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Nucleus
Summary
The nucleus , the largest organelle of the cell, houses the nucleoplasm , nucleolus, and the chromatin . The nucleus is separated from the cytoplasm by a double membrane, known as the nuclear envelope , which is perforated by numerous openings, known as nuclear pores and their associated structures that, together with the pore, form the nuclear pore complex that functions in a bidirectional nucleocytoplasmic transport. Chromatin is a complex of DNA and associated proteins that, during cell division, are folded to form chromosomes . It is the DNA that comprises the genetic material of the cell and acts as a template for RNA transcription . The nucleolus is the deeply staining region within the nucleus where ribosomal RNA synthesis and ribosome assembly occur. The cell cycle is a series of exquisitely controlled events that prepare the somatic cell for mitosis and the gametes for a unique nuclear division known as meiosis .
The nucleus , the largest organelle of the cell ( Fig. 3.1 ), contains nearly all of the deoxyribonucleic acid ( DNA ) possessed by the cell, as well as the mechanisms for ribonucleic acid ( RNA ) synthesis. Its resident nucleolus is the location for rRNA synthesis and for the assembly of the ribosomal subunits. The nucleus, bounded by the nuclear envelope , composed of two concentric phospholipid bilayer membranes, houses three major components: chromatin , nucleoplasm , and the nucleolus .
Cell nuclei. Light micrograph (×1323). Typical cells, each containing a spherical nucleus (N). Observe the chromatin granules (ChG) and the nucleolus (n).
The nucleus is usually spherical and is centrally located in the cell. In some cells, however, it may be spindle-shaped to oblong-shaped, twisted, lobulated, or even disk-shaped ( Figs. 3.2 and 3.3 ). Although each cell usually has a single nucleus, some cells (such as osteoclasts) possess several nuclei, whereas mature red blood cells have extruded their nuclei and are anucleated. The size, shape, and form of the nucleus are generally constant for a particular cell type, a fact useful in clinical diagnoses of the degree of malignancy of certain cancerous cells.
Note that the nucleus of the eosinophil has two lobes (arrows) that are connected to each other by a slender filament (arrowhead) and that its cytoplasm is filled with specific granules (Gr). The red blood cells (RBC) extruded their nuclei during development and platelets (P) are cell fragments that have no nuclei. (×1,325)
Observe that the nucleus of the white blood cell neutrophil has several lobes (arrows) connected to each other by slender filaments (arrowheads) . The red blood cells (RBC) extruded their nuclei during development; therefore, they are anucleated. The platelets (P) are cell fragments and have no nuclei. (×1,325)
Nuclear Envelope
The nuclear envelope is composed of two parallel unit membranes that fuse at certain regions to form perforations known as nuclear pores.
The nucleus is surrounded by the nuclear envelope , composed of two concentric parallel unit membranes: the inner and outer nuclear membranes , separated from each other by a 20- to 40-nm space called the perinuclear cisterna ( Figs. 3.4 and 3.5 ).
Inner Nuclear Membrane
The inner nuclear membrane is about 6 nm thick and faces the nuclear contents. It is in close contact with the nuclear lamins , an interwoven meshwork of intermediate filaments , 80 to 300 nm thick, composed of lamins A, B 1 , B 2 , and C and located at the periphery of the nucleoplasm. The nuclear lamins bind to integral membrane proteins, such as lamina-associated polypeptides and emerin , of the inner nuclear membrane. They function in organizing and providing support to the lipid bilayer membrane and the perinuclear chromatin, assist in the formation of nuclear pore complexes, and aid in the assembly of vesicles to reform the nuclear envelope subsequent to cell division.
Outer Nuclear Membrane
The outer nuclear membrane is also about 6 nm thick, faces the cytoplasm, is continuous with the rough endoplasmic reticulum (RER), and is considered by some authors as a specialized region of the RER, whose lumen is continuous with the perinuclear cistern (see Figs. 3.4, 3.5, and 3.6 ). Its cytoplasmic surface—surrounded by a thin, loose meshwork of the intermediate filaments, vimentin —usually possesses ribosomes actively synthesizing transmembrane proteins that are destined for the outer or inner nuclear membranes.
Nuclear Pore and Nuclear Pore Complex
The nuclear pores are circular openings in the nuclear envelope, each plugged by a complex of proteins known as the nuclear pore complex, providing controlled passage between the nucleus and the cytoplasm.
The nuclear envelope is perforated at various intervals by nuclear pores , where the inner and outer nuclear membranes are continuous with one another. In order to regulate the movement of larger molecules across the nuclear pore, a complex of proteins, collectively known as the nuclear pore complex , is inserted into each nuclear pore. Some cells may have as many as 4000 nuclear pores, with associated nuclear pore complexes.
The nuclear pore complex is about 100 to 125 nm in diameter, spans the two nuclear membranes, and has an average molecular weight of 125 MDa. It is composed of about 500 different proteins, collectively known as nucleoporins , arranged in three ring-like arrays of proteins stacked one on top of the other. Each ring displays an eightfold symmetry and is interconnected by a series of spokes arranged in a vertical fashion. In addition, the nuclear pore complex has cytoplasmic fibers, a central plug, and a nuclear basket ( Figs. 3.7 through 3.9 ).
The cytoplasmic ring , composed of eight subunits, is located on the rim of the cytoplasmic aspect of the nuclear pore. Each subunit possesses a cytoplasmic filament believed to be a Ran-binding protein (a family of guanosine triphosphate [GTP]–binding proteins), that extends into the cytoplasm and may mediate access to the nucleus through the nuclear pore complex by moving substrates along their length toward the center of the pore.
The luminal spoke ring ( middle ring ), a set of eight transmembrane proteins, projects into the lumen of the nuclear pore, as well as into the perinuclear cistern, probably anchoring the glycoprotein components of the nuclear pore complex into the rim of the nuclear pore.
The central lumen of the middle ring is believed to be a gated channel that restricts passive diffusion between the cytoplasm and the nucleoplasm. It is associated with additional protein complexes that facilitate the regulated transport of materials across the nuclear pore complex.
A nuclear ring ( nucleoplasmic ring ), analogous to the cytoplasmic ring, is located on the rim of the nucleoplasmic aspect of the nuclear pore and assists in the export of several types of RNA. A filamentous, flexible, basket-like structure, the nuclear basket , which becomes deformed during the process of nuclear export, appears to be suspended from the nucleoplasmic ring, protruding into the nucleoplasm. Attached to the distal aspect of the nuclear basket is the distal ring .
Function of the Nuclear Pore Complex
The nuclear pore complex functions in bidirectional nucleocytoplasmic transport.
Although the nuclear pore is relatively large, it is nearly filled with the structures constituting the nuclear pore complex; as many as 1000 molecules may pass through any one of these pores every second. Because of the structural conformation of those subunits, several 9- to 11-nm-wide channels are available for simple diffusion of ions and small molecules. However, macromolecules and particles larger than 11 nm cannot reach or leave the nuclear compartment via simple diffusion. Instead, they are selectively transported via a receptor-mediated transport process. Signal sequences of molecules to be transported through the nuclear pores must be recognized by one of the many receptor sites of the nuclear pore complex. Transport across the nuclear pore complex is frequently an energy-requiring process.
The bidirectional traffic between the nucleus and the cytoplasm is mediated by a group of target proteins containing nuclear localization signals ( NLSs ) known as importins and nuclear export signals ( NESs ) known as exportins (also known as karyopherins , PTACs , transportins , and Ran-binding proteins ). Exportins transport macromolecules (e.g., RNA) from the nucleus into the cytoplasm, whereas importins transport cargo (e.g., protein subunits of ribosomes) from the cytoplasm into the nucleus. Exportin and importin transport is regulated by a family of GTP-binding proteins known as Ran (see Fig . 3.9 ). These specialized proteins, along with other nucleoporins located along receptor sites in the nuclear pore complex, facilitate the signal-mediated import and export processes. Some protein trafficking is more like shuttling, because some proteins pass back and forth between the cytoplasm and the nucleus in a continuous fashion. Recently, it has been reported that certain other transport mechanisms literally shuttle in both directions. These transport signals are called nucleocytoplasmic shuttling ( NS ) signals. Proteins that carry this signal interact with messenger ribonucleic acid (mRNA).
Clinical Correlations
A number of diseases are associated with mutations in genes coding for various nucleoporin components of the nuclear pore complex, such as infantile bilateral striatal necrosis ( IBSN ). There are two forms of this condition, the less common familial and the more prevalent sporadic. The familial form is a mitochondrial disorder, in which the malformation occurs in the ATP-synthase-6 molecule. In the sporadic form, the mutation is in one of the nucleoporin genes (specifically, NUP62 ). The sporadic form usually follows an occurrence of high fever as a result of various acute systemic conditions, such as measles or bacterial infections. As such, it has a sudden onset anytime during the first few years of life (in some instances, even during adolescence). Clinical manifestations include spasticity, rigidity, nystagmus, weakness in the arms and legs, as well as other musculoskeletal symptoms. Prospects for the familial form are poor, with quick degeneration of skeletal muscles, followed by early death. The sporadic form has a much better rate of recovery once the cause of the high fever is eradicated. The patient may recover completely; however, in some instances, the patient may suffer various neurological complications.
Chromatin
Chromatin is a complex of DNA and proteins and represents the relaxed, uncoiled chromosomes of the interphase nucleus.
DNA , the cell’s genetic material, resides in the nucleus in the form of chromosomes , which are clearly visible during cell division. In the interval between cell divisions, the chromosomes are unwound or partially unwound in the form of chromatin (see Figs. 3.4, 3.5, 3.7, and 3.10 ), specifically, heterochromatin or euchromatin.
Heterochromatin , a condensed and inactive form of chromatin, stains deeply with basic stains such as hematoxylin, which make it visible with the light microscope. It is located mostly at the periphery of the nucleus, comprises almost 90% of the total chromatin of the nucleus, and is not being transcribed. The remainder of the chromatin scattered throughout the nucleus and not visible with the light microscope is euchromatin . This represents the active form of chromatin, in which the genetic material of the DNA molecules is being transcribed into some forms of RNA.
When euchromatin is examined with electron microscopy, it is seen to be composed of a thread-like material 30 nm thick. More careful evaluation indicates that these threads may be unwound, resulting in a 10 to 11-nm-wide structure resembling “beads on a string.” The beads are termed nucleosomes , and the string, which is the DNA molecule , appears as a thin filament 2 nm in diameter (see Fig. 3.10 ).
Each nucleosome is composed of an octomer of proteins, duplicates of each of four types of histones ( H 2 A, H 2 B , H 3 , and H 4 ). The nucleosome is also wrapped with two complete turns (∼150 nucleotide pairs) of the DNA molecule that continues as linker DNA extending to the next “bead.”
Electron microscopic studies of the nuclear contents following more careful manipulation have revealed chromatin fibers exhibiting diameters of 30 nm. Packaging of chromatin into 30-nm threads is believed to occur by helical coiling of consecutive nucleosomes at six nucleosomes per turn of the coil and cooperatively bound there with histone H 1 (see Fig. 3.8 ). Nonhistone proteins are also associated with the chromatin, but their function is not clear.
Chromosomes
Chromosomes are chromatin fibers that become so condensed and tightly coiled during mitosis and meiosis that they are visible with the light microscope.
As the cell leaves the interphase stage and prepares to undergo mitotic or meiotic activity, the chromatin fibers are extensively condensed to form chromosomes , visible with light microscopy. The process of packing the long, 30-nm-wide fibers into chromosomes occurs with the assistance of two large ring-shaped protein complexes known as condensin I and condensin II . Condensin II is located in the nucleus; it begins the process during the prophase of the mitotic division by forming large 300-nm-wide loops of the 30-nm fibers and, by forming a helical scaffold, causing these loops to wind around the scaffold. During prometaphase, the nuclear membrane disappears and the helically arranged loops become exposed to condensin I that is located in the cytoplasm. Condensin I partitions the 300-nm-wide loops into smaller, nested loops that can be packaged into the compact cylindrical structures, the metaphase chromosomes ( Fig. 3.11 ). Amazingly, the majority of this packaging takes place in about 15 minutes; 45 more minutes are spent on quality control of this remarkable process.
The number of chromosomes in somatic cells is specific for the species and is called the genome , the total genetic makeup. In humans, the genome consists of 46 chromosomes, representing 23 homologous pairs of chromosomes. One member of each of the chromosome pairs is derived from the mother; the other comes from the father. Of the 23 pairs, 22 are called autosomes ; the remaining pair that determines gender is the sex chromosomes . The sex chromosomes of the female are two X chromosomes ( XX ); those of a male are the X and Y chromosomes ( XY ; see Fig. 3.11 ).
Telomeres are short, repeated DNA sequences at the ends of chromosomes. They appear to protect the ends of the chromosomes from degradation and, in oocytes and spermatogonia, as well as in stem cells, an enzyme-RNA complex known as telomerase , maintains the telomere length. Interestingly, the RNA portion of the enzyme is used as a template to synthesize the additional DNA necessary to maintain telomere length. Somatic cells do not possess telomerase. With each successive cell division, the telomeres become shorter; eventually, they become short enough that they can no longer protect the chromosome and the cell becomes unable to replicate itself. This built-in senescence is absent in cancer cells because many malignant cells are able to express the gene that codes for telomerase.
Sex Chromatin
Only one of the two X chromosomes in female somatic cells is transcriptionally active. The inactive X chromosome, randomly determined early in development, remains inactive throughout the life of that individual (see discussion in this chapter: section on RNA) as a clump of chromatin, the sex chromatin ( Barr body ), at the periphery of the nucleus.
Clinical Correlations
It has been reported that individuals who exercise and people with higher education appear to possess longer telomeres, whereas people who are long-term smokers, individuals who drink alcohol excessively, and those who are under very high stress levels have shorter telomeres. It has been suggested that people with shorter telomeres tend to have a shorter life span.
In some individuals, mostly males, the X chromosome displays a narrowed region near its terminus. About 80% of the males possessing such X chromosomes are mentally challenged, display a decreased ability to accomplish certain tasks, are hyperactive, and display anxious behavior. This condition is known as the fragile X syndrome owing to the morphology of the X chromosome, whose tip appears to be almost broken. The altered region of the X chromosome is the locus for the FMR1 gene ( fragile X mental retardation 1 gene ) that codes for the FMR protein . This protein represses translation of certain mRNAs, thereby inhibiting the formation of cytoskeletal elements at synapses and, in that fashion, interfering with neuronal plasticity.
Microscopic study of interphase nuclei of cells from females displays a very tightly coiled clump of chromatin, the sex chromatin ( Barr body ), the inactive counterpart of the two X chromosomes. Epithelial cells obtained from the lining of the cheek and neutrophils from blood smears are especially useful for studying sex chromatin. The sex chromatin is observed at the edge of the nuclear envelope in smears of the oral epithelial cells and as a small drumstick-like evagination of the nuclei of the neutrophils. A number of cells must be examined to observe sex chromatin because the X chromosome must be in the proper orientation to be displayed for observation.
Ploidy
Cells containing the full complement of chromosomes (46) are said to be diploid ( 2n ). Germ cells (mature ova or spermatozoa) are said to be haploid (1n) ; that is, only one member of each of the homologous pairs of chromosomes is present. Upon fertilization, the chromosomal number is restored to the diploid (2n) amount as the nuclei of the two germ cells unite.
Certain alkaloids, such as colchicine, a plant derivative, arrest a dividing cell in the metaphase stage of mitosis when the chromosomes are maximally condensed, thus permitting the pairing and numbering of the chromosomes via a conventional system of karyotyping , an analysis of chromosome number (see Fig. 3.11 ).
Clinical Correlations
One item that may be observed from the karyotype is aneuploidy , an abnormal chromosome number. Individuals with Down syndrome , for example, have an extra chromosome 21 ( trisomy 21 ); they exhibit intellectual disability, stubby hands, and many congenital malformations, especially of the heart, among other manifestations.
Certain syndromes are associated with abnormalities in the number of sex chromosomes. Klinefelter syndrome results when an individual possesses three sex chromosomes ( XXY ). These persons exhibit the male phenotype, but they do not develop secondary sexual characteristics and are usually sterile. Turner syndrome is another example of aneuploidy, called monosomy of the sex chromosomes. The karyotype exhibits only one sex chromosome ( XO ). These individuals are females whose ovaries never develop and who have undeveloped breasts, a small uterus, and intellectual disability.
Deoxyribonucleic Acid (DNA)
DNA, the genetic material of the cell, is located in the nucleus, where it acts as a template for RNA transcription.
DNA is composed of two types of bases: purines (adenine and guanine) and pyrimidines (cytosine and thymine). A double helix is established by the formation of hydrogen bonds between complementary bases on each strand of the DNA molecule. These bonds are formed between adenine (A) and thymine (T) and between guanine (G) and cytosine (C).
Genes
The biological information that is passed from one cell generation to the next—the units of heredity—are located at specific regions on the DNA molecule called genes . Each gene represents a specific segment of the DNA molecule that codes for the synthesis of a particular protein, as well as for the regulatory sequences responsible for their expression. The sequential arrangement of bases constituting the gene represents the sequence of amino acids of the protein. The genetic code is designed in such a manner that a triplet of consecutive bases, a codon , denotes a particular amino acid. Each amino acid is represented by a different codon. The complete set of genes—that is, both the coding and noncoding segments of the DNA—are known as the genome . Coding segments possess the codons that determine the sequence of amino acids in a protein (or polypeptide) and noncoding segments possess regulatory or other functions.
Currently, the data indicates that the human genome contains about 25,000 genes, all of which were sequenced and mapped, which represents only 2% of the genome; 98% of the genome has regulatory or other functions.
Epigenetics
Epigenetics is a relatively new field of study that explores chemically induced heritable changes that occur to the genome without altering the sequence of nucleotides of the DNA molecule. These changes are caused by the addition of small molecules, such as methyl groups or acetyl groups , to the histones that compose the core of the chromatid. These small molecules act as markers that either silence the genes or cause the expression of the genes that are wrapped around the methylated or acetylated histones. The addition of these small molecules can transpire not only during embryogenesis but also in the adult individual. They may be caused by various environmental insults, such as toxic agents, or environmental stimuli, such as stress. It is important to realize that these are inheritable alterations in the same fashion that mutations in the sequence of DNA nucleotides are inheritable. Methylation tends to silence genes, whereas acetylation facilitates gene expression.
Clinical Correlations
Recent evidence has demonstrated that individuals who committed suicide had a much greater degree of methylation of the chromosomes of their hippocampus (the part of the brain responsible for memory formation) than did members of the control group who died suddenly but not due to suicide.
In a related study, it was shown that children who grew up in an orphanage exhibited a greater degree of chromosome methylation than did the control group consisting of children who grew up in the home of their biological parents. Most of the methylated genes were related to brain development and neural function . Although the inheritance of these traits has not been proven in humans, mouse studies have shown that stress-related epigenetic alterations are transmitted from parents to pups.
Ribonucleic Acid
RNA is similar to DNA except that it is single stranded, one of its bases is uracil instead of thymine, and its sugar is ribose instead of deoxyribose.
RNA is similar to DNA, with both composed of a linear sequence of nucleotides, but RNA is single stranded and the sugar in RNA is ribose, not deoxyribose. One of the bases, thymine, is replaced by uracil (U), which, similar to thymine, is complementary to adenine. There are two major types of RNA, coding RNA and noncoding RNAs . Coding RNA—namely, mRNA—carries the code for protein synthesis. Noncoding RNAs assist in protein synthesis (transfer RNA and ribosomal RNA) as well as in regulatory functions ( Table 3.1 ).
TABLE 3.1
Types of RNA
| Abbreviation | Name | Function |
|---|---|---|
| mRNA | Messenger RNA | A coding RNA that functions as the template for protein synthesis |
| rRNA | Ribosomal RNA | Combines with proteins to form the two ribosomal subunits to function in protein synthesis |
| tRNA | Transfer RNA | Binds to amino acids to carry them to the correct sites on the mRNA in protein synthesis |
| miRNA | Micro RNA | Short RNA segments (19–25 nucleotides) that have regulatory functions by blocking protein synthesis; they also promote cancerogenesis by blocking apoptotic pathways |
| siRNA | Small interfering RNA, also known as Silencing RNA |
Short, double-stranded RNA segments (20–22 nucleotides) that interfere with protein synthesis. They are released by viruses or are transposons that enter the cell. There are synthetic siRNAs that are manufactured for therapeutic purposes. |
| lincRNA, also known as lncRNA | Long intergenic noncoding RNA Long noncoding RNA |
Long-chain RNA (≥200 nucleotides) that regulate cancerogenesis and embryogenesis and also inactivate the second X chromosomes in females |
| piRNA | Piwi-interacting RNA | Interferes with the expression of transposons; facilitates the placement of epigenetic markers on chromosomes |
The DNA in the nucleus serves as a template for synthesis of a complementary strand of RNA, a process called transcription . Synthesis of three of the various types of RNA is catalyzed by three different RNA polymerases :
-
Messenger RNA ( mRNA ) by RNA polymerase II
-
Transfer RNA ( tRNA ) by RNA polymerase III
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Ribosomal RNA ( rRNA ) by RNA polymerase I
The mechanism of transcription is generally the same for all three types of RNA. It should be noted that only mRNA is transcribed from the coding segments of the DNA. rRNA, tRNA, and regulatory RNAs are transcribed from the noncoding segments of the DNA.
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