Organization of Eukaryotic DNA

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Chapter: Biochemistry : DNA Structure, Replication, and Repair

A typical (diploid) human cell contains 46 chromosomes, whose total DNA is approximately 2 m long! It is difficult to imagine how such a large amount of genetic material can be effectively packaged into a volume the size of a cell nucleus so that it can be efficiently replicated, and its genetic information expressed.


ORGANIZATION OF EUKARYOTIC DNA

A typical (diploid) human cell contains 46 chromosomes, whose total DNA is approximately 2 m long! It is difficult to imagine how such a large amount of genetic material can be effectively packaged into a volume the size of a cell nucleus so that it can be efficiently replicated, and its genetic information expressed. To do so requires the interaction of DNA with a large number of proteins, each of which performs a specific function in the ordered packaging of these long molecules of DNA. Eukaryotic DNA is associated with tightly bound basic proteins, called histones. These serve to order the DNA into fundamental structural units, called nucleosomes, which resemble beads on a string. Nucleosomes are further arranged into increasingly more complex structures that organize and condense the long DNA molecules into chromosomes that can be segregated during cell division. [Note: The complex of DNA and protein found inside the nuclei of eukaryotic cells is called chromatin.]

 

A. Histones and the formation of nucleosomes

There are five classes of histones, designated H1, H2A, H2B, H3, and H4. These small, evolutionally conserved proteins are positively charged at physiologic pH as a result of their high content of lysine and arginine. Because of their positive charge, they form ionic bonds with negatively charged DNA. Histones, along with ions such as Mg2+, help neutralize the negatively charged DNA phosphate groups.

 

1. Nucleosomes: Two molecules each of H2A, H2B, H3, and H4 form the octameric core of the individual nucleosome “beads.” Around this structural core, a segment of dsDNA is wound nearly twice, causing supercoiling (Figure 29.26). [Note: The N-terminal ends of these histones can be acetylated, methylated, or phosphorylated. These reversible covalent modifications influence how tightly the histones bind to the DNA, thereby affecting the expression of specific genes. Histone modification is an example of “epigenetics” or heritable changes in gene expression without alteration of the nucleotide sequence.] Neighboring nucleosomes are joined by “linker” DNA approximately 50 base pairs long. H1, of which there are several related species, is not found in the nucleosome core, but instead binds to the linker DNA chain between the nucleosome beads. H1 is the most tissue specific and species specific of the histones. It facilitates the packing of nucleosomes into more compact structures.


Figure 29.26 Organization of human DNA, illustrating the structure of nucleosomes. H = histone.

 

2. Higher levels of organization: Nucleosomes can be packed more tightly to form a polynucleosome (also called a nucleofilament). This structure assumes the shape of a coil, often referred to as a 30-nm fiber. The fiber is organized into loops that are anchored by a nuclear scaffold containing several proteins. Additional levels of organization lead to the final chromosomal structure (Figure 29.27).


Figure 29.27 Structural organization of eukaryotic DNA. [Note: A 104 compaction is seen from to1 to 4  .] H = histone.

 

B. Fate of nucleosomes during DNA replication

Parental nucleosomes are disassembled to allow access to DNA during replication. Once DNA is synthesized, nucleosomes form rapidly. Their histone proteins come both from new synthesis and from the transfer of intact parental histone octamers.

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