous lamina lining the inner side of the nuclear envelope.
Nuclear lamina is made up of three types of proteins, namely lamin
A, B and C. Lamin proteins are homologous in structure to IF
proteins and serve the following functions :
1. They anchor parts of interphase chromatin to the nuclear
membrane. They tend to interfere with chromatin
condensation during interphase of cell cycle.
2.
2. Lamins may play a crucial role in the assembly of interphase
nuclei after each mitosis.
2. Nuclear envelope and nucleoplasm. Nuclear envelope comprises
two nuclear membranes an inner nuclear membrane which is lined
by nuclear lamina and an outer nuclear membrane which is
continuous with rough ER. At certain points the nuclear envelope is
interrupted by structures called pores or nucleopores. Nuclear pores
contain octagonal pore complexes which regulate exchange between
the nucleus and cytoplasm. The number of nucleopores is found to be
correlated with the transcriptional activity of the cell. For example,
in the frog Xenopus laevis oocytes (which are very active in
transcription) have 60 pores/ µm 2 (and up to 30 million pore
complexes per nucleus) , whereas frog’s mature erythrocytes
(inactive in transcription) have only about 3 pores/μm2 (and a total
of only 150 to 300 pores per nucleus)
The nuclear envelope binds the nucleoplasm which is rich in
those molecules which are needed for DNA replication, transcription,
regulation of gene actions and processing of various types of newly
transcribed RNA molecules (i.e., tRNA, mRNA and other types of
RNA).
3. Nucleolus. Nucleus contains in its nucleoplasm a conspicuous,
lacks any limiting membrane and is formed during interphase by the
ribosomal DNA (rDNA) of nucleolar organizer (NO). Nucleolus is the
site where ribosomes are manufactured. It is here where ribosomal
DNA transcribes most of rRNA molecules and these molecules
undergo processing before their step-wise addition to 70 types of
ribosomal proteins to form the ribosomal sub-units. Differences
between prokaryotic and eukaryotic cells (Source : Maclean and
Hall, 1987).
DNA STRUCTURE AND THE GENETIC CODE
DNA molecules are very large. The single chromosome of the
bacterium Escherichia coli is made up of two strands of DNA that are
hydrogen-bonded together to form a single circular molecule
comprising 9 million nucleotides. Humans have 46 DNA molecules in
each cell, each forming one chromosome. We inherit 23 chromosomes
from each parent. Each set of 23 chromosomes encodes a complete
copy of our genome and is made up of 6 × 109 nucleotides (or 3 × 109
base pairs.We do not yet know the exact number of genes that encode
messenger RNA and therefore proteins in the human genome. The
current estimate is in the range of 30,000. compares the number of
predicted messenger RNA genes in the genomes of different
organisms. In each organism, there are also approximately 100 genes
that code for ribosomal RNAs and transfer RNAs. The role these
three types of RNA play in protein synthesis
As nucleotides are added to the chain by the enzyme
DNApolymerase , they lose two phosphate groups. The last (the α
phosphate) remains and forms a phosphodiester link between
successive deoxyribose residues. The bond forms between the
hydroxyl group on the 3_ carbon of the deoxyribose of one nucleotide
and the α-phosphate group attached to the 5_ carbon of the next
nucleotide. Adjacent nucleotides are hence joined by a 3_–5_
phosphodiester link.
Table 4.1. Numbers of Predicted Genes in Various Organisms
Organism
Number of Predicted Genes
Bacterium—Haemophilus influenzae 1,
709
Yeast—Saccharomyces cerevisiae
6,241
Fruit fly—Drosophila melannogaster
13,601
Worm—Caenorhabdites elegans
18,424
Plant—Arabidopsis thaliana
25,498
Human—Homo sapiens ∼
30,000
The linkage gives rise to the sugar–phosphate backbone of a
DNA molecule. A DNA chain has polarity because its two ends are
different. In the first nucleotide in the chain, the 5_ carbon of the
deoxyribose is phosphorylated but otherwise free. This is called the
5_ end of the DNA chain. At the other end is a deoxyribose with a
free hydroxyl group on its 3_ carbon. This is called the 3_ end.
The DNA Molecule Is a Double Helix
In 1953 Rosalind Franklin used X-ray diffraction to show that
DNA was a helical (i.e., twisted) polymer. James Watson and Francis
Crick demonstrated, by building threedimensional models, that the
molecule is a double helix
As the genomes of more and more organisms were sequenced,
the most surprising feature to emerge was just how few genes
supposedly “complex” organisms possess. The first eukaryotic
genome to be sequenced was that of the lowly budding yeast,
Saccharomyces cerevisiae, the simple unicellular fungus that we use to
make bread and beer. S. cerevisiae has about 6000 genes. The fruit
fly, Drosophila melanogaster, a much more complex organism with a
brain, nervous and digestive systems, and the ability to fly and
navigate, on the other hand, has 13,600 genes, or roughly twice the
number in a yeast. Even more surprising was the case of the human
genome. Prior to the completion of the Human Genome Project
predictions of the number of human genes were in the order of
100,000. Surely this complex vertebrate that could send a spaceship
to Mars and write War and Peace would need vastly more genes than
the fruit fly. In the event, the number of human genes turned out to
be much lower than expected, about 30,000, only twice as many genes
as in Drosophila.
If complex biological and social achievements are not the result
of having more genes, where do they come from?
Two factors help the human genome generate a more complex
organism. First, having more DNA per gene means that more DNA
can be used in enhancer sequences allowing more subtle control of
where, when, and to what extent a gene is expressed. Second, there is
not a straight forward one-to-one relationship between genes and
proteins. Alternative splicing allows the cell to “cut and paste” a
messenger RNA molecule in different ways to produce many
different proteins from the same gene. Estimates are that something
like 50% of human genes show alternative splicing with the pattern
of splicing (the range of proteins produced) varying from tissue to
tissue. Drosophila genes also show alternative splicing but those of
yeast, which contain few introns, do not.
. THE STRUCTURE OF DNA
Phosphodiester link sugar-phosphate backbone of DNA many
repeating units. Sugar–phosphate backbones lie on the outside of the
molecule, and the purines and pyrimidines lie on the inside of the
molecule. There is just enough space for one purine and one
pyrimidine in the center of the double helix. The Watson–Crick
model showed that the purine guanine (G) would fit nicely with the
pyrimidine cytosine (C), forming three hydrogen bonds. The purine
adenine (A) would fit nicely with the pyrimidine thymine (T),
forming two hydrogen bonds. Thus A always pairs with T, and G
always pairs with C. The three hydrogen bonds formed between G
and C produce a relatively strong base pair. Because only two
hydrogen bonds are formed between A and T, this weaker base pair
is more easily broken. The difference in strengths between a G–C
and an A–T base pair is important in the initiation and termination
of RNA synthesis The two chains of DNA are said to be antiparallel
because they lie in the opposite orientation with respect to one
another, with the 3_-hydroxyl terminus of one strand opposite the 5_phosphate terminus of the second strand. The sugar–phosphate
backbones do not completely conceal the bases inside. There are two
grooves along the surface of the DNA molecule. One is wide and
deep—the major groove—and the other is narrow and shallow—the
minor groove Proteins can use the grooves to gain access to the bases
The Two DNA Chains Are Complementary A consequence of the
base pairs formed between the two strands of DNA is that if the base
sequence of one strand is known, then that of its partner can be
inferred. A G in one strand
cytosine (C)
thymine (T)
guanine (G)
adenine (A)