2-43 The nucleus holds the cells genetic material in eukaryotes

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• The genome of eukaryotes is sequestered to a membrane bound organelle called the nucleus.
• The nucleus is the site of replication and transcription.
• Most eukaryotes have more than one chromosome in their nucleus and replication of these chromosomes proceeds through a sequence of steps that are visible with a light microscope.
• The nucleus contains visible spots called nucleoli, which are the location or ribosome synthesis.

While the bacterial cell does seem to sequester its chromosome to a portion of the cytoplasm, there is no demarcation that divides the nucleoid from the rest of the cell. In eukaryotes the nuclear membrane separates the cell's DNA from the cytoplasm. The nucleus is the largest and most clearly visible organelle of eukaryotic cells. It contains almost all the cell's DNA and is the site of chromosome replication and transcription. It has two layers of membrane encircling it called the nuclear envelope, with the outer layer being contiguous with the ER. Scattered throughout this nuclear envelope are circular openings known as nuclear pores. These pores are highly discriminatory, allowing easy movement in and out of the nucleus of only appropriate macromolecules such as proteins with specific sequences.

In eukaryotes, the chromosome is not a single circular piece of DNA as in most prokaryotes. Rather, it is split into a number of linear chromosomes with each cell containing at least two copies of each chromosome. The exceptions are those cells that specialize in reproduction and only contain one copy of the cell's chromosomes. Each piece of DNA is complexed with special basic structural proteins called histones that seem to be important in keeping the DNA organized. The DNA is also bound by other proteins involved in its maintenance and the entire set of DNA and associated proteins is called chromatin. For much of the cell cycle chromatin consists of long DNA strands formed into beads by association of histones along it length. Figure 2-71 shows a nucleus in the midst of mitosis, with the chromosomes visible.

In actively growing cells the DNA is replicated from numerous sites, rather than the single bi-directional origin in prokaryotes. This is necessary due to the much larger amount of DNA found in most eukaryotic cells. During division in prokaryotes, the cell appears to simply split in two with each daughter cell receiving a chromosome. In contrast, eukaryotic cells go through a morphologically distinct phase, mitosis, to achieve separation of the chromosomes. One of the more important events of mitosis is the binding of additional histones and the contraction of the chromatin into compact structures that were called chromosomes due to their staining properties. (The original meaning of the term chromosomes is a colored body, but is now synonymous with a cell's DNA). The two daughter chromosomes formed during replication are physically separated into the separate daughter cells by the filaments called microtubules. These attach at one end to the chromosome at a region termed the kinetochores and at the other end they attach to one of two regions of the cell called a centrosome. By depolymerization of the microtubules at each centrosome, each daughter chromosome is pulled away from its partner and toward a region that eventually reforms as a new nucleus.

There are also a number of important differences in transcription between eukaryotes and prokaryotes. In eukaryotes, mRNA transcription takes place in the nucleus and the finished mRNA moves through the nuclear pores and into the cytoplasm for translation by the ribosomes. The genes of eukaryotic cells also contain regions of largely unimportant DNA, termed introns, that do not code for protein. After a gene is transcribed into mRNA these introns are removed before translation. One set of nuclear proteins removes these sequences and splices the actual coding sequences (exons) together to make the finished mRNA. The finished mRNA then travels from the nucleus to ribosomes in the cytoplasm. The mRNA of eukaryotic cells is also decorated with modifications at each end that affect the stability of the mRNA. At the front end is usually a 5’-cap made of 7-methylguanine attached to the mRNA by a triphosphate linkage. At the 3' end of the mRNA is a long stretch of A bases (a poly-A tail) that have a role in mRNA stability as mentioned earlier in this chapter. Finally, while it is quite common in bacteria to have a number of genes on each mRNA transcript, the vast majority of mRNAs in eukaryotes code for only a single protein product. Figure 2-72 shows the steps in gene expression in eukaryotes.

Eukaryotic cells also contain one or more dark-staining structures within the nucleus called nucleoli. Although they are not enclosed within a separate membrane the nucleoli are complexes with separate granular and fibrillar regions. They are present in non-dividing cells, but frequently disappear during mitosis and again reappear after cell division is over. The nucleolus is the initial site of ribosome synthesis. This structure contains the DNA that codes for the ribosomal RNA genes. The ribosomal RNAs are synthesized and then processed to form the final rRNA molecules. These are then combined with several ribosomal proteins synthesized in the cytoplasm to form an initial ribosomal complex. The entire complex then migrates out of the nucleus into the cytoplasm where it combines with other proteins to form a ribosome.

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