1. The human immunodeficiency virus (HIV) is a single stranded RNA retrovirus that infects humans.

Following entry into a cell, the virus genome goes through several steps and ultimately becomes embedded into the host cells DNA as a provirus. 1. Describe the structure of the HIV 2. Describe how the HIV gains entry into a cell 3. Describe each stage of the HIV infection from single stranded RNA to provirus 4. Describe how, as a provirus, the HIV replicates 5. Explain why the disease caused by the HIV is called AIDS The structure of HIV is very different from other viruses. It is roughly spherical and is about 60 times smaller then a red blood cell yet it is still larger for a virus. The outer coat of the virus is known as the viral envelope. The viral envelope is composed of two layers of lipids, taken from the membrane of a human cell when a newly formed virus particle buds from the cell. Embedded throughout the viral envelope are proteins from the host cell, as well as 72 copies (on average) of a complex HIV protein known as Env. These Env copies protrude or spike through the surface of the virus particle. Within the viral envelope is a bullet-shaped core or capsid, made up of 2,000 copies of the viral protein, p24. The capsid surrounds two single strands of HIV RNA, each of which has a complete copy of the virus's genes. HIV has three structural genes that contain information needed to make structural proteins for new virus particles. Helper T-Cells bind to antigen presenting cells (APCs) by means of a receptor on the cell surface called CD4. HIV is able to use its own gp120 (a protein on the surface of HIV) to bind to a cells CD4. HIV also binds to coreceptors CCR5 and CXCR4 of the cell surface. HIVs membrane fuses to the cell membrane and gains entry into the cell. HIV is one of the few retroviruses, meaning that it can convert its two strands of RNA into DNA by use of the enzyme reverse transcriptase. Because it has two copies of its RNA, it has two chances to in case one of the strands does not work properly or is damaged. The virus then permanently integrates the newly formed DNA into the hosts genome. This means the cells is able to release more HIV into your body, and the process continues. HIV can only replicate (make new copies of itself) inside human cells. The process typically begins when a virus particle bumps into a cell that carries on its surface a special protein called CD4. The spikes on the surface of the virus particle stick to the CD4 and allow the viral envelope to fuse with the cell membrane. The contents of the HIV particle are then released into the cell, leaving the envelope behind. Once inside the cell, the HIV enzyme reverse transcriptase converts the viral RNA into DNA, which is compatible with human genetic material. This DNA is transported to the cell's nucleus, where it is spliced into the human DNA by the HIV enzyme integrase. Once integrated, the HIV DNA is known as provirus. HIV provirus may lie dormant within a cell for a long time. But when the cell becomes activated, it treats HIV genes in much the same way as human genes. First it converts them into messenger RNA (using human enzymes). Then the messenger RNA is transported outside the nucleus, and is used as a blueprint for producing new HIV proteins and enzyme. Among the strands of messenger RNA

produced by the cell are complete copies of HIV genetic material. These gather together with newly made HIV proteins and enzymes to form new viral particles. The HIV particles are then released or 'bud' from the cell. The enzyme protease plays a vital role at this stage of the HIV life cycle by chopping up long strands of protein into smaller pieces, which are used to construct mature viral cores. The newly matured HIV particles are ready to infect another cell and begin the replication process all over again. In this way the virus quickly spreads through the human body. And once a person is infected, they can pass HIV on to others in their bodily fluids. It is called AIDS because HIV destroys the immune system. 2. Illness can be caused by many different kinds of agents. In response, multiple mechanisms are available to defend the body against these agents. 1. Contrast how bacteria and viruses cause illness. 2. Describe how the immune system defends the body against a toxin 3. Describe how the immune system defends the body against a virus 4. Describe how a vaccine works. What is it about the human immunodeficiency virus (HIV) or the common cold virus that makes it so difficult to create an effective vaccine against them? Viruses invade the host cell as most cannot multiply on their own. Once they invade they cell they insert their genes into the nucleus and take over the cell's machinery (organelles) and reproduce within the cell. This in turn kills the cell, and as more viruses are produced within the cell, it expands until it eventually bursts and releases the replicated viruses to other cells to start the process again. This hi-jacking of cells is where the problem occurs, as the immune system cannot recognize a foreign body to get rid of it, and so more and more cells become affected. Bacteria are single-celled prokaryotic organisms which can reproduce on their own. They normally cause disease due to the toxins which they release upon excretion. These toxins affect the host's cells in a negative way such as the destruction of certain proteins, which leads to the disease. The body's first line of defense is to prevent toxins from entering the body. The skin serves as a protective barrier. Bacteria can not penetrate intact skin, and the salt concentration in sweat creates a hostile environment for most bacteria. The parts of our mouth, lungs, digestive tract and other orifices such as eyes, nose, and ears that come in contact with the environment are protected by saliva, mucus, tears or minute hairs. Stomach acidity and friendly bacteria provide additional protection from things we ingest. These passive defenses are very effective at prevention. More active responses to rid the body of unwelcome guests include coughing, sneezing, runny nose, vomiting and diarrhea, which help the body quickly expel unwanted substances. Elevated temperature helps kill invading microorganisms, and the digestive tract excels at differentiating between what to keep and what to expel as waste. Our immune system protects us against threats. These include viruses, bacteria and parasites causing infectious diseases, from ordinary flu to full-blown malaria. The white blood cells of the defense system are produced in the marrow of our bones. The cells are carried in the blood to specialized organs, where they develop and communicate

to launch immune responses against infections. Immune responses are aggressive and must be controlled. They should be activated only when the body is threatened by disease. To learn how to start or stop the immune system we must understand how microorganisms and sick cells are recognized by white blood cells. Some white blood cells, like macrophages, destroy and eat bacteria and damaged cells. The B cells produce antibodies, which can neutralize viruses, bacteria or toxic proteins in the blood and other body fluids. The T cells can trace microorganisms that leave the body fluids to invade cells. Each T killer cell carries receptors for one type of foreign substance, "antigen". T cells can bind to infected cells and kill them. This can prevent spread of the microorganism within the body. Vaccines help a body prepare in advance to fight illnesses and potentially deadly diseases. Essentially, vaccines give the body a preview of a bacterium, virus, or toxin, allowing it to learn how to defend itself in advance. If the body is ever invaded by that particular pathogen after the vaccine has done its work, the bodys immune system is ready. Most vaccines are administered in the form of a shot or a liquid that is consumed by mouth. However, some vaccines are inhaled as aerosols or powders. The majority of vaccines contain viruses or bacteria that have been weakened or killed. Others contain inactivated toxins. In their altered states, vaccine pathogens are typically safe and unable to cause disease. When a weakened or dead pathogen is introduced into the bloodstream, the bodys B-cells go to work. It is these cells that are responsible for fighting diseasecausing pathogens. Once the B-cells are stimulated to act, antibodies are formed and the body develops immunity to the particular pathogen. Once a person receives a vaccine and develops immunity, he or she is usually protected for life. The virus mutate and change shapes quickly and also aim at destroying the white blood cells at a faster rate than other diseases. The big problem in all treatments is HIV's rapid rate of mutation. Every virus that comes out of a cell is slightly different from the one that went in. It doesn't take long for drug resistant viruses to appear in the blood. Like the common cold, the HIV virus changes so fast that it's difficult to develop an effective vaccine. AIDS is a retro virus that changes its DNA so it is hard to destroy

3. Biologists have discovered that many mycorrhizal fungi are sensitive to a low pH. What human caused environmental problem may prove catastrophic for these fungi? How may this problem affect their plant partners? Mycorrhizal fungi in nature are lost due to soil disturbances such as mining, construction or erosion; strong acid or chemical treatments; pesticides, excessive heat, drought or flooding; and denial of oxygen or water by asphalt, concrete, soil compaction and roads. In indoor gardens mycorrhizae must be introduced into sterilized soils and maintained because of losses due to the use of strong sterilizers, waterlogged soils low in oxygen and excessive fertilization. Mycorrhizae work well within integrated pest management (IPM) programs and organic programs; are effective in resistance management; break down crop residue thus freeing up valuable nutrients for plants; and are nonburning and nonphytotoxic to plants. There are two main types of mycorrhizae: ecto and endo

There are two main types of mycorrhizae: ecto and endo. (endo) This group of mycorrhizal fungi is important in non-woody plants, including many agricultural crops, grasses and turf. They are sometimes called vesicular-arbuscular mycorrhizae (VAM) due to specialized structures that the fungus creates. Although this type of mycorrhizae invades plant roots it does not harm the plant. (ecto) This group of mycorrhizal fungi grows between root cells and forms a sheath or mantle around plant roots, but it does not actually invade the plant cells. They are important to many woody perennials, bushes, shrubs and trees. There is a great potential for the use of mycorrhizal fungi as inoculants especially in the production and protection of high-value greenhouse-grown crops or transplanted vegetable crops such as tomatoes and other bedding plants. If using mycorrhizae as a control rather than preventative it is best to treat infections early. If mycorrhizae are applied too late then