MCDB 1030 Spring 2005 Homework Set 3 Viruses and The Immune System 1. What kinds of nucleic acids may be found in viruses? Viruses can contain ds DNA, ss DNA, ds RNA, or ss RNA. They never contain both DNA and RNA. 2. What is the difference between a + strand and a – strand of RNA? The + strand codes for proteins, and can be directly translated at the ribosome. The – strand is the complement of the strand that can be translated, and must be copied before proteins can be made. 3. Describe the principle events that occur in the life cycle of a + strand RNA virus. i) entry into the cell; ii) replication of the genome using an RNA-dependent RNA polymerase, which must copy the + strand into – strands, which are then copied to provide the + strands that will be packaged into the progeny virions; iii) production of viral proteins by translation of + strands at the ribosome; iv) assemply of new viral particles; v) exit from the cell by lysis or budding 4. What do the following enzymes do? In each case, indicate the type of organism in which the enzyme is required. (For viruses, specify the type of virus.) a) RNA-dependent DNA polymerase copies RNA and synthesizes DNA (required in retroviruses) b) RNA-dependent RNA polymerase copies RNA and synthesizes RNA (required in RNA viruses) c) DNA-dependent DNA polymerase copies DNA and synthesizes DNA (involved in replication in cells and in DNA viruses) d) DNA-dependent RNA polymerase copies DNA and synthesizes RNA (involved in transcription in bacteria, eukaryotes, and DNA viruses) 5. Summarize the first, second, and third lines of defense against invading pathogens. See Figure 15.1 in Bauman 6. What is phagocytosis? Why is it important? Phagocytosis literally means cell-eating. It is the process by which cells such as macrophages engulf pathogens. It is important because the engulfed pathogens are killed, and because fragments of the digested pathogen are presented to the immune system to initiate the acquired immune response. 7. The complement system contributes to destruction of bacteria in three important ways. What are they? i) Opsonization, which increases the ability of phagocytic cells to ingest bacteria; ii) increase in inflammation increases the delivery of the cells and protein mediators needed to fight an infection; and iii) formation of membrane attack complexes that pole holes in the membranes of bacteria 8. What is inflammation? Is it beneficial or harmful? Inflammation is a process in which increase blood flow and increased vascular permeability result in increased delivery of phagocytic cells to a site of infection or injury. The ultimate effect of inflammation is clearing of infectious agents and repair of tissue. It is beneficial as long as it doesn’t get out of hand and become either too severe or chronic. 9. Define the following terms: a) Antigen – molecules with molecular weights between 5,000 and 100,000 that are recognized as foreign by the immune system b) humoral immunity – the immunity provided by antibodies secreted by B cells c) cell-mediated immunity – the immunity provided by T-cells d) interferon - proteins that are secreted by virally infected cells that provide an early warning system that allows adjacent cells to prepare for a viral attack e) lymph - the fluid in the lymphatic system that filters the tissues and delivers foreign materials to the lymph nodes 10. Diagram an antibody molecule and label the heavy and light chains, and the constant and variable regions. Draw a cartoon of two antibodies that are specific for molecules of different shapes, and show why they would not cross-react. 11. What are the roles of each of the following in the immune response? a) helper T cells – secrete lymphokines that stimulate B cells to divide and become plasma cells (which secrete antibodies) and that stimulate cytotoxic T cells that kill infected cells b) cytotoxic T cells ( a.k.a. killer T cells) – kill infected cells to prevent further replication of an intracellular pathogen c) B cells – the cells that are capable of maturing into plasma cells and produce antibodies d) Cytokines – chemical messengers that allow cells to communicate with each other e) MHC proteins – proteins on the surfaces of cells that present antigens to the immune system; MHC-I molecules are found on the surface of all nucleated cells, while MHC-II molecules are found on antigen-presenting cells such as macrophages and their relatives and B cells (make sure you understand why it is important that there are two types of MHC molecules) f) Antigen-presenting cells – macrophages and other phagocytic cells and B cells that present antigens to the immune system on MHC-2 molecules g) CD4 receptor – a protein on T helper cells that recognizes MHC-II molecules in a complex with the T-cell receptor h) CD8 receptor - a protein on cytotoxic T cells that recognizes MHC-I molecules in a complex with the T-cell receptor 12. Why are both humoral immunity and cell-mediated immunity important for fighting a viral infection? Humoral immunity is important because antibodies that bind to surface proteins on a virus can prevent the virus from attaching to its cellular target. Cell-mediated immunity is important because it allows for killing of virally-infected cell to prevent production of more virus.