Essential Questions For Viruses - Assignment Example

MB12 – Review Questions on Viruses What are some properties of viruses that distinguish them from living cells? A living cell is capable of independent metabolism whereas viruses are dependant on a living cell for being alive. They are incapable of reproduction without enzymes of the host cell and they make use of the metabolized products of the host like ATP for its vital functions. 2. What is the general structure of a non-enveloped virus? What about enveloped viruses? Non enveloped viruses have a nucleic acid covered by a capsid layer whereas enveloped viruses have a phospholipid bilayer derived from the host cell that it infected covering its nucleic acid and capsid layer. 3. What creates the specificity of a virus for its host cell(s)? Why are different individuals more or less susceptible to particular viral infections when compared to other individuals? Specificity of virus for a particular host cell is due to complimentarity of the viral surface proteins with the cell surface receptors. During infection, viral proteins attached to host surface receptor molecules which are proteins. These receptor proteins are coded by genes which show variability in a population. Gene variations account for the varying susceptibility to viral infections among different individuals. 4. What are some features of the host cell that many viruses need in order to reproduce? Host cell surface need the receptor protein to which the viral surface protein attaches and thus gains access to the host cell. Host cell nucleus is the site where viral DNA duplicates and the capsid proteins are imported into nucleus for assembly. Packaging of the viral particle occurs in the cytoplasm of the host cell. 5. What type of information do the genes of most viruses contain? Viral genes code for capsid proteins, enzymes for processing nucleic acid, and viral proteins. They regulate the reproduction using host cell machinery and transmission of the newly formed viruses. 6. What are the different ways viral genomes can be organized? viral genome can be organized in helical or icosahedral shapes. 7. Describe the process of infection by animal viruses. You should be able to do this for DNA viruses and the four types of RNA viruses described in lecture. The basic outline of steps includes attachment, penetration, uncoating, expression of viral genes, replication of viral genomes, packaging/maturation, and release. a) Attachment: Viral coat proteins get attached to specific cell surface receptors. b) Penetration: Injection of the nucleic acid into the host cell or endocytosis into the host cell (in case of enveloped viruses) takes place. c) Uncoating: Viral capsid is digested and nucleic acid is released. d) Biosynthesis: DNA viruses start with transcription whereas RNA viruses proceed to translation if it is a + plus strand. Viral DNA is replicated in the host nucleus and capsid proteins are imported into the nucleus for assembly. e) Packaging: assembly of the viral particles occur in the host cytoplasm. f) Release: lysis of the host cell results in release of new viral particles or budding of viral particles to the outside, acquiring an envelope from the host cell membrane. 7a. What is the first step during the biosynthesis stage of each type of viral infection? In case of infection by a DNA virus, first step of biosynthesis is transcription of viral genes and in case of RNA viruses with a + strand, translation is the first step. For RNA viruses with a minus strand RNA is processed before translation. 8. What are some possible "side effects" of integration of retroviral DNA? Retroviral DNA may sometimes disrupt host genes, such mutations may lead to malignancies like cancer. It is postulated that this kind of genetic shifts or mutations are responsible for evolutionary changes. It is also found to be a powerful tool for gene therapy. 9. How is the life cycle of animal retroviruses similar to lysogenic phages? In retroviral infection, the viral RNA produces ss DNA, which is transported to the nucleus and integrates as a provirus. This provirus is capable of dividing indefinitely along with the host DNA as in the case of the lysogenic conversion, where a viral genome integrates to the host chromosome. 10. Why might it be a disadvantage for a virus to rapidly destroy its host cell as opposed to a slow course of infection? Virus replicates with the help of host enzymes and proteins, therefore destruction of the host cell soon after infection would in turn the virus also inactive. Outside the host cell viral particles are inactive. 11. What are some different types of anti-viral treatments? How does each of these work? Nucleoside analogs like acyclovir and deoxy guanosine are used for the treatment of viral infections. Acyclovir acts by blocking viral DNA replication. Small molecules or peptides capable of binding to the viral proteins can prevent the viral –host cell fusion. Small double stranded RNA called as the interfering RNA is also used that destroys the viral m RNA on binding to it. 12. Why are certain anti-viral drugs likely to have side effects? Viruses thrive inside the host system and so any drug aimed at killing the virus will ultimately turn harmful to the host cell machinery. 13. Why do most anti-viral drugs have limited efficiency? Viruses tend to undergo frequent mutations. A drug designed to target a particular virus may not be effective for long due to genetic changes which alter the virus. A treatment aimed solely to destroy virus is difficult as it is living like a parasite in the host cell. MB12 – Origins of Life on Earth 1. What is the evidence that life may have been present on Earth over 3 billion years ago? Microfossils of bacteria from old rocks that date back to 3.5By have been recovered by scientists. Geological records which give composition of the earth at that time also give supporting evidences. 2. What is the main experiment that has been done to try and simulate the origin of biological molecules on Earth? Describe the experimental set-up, the results, and the conclusions. Miller Urey experiment was main experiment done to simulate the conditions on primitive earth. This experiment explored if organic compounds could be generated from its inorganic substrates. Inorganic components were subjected to conditions of high temperature and pressure in presence of electric current and the whole set up was connected to another chamber where cooling and condensation took place. The final cooled product showed the presence of hydrogen cyanide and formaldehyde within hours and it was found that it also had amino acids, purines and pyramidine which are the building blocks of life. This experiment helped to conclude that the conditions that prevailed on primitive earth helped in synthesis of organic molecules from simpler inorganic molecules in the ‘primordial soup’. 3. How may have the first cells organized themselves from a random collection of lipids and RNA? Small molecules aggregated to form larger ones called coacervates in the ocean, these aggregates later attained chemical characteristics under the extreme temperature and high voltage thunder and lightning on primordial earth giving rise to primordial cells. 4. Why do scientists propose an RNA world? How can living things use RNA instead of DNA and/or proteins? RNA molecule is capable of self replication, it has catalytic properties and has the capacity to store information .For these reasons it would have been the initiator molecule for life to begin. 5. How might the earliest cells have obtained energy from their environment? Earlier life forms had a H2 based metabolism from which they derived energy. 6. According to science, how may life have first appeared on Earth if it did not form in the way covered in the previous questions? Another theory called the Panspermia says that A 4.5 billion year old meteorites ALH 84001 which left Mars 16 million years ago landed in Antarctica 11000 years ago would have brought life to earth. MB12 – Review Questions on Biotechnology 1. What properties of DNA and gene expression enable modern genetic engineering? Chemical structure of DNA is universally the same in all life forms and gene expression follows the same pattern in all life forms due to universal nature of the genetic code. 2. How is modern genetic engineering similar to traditional breeding? What are the differences? Are these differences strong enough to consider the two entirely different processes? 3. What are the limits to our ability to predict outcomes of our genetic engineering? Gene expression patterns may vary due to environmental effects on the gene and hence we can’t predict the result of genetic engineering. 4. What are the microbiologically-derived tools that are used to create recombinant DNA? You should be able to describe how the various enzymes, plasmids, and E. coli cells are used. DNA is isolated from cells, and cut into fragments using restriction enzymes. The cut fragments can be mixed with the desirable foreign DNA bits and this can be mixed and combined using enzyme DNA ligase. This hybrid DNA is then incorporated into a plasmid having compatible ends. Plasmids enable the DNA replication in E. Coli cells each time it reproduces producing the recombinant protein. 5. What are some examples of pharmaceuticals that are produced in bacteria? You should be able to use #4 to describe how these pharmaceuticals are produced. Insulin is the best example for a genetically engineered product. Using the same restriction enzyme DNA isolated from human cell and a plasmid DNA is cut to produce complimentary sticky ends. These complimentary ends when they come together join by base pairing. DNA ligase is used to join the backbone of DNA fragments. The gene for insulin production is thus incorporated into a plasmid vector which then replicates along side the E. coli bacterium replication producing the recombinant protein. 6. How is DNA observed in a laboratory setting? Describe the procedure and how it works. DNA is extracted from cell, cut with restriction enzymes into fragments and separated on an agarose gel. Electric current helps migration of the DNA fragments due to its negative charge and gets separated as fragments which can be visualized by ethidium bromide staining. 7. Give some examples of foods that have been genetically-engineered. You should name the food, the source of the transgene, and the new trait that is conferred by the transgene. Corn and Soy plants have a herbicide resistance gene from Salmonella. This product has been marketed as “Round Up Ready” by Monzanto. Corn and Potato have insecticide genes from the bacterium Bacillus thuringiensis, marketed as Bt-Corn by Monzanto. Rice has been genetically engineered to produce β-carotene called “Golden rice”. 8. What are some of the safety concerns (human health, environmental) with the genetic engineering of food? People are concerned as to how safe or good genetically modified foods are because of the greater use of chemicals, pesticides and unexpected environmental problems like pollen contamination etc. 9. Describe other types of concerns (economic, religious, etc.) about the genetic engineering of food. Genetically engineered tomato with a fish gene may not be acceptable to vegetarian people. Economically the recombinant products are costlier and hence may not be affordable for the common man. Round –up ready crops demand greater use of chemicals and Bt-crops are found to have pesticides. 10. What are some of the rationales given for genetically engineering various food crops (or animals)? What are the ways in which these rationales may not hold up? Greater productivity, increased pest resistance, faster growth rate are some the reasons for genetic engineering of natural breeds. Food scarcity in a country cannot be attributed to low productivity alone it is also a result of lack of proper distribution and lack of wastage. 11. How can viruses be used for gene therapy? What is the concept behind gene therapy? Viruses are good shuttles for delivery of the normal gene into a patient. Normal allele of the defective gene is inserted into the retroviral RNA. Viruses are used for infecting bone marrow cells isolated from the patient and grown in culture. Viral DNA carrying the normal allele integrates into the cultured cell genome thus repairing the defect. This engineered bone marrow cells are then injected back into the patient. Replacing the ‘defective’ gene with a ‘working one is the concept behind gene therapy. 12. What are some dangers of gene therapy? Viral genes can randomly integrate into the host genome sometimes interrupting the function of some vital genes thus causing mutations responsible for cancer. If two viruses happen to infect the same cell they can recombine which can be dangerous if a stronger virus evolves. Immune over reactions can occur sometimes due to gene therapy. 13. Describe the process of PCR and how it can be used to diagnose infections such as HIV. Polymerase chain reaction makes use of DNA polymerase to amplify a specific piece of DNA. Primers are designed which are complimentary to a specific conserved sequence of the target DNA. Using heat the template DNA is denatured making it single stranded. This is followed by cooling when annealing of the specific primer takes place with the target DNA. Next step is the extension of the new strand using DNA polymerase. The amplified genome can be visualized by agarose gel electrophoresis followed by visualization with ethidium bromide staining. PCR can detect the presence of HIV virus particles in blood or any other body fluid using this principle. 14. How is a piece of DNA sequenced? What are some limits to understanding a living organism that a complete genome sequence does not help overcome? Refer Dideoxy method of sequencing 15. In your opinion, are there any beneficial uses of the various modern biotechnologies? Are there any uses of biotechnologies that should be banned? Be sure to explain your opinions with clear, thorough, and detailed explanations. Your explanations should include examples of specific technologies and how/why they bring benefits or cause harm. Your goal is to try and convince someone who initially disagrees with you that your opinion is a good one. Modern technology of genetic engineering has been a boon to mankind in so many ways. It has contributed many valuable therapeutics like human insulin ( a recombinant protein produced in E.coli), human growth hormone, bovine growth hormone and human clotting factors. These have been life saving to many. Patenting of genetically modified seeds may have undesirable effects in the agriculture sector. Genetically modified food stuffs also need to be closely monitored before being marketed. Human experiments should also be restricted in genetic engineering. Exam questions 1. Recombinant DNA technology is used to produce certain pharmaceuticals various food crops. A. Choose one pharmaceutical or crop and describe how the recombinant DNA is created. Be sure to describe each step, including how the various enzymes work. Refer answer to question no: 5 B. How is the recombinant DNA introduced into the soon-to- be transgenic organism? Recombinant DNA can be introduced by electroporation or microinjection technique. Transformation can be done using a “gene gun” –DNA coated gold particle which can penetrate the cell wall of plants. Microinjection is done in egg or embryo cells where foreign DNA is injected into the nucleus for recombination to occur between the two genomes. 2. Choose another of a transgenic organism. A. What organism is the source of the transgene and what is the trait it gives to the recipient organism? Salmon with extra growth hormone genes is an example of a transgenic organism. Organism with desirable traits form the source of the gene this can give many desirable traits to the recepient organism like increased productivity, disease resistance and stress resistance. Refer: insulin gene cloning. B. What is a one problem that could result from the use of this transgenic organism? Be sure to explain why this is a problem. There is a serious concern about consuming a fish that has genes for over production of growth hormone. 3. A. Describe the process of inflammation. Inflammation is an innate immune response of the body against infection or irritation. Blood vessels dialate to increase their permeability, supplying more blood to the site of infection. This causes heat and redness in the area. Antibodies reach the site through blood. Interleukins like IL-1, IL-6 and IL8-Chemotactically attract phagocytes to the site of infection. Margination or sticking of phagocytes to the endothelium occurs. Phagocytes squeeze out of endothelial cells (emigration) to engulf the foreign particle or invading bacteria. B. What are two events that can happen more easily as a result of inflammation? Describe these events. 1) Vasodilation: Blood vessels swell up bringing more blood to the site of the injury. Histamines are released by the damaged cells and basophils which also cause vasodilation. 2) Phagocytosis: Antibodies reach the site through blood. Interleukins like IL-1, IL-6 and IL8-Chemotactically attract phagocytes to the site of infection. Margination or sticking of phagocytes to the endothelium occurs. Phagocytes squeeze out of endothelial cells (emigration) to engulf the foreign particle or invading bacteria. 4. A minus strand RNA virus has just been uncoated in its host cell. How will this viral genome be replicated and packaged into new viral particles? Describe the events in the order that they occur. The – strand serves as a template for m RNA synthesis. They also possess RNA dependant RNA polymerase. m RNA serves as template for the synthesis of new – strand which is then packaged into new viral particles. 5. A. Why are retroviruses often used for gene therapy? What are two key viral enzymes that must function to get the virus RNA genome into the patients chromosomes? B. What is one concern with this type of medicine? Retroviruses can also transform cells by integrating near to a cellular proto-oncogene & driving inappropriate expression from the LTR, or by disrupting a tumor suppresser gene. This event, termed insertional mutagenesis, though extremely rare could still occur when retroviruses are used as vectors. 6. What do you think about the use of recombinant DNA technologies? When might their use be justified? When they are dangerous? Explain your responses. Refer to answer for question no: 15 Modern technology of genetic engineering has been a boon to mankind in so many ways. It has contributed many valuable therapeutics like human insulin (marketed as human mixtard which is a recombinant protein produced in E. coli), human growth hormone, bovine growth hormone and human clotting factors. These have been life saving to many. Patenting of genetically modified seeds may have undesirable effects in the agriculture sector. Genetically modified food stuffs also need to be closely monitored before being marketed. Human experiments should also be restricted in genetic engineering. 7. Other than fossils, describe one experiment or one observation that explains some aspect of how microbial life may have first evolved on earth. Be as thorough as possible. Miller Urey experiment was main experiment done to simulate the conditions on primitive earth. This experiment explored if organic compounds could be generated from its inorganic substrates. Inorganic components were subjected to conditions of high temperature and pressure in presence of electric current and the whole set up was connected to another chamber where cooling and condensation took place. The final cooled product showed the presence of hydrogen cyanide and formaldehyde within hours and it was found that it also had amino acids, purines and pyramidine which are the building blocks of life. This experiment helped to conclude that the conditions that prevailed on primitive earth helped in synthesis of organic molecules from simpler inorganic molecules inthe ‘primordial soup’. 8. A DNA virus has just been uncoated inside its host cell. What are the steps that it goes through to produce new mature viral particles: 1) Uncoating: Viral capsid is digested and nucleic acid is released. 2) Biosynthesis: DNA viruses start with transcription whereas RNA viruses proceed to translation if it is a + plus strand. Viral DNA is replicated in the host nucleus and capsid proteins are imported into the nucleus for assembly. 3) Packaging: assembly of the viral particles occurs in the host cytoplasm. 4) Release: lysis of the host cell results in release of new viral particles or budding of viral particles to the outside, acquiring an envelope from the host cell membrane 9. What is one protein that is expressed in the early phase? What is one protein that is expressed during the late phase? 10. What is the type of drug that one might take to treat viral infections? Explain how it works. Refer to answer no: 11. A. How does the "dideoxy" method of DNA sequencing work? This technique commonly called Sanger sequencing utilizes 2, 3-dideoxynucleotide triphospates (ddNTPs), molecules that differ from deoxynucleotides by the having a hydrogen atom attached to the 3 carbon rather than an OH group. These molecules terminate DNA chain elongation because they cannot form a phosphodiester bond with the next deoxynucleotide. First step is conversion of double stranded DNA into single stranded DNA which is done by denaturing the double stranded DNA with NaOH. A Sanger reaction consists of the following: a strand to be sequenced (one of the single strands which was denatured using NaOH), DNA primers (short pieces of DNA that are both complementary to the strand which is to be sequenced and radioactively labeled at the 5 end), a mixture of a particular ddNTP (such as ddATP) with its normal dNTP (dATP in this case), and the other three dNTPs (dCTP, dGTP, and dTTP). On adding DNA polymerase, the polymerization will take place and will terminate whenever a ddATP is incorporated into the growing strand. This reaction is performed four times using a different ddNTP for each reaction. When these reactions are completed, a polyacrylamide gel electrophoresis (PAGE) is performed. One reaction is loaded into one lane for a total of four lanes. The gel is transferred to a nitrocellulose filter and autoradiography is performed so that only the bands with the radioactive label on the 5 end will appear. In PAGE, the shortest fragments will migrate the farthest. Therefore, the bottom-most band indicates that its particular dideoxynucleotide was added first to the labeled primer. ddATP must have been added first to the primer, and its complementary base, thymine, must have been the base present on the 3 end of the sequenced strand. One can continue reading in this fashion. The sequenced strand can be read 5 to 3 by reading top to bottom the bases complementary to those on the gel. B. What are some ways this technology may be used in human health? Sequencing of the human genome has helped in treating many diseases which were considered incurable. Huntington’s disease manifests itself when the victim is in his or her 30s or 40s by causing uncontrolled movements and dementia. Up until 1991, those that are tested for Huntington’s disease before manifestation of the symptoms were given counseling before and after the tests. Experience has shown that the psychological burdens of know whether or not there is a propensity for such a disease can be immense. Genomic information helps gene therapy. C. What is one potential abuse at this technology? Genomic data or risk possibility of an individual will influence the decisions of insurance companies. They will choose only low risk clients. Possibility of developing a serious illness in future will be psychologically discouraging for individuals. 12. A. Describe the process of producing either a pharmaceutical or a food crop that relies on recombinant DNA. One component of the recombinant DNA should be bacterial DNA. Refer production of Insulin hormone by gene therapy or production of Human growth hormone production in expression vectors B. What is one potential objection to any recombinant DNA technology? This can be used for bad motives which should be prevented. Patenting of genetically modified seeds may have undesirable effects in the agriculture sector. Genetically modified food stuffs also need to be closely monitored before being marketed. Human experiments should also be restricted in genetic engineering. 13. Inflammation is a useful way to recruit additional antibodies to the site of an infection. A. How does the process of inflammation work? Inflammation is an innate immune response of the body against infection or irritation. Blood vessels dilate to increase their permeability, supplying more blood to the site of infection causing heat and redness in the area. Antibodies reach the site through blood. Interleukins like IL-1,IL-6 and IL8-Chemotactically attract phagocytes to the site of infection. Margination or sticking of phagocytes to the endothelium occurs. Phagocytes squeeze out of endothelial cells (emigration) to engulf the foreign particle or invading bacteria. B. What are two ways that antibodies can stimulate the destruction of the antigen? 1) Neutralisation: Antibodies that recognize viruses can block these by binding them directly.[2] In doing so, the virus will be unable to dock to its preferred receptor on a host cell in order to infect it. Some antibodies, like IgA, also directly bind to microbes in mucus to prevent the colonization of mucosal tissues. Some antibodies, like those in anti venoms, neutralize toxins by binding to them. 3) Agglutination: Antibodies are clonally generated for binding single specific antigens, which may compose specific molecules on the surfaces of viruses or cells. The antibodies can link these viruses or cells together, causing them to agglutination (coagulate) so phagocytes can capture them. Work Referred Atlas, Ronald. M. Principals of Microbiology. Kuby, Janis. Immunology. Pelczar, Micheal. J., CHAN, E.C.S., Krieg, Noel .R. Microbiology. Tata Mc Graw Hill Edition. Web: http://fog.ccsf.cc.ca.us/~kesler/microbiology.htm Read More