Since viruses must use the cell for replication, it is necessary to understand what is going on in the cell and how a virus can utilize these processes. A virus must use cellular energy sources and protein synthetic machinery. Further, many viruses use all or part of the cell's machinery to extract information maintained in the viral genome and convert it to mRNA (the process of transcription). While cellular mechanisms for gene expression predominate, virus infection can lead to some important variations. Various RNA viruses face a number of special problems that differ for different viruses. Also, many viruses modify or inhibit cellular processes in specific ways so that expression of virus-encoded proteins is favored.

To understand how viruses parasitize cellular processes, these processes should be understood. Indeed, the study of virus gene expression has served as a basis for the study and understanding of processes in the cell. All gene expression requires a mechanism for the exact replication of genetic material and the information contained within, as well as a mechanism for "decoding" this genetic information into the proteins that function to carry out the cell's metabolic processes.

Whether prokaryotic or eukaryotic, the cell's genetic information is of two fundamental types: cis-acting genetic elements or signals, and trans-acting genetic elements. Genetic elements that act in cis work only in the context of the genome in which they are present. These include the following:

1 Information for the synthesis of new genetic material using the parental genome as template.

2 Signals for expression of information contained in this material as RNA.

Trans-acting elements are just that information expressed to act, more or less freely, at numerous sites within the cell. Such information includes the genome sequences that are transcribed into mRNA and ultimately translated into proteins, as well as the sequences that are transcribed into RNA with specific function in the translational process: ribosomal RNA (rRNA) and transfer RNA (tRNA). Certain other regulatory RNA molecules such as microRNAs and small interfering RNAs (siRNAs) also can be included in this category.

While both prokaryotic and eukaryotic cells utilize DNA as their genetic material, a major difference between eukaryotic and prokaryotic cells is found in the way that the double-stranded (ds) DNA genome is organized and maintained in the cell. Bacterial chromosomes are circular, and whereas they have numerous proteins associated with them at specific sites, genomic DNA can be considered as "free" DNA (i.e., not associated with any chromosomal proteins).

By contrast, eukaryotic DNA is tightly wrapped in protein, mainly histones. Thus, the eukaryotic genome is the protein—nucleic acid complex chromatin. The unique structure of this chromatin and its condensed form of chromosomes, and the ability of these to equally distribute into daughter cells during cell division, are manifestations of the chemical and physical properties of the deoxyribonucleoprotein complex.

There are also differences in the way that genetic information is stored in bacterial and eukaryotic chromosomes. In bacterial chromosomes, genes are densely packed and only about 10—15% of the total genomic DNA is made up of sequences that do not encode proteins. Non-protein-encoding sequences include mainly short segments that direct the transcription of specific mRNAs, short segments involved in initiating rounds of DNA replication, and the information-encoding tRNA and rRNA molecules.

In some eukaryotic genomes, on the other hand, 90% or more of the DNA does not encode any stable product at all! Some of this DNA has other functions (such as the DNA sequences at the center and ends of chromosomes) but some of these non-protein-encoding DNA sequences have accumulated over evolutionary time, and their current function (if any) is the subject of continuing experimental investigation and vigorous debate. While the function of such DNA sequences may not be clear, the origin of much of it is much better understood. Detailed sequence analysis of the human genome has demonstrated that about 10% is composed of simple sequence repeats and segment duplications, another 10% comprises retroviral cDNA elements that no longer can replicate, and 30% or so are transposable elements clearly related to retroviruses. Thus, more than four times more DNA in the human chromosome is related to retroviruses than is involved in protein-encoding information! This is a striking demonstration of the importance of viruses in the biosphere and of their coevolution with their hosts.

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