LESSON 1.4 WORKBOOK. Viral structures. Just how small are viruses? Workbook Lesson 1.4 1

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1 Eukaryotes- organisms that contain a membrane bound nucleus and organelles Prokaryotes- organisms that lack a nucleus or other membrane-bound organelles Viruses-small acellular (lacking a cell) infectious agents that can replicate only within the cells of living organisms. For a complete list of defined LESSON 1.4 WORKBOOK Viral structures In this lesson we will focus on the structures of viruses that directly relate to infectious diseases. As with bacterial structures, viral structures are precisely adapted, in this case for replication. You may also notice that many of the structures are quite similar those that you saw in the last lesson, in fact you may be able to predict the function of the viral structures by extrapolating on what you know about bacteria structure and function. Just how small are viruses? As we mentioned before, microbes come in a variety of flavors. The larger microbes, such as fungi and many parasites, are eukaryotic, which means they have a membrane-bound nucleus. Bacteria are prokaryotic, which, as we saw before, means they lack a membrane-bound nucleus. Viruses are neither prokaryotic nor eukaryotic, in fact, they are not even alive! They are simply a collection of genetic material and proteins that are able replicate with the help of the cell they infect. Viruses are much, much smaller that bacteria and this impacts every aspect of their structure, how they replicate and how they infect. Their small size also impacts how we are able to detect them, because they are too small to see under a normal microscope. Lesson 1.4 1

2 How big are viruses compared with other pathogens? The microbial world generally exists below the limit of what the unaided human eye can see. Sizes can vary considerably within each category. Eukaryotes are the biggest, followed by prokaryotes, and then by viruses. Viruses can vary in volume by a thousand fold. The largest viruses fall within the lower size range of prokaryotes - similar to the size of small bacteria such as chlamydiae that casue chlamydia infections. Only the largest viruses such as smallpox virus are visible with the light microscope, and then only barely. Because the differences in microbe sizes are so large we need more that one unit of measurement Most bacteria are on the order of 1 micron in diameter. A micron, or a micrometer, is one millionth of a meter. To give you an idea of how small this is, bacteria are so small that when they are in suspension in a fluid like urine, it only becomes cloudy only after there are between one million to ten million bacteria per milliliter. This means that even when water looks completely clear, it can contain millions of bacteria. Viruses are even smaller, at about one one-hundredth of the size of a bacterium. To give you a sense of scale, if a virus were the size of an orange, a bacterium would be about the size of a sofa. Practice Calculation: Conversion Conversion between units is important for every apect of science. Fortunately in this course we are only concerned with a few conversions that relate to microbe size. So let s practice: How big is a micron? 1 millimeter= 1 X 10-3 meters or meters 1 micron = 1 X 10-6 meters, or meters 1 nanometer = 1X 10-9 meters or meters For example: How many microns are in a millimeter? Answer: 1 micron = ( meters) 1 millimeter = (0.001 meters) A millimeter is 1000 times bigger than a micron so there are 1000 microns in a millimeter. Lesson 1.4 2

3 DEFINITION OF TERMS Genome - the genetic material a cell (or a virus) uses to replicate itself. Icosahedral- a regular polygon with 20 identical equilateral triangular faces (top picture). Helical having the shape of a helix or spiral (middle picture) Complex- having a structure that is neither purely helical nor icosahedral, possibly with additional structures (bottom picture). For a complete list of defined Viral structure: Its all about delivering the genome to the host cell. Now back to viral structures. When you are reading about viral structures it is important to keep in mind that viruses require their host cells to supply everything they need to replicate with the exception of a few key viral proteins and the viral genome. For this reason viruses can be thought of simply as vessels that transport genetic information. Because the virus uses so many of the host cell proteins to replicate, it does not need to code for these genes because the host cell does. Hence viral genomes are much smaller than either bacterial or eukaryotic genomes. Viral genomes can be either DNA or RNA, as we will discuss later. Viral genomes are packaged in two structures: 1. The protein coat (capsid) 2. The envelope The capsid protects the genome: All viruses have capsids that protect their genomes. The capsid can be a single or double layer, and fits into one of three symmetrical patterns: Icosahedral, helical or complex (as shown above left). The capsid is composed of proteins, without the lipids that are in envelopes and other membranes. Some of the capsid proteins are not found in the host and are required for viral replication. For naked or non-enveloped viruses the capsid is the only protection the genome has from the environment.. Figure 1.4.1: The viral genome sits inside the capsid. The envelope is made of host cell lipids/proteins and viral proteins: Only some viruses have an envelope. For those that do, it is vital for their function. The envelope is made of viral proteins that help viruses enter host cells, plus lipids and proteins stolen from the cell membrane of the host cell. The inner surface of the envelope has virus-specific proteins that contacts the capsid. These proteins stabilize the interactions between the lipids in the envelope and the capsid. As we will see later, they also determine where the What is the function of the capsid? Where do the lipids in an envelope come from? Do you think the source of the viral lipids will affects how well the immune system will recognize the virus? Why? The genome of a virus can be or (fill in the blanks). How does this differ from Eukaryotes and Prokaryotes? Figure 1.4.1: All viruses have capsids, only some virus will assemble in the host cell. Lesson 1.4 have envelopes. 3

4 Uncoating- a process whereby the viral capsid is removed. Virion- a virus particle that includes all of the components of a complete virus Receptor- a molecule in or on a cell that receives chemical signals Affinity- preference Tropsim the affinity of a particular virus for a particular cell type because of the presence of a specific receptor. Sialic acid- a monosaccharide (sugar) used as a building block for molecules in cells throughout the body. The four stages of the viral life cycle The rest of this reading describes viral structures in the context of how they function. To simplify we can divide the viral life cycle into four steps: 1) attachment, 2) entry, 3) replication, 4) exit. We will focus on viral replication later. While you are reading keep in mind that, like bacterial structures, each viral structure performs its own unique key function. The virus has one goal to make more virus. To reproduce, viruses need to enter their host cell where they make more virus and then leave. First, the virus attaches to the cell it is going to infect, then the virus enters the cell and uncoats its genome so that it can begin to replicate. Viruses replicate their genomes and make the structural proteins they need to assemble a new virus particle. Once the virus has made all its parts it assembles new virions that exit into the environment to infect other cells. Figure 1.4.3: An overview of the virus life cycle. 1) Attachment usually requires a specific receptor. Both naked and enveloped viruses need to attach to a host cell before they can enter it. To do this all viruses have receptors on their surface that act like keys, which interact with select receptors on the host cell surface that act like locks. For example, HIV is an enveloped virus that uses the receptor protein gp120 to attach to a receptor on the host cell surface called CD4. Like other viruses, HIV can only infect cells that have the right host receptor. This means that different viruses have affinity for different cell types. In the case of HIV, only cells of the immune system like helper T cells and dendritic cells have the CD4 receptor. Why would a virus need to enter a cell in order to reproduce? Could an HIV virus infect any cell? Why or why not? What do H and N stand for in H1N1? What does Hemaglutinin bind to on host cells? How might binding of Hemaglutinin impact how severe the disease is? All viruses have affinity for particular host cell targets, called tropism. Consider influenza virus. Influenza virus has a receptor in its envelope called hemaglutinin (the H in H1N1). Hemaglutinin binds to sialic acid sugars that are on epithelial cells in the respiratory tract - it is tropic for those cells. Different variants of influenza have different H receptors that attach to different sialic acid sugars. These different sialic acid sugars are located on different cells in the respira- Figure 1.4.4: Viruses attach to their host tory tract. This means that different variants of H1N1 infect Lesson 1.4 cells using a receptor. different sites in the respiratory tract. 4

5 Cytoplasm- the inner material of the cell that is enclosed by the plasma membrane and surrounding the nuclear membrane (when present). Endocytosis- the process by which cells absorb small molecules by engulfing them. It differs from phagocytosis, which is used to internalize large particles like bacteria, in the size of particle ingested. Extracellular- outside of the cell. Endosome- a membrane bound vesicle that is produced when a cell engulfs material from the extracellular space. 2) Entry depends on whether the virus is enveloped or naked. In order to replicate all viruses must cross the plasma membrane and get inside the host cell. As we will see, enveloped and naked viruses enter cells differently. Enveloped Viruses fuse with the host membrane. The most direct way for enveloped viruses to deliver their capsid to the host cell cytoplasm is to fuse their own envelope membrane with the membrane of the host. Because both viral envelopes and host cell membranes are composed of similar host cell membrane lipids, fusion happens easily, like two oil droplets combining in water. After the membranes have fused the virus can then spill its capsid, which contains its genome, into the cytoplasm. HIV is an example of a virus that fuses its envelope with the T cell membranes like this. A less direct route enveloped viruses can take is via endocytosis, using the same mechanism the host cell uses to take up molecules from the extracellular space. A virus particle that hijacks endocytosis to enter the host cell ends up in a vesicle, called an endosome. Once in the cell inside the endosome the virus gets its capsid into the cytoplasm by fusing with the endosome membrane - just like the other virus did when it fused with the plasma membrane. Influenza is an example of a virus that enters the cell by endocytosis and then fuses its membrane with the endosome membrane. Once it is in the cytoplasm the virus can begin to replicate. Naked viruses cross the host membrane Figure 1.4.5: Naked viruses inject themselves into the host cell. Figure 1.4.5: Enveloped viruses fuse with the membrane. Naked viruses aren t coated in a lipid envelope, so they can t fuse with membranes. Instead, naked viruses either inject their genomes into the host cell cytoplasm through the plasma membrane, or are taken up through endocytosis. Either way the virus needs to get its capsid through host cell membranes into the cytoplasm. Some very small naked viruses like Poliovirus can feed their genomes through tiny pores present in the endosome membrane. Other naked viruses release enzymes that punch holes in the host cell endosome membrane before injecting their genome and other viral proteins into the host cell cytoplasm. Again, once the virus has its Describe how enveloped viruses get their genomes into the host cell cytoplasm. Make sure you understand how endocytosis works. Describe how naked viruses get their genomes into host cell cytoplasm. Why would a naked virus in an endosome use enzymes for? Lesson 1.4 genome inside the host cell it is able to replicate. 5

6 Budding-a form of viral shedding by which enveloped viruses obtain their envelope from the host cell membrane by bulging. Lysis- the breaking down or rupture of a cell For a complete list of defined 3) Exit also depends on whether the virus is enveloped or naked. Once replication has occurred, the virus must leave the host cell so it can carry on its cycles of infection and replication. Again viruses have two different exit strategies depending on whether they are enveloped or naked. Enveloped viruses bud off of host cells: Enveloped viruses leave the cell in distinct stages. First, the envelope proteins collect in the host cell membrane close to where the genome is making the capsid proteins. Then the genome and capsid proteins travel together to the site on the host cell membrane where the envelope is located, and attach to the envelope proteins on the inside of the membrane. Next, the fully formed capsid containing the genome buds out of the host cell. As it does so it gathers the virus envelope proteins and stolen host membrane surrounding the capsid and forming a complete new virus particle or virion. This is true of both HIV and influenza. Whether or not the budding off of virus particles will cause the host cell to die depends on how fast the virus is replicating; if a virus is replicating slowly the cell may survive, but quickly budding viruses will probably cause the host cell to die. Naked viruses lyse the host cell: Naked viruses employ a rather more straightforward exit strategy than enveloped viruses. Quite simply, the virus replicates rapidly, and the huge numbers of virus particles that accumulate in the cytoplasm burst the cell open by force. This process of rupturing a cell is termed lysis. It is an important phenomenon and we will use the term routinely to describe when a cell is broken open. An example of a naked virus that exits by budding is human papilloma virus or HPV, the virus that causes genital warts, and that is linked to forms of cervical cancer. What might be some advantages to budding slowly? What might be some advantages to budding quickly? What will happen to the host cells if they are lysed? Figure 1.4.6: Enveloped viruses release by budding. Naked viruses lyse the host cell. Lesson 1.4 6

7 For a complete list of defined The exit strategy must also prevent viruses re-entering into the same infected cell: An important part of exiting the host cell successfully is not re-infecting the same cell. Think about this - if a virus keeps re-infecting the same host cell it will not be able to spread and eventually the host cell too will die. Without being able to replicate the virus will eventually disappear. In fact, mutations that prevent influenza from detaching from their host cell result in disabled viruses that are not virulent. Since viruses are designed to attach to and then enter a cell they are coated in receptors, like the Hemagglutinin receptor we discussed previously, that bind very specifically to their host cells. How do they prevent themselves from remaining attached to the host cell and reinfecting the same cell, rather than moving off to infect new targets? Even though not all enveloped viruses kill their host cells, a host cell that has been hijacked by a virus will no longer be healthy, so re-infection of the cell would be unproductive for the virus The Influenza virus solves the problem of detachment very neatly by carrying another protein in its envelope, the enzyme Neuraminadase (the N in H1N1). Neuraminanidase is able to cut the host cell sialic acid, destroying it. This lowers the number of sialic acid molecules on the host cell, thereby preventing any newly budded virius particles from using them to either remain attached, or to reattach to the host. Conversely, inhibiting Neuraminidase function will prevent viruses being released from the host cell. This in turn will reduce the number of infective viruses that are circulating (the viral load). The drugs Tamilfu and Relenza target Neuraminidase and inhibit it, thereby reducing the number of infective virus particles and the viral load. Why doesn t H1N1 re-infect the same cell? Would a naked virus have the same re-infection problem that a enveloped virus has? Why or why not? Figure 1.4.7: Influenza virus destroys its host cell receptor as it leaves, preventing reinfection. How do anti-influeza medications like Tamiflu work? Lesson 1.4 7