The Nucleus of a Eukaryotic Cell and Chromatin Organization

By | August 20, 2021
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The nucleus of a eukaryotic cell is essential for the storage and utilization of genetic information. The contents of the nucleus are enclosed by a complex nuclear envelope that separates the nucleus from the cytoplasm. The nucleus of a non-mitotic cell contains:

  • Chromosomes, highly extended nucleoprotein fibers, also called chromatin.
  • An irregularly shaped electron-dense structure, that function in the synthesis of ribosomal RNA and the assembly of ribosomes, called nucleoli.
  • Nucleoplasm, the fluid substance of the nucleus in which the solutes and contents dissolve.
  • Protein-containing fibrillar network called nuclear matrix.

The Nuclear Envelope

The nuclear envelope is a double membrane structure, such that the two cellular membranes are separated by 10 to 50 nm. This envelope does not allow the passage of ions, macromolecules, and solutes into the nucleus. The two membranes are fused with circular pores at sites, formed of complex assemblies of proteins. A typical mammalian cell contains several thousands of such nuclear pores. The outer membrane of the nuclear envelope is continuous with the membrane of the endoplasmic reticulum and studded with ribosomes.

The inner surface of the nuclear envelope is associated with the thin filamentous meshwork, called nuclear lamina, through integral proteins. The nuclear lamina also serves as a site of attachment for chromatin fibers at the periphery of the nuclear and it also, serves an unclear function in DNA replication and transcription. The filaments, belonging to the family of intermediate filaments, of the nuclear lamina are 10 nm in diameter and are composed of polypeptides called lamins. Like in the cytoplasm, the integrity of intermediate filaments is regulated by phosphorylation and dephosphorylation in the case of the nuclear lamina as well.

The two-dimensional image depicts the nucleus of a cell as a circular object with two membranes; several gaps appear in the circle, representing nuclear pores. Surrounding the nucleus are membranous sacks representing the endoplasmic reticulum. Inside the nucleus is another circle, approximately ten percent of the total size of the nucleus, representing the nucleolus.

The Nuclear Pore Complex and its Function in Nucleocytoplasmic exchange

The nuclear pore complex (NPC) is a gateway across the barrier of the nuclear envelope. Unlike the plasma membrane that does not allow macromolecules into the cell from the extracellular matrix, the NPC allows the movement of RNAs and proteins between the nucleus and the cytoplasm. The best example is the process of replication and transcription, where the nucleus requires large numbers of proteins that are transported from the cytoplasm after the process of translation. Whereas, the ribosomal subunits, mRNAs, and the tRNAs synthesized in the nucleus are transported in the opposite direction, to the cytoplasm.

Materials as large as gold particles and ribosomal units can pass through the NPC. The NPC is a large, supramolecular complex that is 15 to 30 times the mass of a ribosome. It exhibits an octagonal symmetry with an eightfold repetition of structures. In this way, the NPC is composed of 30 different types of proteins called nucleoporins. These nucleoporins are conserved along with evolution, between yeast and vertebrates. The subset of proteins of nucleoporins is composed of amino acid sequence with a large number of phenylalanine-glycine repeats (FG repeats). The FG repeats clustered together from the FG domain. The NPC contains the FG repeats lining along the center of the channels, the heart of the 20 to 30 nm wide channel. The FG domain forms a hydrophobic mesh that blocks molecules with a molecular weight greater than 40,000 Daltons.

Multiple ubiquitin groups combine to bind to a protein. The tagged protein is then fed into the hollow tube of a proteasome. The proteasome degrades the protein. This produces ADP and amino acids, and the ubiquitin is also released.

Nuclear localization signal (NLS) consists of one or two stretches of positively charged amino acids, that are part of the macromolecules traveling, enables a protein to pass through the NPC and enter or leave the nucleus. The proteins consist of such a specific “address” recognized by a specific receptor that mediates its movement across the organelle. Such mobile transport receptors ferry macromolecules across the nuclear envelope. Importins, move the macromolecules from the cytoplasm to the nucleus, whereas exportins move them in the opposite direction.

Chromosomes and Chromatin

An average human cell contains 6.4 billion base pairs of DNA, diving into 46 chromosomes. Since each base pair is about 0.34 nm in length, therefore the entire DNA is 2 m long. The nucleus is just 10 micrometers in diameter, how is it able to contain the DNA as well as enzymes and other regulatory proteins? The answer lies in how well the DNA is packaged and precisely organized so that it does not become a hopeless entanglement!

The chromosome organization: The chromosomes contain DNA and associated proteins, which together are called chromatin. Histones are a remarkable group of small proteins that contain high numbers of basic amino acids, such as arginine and lysine. These proteins help in the orderly packaging of eukaryotic DNA.

Histones are divided into five different classes: depending on the ratio of arginine and lysine. The amino acid sequence of histones, H3 and H4 are highly conserved along evolutionary time. This is because these proteins interact with the backbone of the DNA. The DNA and the histones are organized into a repeating subunit, called nucleosomes. It was found in the early 1970s when the chromatin was treated with nucleases and resulted in fragments approximately of 200 base pairs in length. But this was not the case when the DNA-devoid-of-proteins (after protease treatment), instead it resulted in a randomly sized population of fragments. This led to the discovery of nucleosomes.

Part a: In this illustration, DNA tightly coiled into two thick cylinders is shown in the upper right. A close-up shows how the DNA is coiled around proteins called histones. Part b: This image shows paired chromosomes.  The chromosomes are shown as a collection of slender tubes.

The Nucleosome: The core particle consists of 146 base pairs of supercoiled DNA. Each histone core has two copies of each histone H2A, H2B, H3, and H4, which assembles as an octamer. H1 type of histones is outside the histone core, the linker histone which links one core particle to another. In this way, the nucleosome spaces every 200 base pairs of the DNA as beads on a string. DNA and core histones are held together by several non-covalent bonds, especially ionic bonds between negatively charged phosphates of DNA backbone and positively charged residues of the histones. H1 histone dissociates and reassociates with the chromatin to facilitate the DNA replication, transcription, and repair, distinguishing the chromatin into euchromatin (coding DNA) and heterochromatin (non-coding DNA).

Higher levels of chromatin organization: The nucleosomes are further packed at the ratio of approximately 7:1. The successive nucleosomes along the DNA are arranged in different stacks and alternating nucleosomes become interacting neighbors. Assembly of the 30 nm fiber increases the packing ratio to an additional 6 fold or about 40 fold altogether. The 30 nm chromatin fiber is gathered into a series of large, supercoiled loops, or domains, compacted even into even thicker (80-100 nm) fibers, chromosomes.

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