Virus Packet - Notes_ Projects_ Webquests etc

					Chapter 26 – Viruses – PowerPoint Notes Sheet                Name:________ Points ___/0
The History of Viruses / Virology
the first written record of a virus infection consists of a heiroglyph from Memphis, the capital of
ancient Egypt, drawn in approximately ______________, which depicts a temple priest called Ruma
showing typical clinical signs of ______________________

variolation involved ______________________________________________________________

Smallpox In the late _____________________ observed and studied Miss Sarah Nelmes, a
milkmaid who had previously caught ____________ and was subsequently found to be immune to
________________ ____________________.
On 14th May 1796, Edward Jenner used cowpox-infected material obtained from the hand of Sarah
Nemes, a milkmaid from his home village of Berkley in Gloucestershire to successfully vaccinate __
On 1st July 1796, Jenner challenged the boy by ________________________________________
__________________! He did not become _____________________- !!!
Jenner developed the __________________, based on these findings, and smallpox is currently all
but wiped out.

Koch’s Postulates which are still generally regarded as the _________________________ is
responsible for a specific disease:
   • The agent must be _______________________________________.
   • The agent must be _______________________________________.
   • The disease must be reproduced when a _____________ of the agent is inoculated into a
   • The same agent must be ______________ once again from the experimentally ___________.

Viruses: The Basics
What are the “requirements” for life?

Are viruses alive?

   •   Most virologists consider them __________________________________________________
   •   They are similar to ___________________________ as they lack the means for self-
       reproduction outside a host cell, but unlike parasites, viruses are generally not considered to
       be true living organisms.
   •   For those who consider viruses living, _______________________________________

   •   A virus is a microscopic ____________________________________________________.
   •   Viruses can only replicate themselves by _______________________________________
   •   At the most basic level, viruses consist of __________________________________
       _______________. They infect a wide variety of organisms: both ______________________.
   •   A virus that infects bacteria is known as a ____________________, often shortened to _____.
   •   The study of viruses is known as virology, and those who study viruses are known as
    •     The word virus comes from the Latin, poison (syn. venenum).

The Nature of Viruses
    •     Viral structure - core of _________________ surrounded by ___________
              – classified by nature of ______________
                      Either ____________________
                      ________________- viruses – retroviruses (more later)
              – Lack ______________ and necessary ________________________
              – nearly all form a protein sheath or __________ around their ______________
                      Many animal viruses form an ______________ around the capsid.
    •     ___________________- suitable cells for a virus

Viral Structure

Viral Replication
    •     Viruses can reproduce only when they ________________________________________.
              – viral genes translated into proteins by the cell’s genetic machinery

Viral Shape
•       _________ - rodlike
•       __________ - spiral
          –    ________________
             – structure with _____________________ facets
             – most ____________________ that linear subunits can form
               a shell with maximum ________________

Viral Genome Structure
    •     Viral genomes types exhibit great diversity
    •     Some use _______________________
    •     Some ___________________________________
    •     __________________________________
    •     In ______________, the genome can contain the same base sequences as the
          ____________ used to produce viral proteins. _______ strand can serve as ________ and is
          called a ______________________
    •     Genome can contain bases _______________ to viral __________ and is called
Types of Viruses - Adenoviruses
   •   Adenoviruses are a frequent cause of acute upper respiratory tract (URT) infections, i.e.
       "colds". In addition, they also cause a number of other types of infection; 5–10% of upper
       respiratory infections in children, and many infections in adults as well
   •   Widespread in nature, infecting birds, many mammals and man.
   •   Several types have _________________ potential. What does this mean?
   •   In recent years, there has been considerable interest in developing Adenoviruses as
       __________ to carry and express foreign genes for _______________________.

Types of Viruses - Retroviruses
   •   They are enveloped viruses possessing _____________, and replicate via a _____________.
   •   The virus itself stores its nucleic acid in the form of a ___________________ and serves as a
       means of delivery of that genome into cells it targets as an _____________________
   •   rely on the enzyme ______________________ to perform the reverse transcription of its
       ______________________________, which can then be _______________ into the host's
       ______________ with an integrase enzyme.
   •   Simply, the retrovirus enters a host cell and provokes the RNA strands inside of the normally-
       functioning cell to undergo reverse transcription, which is violating the 'central dogma of
       biology.' DNARNAProtein
   •   When a retrovirus is inside of a cell, the first two steps of that process would be switched.
       (Rather than DNA --> RNA --> Protein, it would be RNA --> DNA) The host cell would become
       a provirus as this has occurred
   •   When retroviruses have integrated their genome into the ___________, their __________ is
       passed on to a following _________________.
   •   These endogenous retroviruses, contrasted with exogenous ones, now make up surprisingly
       ______________ of the human genome. Most insertions have ______________ and are often
       referred to as "junk DNA".

Types of Viruses – Herpesviruses
   •   all herpesviruses are composed of relatively large double-stranded, linear DNA genomes
       encoding 100-200 genes encased within an icosahedral protein cage.
   •   There is no known _____ for HSV infection, but treatments can reduce the likelihood of viral
       shedding and spread.

   •   ______________________ - viruses that infect bacteria
          – Bacteriophages are among the most ____________ biological entities on Earth.
          – The term is commonly used in its shortened form, phage.
          – some named as members of a “T” series
          – They have been used for over 60 years as an _______________________ in the
            former Soviet Union and Eastern Europe.
          – They are seen as a possible therapy against ______________________________

Lytic and Lysogenic Cycles
Lytic Cycle
   • tail fiber contacts lipoproteins of host bacterial cell wall
          – tail _____________ and tail tube passes through opening in base plate, __________
              bacterial cell wall
                  contents _____________ into host cytoplasm
          – will _________________
        – virulent viruses
Lysogenic Cycle
   • Does not _____________________ the cell
   • __________________ their nucleic acid into the genome of the infected host cell (prophage).
               prophage - phage genome ______________________________________
                 __________ of a bacterium
        – The integration of a virus into a cellular genome is termed _________________.
        – prophage may exit genome and initiate virus replication

Cell Transformation and Phage Conversion
   •   Transformation - ________________ of a cell’s genome by the introduction of ____________
          – phage conversion - foreign DNA contributed by bacterial virus
                 disease-causing bacteria Vibrio cholerae usually exists in harmless form
                         bacteriophage that infects V. cholerae introduces into the __________
                          _________________________________ for the cholera toxin

   •   Acquired Immunodeficiency Syndrome (AIDS) was first reported in the US in ________.
           – estimated over ________________ worldwide are infected with Human
               Immunodeficiency Virus (HIV)
   •   Infection cycle
           – In normal individuals, ___________________ patrol the bloodstream and attack
               invading bacteria or viruses.
   •   In AIDS patients, the virus hones in _______________, infecting and killing them.
           – Without T cells, the body _______________________________________________.
           – After docking onto the macrophage CD4 receptor, HIV requires a second macrophage
               receptor (CCR5) to cross the cell membrane.
           – Once inside the macrophage, the HIV particle sheds its protective coat.
           – RNA and reverse transcriptase left floating in cytoplasm
– double strand of DNA, complementary to RNA, produced
– viruses released via exocytosis
Disease Viruses
   •   Many human diseases are caused by viruses:
           – _______________________________________
   •   Viruses may also play a role in ______________________ such as _____________________
   •   Recombination
   •   Viral genes are readily re___________________________.
       • inability to make perfect vaccines
              • flu pandemics
              • How? And Why?
   •   Emerging viruses
           – viruses that originate in one _____________________________________________
                 • _____________ –one strain has 90% lethality
                 • Severe Acute Respiratory Syndrome (SARS) –
                        • Unrelated to any previous coronovirus
                        • most likely came from ________________________ in China eaten as

Viruses and Cancer
   •   Viruses are capable of ____________________________________________ they infect by
       triggering _________________________.
           – Association between ___________________ infections and _____________________
           – ________________________ linked to certain strains of HPV (human papilomaviruses)
                   Why are some groups against vaccine?
           – ____________ of all cancers worldwide

   •   Prions – _________________________
           – infectious proteins that some believe may be responsible for __________________
              ____________________ (TSE’s)
                  __________ in sheep & _________________________ in cattle
                  Humans
                         __________ in Fore people of New Guinea
                         Creutzfeldt-Jakob disease
   •   tiny, naked molecules of ______________ that are an important ________________
       _______________ in plants
           – recent outbreak killed ______________________________- in Phillipines
   •   Not clear how they cause disease
   •   Viroid nucleotide sequences resemble sequences of introns within ribosomal RNA genes

Human Viral Diseases
Rabies                              HFMD                             SARS
Chicken Pox and related disorders   Lassa Fever                      Menigitis
Ebola / Marburg                     Machupo                          West Nile
Epstein Barr                        Norovirus                        Yellow Fever
Herpes, Genital                     Pneumonia                        Winter Vomiting Virus
Hepatitis                           Polio
Viral Disease (or prions) Presentation (30 points)                                      Due March Something In Class
         For this assignment you are to research a human disease or condition that is a result of a virus. The presentation
should be rehearsed or practiced and look polished. There should not be any words that you have trouble pronouncing.
If you do not know what the word means, then do not include it in your presentation, or look up what it means and tell the
class. When you are presenting the material in class, you should be able to discuss the information without having to
read your PowerPoint or Poster. Specific information such as statistics or complicated names or organizations can be
referenced but the basic science behind the disease should be completely understood.
         A PowerPoint presentation is not required. It is recommended that some sort of visual aid be used to enhance
the understanding of the material. If you wish to use a PowerPoint presentation, then you must email it to the instructor at
least a day prior to your presentation. The PowerPoint cannot have more than 10 words per page. Use pictures/ graphs/
tables to convey information instead of words on the screen.
         On the next test/quiz there will be a matching section where you will have to match the virus (name) with
symptoms/features. If you want to make a notes sheet for your classmates to help them learn this better, then email it to
me 1 day in advance and I will make copies.

1. Visual Aid
2. The “discovery”, discoverer or historical background of virus.
3. The specific type of virus. Included in this section should be:
    o Type of genetic material                                     o How is it transmitted
    o Specific Structural Information                              o Any other
4. Any demographic information regarding affected individuals
       o    Frequency of occurrence                              o Areas, cultures or types of people affected
5. How humans are affected by the virus
6. Sources of information.

Grading                       30 points total
                                         Presentation 17 Points
 Flow of Material (up to 6 points)
      0-2         Students (audience) unable to follow presentation
      3-4         Somewhat clear, somr parts of presentation confusing or hard to understand
      5-6       Very clear! All materials understandable and in a logical order.
 Visual Aid (PowerPoint / Poster) (up to 5 points)
      0-2         Wordy, wordy, wordy. Your visual aid is all words and no pictures
      3-4         OK, but still too words. Almost theres
       5          Picture perfect!
 Preparedness (up to 6 points)
      0-2         Students (audience) unable to follow presentation
      3-5         Somewhat clear, somr parts of presentation confusing or hard to understand
      6-7         Very clear! All materials understandable and in a logical order.

                                           Information 13 Points
 Quality of Material (up to 7 points)
       0          Seriously…are you aware there were requirements?
       2          3 missing or insufficient requirements
       4          2 missing or insufficient requirements
       5          1 missing or insufficient requirements
       6          0 missing or insufficient requirements
 Students understanding material (up to 6 points)
       0          Student mispronounces or does not understand more than two important terms and misses a few key points
       3          Student mispronounces or does not understand 2 important terms and misses 1 key point
       5          Student mispronounces or does not understand one important term and misses 1 key point
       6          Student understands and pronounces all terms well and completely understands material
Chapter 26 Virus Study Guide
   1. What is a bacteriophage?
   2. What is the difference between even and odd T series phages
   3. What is the difference between the lytic and lysogenic cycles?
   4. How do viruses contact bacterial cells?
   5. Describe the process of bacterial infection by a virus?
   6. What makes a virus virulent?
   7. What is a prophage?
   8. How is DNA differently replicated in the lysogenic cycle?
   9. What is the lamba phage?
   10. Compare temperant viruses to virulent viruses?
   11. Imagine you are a virologist examining a patient who looks to have a virus that has attacked
       their red blood cells. How could you tell by only looking at RBCs under a microscope if the
       virus is virulent or temperant?
   12. What is cell transformation?
16.3 (pg 333-334)
   13. What is gene therapy?
   14. What are subunit vaccines? (read 1035 for more info on DNA vaccines)
   15. How are these vaccines different from other vaccines?
13.2    (pg 263-264)
   16. What is gene transfer therapy?
   17. What types of diseases would gene transfer therapy attempt to cure?
   18. What are some problems with gene therapy?
   19. What is so promising about the adeno-associated virus?
   20. Has gene therapy with AAV ever worked? How and in what organism?
   21. What are some major diseases caused by viruses?
   22. What kind of virus is Influenza? What are the differences between the types?
   23. How does recombination effect the influenza virus?
   24. Why is recombination more of a problem then mutation?
   25. Why is it a bad idea to come to school if you have a bad case of the flu?
   26. What is an emerging virus? What are some examples of emerging viruses?
   27. How are viruses and cancers linked? (see pages 406-409 for more detail)
   28. How are prions different from viruses?
   29. What is a viroid? Are you susceptible to viroids?

Now you have seen And the Band Played On which should serve as a good introduction to the AIDS
epidemic. Read the pages in the text in section 26.3 (536-539) and answer the following questions.
The material in the text will be on the test.

   1.   What kind of virus is HIV?
   2.   Was HIV an emerging virus?
   3.   What is AIDS?
   4.   Explain the HIV infection cycle?
   5.   What kind of cells does HIV infect? How does it recognize these cells?
   6.   What is reverse transcriptase’s role in HIV infections?
   7.   What is the significance of the gp120 protein?
8. (Not in the book) Imagine you were to designing a drug that would help patients with HIV.
   What approach would you use to help an HIV+ patient from getting AIDS?
9. How do AZT drugs work? What is combination therapy?
10. What is vaccine therapy?
11. What are chemokines? How would they help fight HIV?
12. How / why do some people not develop AIDS?

Extended Response: (Not in the book) In some impoverished sub-Saharan African nations as
many as 25% of the population has HIV which amounts to 24.5 million people in all of Africa.
Some people (too many really) believe that AIDS does not come from HIV.

(Check this website for some info: whenever
you have time)

Some of the “reasons or evidence” given in support of this idea generally discuss how people
compromise their immune systems in other ways (i.e. malnutrition, drug use, immunosuppressive
drugs given to hemophiliacs and organ transplants, and specific homosexual drug use.) Other
people believe that the medications that are given to HIV infected people cause AIDS. Propose
an experiment (or data analysis) that would demonstrate that AIDS results from being HIV+.
And the Band Played ON                                  Movie Worksheet                                            10 Points
This worksheet is not necessarily in chronological order. The questions and prompts should be read
prior to viewing the movie. After the movie is finished, you will have time to complete the worksheet.
It is advisable to make notes during the movie, but don’t try to answer the questions in depth while the
movie is playing. More important then getting the questions correct is an understanding of the history
of HIV/AIDS on how prejudice/stereotyping played a role in the early understanding of the disease.
The final submission needs to be in complete sentences. If you wish to turn in a typed coy, then it
needs to be submitted via

   1. What was HIV / AIDS originally referred to and what do HIV and AIDS stand for?

   2. Who was Don Francis and what prior experience did he have that helped him to understand
      HIV and AIDS?

   3. What portion/subgroup of the population was first affected by HIV/AIDS?

   4. Who was Bill Kraus and how did he help the HIV / AIDS cause? (Side note – he went on to
      work with Harvey Milk.)

   5. Who was Dr. Robert Gallo and what was his role in the early understanding of HIV/AIDS?

   6. The following is a quote of Dr. Francis. Why do you think he said it and do you agree/disagree
      with his statement?
      How many people have to die before it'll be cost effective for you people to do something about it? A hundred? A thousand? Give us a number
      so we won't annoy you until the amount of money you start losing on LAWSUITS makes it PROFITABLE for you to save people than to kill

   7. Who was “Agent Zero” and what does it mean for someone to be “Agent Zero?”

   8. Several viral disease investigators sparred over who should be credited with “discovery” of HIV
      AIDS. Give your opinion to whom you think should be credited with the discovery?

   9. The tagline of the movie is below. What current disease, epidemic or social concern would
      you compare to the situation faced in the movie that would also warrant the same tagline?
      A threat no one dared face. A word no one wanted to speak. A fight for many, fought by few.

   10. What is your opinion of how the Centers for Disease Control (CDC) and the American Red
       Cross handled the epidemic?
VIEWING GUIDE TO OUTBREAK                                                                               10 Points
           The film, Outbreak, portrays the efforts of an army virologist, Sam Daniels, to prevent a global biological disaster.
A rare killer virus from the African jungle has started an epidemic in a small northern California community. The virus has
a 100% mortality rate. The film follows the scientists and army officers as they trace the epidemic and seek to contain it.
The story in the film is fictional. Could something like this really happen?
           The questions in Part 1 are listed for you to think about. They follow, in order, the events of the film. You may wish
to take notes as you watch the tape. Part 2, which can be done after you view the tape, is a list of things that happen
during the story. Some of them seem to be minor incidents, but each one has importance in advancing the plot. Your job
is to tell how each event is important to the story.

1. Why was the mercenary camp in the Motaba River Valley of Zaire bombed in 1967?

2. In the film, we see a progression of laboratory safety levels at the U.S. Army Medical Research Institute of Infectious
Diseases (USAMRIID) at Fort Detrick, Maryland. Below is a description of each level. As one progresses from level to
level, describe the differences shown and the procedures and safety methods observed.
         Biosafety level 1 (BS1) - Minimum biohazard; study of low risk infectious agents: Pneumococcus, Salmonella

        Biosafety Level 2 (BS2) - Moderate biohazard; infectious agents: hepatitis, Lyme Disease, influenza

        Biosafety Level 3 (BS3) – High biohazard; multiple vaccinations required; infectious agents: anthrax, typhus, HIV

        Biosafety Level 4 (BS4) – Extreme biohazard; maximum security; highly virulent; no known cures or vaccines;
        infectious agents: Ebola, Lassa, Hanta viruses

3. Why were Sam Daniels and his crew sent to the Motaba Valley, Zaire?

4. What are the conditions in the Motaba Valley?

5. How did the mystery disease get to the Motaba Valley?

6. What is the tribesman’s explanation of why the disease was affecting the tribe? Do you feel that there could be any
truth to the explanation?

7. What are the characteristics of the mystery disease?

8. Why was it said that the virus was contained?

9. Why did Casey show so much concern about the small tear in Daniels’ suit as they were about to enter the BS4 area of
the lab?

10. What did the electron microscope show about the Motaba virus in kidney cells?

11. One of the staff describes the name “Motaba virus” as sounding like the name of a perfume…”one drop and you’ll feel
so different, your lover will melt in your arms.” How did these words have a prophetic significance?

12. Why did the generals want Daniels off the case? What did they want him to do? What is Daniels’ reaction?

13. What measures were taken in Cedar Creek to contain the outbreak?

14. What was Operation Clean Sweep? Why did many officials think it was necessary?

15. What was the reason that the E-1101 antiserum against Motaba virus was kept secret?

16. Why was Daniels so intent on capturing the monkey in Palisades, California?

17. Why did General McClintock want to get rid of Daniels?

18. After capturing the monkey, what were Daniels and his team able to do?

19. How did Daniels prevent the success of Operation Clean Sweep?
PART 2 - Each of these incidents from the film has some significance to the story. Describe how each
one is important either in the spread of the epidemic or in efforts to trace and contain it.
1. The disease affects many people at the mercenary camp on Motaba Valley, Zaire.

2. The camp in Zaire is firebombed.

3. Daniels receives a telephone call as he is bathing the dogs.

4. The new man on the team is briefed before leaving for Zaire.

5. The monkey is trapped in the Motaba Valley.

6. A phone call is made by Jimbo Scott from the animal holding facility in San Jose, California.

7. The monkey scratches Rudy Alvarez at the pet shop.

8. Jimbo Scott releases the monkey into the woods in California.

9. Henry Seward, hospital laboratory technician, is accidentally sprayed with Rudy Alvarez’ blood from a tube in the

10. Jimbo Scott kisses Allison at Logan Airport in Boston.

11. Henry Seward coughs during a movie in a crowded theater.

12. A patient is discovered at Cedar Creek Hospital who has the disease but has had no contact with others who are sick.

13. Two different strains of the Motaba virus are discovered in Cedar Creek.

14. Casey becomes ill.

15. Robbie is stuck with a needle that she was injecting into Casey.

16. The dead man is found on the ship and a picture of a monkey is found above his bunk.

17. Mrs. Jeffries sees a picture of the monkey on television.

18. Daniels’ helicopter blocks the path of the airplane carrying the firebomb.

1. Describe how the virologists determined the identity of the virus causing the disease, how they tracked the
epidemic and how they eventually conquered the virus.

2. What do you think was the largest scientific guffaw, blunder, inaccuracy in the film? Did it affect your opinion
of the movie? What was a realistic scientifically accurate part of the movie that was the most interesting or
thought provoking?

3. At the beginning of the film is a quote by Nobel Prize Winner Joshua Lederberg.
“The single biggest threat to man’s continued dominance on this planet is the virus.”
Discuss this quote. Do you agree with it? Why or why not? What evidence from this film supports Lederberg’s
view? What evidence from other sources that you have read or viewed lends support? What do you feel is
significant about Lederberg’s statement in light of recent news regarding bioterrorism? What do you feel will
be the future of human dominance on earth? Support your views with facts and logical thought.
Gene Therapy and HIV/AIDS Webquest                                                     30 Points
You must either handwrite the answers to this assignment or turn it in via Obviously, I
don’t want you to cut and paste information from websites without reading and understanding the
Gene Therapy
Respond in complete sentences to the following prompts
1. What is gene therapy?
2. When was gene therapy first attempt or proposed
3. What is the goal of gene therapy?
4. What are some of the pros and cons of gene therapy?
5. Explanation of the mechanism of gene therapy.
6. What types of viruses are used in gene therapy, and how can they be used safely?
7. What are some diseases that scientists/doctors have tried to cure/treat with gene therapy?
8. The first disease approved for treatment with gene therapy was adenosine deaminase (ADA)
    deficiency. What is this disease and why was it selected?
9. What is SCID and how does it affect humans?
10. What are the major negative aspects/risks of gene therapy?
11. Which diseases that have had experimental gene therapy treatments have shown positive or
    promising results?
12. How has gene therapy been used to treat a hereditary eye disease?
13. How has gene therapy been used in veterinary medicine. Explain which diseases have used
    gene therapy as a treatment.
14. What are some of the social and ethical issues surrounding human gene therapy?
15. How was gene therapy used to treat the “brain wasting disease” in the following article?
Respond in complete sentences to the following prompts:

1.  When was the first case of AIDS reported in the United States?
2.  How long has AIDS been in the human population?
3.  What two diseases had a huge increase in cases in 1981 in both New York and California?
4.  What did KSOI refer to? When did the name AIDS become accepted?
5.  What were the first groups (plural as in more than one) that were mostly affected by AIDS?
6.  When was the name of the virus HIV decided on? What were the other options? Why do you
    think any cared about other names?
7. According to, what group in the US has the largest number
    of HIV positive individuals? What age group has the largest number of infected individuals and
8. Extended response: How serious of a problem is AIDS in Africa?
9. Which part of Africa is worst affected?
10. According to, what is evidence the HIV cause AIDS?
11. Why is Dr. Peter Duesberg unconvinced that HIV causes AIDS?

12. Who are other people that doubt that HIV causes AIDS? What “proof” or “evidence” or reasons do
    individuals/groups use to substantiate their claim that HIV does not cause AIDS?
(Read the whole pages, I think it is worth it)
13. What is the story of Christine Maggiore and Eliza Jane?
14. What is the story of Sean Current? Why did he change his mind?
15. Which side of the “HIV causing / not causing AIDS” issue do you side with?

Check out the AIDS Game!

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