The interphase chromosomes of eucaryotic cells are complex molecular structures composed primarily of a DNA core and a protein matrix complexed into a long thread-like structure. This basic chromosome thread is then coiled through several layers of organization and ultimately gives rise to a structure that can be visualized with a light microscope.
Chemically, the interphase nucleus is composed of a substance known as "chromatin," which is further subdivided into euchromatin and heterochromatin. The distinction between these subdivisions is based on quantitative distribution of the basic chromosome fiber, with a higher concentration found in heterochromatin. Heterochromatin, therefore, will stain more intensely than euchromatin, since the fiber is packed tighter within a given volume.
Proteins extracted from chromatin have been classified as either basic or acidic in nature. The basic proteins are referred to as "histones" and the acidic as "non-histone proteins". Histones play an integral part in the structural integrity of a eucaryotic chromosome. They are organized into specific complexes, known as nucleosomes, and around which the DNA molecule is coiled. Acidic proteins within the nucleus compose many of the DNA replication and RNA transcription enzymes and regulatory molecules. They vary in size from small peptides of a few amino acids to large duplicase and replicase enzymes (respectively DNA and RNA polymerases).
Transcription of DNA on the chromosome fiber results in the presence of a host of RNA species found within the nucleus of the cell. When the RNA is transcribed from the "nucleolar organizer" region of a genome and complexed with ribosomal proteins, granules are formed which collectively produce a "nucleolus," visible at the light microscope level of resolution. When transcribed from other portions of the genome, the RNA is either in the form of pre-transfer RNA, or heterogeneous nuclear RNA (hnRNA). The precursor tRNA must be methylated and altered before becoming functional within the cytoplasm, and the hnRNA will also be significantly modified to form functional mRNA in the cytoplasm.
Thus, a chemical analysis of chromosomes will yield DNA, RNA and both acidic and basic proteins. 1 It is possible to extract these compounds from an interphase nucleus (i.e. from chromatin) or to physically isolate metaphase chromosomes and then extract the components. For the former, the nuclear envelope will be a contaminating factor, as will the nucleolus. For isolated chromosomes, many of the regulatory molecules may be lost, since the chromosomes are essentially non- functional during this condensation period.
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