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Week 9

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.

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!

Week 9 Viruses

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

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.
  • ALSO be sure to read the article in Vancko Hall on Influenza!
  • Here is the link to the CDC information on H1N1 for you.

From your reading you should have an understanding of influenza infection as well as

  • the structure of the influenza virus and the significance of the different  “H#N# combinations.
  • the importance and meaning of genetic drift and genetic shift in terms of influenza.
  • the significance of the 1918 influenza epidemic and its possible relationship to the current H1N1 influenza virus pandemic.

Week 6

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 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.

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?

Looking Ahead to Week 7:

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.

Week 5: Prokaryotes!

Prokaryotic Cell Structure

  • 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 vs. eukaryotes.
  • Be able to show that you understand the ways that  microbiologists use the differences between these basic cell types to their advantage.
  • 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.
    • Why can exotoxins be inactivated and used as vaccines while enodoxoins cannot be used in 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 within 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 reagents that are used as well as why Gram positive cells are purple and Gram negative cells are pink.
  • Be able to compare and contrast Eukaryotic and Prokaryotic Cell Structure.  There is a table in Vancko Hall in this unit that you can use as a template to fill in this comparison.

I have also posted the NY Times article about pets and bacteria that can infect humans entitled “Tie to Pets has Germs Jumping To and Fro.  It is in Vancko Hall Lecture  in this unit.

Week 4

Microbiology and the Progress of Science

  • Be able to show an understanding of how science progresses by listing the major discoveries that lead to the understanding of what microbes could do (including cause disease).
    • What was the result of the understanding that microbes caused disease?
    • When were there first cures for infectious diseases?
  • Be able to describe process that scientists go through to make scientific discoveries.
    • Be able to describe the steps in the scientific method using either Pasteur’s confirmation that biogenesis was true OR the use of Koch’s postulates.
    • Using Redi’s experiments with meat and maggots describe the scientific method.
    • Using Redi’s experiments with meat an maggots to explain the importance of Pasteur’s later work with crook-necked flasks.

Eukaryotic Cell Structure

  • Know the structure and function of organelles typical of eukaryotic cells
  • Compare and contrast the structure and function of mitochondria and chloroplasts.
  • Know the structure and role of cell membranes.
  • Know and be able to describe the steps in the process of phagocytosis (see the diagram of phagocytosis)

Exam 1 Will be Tuesday September 29th

It will consist of 35 multiple choice and matching questions that will be scantron graded so bring a #2 pencil to fill in the answer sheet.  This portion is worth 70 points.  For 30 points you will be asked to answer 3 (out of several) essay questions.  You will have 1 hour and 15 minutes to complete the exam.

It will cover everything we have gone over in lecture so far this semester.  Remember that lab overlaps lecture in this portion of the course!

Potential Essays:

1. Explain Koch’s postulates. Why are they important?

2. Explain how Pasteur was able to prove biogenesis.

3. Show and explain the steps in the Scientific Method using Pasteur’s proof of biogenesis. [The answer to this questions includes a list of the steps in the Scientific Method and THEN how Pasteur's experiments fit into those steps.]

4. Explain why infectious diseases are important in the world today. What measures can be taken to lower the deaths from infectious diseases in the world.

5. Compare and contrast the following pairs of terms. OR Tell what each of the items is and how it is related to the other item. [If it isn't related in any way, say so.]

  • Algae and Protozoa (e.g. Volvox and Paramecium )
  • Algae and Cyanobacteria (Spirogyra and Oscillatoria )
  • Eukaryote and prokaryote
  • Ectoparasite and endoparasite
  • Infection and Intoxication
  • Trophozoite and cyst
  • Apical complex and cyst
  • Sporozoite and merozoite
  • Cestode and Nematode and Trematode

6. Draw a simple diagram of the life cycle of the malarial parasite and label it. OR Label the drawing and explain the life cycle of the malarial parasite.

7. Should organisms like Euglena (which has chloroplasts, a flagellum, but can be heterotrophic, be place in with the Algae or the Protozoa? Why or Why not?

8. Where do you think organisms like Oscillatoria should be placed, in the Cyanobacteria or the Algae? Explain your reasoning.

9. Explain the factors that have contributed with the difficulties in controlling malaria.

10. Label and explain the diagram of phagocytosis.

11. Explain the ways that humans can become ill from fungal (or protozoan) diseases; give examples.

12. Discuss two important diseases caused by trypanosomes.

13. Compare and contrast the structure and function of chloroplasts and mitochondria.

14. Explain the structure of DNA and how it controls what goes on in the cell.

Week 3

Protozoan Diseases

  • Be able to discuss the major ways that protozoa cause disease and any structural adaptations they may have for this.
  • Be able to label and explain a diagram of the life cycle of the malaria parasite.
  • Be able to discuss the reasons why malaria has been so difficult to eliminate world-wide.

The Fungi (Kingdom Myceteae)

  • Know the characteristics of the fungi.
  • Be able to explain and give examples of their inability to compete with bacteria
    • and how this can be medically important.
  • Know the way that fungi are classified and the classification of fungi with examples.
  • Know the types of asexual and sexual spores produced by the fungi.
  • Be able to list the ways that fungi cause disease and give examples.
    • Know about fungal intoxications:  aflatoxicosis, ergotism, and mushroom intoxication.
    • Fungal infections:  histoplasmosis, and candidiasis.

Quiz 1 — On-line

Quiz 1 is online:

  • Worth 33 points.
  • There are 22 questions — two are  matching questions that have 5 or 6 matches.
  • Once you log on and start the quiz you have 45 minutes to complete it.
  • It must be completed by 11:55 PM EDT Wednesday September 23rd.
  • It covers:
    • Kingdoms
    • Importance of Infectious Diseases World-Wide
    • The Kingdoms Protista and Myceteae
    • Diseases that are characteristic of those kingdoms.
    • Chemistry — especially the 4 groups of organic compounds (carbohydrates, etc.)

Week 2 Review

Protozoan Diseases (I’ll actually cover this at the start of lecture week 3.)

  • Be able to discuss the major ways that protozoa cause disease and any structural adaptations they may have for this.
  • Be able to label and explain a diagram of the life cycle of the malaria parasite.
  • Be able to discuss the reasons why malaria has been so difficult to eliminate world-wide.

Importance of Infectious Diseases World-Wide

  • Be able to illustrate (give examples) and explain the two major points of the lecture on the importance of infectious diseases world-wide based on the 1999 WHO article (link to which is available in the lecture schedule found on-line).
  • Be able to give details in explaining the bar graph of the 6 major categories of infectious diseases that cause 90% of all deaths world-wide.
  • Be able to give examples of successes and failures in the struggle to control infectious diseases and some ways that might be used to control them.

Chemistry:

I’ve learned that biology is really, when you get right down to it, all about chemistry.  So you’ll have to keep in mind some chemistry as a part of this course.  It comes up over and over.

First of All be Aware of the Following:

  • Atoms, elements, compounds, and molecules.
  • The nature of chemical bonds (ionic, covalent, and hydrogen).
  • The difference between organic and inorganic compounds.
  • Remember that electrons = energy.
  • The loss of electrons is oxidation and results in a loss of energy which may escape as heat and/or light or be converted to a form of energy that is readily used by living systems — like the high-energy phosphate bond on between ADP and a phosphate to make ATP.

Be sure to know the 4 groups of large organic compounds that are important in living systems.

  • They are carbohydrates, lipids, proteins, and nucleic acids.
  • Know their basic composition in terms of elements as well as the subunits they are made up of.  [Most are made up of identical or nearly identical subunits.]
  • Know how they function in living cells and when they form structural elements what those structures are.
  • Especially be aware of the importance of proteins in their function as enzymes.
    • The shape of proteins is especially important to their function.
    • Know how the shape or proteins is determined and what primary, secondary, and tertiary structures of proteins are.
  • Know the function of nucleic acids and their subunits (nucleotides which are made of a nitrogen base, sugar, and phosphate).
    • Know how the order of nucleotides in a nucleic acid determines the shape of proteins.
    • What is the genetic code and what does it code for?
  • Try the sample short answer questions that are posted in Vancko Hall.

Multicellular Parasites

Don’t forget to view the lecture on multicellular parasites on Vancko Hall — I won’t be lecturing on this but you will be responsible for the information.

  • Know the characteristics of the parasitic members of the Trematodes, Cestodes, and Nematodes.
  • Pay particular attention to the life cycles of the significant examples of these parasites that are given in the lecture:
  • How they get into the human host.
  • What the definitive and intermediate hosts are.
  • How they cause damage.
  • Important diseases include:
  • Flukes (Trematodes) — Liver and blood flukes
    • Schistosomiasis
    • Liver flukes
  • Tapeworms (Cestodes):
    • Beef tape worm disease of humans
  • Roundworms (Nematodes)
    • Ascariasis
    • Trichinosis
    • Fiariasis

Week 3 I’ll be finishing up with the Chemistry lecture and the Protozoan diseases and moving on to the Fungi.  Quiz 1 which will be on line toward the end of the week will cover:

  1. Characteristics of the kingdoms + viruses and pirions
  2. Importance of Infectious Diseases World-Wide
  3. Essential Chemistry
  4. The Kingdom Protista and associated diseases
  5. The Kingdom Mycetea and associated diseases
The quiz will probably be posted Thursday and will be due the following Tuesday night:  Sept. 17-Sept. 22.
Here are a few from the Spring and Summer first exams on the subjects we’ve covered.  I’ll also post them as a practice quiz on Vancko Hall; doing so will give you the correct answers.  I’ve crossed out questions on History because they will not be covered for the first quiz.

Spring ‘09 Questions

_____1. Which of the following is not true of microorganisms?
a. they produce antibiotics; b. they are used in the production of many types of food and beverages; c. they decompose dead organisms; d. they all cause disease in humans.

_____2. In this kingdom there is no sexual reproduction:
a. Monera; b. Protista; c. Fungi; d. Plantae; e. Animalia

_____3. Which of the following groups or organisms contains members better known for transmitting agents of disease than for causing disease themselves?
a. arthropods; b. protozoa; c. fungi; d. helminths (parasitic worms).

_____4. The first person to use a microscope to observe living cells was
a. Robert Hooke; b. Matthias Schleiden; c. Anton van Leeuwenhoek; d. Louis Pasteur

_____5. The Germ Theory of Disease
a. states that germs are the fundamental units of life;
b. states that germs can invade other organisms and cause disease;
c. states that germs will spontaneously arise from decaying meat;
d. is another name for the Cell Theory.

_____6.  Proper sanitation would help control this (these) disease(s)
a. acute respiratory infections; b. malaria; c. tuberculosis; d. measles; e. diarrheal diseases.

_____7. This chemical is an insect repellant that, when applied to bed nets is effective at controlling the spread of malaria:
a. DEET; b. DDT; c. LSD; d. ergotamine

_____8. Which of the following is NOT true of algae?
a. They photosynthesize to produce their own food;
b. They are found in both fresh- and salt- water.
c. They have a nucleus;
d. They usually cause disease in humans.

_____9. Which of the following subatomic particles is NOT found in the nucleus of an atom
a. proton; b. neutron; c. electron; d. All are found in the nucleus of an atom.

_____10. Chemical bonds between atoms occur because of the interaction of
a. electrons; b. neutrons; c. protons; d. isotopes.

_____11. Electrons are shared equally in the formation of ___ bonds.
a. hydrogen; b. covalent; c. ionic.

_____12. Carbohydrates do not include which of these?
a. glucose; b. starch; c. cellulose; d. lipids.

_____13. Proteins are built from subunits called
a. nucleic acids; b. amino acids; c. nucleotides; d. phospholipids.

_____14. The sequence of amino acids in a protein is the protein’s
a. primary structure; b. secondary structure; c. tertiary structure; d. quaternary structure.

_____15. Which of the following are considered roundworms?
a. Nematodes; b. Trematodes; c. Cestodes; d. None, they are all flatworms.

_____16. Malaria is the result of an infection by a
a. mastigophoran; b. sacrodine; c. apicomplexan; d. ciliate.

_____17. The proper order of develop Trichinosis ment of Plasmodium in human blood is
a. gametocyte; b. merozoite; sproozoite;
b. sporozpoite; merozoite; gametocyte;
c. gametocyte; sporozoite; merozoite
d. sporozoite; gametocyte; merozoite.

_____18. The major characteristic used to divide up protozoans into four major groups is
a. type of motility; b. type of feeding behavior; c. reproductive strategies; d. habitat.

_____19. Some protozoan infections are contracted via the “fecal oral route”.  In these cases the person ingests the ___ stage of the parasite.
a. trophozoite; b. gametocyte; c. cyst.

_____20. Which of the following fields is concerned with the study of fungi?
a. bacteriology; b. virology; c. phycology; d. mycology.

_____21. Fungi are classified according to
a. the type of cell wall; b. type of photosynthetic pigments; c. nature of their sexual cycle; d. nature of their asexual cycle.

_____22. The intermediate host of many flukes are
a. humans; b. cattle; c. snails; d. tapeworms.

_____23. Humans are accidental defiinitve hosts of
a. liver flukes; b. malarial parasite; c. histoplasmosis; d. PSP

_____24. Mushrooms produce sexual spores called
a. basidiospores; b. ascospores; c. zygospores.

Summer ‘09 Questions:

Match the Kingdom or group with its description:

______1. Eukaryotes — some are heterotrophs and some are phototrophs. a. Monera (Prokaryotae)
______2.  Includes the heminths. b. Protista
______3.  Includes unicellular as well as multicellular saprobic organisms. c. Prions
______4. Nonliving entities that are intracellular parasites. d. Animalia
______5. Unicellular prokaryotes includes both heterotrophs and phototrophs. e. Viruses
______6. Nonliving entities that are made only of proteins. ab. Myceteae
______7. Diseases caused by these include Paralytic Shellfish Poisoning and Chagas Disease.
______8. Diseases caused by these include Histoplasmosis and Aflatoxicosis.

Matching on deaths due to infectious diseases in the world:

_____9. Accounts for the greatest number of deaths each year. a. HIV/AIDS
_____10. Difficult to control primarily due to multiple drug resistance. b. Tuberculosis
_____11. Almost all deaths are children. c. Acute Respiratory Diseases
_____12. Would be easy to decrease with proper sanitation. d. Diarrheal Diseases
e. Measles
ab. Malaria

Matching on chemistry:

_____13. Bonds formed between carbon atoms. a.  ions
_____14. Form biologically important catalysts. b. covalent bonds
_____15. Polymers form many organisms’ cell walls. c. hydrogen bonds
_____16. With an attached phosphate these form cell membranes. d. proteins
_____17. These determine the sequence of amino acids in proteins. e. lipids
ab. nucleic acids
ac. carbohydrates

More Matching

_____18. When they cause disease do so by causing infections. a. Algae
_____19. Cause disease by intoxications. b. Protozoa
_____20. Some cause infections and some intoxications. c. Fungi
_____21. Categorized by their form of motility.
_____22. Categorized by type of sexual reproduction.

_____23.  Pick the term that does not belong with the others:
a. trophozoite; b. merozoite; c. sporozoite; d.spermatocyte.

_____24. Pick the term that does not belong with the others:
a. gametocyte; b. conidiospore; c. sporangiospore.

_____25. Pick the term that does not belong with the others:
a. Mastigophora; b. Deuteromycota; c. Sarcodina; d. Ciliata.

Tell if the following are a. true statements or b. false statements.

_____26. Fungi are poor competitors when it comes to bacteria.

_____27. Plant cells do not contain mitochondria.

_____28. Aerobic respiration requires oxygen.

_____29. Eukaryotic chromosomes contain DNA that does not code for anything.

_____30. Filarial diseases are caused by insects that carry helminths.

_____31. In this disease cysteceri form in muscle which are then ingested to cause the intestinal form of the disease.  Humans are the definitive host.
a. Trichinosis; b. Beef tapeworms; c. Schistosomiasis; d. Ascariasis.

_____32. In this disease humans are the definitive host and snails are the intermediate host.
a. Trichinosis; b. Beef tapeworms; c. Schistosomiasis; d. Ascariasis

_____33. Ingested eggs hatch in the intestine and make their way to the intestine again after entering the bloodstream and getting to the lungs where they are coughed up and swallowed!
a. Trichinosis; b. Filariasis; c. Schistosomiasis; d. Ascariasis

_____34. This disease is acquired via the bite of a mosquito.  The worm circulates in the blood and to the lymphatic system.
a. Trichinosis; b. Filariasis; c. Schistosomiasis; d. Ascariasis

Week 1 Review

Characteristics of the Kingdoms and Introduction to the Kingdom Protista

Word cloud created from this week's terms using wordle.net

Word cloud created from this week's terms using wordle.net

The Kingdoms:

Be able to distinguish among the 5 kingdoms of living organisms and the viruses and prions.

  • Know the basic characteristics of each of these 7 groups and the kinds of organisms or entities that are included in each.
  • Be able to explain the Five Kingdom System of classification and how it is depicted.

Kingdom Protista — Protozoa and Algae

  • Know the characteristics that apply to all members of this kingdom.

Protozoa:

  • Be sure to review the basics of Parasitology and its associated terms.
  • Know the characteristics of the Protozoa.
    • In general be able to describe how protozoans cause disease.  [Later we cover specific diseases.]
  • Know the characteristics of the Phyla of Protozoa and how they are distinguished from one another.
  • Know examples of those that cause disease.

Algae:

  • Show an understanding of algal structure and function.
    • Be able to show how algae are important to humans.
    • Know about PSP and Ciguatera
  • Be able to compare and contrast Protozoa and Algae
  • Know why Cyanobacteria are bacteria and not algae.

The lecture on this kingdom is available online.  There are also sample exercises (some of which come from previous exams) for you to try that will give you an idea of the kinds of questions I ask on exams.  All of these are available on Vancko Hall.

This week (Week 2) I’ll be finishing up Protista, talking about malaria and other diseases caused by protozoans.  Then I’ll lecture on a bit of History and introduce the fungi because you’ll be looking at them in lab on Week 3.

Welcome to General Microbiology at SUNY Delhi

What is this?

  • Well this is a blog to help you in the course.  I will post weekly to this blog with review material.
  • Each weekend I update the blog by reviewing the material that we’ve covered during the week in lecture.
    • I have another blog that is a preview or briefing for each week’s lab.
    • The lab briefing blog is posted by the end of one week and gives you a preview of the next week’s lab.
    • I expect that you will print out that briefing and bring it to lab with you.
  • This is a review blog.  It will contain such things as
    • an outline or review sheet of important things we’ve gone over.
    • sample multiple choice and matching questions (some of these will be in Vancko Hall as “Hot Potatoes Quizzes” which are just practice quizzes.
    • sample essay questions for exams.

Why a blog?  Why not just post a review in Vancko Hall?

  • Primarily because I can (and have) add a RSS feed for you.
    • What does that mean?  Well it means that you can subscribe to this blog.  So that every time I update it or make a new posting, you get a message that tells you that I’ve updated it.  You can also add the RSS feed to your feed burner if you want.  [A feed burner is a program that holds your subscriptions.  Google Reader, for example, is a feed burner.]
  • Also you can send it comments or questions easily.
  • AND it puts all of the review material in one readily accessible place.
  • I suggest that you bookmark the blog.  That way if the Delhi system goes down you can get to the blog at least!

So… Welcome!  Use the blog and the other resources I provide for you and you’ll do fine in the course!

Dr. Stock