Outside their host cells viruses survive as virus particles also known as virions The virion is a gene delivery system it contains the virus genome and its functions are to protect the genome and to aid its ID: 1014976
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1. Virus structure
2. Introduction to virus structure Outside their host cells, viruses survive as virus particles, also known as virions. The virion is a gene delivery system; it contains the virus genome, and its functions are to protect the genome and to aid its entry into a host cell, where it can be replicated and packaged into new virions. The genome is packaged in a protein structure known as a capsid.Many viruses also have a lipid component, generally present at the surface of the virion forming an envelope, which also contains proteins with roles in aiding entry into host cells. A few viruses form protective protein occlusion bodies around their virions. Before looking at these virus structures we shall consider characteristics of the nucleic acid and protein molecules that are the main components of virions.
3. Virus genomesA virion contains the genome of a virus in the form of one or more molecules of nucleic acid. For any one virus the genome is composed of either RNA or DNA. If a new virus is isolated, one way to determine whether it is an RNA virus or a DNA virus is to test its susceptibility to a ribonuclease and a deoxyribonuclease. The virus nucleic acid will be susceptible to degradation by only one of these enzymes. Each nucleic acid molecule is either single-stranded (ss) or double-stranded (ds), giving four categories of virus genome: dsDNA, ssDNA, dsRNA and ssRNA.The dsDNA viruses encode their genes in the same kind of molecule as animals, plants, bacteria and other cellular organisms, while the other three types of genome are unique to viruses.
4. It interesting to note that most fungal viruses have dsRNA genomes, most plant viruses have ssRNA genomes and most prokaryotic viruses have dsDNA genomes. The reasons for these distributions presumably concern diverse origins of theviruses in these very different host types.A further categorization of a virus nucleic acid can be made on the basis of whether the molecule is linear,with free 5 and 3 ends, or circular, as a result of the strand(s) being covalently closed. Examples of each category are given in Figure 3.1. It should be noted that some linear molecules may be in a circular conformation as a result of base pairing between complementary sequences at their ends (see Figure 3.7 below). This applies, for example, to the DNA in hepadnavirus virions and to the RNA in influenza virions.
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10. Modifications at the ends of virusgenomesIt is interesting to note that the genomes of some DNAviruses and many RNA viruses are modified at one orboth ends (Figures 3.4 and 3.5). Some genomes have acovalently linked protein at the 5 end. In at least someviruses this is a vestige of a primer that was used forinitiation of genome synthesis. Some genome RNAs have one or both of the modifications that occur in eukaryotic messenger RNAs (mRNAs): a methylated nucleotide cap at the 5 end and a sequence of adenosine residues(a polyadenylate tail; poly(A) tail) at the 3 end
11. The genomes of many RNA viruses function as mRNAs after they have infected host cells. A cap and a poly(A) tail on a genome RNA may indicate that the molecule is ready to function as mRNA, but neither structure is essential for translation. All the ssRNAs in Figure 3.5 function as mRNAs, but not all have a cap and a poly(A) tail.The genomes of some ssRNA plant viruses are basepaired and folded near their 3 ends to form structures similar to transfer RNA. These structures contain sequences that promote the initiation of RNA synthesis.
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14. Proteins non-covalently associatedwith virus genomesMany nucleic acids packaged in virions have proteins bound to them non-covalently. These proteins encoded in two or more nucleic acid molecules. regions that are rich in the basic amino acids lysine, arginine and histidine, which are negatively charged and able to bind strongly to the positively charged nucleic acids.Papillomaviruses and polyomaviruses, which areDNA viruses, have cell histones bound to the virusgenome.
15. Segmented genomesMost virus genomes consist of a single molecule of nucleic acid, but the genes of some viruses are encoded in two or more nucleic acid molecules. These segmented genomes are much more common amongst RNA viruses than DNA viruses. Examples of ssRNA viruses with segmented genomes are the influenza viruses , which package the segments in one virion, and brome mosaic virus,which packages the segments in separate virions.Most dsRNA viruses, such as members of the familyReoviridae , have segmented genomes.
16. Repeat sequencesThe genomes of many viruses contain sequences that are repeated. These sequences include promoters, enhancers, origins of replication and other elements that are involved in the control of events In virus replication. Many linear virus genomes have repeat sequences at the ends (termini), in which case the sequences are known as terminal repeats (Figure 3.7). If the repeats are in the same orientation they are known as direct terminal repeats (DTRs), whereas if they are in the opposite orientation they are known as inverted terminal repeats (ITRs). Strictly speaking, the sequences referred to as ‘ITRs’ in single-stranded nucleic acids are not repeats until the second strand is synthesized during replication. In the single-stranded molecules the ‘ITRs’ are, in fact, repeats of the complementary sequences (see ssDNA and ssRNA (−) in Figure 3.7).
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18. Virus proteinsThe virion of tobacco mosaic virus contains only one protein species and the virions of parvoviruses contain two to four protein species. These are viruses with small genomes. As the size of the genome increases, so the number of protein species tends to increase; 39 protein species have been reported in the virion of herpes simplex virus 1, and over 100 in the virion of the algal virus Paramecium bursaria Chlorella virus 1.Proteins that are components of virions are known as structural proteins. They have to carry out a wide range of functions, including:• protection of the virus genome attachment of the virion to a host cell (for many viruses)• fusion of the virion envelope to a cell membrane (for enveloped viruses).
19. Virus proteins may have additional roles, some ofwhich may be carried out by structural proteins, andsome by non-structural proteins (proteins synthesizedby the virus in an infected cell but they are not virioncomponents). These additional roles include:- enzymes, e.g. protease, reverse transcriptase - transcription factorsprimers for nucleic acid replication, interference with the immune response of the host.
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