The Final Exam will be Tuesday May 18th from 10AM-12PM in Sanford 001.

Here is some information on the exam:

• 100 questions all matching, multiple choice etc.
• It covers pretty much everything that we have covered.
• There are no questions from lab except those that directly pertain to lecture material.
• Breakdown is as follows with the topic followed by the (approximate)  number of questions:
  1. Kingdoms 14
  2. Chemistry 7
  3. History 4
  4. Protista 2
  5. Fungi 2
  6. Multicellular Parasites 4
  7. Eukaryotic Cell Structure 5
  8. Prokaryotic Cell Structure 8
  9. Eukaryote vs Prokaryote Structure 7
  10. Viruses and Prions 11
  11. Bacterial Growth and Control (includes antibiotics) 11
  12. How Microbes Cause Disease 5
  13. Epidemiology and Nosocomial Infections 10
  14. Defense Systems 10
  15. Identify the Diagrams 5
• You may bring a single piece of paper that is no larger than 3″x5″ with writing/printing on both sides.  This must be a single piece of paper — not two pieces stuck together.
• You have 2 hours to complete the exam which is held in the lecture hall.
• It will be scantron graded so bring a pencil.
• The exam will be graded on later on Tuesday.
• The exam grades probably be posted Tuesday evening.

Final Exam Review

• Results of the survey indicate that a few wanted each time I suggested with the majority requesting 4 and 5 PM.  So…
• I’ll be in my office by 3PM on Monday.  If you want to come in and ask questions, pick up your Exam 3 or your Staphylococcal Study papers you may do so any time after 3.
• I’ll be available in the lab for a more formal review at 4 and 5.  [Most people should not have a conflicting exam that way.]
• If this absolutely doesn’t work for you please let me know.

1. Control of Microbial Growth   (includes physical and chemical factors as well as chemotherapeutic agents).
2. Prions and Prion Diseases
3. Infection and Disease (Disease Processes)
4. Epidemiology
5. Host Defense Systems

Some sample essay questions for exam 3 (Thursday May 12th):

1.  Based on your knowledge of microbiology design a perfect bacterial pathogen.  Be realistic in your answer.  [For example, it can only be spread one major way – not every way possible!]  Explain why you gave it the characteristics you did.
OR Design your own pathogen and justify your answers to each of the following.
a) spread by ___
b) portal of entry and exit
c) lives intra- or extra-cellularly
d) produces exotoxins or endotoxins
e) avoids the immune system by ___
f) affects ___ system.

A similar question is to explain the same things using a bacterial pathogen that you have researched.

2.  Explain the factors that contribute to the development of nosocomial infections and the control methods that are taken to prevent them.
OR Discuss nosocomial infections in terms of the following:
a) What are nosocomial infections?
b) What factors lead to nosocomial infections?
c) What bacteria commonly cause nosocomial infections?
d) What levels of control are taken to prevent these infections?

3.  Briefly explain how a specific infectious bacterial disease organism causes disease.

4.  Discuss the factors that lead to the emergence and re-emergence of infectious diseases?

5.  Discuss the reasons why, even though we know a great deal about what causes infections diseases and how to control the spread of disease, people continue to sicken and die of infectious disease.  (Apply this to the U.S. only.)

6.  Discuss the various ways by which food is preserved based on what you know about the ways that microbial growth is controlled – include the advantages and disadvantages of each.

7.  Thoroughly discuss the control of diseases in hospitals.  Include levels of control as well as problems that arise in the control of diseases in hospitals.  [This question includes the answer to number 2 above and might also include the use of antiseptics, disinfectants, and sterilization techniques to control pathogens in the hospital setting.]

8.  Discuss the side-effects of antimicrobial therapy.  Be sure to give examples of each.

9.  Compare and contrast the production and effects of exotoxins and endotoxins by bacteria.

10. Discuss the advantages and disadvantages of having a normal flora.

11. Explain how the complement system works to destroy or incapacitate pathogens.

12. Explain the ways that constitutive and induced defenses interact.

Host Defense Systems

• Be able to distinguish between constitutive and cell-mediate defense systems.
• Know which white blood cells are associated with each.
• Know how various portions of each are stimulated and what happens when they are.
• Know the ways in which the defense system act to neutralize, destroy, or aid in the destruction of invading organisms.
• Be able to discuss the ways (two) that the constitutive and induced defense systems interface.

Here is an outline:

I.  Constitutive Defense is always present and nonspecific

• Phagocytosis
  • Neutrophils
  • Macrophages
• Inflammation
  • Triggered by degranulation by granulocytes
• Complement System (complement activation or fixation)
  • Triggered by antigen-antibody complexes OR
  • Directly by antigens
  • Leads to Destruction via
    • Inflammation
    • Cytolysis
    • Complement Activation

II. Cell Mediated Defense (Immunity) must be activated and is specific

• Humoral Immunity acts against bacterial cells and viruses
  • B-lymphocytes (B-cells)
    • Stimulated by antigens or by Helper T-cells
    • Divide into specialized B cells
      • Plasma cells that produce antibodies
      • Memory B Cells
• Cell-mediated Immunity acts against eukaryotic cells (host cells that are infected with viruses or bacteria, transplanted cells, cancer cells etc.)
  • T-lymphocytes (T-Cells)
  • Stimulated by APC’s (Antigen presenting Cells) — usually macrophages
  • Divide into specialized T-cells
    • Helper T-cells (stimulate B cells)
    • Cytotoxic T-cells
    • Memory T-cells

What is the normal flora?

• You should know what the normal flora, examples of the normal flora and the roll that it plays in the protection of the the body against infectious diseases.
• Know which parts of the body are colonized by microbes and which are microbe-free under normal conditions.
• Refer to Lab Exercise information of the normal flora of the GI and Urinary tract.
  • What are the growth conditions in the GI tract?
  • How does that affect microbial growth there?
  • What kinds of microbes comprise the normal flora of the GI tract?
  • What are some things that can go wrong?
  • How do urinary tract infections occur?
    • What kinds of microbes cause them?
    • How would you grow and identify them?

Microbes and Disease Processes

• Strategies for Colonization of Host Tissue
  • Know the pros and cons of a microbe colonizing host tissue and living within host cells (intracellularly) or outside of host cells (extracellularly).
• Be able to compare terms such as colonization, infection, and disease.
• Understand what a pathogen must accomplish to cause a disease.
  • What are the 6 requirements?  Can you name examples of each stage in the process?
    • Can you do that for a disease we studied like E. coli gastroenteritis, or Smallpox, for example.
• Microbes cause disease by interfering with normal bodily functions.  They usually do so by destroying host tissues.
  • You should be able to name the ways that bacteria destroy host tissues and give examples.
    • How do they attach and then invade host tissue?
• Be able to compare and contrast exotoxins and endotoxins in their chemical composition as well as their toxic effects and the types of bacteria that produce them.
• Know the types of infections diseases.
• Know the stages of an infection with an infectious disease.

Epidemiology and Nosocomial Infections (Week 13 Tuesday)

Epidemiology

• You should be able to explain what epidemiologists do.
• Know the terms that pertain to epidemics —
  • Rates of Occurrence, Death, and Infection
  • Types of Outbreaks (epidemic, endemic, sporatic, pandemic)
    • Be able to identify these by their illustrations in the text.
  • Methods of analysis of epidemics.
• Identify the three types of reservoirs of infectious diseases and give specific examples of diseases associated with each.
• Be able to name portals of entry and exit of infectious diseases and give examples of each.
  • Specifically know diseases that may be transmitted to the fetus from the mother.
• Know the three ways that diseases may be transmitted.
  • Understand the different types of each.
  • Be able to give or identify specific examples of each.
• Know the 4 general ways that epidemics can be controlled and examples of each.
• If we know all this about infectious diseases, why do people still get sick and die?
  • Part of the answer is in the occurrence of new (emergent) and reoccurring (resurgent) diseases.
  • Know what factors contribute to emergent (and resurgent) diseases.
    • Be able to give specific examples.

Nosocomial Infections

• Why do people who are in the hospital get sick from being in the hospital?
  • What factors cause nosocomial infections?
  • What kinds of infections are most commonly nosocomial?
  • What microbes most often cause nosocomial infections?

• Be able to characterize prion diseases of humans and animals.  Specifically:
  Scrapie, Chronic Wasting Disease, and Bovine Spongeoform Encephalopathy in animals
  CJD, vCJD, and Kuru in humans
• Exhibit an understanding of how human prion diseases are acquired.
• Exhibit an understanding of the difference between prions and viruses in the way they “replicate”.
  Be able to explain why scientists feel there are no nucleic acids associated with prions.

Control of Microbial (Bacterial) Growth

Chemical Agents:  Disinfectants and Antiseptics

• Be able to compare
  • antiseptics and disinfectants
  • sterilization vs. disinfection
  • bacteriostatic vs. bacteriocidal
  • NOTE:  the terms in Table 12.1 on pg. 343 in the text.
• How is the effectiveness of antibacterial chemicals evaluated?
  • To what disinfectant are new ones compared?
• What are requirements for a good disinfectant or sanitizing agent?
• The following categories of chemical agents were discussed:
  • soaps and detergents
  • acids and alkalis
  • heavy metals
  • halogens
  • alcohols
  • phenols
  • oxidizing agents
  • alkylating agents
  • dyes
• You should know examples of each, how they work, and under what circumstances each is used.  Table 12.3 on page 352 is an excellent summary.

Physical Antimicrobial Agents: heat, refrigeration, freezing, drying, freeze-drying, radiation (UV and ionizing), filtration, osmotic pressure.

• You should know how each of these physical methods works to kill bacteria and other microbes.
• Which are methods of sterilization?
• Under what circumstances are each used?
• Which are used to control microbial growth in food?  Are some used in combination with chemical methods of control?
• The summary table (table 12.5) on page 361 is excellent.

Which of these techniques is used to preserve food?  How are they used?

Antimicrobial Therapy (Chemotherapeutic Agents)

• What is antimicrobial chemotherapy?
• Name the properties of antimicrobial chemicals and how these properties are used to control disease.
• Know the 5 modes of action of antimicrobial agents and how they are selective.
• Be able to list the characteristics of an ideal antibiotic.
• What are three kinds of side effects to chemotherapeutic agents?  Be able to give examples of each.

Exam 2 Covers Bacteria and Viruses

• See Weekly Reviews for Weeks 6-9 for outlines of what we have covered.
• Practice short answer (matching, multiple choice, crosswords) are posted in Vancko Hall.
• Sample essays are below.
• Note that this maybe a diagram-heavy exam as there are lots of possibilities for diagrams of such things as:
  • cell wall structure in prokaryotes
  • cell structure (both prokaryotes and eukaryotes but mostly the former)
  • viral structure
  • viral replication cycles — both bacteriophages and animal viruses
  • bacterial growth curve
  • viral growth curve
• Diagrams may be presented as parts of essays, i.e. label the diagram and explain what is going on in it, and multiple choice questions where the structures have letters and you have to choose the correct letter to go with the name of the structure.

Possible Essays for Exam 2

1. The 1918 influenza pandemic had a huge impact, costing may lives.  Explain the historical, scientific, and intrinsic (due to the virus itself) factors that made this possible.
2. Could an influenza outbreak be this devastating today?  Explain why or why not.
3. Explain the infective cycle of an animal virus using the diagram below.  Be sure to label the diagram.  [The diagram was from your text.]
4. Compare and contrast the infective cycle of a bacteriophage with that of an animal virus.
5. Thoroughly describe the infective cycle of an animal virus using HIV as an example.
6. Discuss the factors that are involved in choosing an agent for biological warfare using anthrax and/or smallpox as examples.
7. Compare and contrast the following pairs of terms:  [Define each; tell how they are related if they are related; and why they are not if they are not.]
   • capsid and capsule
   • glycocalyx and capsule
   • spikes and fimbriae
   • nucleoid and nucleus
   • chromosome and plasmid
   • eukaryotic and prokaryotic ribosomes
   • eclipse period and latent period
   • virulent and temperate phages
   • chickenpox and shingles
   • fimbriae and flagella
   • naked and enveloped viruses
   • lytic and lysogenic cycles

I will be available for review Tuesday, April 5th at 5 PM and at 6 PM in the lab as well as by appointment.

• Note that I cannot be available from 3:30-5 on Tuesday.
  

Viruses

Basic Viral Structure and Replication

• Know the structure of bacteriophages as well as animal viruses.
• Be able to identify and explain the steps in viral replication.
• Know the difference between lysogenic and lytic viral cycles.

Bacteriophages vs. Animal Viruses

• Be able to compare and contrast the infective cycles of bacteriophages and animal viruses.
• Be able to explain the steps of the infective cycle of an animal virus; use HIV as a specific example.

Effects of Infection by a Virus

• Be able to explain the possible outcomes of infection by a virus:
  • Disease process (as exemplified by influenza, herpes, smallpox, or rabies).
  • Teratogenesis
  • Cancer
• Be able to discuss in detail the influenza virus:
  • Its structure and the role of this structure in infection as well as genetic drift and shift.
  • Why the 1918 influenza pandemic was so devastating;
  • What its reservoir is and how it goes from infecting birds to infecting humans;
  • What steps are taken to prevent a pandemic like the 1918 one;
  • The dangers of avian flu.
• How can viral infection lead to secondary bacterial infections?

Viral Diseases –Lectures are online in Vancko Hall

• Small Pox, Influenza, Rabies, Herpes
• Also Avian Influenza!

Viral “Activity” as Obligate Intracellular Parasites

Know the ideas about the origin of viruses as outlined in your text.

• In what ways are they living?  …nonliving?

Reading:

• Be sure to read the introduction to viruses in your text (pp.271-276)
• Read up on Herpesviruses in your text:  pp. 627-632
• Read about influenza in your text pp. 660-665.

It will cover:

• prokaryotic structures and their function
• a comparison of eukaryote and prokaryote cell structure
• the origin of eukaryotes from prokaryotes
• the different kinds of bacteria and how we see/identify them.
  • three domains
  • types of bacteria withing the Eubacteria
  • kinds of microscopy
  • ways to increase contrast
• bacterial growth and nutrition

Bacterial Growth

By what process to bacteria grow?

• Know the phases of growth as exhibited in a closed container.
• What contributes to each phase?
• How do we use this knowledge to control microbial growth

What are several methods that are used to measure the growth of bacteria?

• Which of these have we used in lab?

We discussed several physical factors that affect the growth of bacteria:

• pH
• temperature
  • Know the terms for bacteria that have different temperature optima.
  • Relate temperature requirements for growth of bacteria and foodborne infections and intoxications.
• oxygen
  • Distinguish between obligate and facultative anaerobes and aerobic bacteria.
  • Know the toxic forms of oxygen and what mechanisms are used to combat them.
  • Understand how peroxide is used as an antiseptic.
  • How are bacterial oxygen requirements related to food safety?
• moisture
  • How is this used to control bacterial growth?  or to preserve bacteria?
• osmotic pressure
  • What is osmotic pressure and how is it used to control bacterial growth?
• nutritional requirements
  • Review the elements that are essential for bacterial growth and the kinds of compounds that they are necessary for.
  • Review nitrogen fixation:  which organisms are capable of it and why it is important.

Viral Structure

• Know the basic structure of viruses including naked and enveloped viruses.  Note the relative sizes and the shapes of viruses as illustrated in Figure 10.2 pg. 274 in your text.
  • Terms include:
    • capsid
    • capsomere
    • nucleic acid
    • spikes
    • virion
    • nucleocapsid

Week 9 will continue viruses including the viral replication cycle of bacteriophages and animal viruses.  Viral diseases:  smallpox, influenza and rabies.

Exam 2 will be given on Thursday April 8th.

The Origin of Eukaryotes from Prokaryotes

• Be able to describe the process by which eukaryotes arose from prokaryotic cells.  [In other words explain the Endosymbiotic Theory of the Origin of Eukaryotes.]

• Be able to give examples of the evidence that exists for this theory using mitochondria and chloroplasts.
  • What eukaryotic organelle is NOT thought to have originated this way?

Kinds of Bacteria (Prokaryotes) and How We See and Identify Them

• Show and understanding of the Three-Domain System of classification and be able to contrast it with the Five Kingdom System we covered earlier in the semester.
  • Which system do you think best describes living organisms and their evolutionary relationships?  Justify your answer.
• Know the differences between the Eukbacteria and the Archaebacteria
  • Why are the Archaebacteria called extremophiles?
• In the Eubacteria know about some specialized bacteria such as:
  • Chlamydias and Rickettsias and how they differ from bacteria such as E. coli and Staphylococcus.
  • Know the diseases caused by Chlamydia and especially the impact of Chlamydia that causes blindness.
    • Be sure to read the NY Times article on Trachoma linked in Vancko Hall.
• Be able to distinguish among light, transmission electron and scanning electron micrographs.
  • What are the advantages and disadvantages of the use of these three kinds of microscopes?
• Know why we stain bacteria cells and which stain and microscope techniques are useful in different situations and for different kinds of bacteria and eukaryotes.
• Know the differences between selective and differential agar as well as some examples of each that we have used in lab.

Biological Warfare:  Anthrax as an Example

• Know the characteristics of an ideal biological weapon.
• Be able to explain how bacterial structure of B. anthracis lends it self to use as a biological weapon.
  • Be able to discuss the problems in developing/using a biological weapon.
    
    • What structures that are typical of some prokaryotic cells, make Anthrax such a prime candidate for use as  a biological weapon?
    • Note that after we have covered viruses you will be asked to compare and contrast smallpox and anthrax for use as biological weapons.
• Be sure to go through this Case Study entitled “Dead Cattle Bloated with Epistaxis“; it is also available in Vancko Hall.

• Be able to describe the structure of a prokaryotic cell as well as the functions of the structures.  Especially pay attention to the contrast in structure and function of prokaryotes with eukaryotes.
• Be able to show that you understand the ways that microbiologists used the differences between these basic cell types to their advantages.
• Be able to show that you understand the relationship between endotoxins and gram-negative cell wall structure.
• Know what exotoxins are, what kinds of bacteria produce them, as well as some examples of diseases caused by bacteria that produce exotoxins.
  • Why can exotoxins be inactivated and used as vaccines while endotoxins cannot be used this way? What diseases are prevented by vaccination with toxoids? What is an antitoxin?
• Know the nature and function of endospores.
  • What diseases are caused by endospore-forming bacteria?
  • if one bacterium in your unknown mixture produces spores, what shape and gram reaction would it most likely have?
• Show an understanding of the variety of structures with in the Prokaryotae, for example the variety in cell walls.
• You should be able to answer questions related to laboratory and the Gram stain — this includes the agents that are used as well as why gram-positive cells are purple and gram-negative cells are red.
• Be able to compare and contrast eukaryotic and prokaryotic cell structure.