1. Outline the classification and include living examples at all levels of classification.

Because viruses are not considered living things, they are not classified by the system of nomenclature. Viruses instead are classified as DNA viruses or RNA viruses depending on the type of nucleic acid in the capsid. Viruses contain either RNA or DNA, never both.

DNA and RNA viruses differ in the manner in which they alter the machinery of a host cell. Once inside the host cell, a DNA virus may directly produce new RNA that then makes more viral proteins. Alternatively the virus DNA may join to the DNA of the host cell and then direct the synthesis of new viruses. Some of the DNA viruses are rhinoviruses which is a virus that causes the common cold and herpes simplex virus that causes herpes.

RNA viruses perform in another way. Some RNA viruses enter the cell and make new proteins directly. They do so by releasing the RNA, which then migrates directly to the cytoplasm, where it uses the host ribosome's to make proteins. The polio virus, which is an RNA virus, acts in this matter. Other RNA viruses, called retroviruses, act differently. In addition to RNA, retroviruses contain an enzyme called reverse transcriptase. Reverse transcriptase is an enzyme that makes DNA from RNA. In normal cells DNA makes RNA. The RNA in turn makes proteins. In retroviruses RNA makes DNA with the aid of reverse transcriptase. The DNA then makes the new RNA. This RNA in turn makes the proteins that become part of the new viruses. The AIDS(HIV - human deficiency virus) virus is a retrovirus.

In the last three decades scientists have isolated certain disease causing particles that are smaller and simpler then viruses. One of these is the viroid. A viroid is a short, single strand of RNA with no surrounding capsid. The strand of viroid RNA under electron microscope looks like a tangled string. A viroid does not contain enough RNA to make proteins. Scientists suggest that this RNA strand somehow interferes with normal cell functions and causes the production of new viroid strands by using the host cell’s enzymes. Diseases caused by viroids include those that harm potato, coconut, chrysanthemum, and citrus crops, as well as other plants.

A prion is a glycoprotein particle containing a polypeptide of about 250 amino acids. Even without nucleic acids prions are capable of reproducing in some mammalian cells. Prions are implicated in diseases with long incubation periods. For instance prions cause scrapie which is a slow degeneration of the nervous system in sheep and goats. Another prion disease is kuru, a degenerative nerve disease that can be contracted by touching the brains of deceased individuals. It occurs among some New Guinea highland tribes whose funeral rites include touching the brains of deceased ancestors.

Viruses were originally and also now classified not only by DNA and RNA but also by symmetry. The chart below is organized according to the symmetry of the DNA and RNA viruses.

2. Discuss phylogeny and evolutionary status.

Many people ask the question how and where did viruses evolve. No fossil evidence of viruses has been found. However, scientist form inferences about the evolution of viruses. Because they are obligate intracellular parasites, viruses probably did not arise until cells had evolved, since their existence requires cells. If this is so, then viruses probably either formed spontaneously from existing nonliving organic material or evolved as simplifications of previously existing cells.

Whatever their origin, existing viruses often evolve very rapidly by natural selection. Suppose that cold viruses invade a human body. The human immune system may destroy most of these viruses. The few that remain will have been naturally selected and will be resistant to immediate attack by the immune system. These resistant viruses enter cells and produce hundreds or thousands of viruses in a few days. The immune system responds to repel the viruses eventually but not until many new ones have been formed. The short generation time of a virus means that natural selection acts quickly to create new viral types that are capable of withstanding destruction in the next host.

3. Describe the main characteristics displayed by the phyla. Show examples of how these characteristics are found among all the members of the phyla.

A virus is a biological particle composed of genetic material and protein. A typical virus consists of either RNA or DNA encased in a protein code called a capsid. When a virus causes a disease it is said to be virulent. If the virus does not cause disease immediately it is said to be temperate.

Viruses are constructed of compounds usually associated with cells, but they are not considered living organisms. They have some but not all of the characteristics of life. Viruses have no nucleus, cytoplasm, organelles or cell membrane. They do not reproduce by either mitosis or meiosis, nor are they capable of carrying out cellular functions. As stated before viruses do not contain nucleus, organelles, cytoplasm and a membrane instead they have a protein and nucleic acid core. While a normal cell has both DNA and RNA a virus can contain only one of either DNA or RNA at a time. Also, cells can reproduce by mitosis and meiosis, however viruses require a host cell and using this cell they can reproduce. Viruses do not have cellular respiration, but they can crystallize which caused a great amount of confusion when viruses were discovered.

As said before because viruses are not like cells, they can only reproduce by invading a host cell and using the enzymes and organelles of the host cell to make more viruses. They are therefore obligate intracellular parasites, which means they require a host cell to reproduce. Outside a host cell a virus is a lifeless particle with no control of its movements. It is spread on the wind, in water, in food or via blood or other bodily secretions.

Many viruses, including the polio virus, are shaped like polyhedrons and typically are covered by a protein coat called capsid. The structure of the polio virus is typical of many viruses. The virus particle is about 20 to 30 nm in diameter. The capsid is shaped like an icosahedron which is a polyhedron with 20 triangular faces. The capsid is made of protein subunits that fit together like pieces of leather on a soccer ball. The capsid surrounds a single strand of RNA.

Most icosahedral viruses are between 15 and 200 nm in diameter. The approximately 200 kinds of viruses that cause the common cold are mostly icosahedral viruses about the size and shape of the polio virus. Some viruses, such as the virus that causes tobacco mosaic disease, a disease of tobacco plants, are rod shaped when viewed under the electron microscope. These viruses have a helical strand of nucleic acid that runs the length of the virus and is surrounded by a hellically arranged protein coat. The protein coat makes up about 95 percent of the mass of this type of virus. Rabies and mumps are caused by helical viruses.

The virus that causes acquired immune deficiency syndrome, or AIDS, is even more complex. The AIDS virus is shown on the right. This virus, called HIV, has two single strands of RNA in its core. These strands are surrounded by two layers of protein. A layer of lipids surrounds these inner protein layers. Glycoprotein molecules, proteins with sugar chains attached, are embedded in the lipid layer and form the capsid of the virus.

In conclusion some of the main characteristics of viruses is they are not classified as living organisms because they cannot reproduce by themselves, they are usually composed of a strand of nucleic acid enclosed in a capsid composed , usually, of several proteins( sometimes there are also specific proteins in the capsid, like reverse transcriptase). Viruses can crystallize. This is the basic summary of the main characteristics of viruses.

4. Explain in detail the reproductive patterns found in the phyla. How do these patterns increase the ability of the organism to survive natural selection.

Scientists first learned about virus reproduction by studying bacteriophages, viruses that infect bacteria. Phages, as they are called, can easily be studied because their bacterial hosts multiply quickly in cell cultures.

The most commonly studied phages are those of the T group. They are named T1, T2, T3 and so forth. the T phages infect bacterium escheria coli, the common bacterium of the human digestive tract. The T-even(T-2,T-4) phages are virulent. They are capable of destroying E. Coli cells.

In the structure of a T4 phage the DNA in the viral core is surrounded by a protein coat that forms a polyhedron. Beneath the head is a collar of protein and a sheath that rests on a base plate. Tail fibers emerge from the base plate.

The lytic cycle is a fundamental reproductive process in viruses. The term lyse means to "break open", which is a reference to the liberation of new viral particles from the host cell. The T4 phage reproduces by the lytic cycle and thus can serve as an example of viral reproduction. The lytic cycle has five phases, each of which is continuous with the others. The phases are adsorption, entry, replication, assembly, and release.

1. During absorption the virus attaches itself to a specific host cell. The tail fibers of the virus contain proteins that have chemical affinity with the bacterial cell wall. In fact, specific areas of the wall, called receptor sites, are the places where the virus attaches itself.

2. During entry the T4 phage releases an enzyme that weakens a spot in the cell wall of the host. The n much like a hypodermic needle, the T4 presses its sheath against the cell and injects its DNA into the host cell through the weak spot in the wall. The empty capsid remains on the outside of the cell. In contrast, many viruses enter their host cell intact. Once inside, the capsid dissolves and the genetic material is released. This process is called uncoating.

3.During replication the viral DNA takes complete control of cell activity. It inactivates the E. Coli DNA. The genes contained in the DNA of the viral genome then take over. They direct the cell to make viral DNA and the viral proteins that make up the structural portions of the phage. This happens when viral DNA makes RNA from nucleotides in the host cell by using the enzymes of the host cell.

4. During assembly proteins coded for by phage DNA act as enzymes that put new virus particles together. The entire metabolic activity of the cell is thus directed toward assembling new T4 phages. The result is a cell stuffed with new viruses.

5. During release the T4 phages release an enzyme that digests the bacterial cell wall from within. The disintegration of the infected host cell called lysis, allows new viruses to leave the cell. The new virus particles can then infect other cells, and the process can start again.

During the lytic cycle viruses enter the cell, use its components to make new viruses, and destroy the cell in one continuos process, which usually takes a day or two. However, some temperate viruses can infect a cell without causing its immediate destruction. Temperate viruses undergo a kind of life cycle called a lysogenic cycle, which has been most throughoutly studied in bacteriophages.

In the lysogenic cycle a temperate phage enters a bacterium in much the same way the T4 bacteriophage does, by attachment of tail fibers and injection of the DNA into the host cell. At this point, however, the lysogenic cycle differs from the lytic cycle. Instead of immediately creating new RNA and proteins the DNA of the temperate phage attaches itself to the host DNA. It becomes, in effect, an additional set of genes. The phage, now represented by only a short segment of DNA, is called a prophage. When host DNA replicates or when the host cell devides, the prophage acts just like an inert segment of the DNA of the host. It causes no harm to the cell.

However, various external stimuli - exposure to radiation or certain chemicals, for instance - can cause the prophage to become virulent. It then takes over the host cell, produces new viruses, and ultimately destroys the cell.

Temperate viruses released during cell lysis may take with them a portion of the DNA of the host cell. When the phage enters a new host, it may introduce genes from the former host into the new host. In this process, called transduction, a virus transfers DNA from cell to cell and thus causes a change in the genetic code of bacterial cells. This results in genetic recombination and hence phenotypic variation in the new host bacterium.

5. Describe the relationship with humans, positive or negative? How do they effect our survival?

Many viruses cause serious diseases in humans and other organisms and plants. Many viruses do not cause death but they weaken the organisms body( in humans immune system) which given the conditions other harmful factors take advantage of.

Often viruses kill livestock and damage plants such as the tobacco mosaic virus.

Some genetically engineered bacteriophages can carry human DNA into bacteria where it incorporates into the bacterial DNA and the bacteria can produce some useful pharmacologicaly active proteins( such as insulin).

Genetically engineered viruses can be used as carriers for human DNA to introduce functional human genes that are missing in the individual( many enzyme deficiencies)

6. Make a running list of all the organisms for each phyla you observe in class.

Size - 45-55 nm

Structure - polyhedral

Diseases caused by - warts

Size - 70-80 nm

Structure - polyhedral

Diseases caused by - Respiratory and intestinal infections, conjunctivitis, sore throat

Size - 150-200 nm

structure - Enveloped polyhedral

Diseases caused by - Herpes, chickenpox, shingles, infectious monoucleosis

Size - 100 times 200 times 300

structure - helical

Diseases caused by - Smallpox

Size - 20-30 nm

structure - polyhedral

Diseases caused by - poliomyelitis, infectious hepatitis, common cold

Size - 80-120 nm

structure - enveloped helical

Diseases caused by - influenze A, B, C

size - 70 times 180

structure - enveloped helical

diseases caused by - rabies

size - 100 nm

structure - glycoprotein enveloped complex

Diseases caused by - AIDS( depressed immune system)