Category: Microorganisms

Chapter 18 – AP Objectives

 

Chapter 18    Genetics of Viruses & Bacteria
Objectives
The Genetics of Viruses
1. Recount the history leading up to the discovery of viruses. Include the contributions of Adolf Mayer, Dimitri Ivanowsky, Martinus Beijerinck, and Wendell Stanley.
2. List and describe the structural components of viruses.
3. Explain why viruses are obligate intracellular parasites.
4. Explain how a virus identifies its host cell.
5. Describe bacterial defenses against phages.
6. Distinguish between the lytic and lysogenic reproductive cycles, using phage lambda as an example.
7. Describe the reproductive cycle of an enveloped virus. Explain the reproductive cycle of the herpesvirus.
8. Describe the reproductive cycle of retroviruses.
9. List some characteristics that viruses share with living organisms and explain why viruses do not fit our usual definition of life.
10. Describe the evidence that viruses probably evolved from fragments of cellular nucleic acids.
11. Define and describe mobile genetic elements.
12. Explain how viral infections in animals cause disease.
13. Describe the best current medical defenses against viruses. Explain how AZT helps to fight HIV infections.
14. Describe the mechanisms by which new viral diseases emerge.
15. Distinguish between the horizontal and vertical routes of viral transmission in plants.
16. Describe viroids and prions.
17. Explain how a non-replicating protein can act as a transmissible pathogen.
The Genetics of Bacteria
18. Describe the structure of a bacterial chromosome.
19. Compare the sources of genetic variation in bacteria and humans.
20. Compare the processes of transformation, transduction, and conjugation.
21. Distinguish between generalized and specialized transduction.
22. Define an episome. Explain why a plasmid can be an episome.
23. Explain how the F plasmid controls conjugation in bacteria.
24. Describe the significance of R plasmids. Explain how the widespread use of antibiotics contributes to R plasmid-related disease.
25. Explain how transposable elements may cause recombination of bacterial DNA.
26. Distinguish between an insertion sequence and a transposon.
27. Describe the role of transposase in the process of transposition.
28. Briefly describe two main strategies that cells use to control metabolism.
29. Explain the adaptive advantage of genes grouped into an operon.
30. Using the trp operon as an example, explain the concept of an operon and the function of the operator, repressor, and corepressor.
31. Distinguish between structural and regulatory genes.
32. Describe how the lac operon functions and explain the role of the inducer, allolactose.
33. Explain how repressible and inducible enzymes differ and how those differences reflect differences in the pathways they control.
34. Distinguish between positive and negative control and give examples of each from the lac operon.
35. Explain how cyclic AMP and catabolite activator protein are affected by glucose concentration.
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Chapter 19 AP Objectives

 

Chapter 19    Eukaryotic Genomes
Objectives
The Structure of Eukaryotic Chromatin

1.  Compare the structure and organization of prokaryotic and eukaryotic genomes.

2.  Describe the current model for progressive levels of DNA packing in eukaryotes.

3.  Explain how histones influence folding in eukaryotic DNA.

4.  Distinguish between heterochromatin and euchromatin.

The Control of Gene Expression

5.  Explain the relationship between differentiation and differential gene expression.

6.  Describe at what level gene expression is generally controlled.

7.  Explain how DNA methylation and histone acetylation affect chromatin structure and the regulation of transcription.

8.  Define epigenetic inheritance.

9.  Describe the processing of pre-mRNA in eukaryotes.

10. Define control elements and explain how they influence transcription.

11. Distinguish between general and specific transcription factors.

12. Explain the role that promoters, enhancers, activators, and repressors may play in transcriptional control.

13. Explain how eukaryotic genes can be coordinately expressed and give some examples of coordinate gene expression in eukaryotes.

14. Describe the process and significance of alternative RNA splicing.

15. Describe factors that influence the life span of mRNA in the cytoplasm. Compare the longevity of mRNA in prokaryotes and in eukaryotes.

16. Explain how gene expression may be controlled at the translational and post-translational level.

The Molecular Biology of Cancer

17. Distinguish between proto-oncogenes and oncogenes. Describe three genetic changes that can convert proto-oncogenes into oncogenes.

18. Explain how mutations in tumor-suppressor genes can contribute to cancer.

19. Explain how excessive cell division can result from mutations in the ras proto-oncogenes.

20. Explain why a mutation knocking out the p53 gene can lead to excessive cell growth and cancer. Describe three ways that p53 prevents a cell from passing on mutations caused by DNA damage.

21. Describe the set of genetic factors typically associated with the development of cancer.

22. Explain how viruses can cause cancer. Describe several examples.

23. Explain how inherited cancer alleles can lead to a predisposition to certain cancers.

Genome Organization at the DNA Level

24. Describe the structure and functions of the portions of eukaryotic DNA that do not encode protein or RNA.

25. Distinguish between transposons and retrotransposons.

26. Describe the structure and location of Alu elements in primate genomes.

27. Describe the structure and possible function of simple sequence DNA.

28. Using the genes for rRNA as an example, explain how multigene families of identical genes can be advantageous for a cell.

29. Using a-globin and b-globin genes as examples, describe how multigene families of nonidentical genes may have evolved.

30. Define pseudogenes. Explain how such genes may have evolved.

31. Describe the hypothesis for the evolution of a-lactalbumin from an ancestral lysozyme gene.

32. Explain how exon shuffling could lead to the formation of new proteins with novel functions.

33. Describe how transposition of an Alu element may allow the formation of new genetic combinations while retaining gene function.

 
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Caught Red-Handed

 

Caught Red-Handed  

 

Introduction:

Bacteria are everywhere. They have evolved the ability to inhabit almost every surface on the planet; however, they are invisible to the naked eye due to their small size. Bacteria have been found living in the deepest part of the ocean, in volcanic vents, in boiling hot springs, and even deep in polar ice caps. Many species of bacteria live inside of other organisms in a harmless commensalistic way such as the intestinal bacteria, Escherichia coli. Bacteria can reproduce at very rapid rates whenever conditions are favorable, as often as every 20 minutes doubling in number. The bacterial population is kept in check by the natural defenses of the host, such as the immune system and proper washing habits. When these natural defenses fail, bacteria can quickly become a problem. Some bacteria produce poisons or toxins that can be life-threatening if the bacterial population isn’t controlled by our natural defenses.

The United States Centers for Disease Control (CDC) states that the best way to prevent bacterial spread and infection is through the use of proper sanitary techniques. Perhaps the most critical step in this prevention is the use of proper hand washing. When improperly washed, your hands are one of the most easily colonized areas of your body and many of our behaviors involve the use of our hands.  Proper hand washing requires the use of water as hot as you can stand, soap, and lots of rubbing. The soap and water serve to destroy bacteria, and the rubbing helps slough off dead skin cells along with lots of bacteria.

Objective:

Students will examine:

  1. The spread of bacteria through surface contact
  2. Surface washing techniques to reduce the spread of bacteria

Materials (Part A):

Black light, Glo-Germ powder, lotion or Glo-Germ oil, hand soap, water, paper towels, pencil, lab sheet

Procedure (Part A):

  1. Choose one student in the lab group and have them spread a SMALL AMOUNT of Glo-Germ powder or lotion evenly over the entire surface of their hands. Be sure to include hard to clean areas such as around & under the fingernail.
  2. Have another student use the Black light to check your hands for the fluorescent “germs”.
  3. Estimate the percentage of your hand that you have covered with Glo-Germ powder and record this percentage in your data table 1 under time “0”.
  4. Wash your hands for 10 seconds and then recheck your hands with Black light and record the percentage of “germs” remaining.
  5. Repeat step 5 for washing times of 30 seconds, 60 seconds, and 120 seconds.
  6. Return Glo-Germ powder, lotion, or oil to lab cart. 

Data Table 1

 

Time of Wash in Seconds Percent of Hand Covered with “germs”
0 (initial observation)
10
30
60
120

 

Materials (Part B):

Tennis ball, “play” money, stuffed toy, pencil, lab sheet

Procedure (Part B):

  1. Choose a different member of your lab group and use the Black light to check their hands for the presence of germs.  IF they are “infected”, have them thoroughly wash their hands to remove the “germs”.
  2. Record the percentage of their hand that is covered with “germs”.
  3. Pick up the basket from the lab cart with your materials for part B.
  4. Handle the tennis ball for at least 20 to 30 seconds.
  5. After handling the tennis ball, have your hands rechecked with the Black light for “germs”.
  6. Record this percentage in data table 2.
  7. Return to your lab table and handle each of the other items ONE AT A TIME, checking for “germs after EACH item and recording this percentage in table 2.
  8. Return the black light and basket with handled items to the lab cart.

Data Table 2

 

Name of Item Percent Coverage
Initial Hand Coverage
Tennis Ball
“Play” money
Toy

 

Questions:

  1. If almost every surface we touch is inhabited by bacteria, why don’t bacterial infections occur more often?
  2. Name 3 ways you  might prevent the spread of bacteria each day.
  3. Name several bacterial diseases.
  4. Name and describe the 3 shapes of bacteria.
  5. Are all bacteria harmful? Explain your answer.
  6. What effect, if any, did increased washing time have on the percentage of “germ” coverage on your hands?
  7. Name 3 areas of your home that are most susceptible to bacterial contamination. Explain steps you could take in each of these areas to prevent the spread of bacteria to other places in your home.

Optional:

Create a graph based on the data from table 1.

Title _____________________________

 

Bacteria Culturing Activity

 

Where are Bacteria Found?  

 

 

Introduction:

They’re everywhere. Bacteria are the huddled masses of the microbial world, performing tasks that include everything from causing disease to fixing nitrogen in the soil. The estimated number of bacteria on Earth is five million trillion trillion — that’s a five with 30 zeroes after it.  When people think of bacteria, they likely first consider the nasty ones that cause disease, but the bacteria inside all animals combined — including humans — makes up less than one percent of the total amount. By far the greatest numbers are in the subsurface, soil and oceans.

 

Objectives:

  1. To take bacterial swabs from various places in the school
  2. To inoculate a petri dish with a bacterial culture
  3. To count bacterial colonies
  4. To determine what kind of environmental conditions influence bacterial growth

Materials: 

Petri dish,  pencil,  incubator, hot water bath, nutrient agar, thermometer

Procedure (Part A): Petri Dish Preparation

  1. Set up a hot water bath at 95oC.
  2. Loosen the caps and place nutrient agar bottle in hot water bath until agar liquefies. (Agar melts above 95oC and remains liquid until cooled to about 45oC.)
  3. Remove agar bottles and allow the agar to cool to about 50-55oC.
  4. Partially lift the cover of the petri dish and pour about 15-20ml of liquid to cover 2/3 of the plate surface.
  5. Lower the lid of the dish and gently swirl the plate to spread the media over all the bottom surface.

  1. Repeat step 5 to fill other petri dishes.
  2. DO NOT MOVE the covered plates until the nutrient agar has solidified.
  3. Once the plates are solidified, turn the plates upside down (presents condensation from getting on the agar surface).
  4. From this moment on, keep the plates upside down (condensation will disappear) in a dark, dust-free place in the room until ready to add bacteria. If plates will not be used for several days, refrigerate them.
  5. Check plates for contamination before proceeding to Part B. Discard contaminated plates.

Materials: 

Petri dish with nutrient agar, sterile cotton swabs, permanent marker, index card with sample location, pencil,  incubator

 

Procedure (Part B): Collecting Bacteria

  1. Choose an index card to determine your sample location
  2. Turn the petri dish upside down, and using your marker, place your initials, date and sample location along the bottom perimeter of the dish, NOT in the middle
  3. Get your sterile Q-tip, being very careful not to touch the side that will collect your sample. Go to your assigned area and quickly swab and return with your sample! (Sample locations included door handles, water faucets, desk tops, etc.)
  4. Carefully open your dish just enough to lightly rub your Q-tip in a zigzag pattern across the agar.

  1. Draw what your dish looks like in Figure 1 and record the number of bacterial colonies, if any, present on the agar surface in table 1
  2. Place your petri dish upside down in the incubator to be examined again in a few days.
  3. Recheck the plates after 1 day, 2 days, and 5 days. Count and record the number of bacterial colonies on each plate. If the plate is  completely covered with bacteria, record “lawn” in the data table.
  4.  Ignore “fuzzy” appearing colonies that are actually fungi!

Example of Bacterial Colonies on Plate

Data:

Reminder — Fuzzy Colonies = Fungus not Bacteria

Figure 1 

Day 1                Day 2                Day 5

   

Table 1:   Number of Colonies on petri dish 

    Location:
Day Number of Colonies

 

Analysis:  

  1. Compare the number of colonies on your plate on day 5 with the plates collected from other locations. Did any of the areas show a greater number of bacteria? How many clusters of bacteria appear to be growing in each petri dish?
  2. Which petri dish had the most growth? The Least?
  3. Why was the agar sterilized before this investigation?
  4. What kind of environmental conditions seem to influence where bacteria are found?
  5. How can you control the amount of bacteria that you will encounter?
  6. Check the plate that the teacher has had open, exposed to the air for several days. What did you observe and why?

Dispose of the petri dishes carefully!  Place them in a biohazard bag to be autoclaved.

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Bacteria

KINGDOMS ARCHAEBACTERIA & EUBACTERIA


All Materials © Cmassengale

Bacterial Evolution & Classification 

  • Most numerous organisms on earth
  • Earliest life forms (fossils date 2.5 billion years old)
  • Microscopic prokaryotes (no nucleus nor membrane-bound organelles)
  • Contain ribosomes
  • Infoldings of the cell membrane carry on photosynthesis & respiration
  • Surrounded by protective cell wall containing peptidoglycan (protein-carbohydrate)
  • Many are surrounded by a sticky, protective coating of sugars called the capsule or glycocalyx (can attach to other bacteria or host)
  • Have only one circular chromosome
  • Have small rings of DNA called plasmids
  • May have short, hairlike projections called pili on cell wall to attach to host or another bacteria when transferring genetic material
  • Most are unicellular

  • Found in most habitats
  • Most bacteria grow best at a pH of 6.5 to 7.0
  • Main decomposers of dead organisms so recycle nutrients
  • Some bacteria breakdown chemical & oil spills
  • Some cause disease 
  • Move by flagella, gliding over slime they secrete ( e.g. Myxobacteria)
  • Some can form protective endospores around the DNA when conditions become unfavorable; may stay inactive several years & then re-activate when conditions favorable
  • Classified by their structure, motility (ability to move), molecular composition, & reaction to stains (Gram stain)
  • Grouped into 2 kingdoms — Eubacteria (true bacteria) & Archaebacteria (ancient bacteria)
  • Once grouped together in the kingdom Monera

 

STRUCTURE FUNCTION
Cell Wall protects the cell and gives shape
Outer Membrane protects the cell against some antibiotics (only present in Gram negative cells)
Cell Membrane regulates movement of materials into and out of the cell; contains enzymes important to cellular respiration
Cytoplasm contains DNA, ribosomes, and organic compounds required to carry out life processes
Chromosome carries genetic information inherited from past generations
Plasmid contains some genes obtain through genetic recombination
Capsule, and slime layer protects the cell and assist in attaching the cell to other surfaces
Endospore protects the cell against harsh environmental conditions, such as heat or drought
Pilus (Pili) assist the cell in attaching to other surfaces, which is important for genetic recombination
Flagellum moves the cell

 

Kingdom Archaebacteria

  •   Found in harsh environments (undersea volcanic vents, acidic hot springs, salty water)
  • Cell walls without peptidoglycan
  • Subdivided into 3 groups based on their habitat — methanogens, thermoacidophiles, & extreme halophiles

Methanogens

  • Live in anaerobic environments (no oxygen)
  • Obtain energy by changing H2 and CO2 gas into methane gas
  • Found in swamps, marshes, sewage treatment plants, digestive tracts of animals
  • Break down cellulose for herbivores (cows)
  • Produce marsh gas or intestinal gas (methane)

Extreme Halophiles

  •   Live in very salty water
  •   Found in the Dead Sea, Great Salt Lake, etc.
  • Use salt to help generate ATP (energy)

Thermoacidophiles (Thermophiles)

  • Live in extremely hot  (1100C) and acidic (pH 2) water
  • Found in hot springs in Yellowstone National Park, in volcanic vents on land, & in cracks on the ocean floor that leak scalding acidic water

Kingdom Eubacteria (true bacteria)

  • Most bacteria in this kingdom
  • Come in 3 basic shapes — cocci (spheres), bacilli (rod shaped), spirilla (corkscrew shape)

  • Bacteria can occur in pairs ( diplo– bacilli or cocci)
  •   Bacteria occurring in chains are called strepto- bacilli or cocci
  • Bacteria in grapelike clusters are called staphylococci
  • Most are heterotrophic (can’t make their own food)
  • Can be aerobic (require oxygen) or anaerobic (don’t need oxygen)
  • Subdivided into 4 phyla — Cyanobacteria (blue-green bacteria), Spirochetes, Gram-positive, & Proteobacteria
  • Can be identified by Gram staining (gram positive or gram negative)  

Gram Staining

  • Developed in 1884 by Danish microbiologist, Hans Gram
  •   Bacteria are stained purple with Crystal Violet & iodine; rinsed with alcohol to decolorize; then restained with Safranin (red dye)

  • Bacterial cell walls either stain purple or reddish-pink

Gram-positive bacteria (Gram +)

  • Thick layer of peptidoglycan (protein-sugar) complex in cell walls & single layer of lipids
  • Stain purple

  • Lactobacilli are used to make yogurt, buttermilk ….
  • Actinomycetes make antibiotics like tetracycline & streptomycin
  • Disease-causing gram + bacteria produce poisons called toxins
  • Clostridium causes tetanus or lockjaw
  • Streptococcus cause infections such as “strep” throat

  • Staphylococci cause “staph” infections

  • Also cause toxic shock, bacterial pneumonia, botulism (food poisoning), & scarlet fever
  • Can be treated with penicillin (antibiotics) & sulfa drugs

Gram-negative bacteria (Gram -)

  • Cell walls have a thin layer of peptidoglycan & an extra layer of lipids on the outside
  • Stain pink or reddish 

  • Lipid layer prevents the purple stain & antibiotics from entering (antibiotic resistant)
  • Some are photosynthetic but make sulfur, not oxygen
  • Rhizobacteria grow in root nodules of legumes (soybeans, peanuts…) & fix nitrogen form the air for plants
  • Rickettsiae are parasitic bacteria carried by ticks that cause Rocky Mountain spotted fever
  • Spirochetes can cause syphilis & Lyme disease

Phylum Cyanobacteria

  • Gram negative
  •   Carry on photosynthesis & make oxygen
  • Called blue-green bacteria
  • Contain pigments called phycocyanin (red & blue) & chlorophyll a (green)
  •    May be red, yellow, green, brown, black, or blue-green
  • Some grow in chains (e.g. Oscillatoria)  & have specialized cells called heterocysts that fix nitrogen


OSCILLATORIA

  •  First bacteria to re-enter devastated areas
  • Anabaena that live on nitrates & phosphates in water can overpopulate & cause “population blooms” or eutrophication
  •   After eutrophication, the cyanobacteria die, decompose, & use up all the oxygen for fish

Phylum Spirochetes

  •   Gram positive
  • Have flagella at each end so move in a corkscrew motion
  •   Some are aerobic (require oxygen); others are anaerobic
  • May be free-living, parasitic, or live symbiotically with another organism  

Phylum Gram Positive bacteria

  • Most are Gram +, but some are Gram –
  • Lactobacilli grow in milk & make lactic acid (forms yogurt, cottage cheese, buttermilk) & also found on teeth & cause tooth decay
  • Actinomycetes grow in the soil & make antibiotics
  • Gram + members are found in the oral & intestinal cavities & slow the growth of disease-causing bacteria

Phylum Proteobacteria

  • Largest & most diverse bacterial group
  • Subdivided into Enteric bacteria, Chemoautotrophic bacteria, & Nitrogen-fixing bacteria  

Enteric bacteria

  • Gram negative heterotrophs
  • Can live in aerobic & anaerobic environments
  • Includes E. coli that lives in the intestinal tract making vitamin K & helping break down food
  • Salmonella causes food poisoning

Chemoautotrophs

  • Gram negative bacteria that obtain energy from minerals  
  • Iron-oxidizing bacteria found in freshwater ponds use iron salts for energy

Nitrogen-Fixing bacteria

  • Rhizobium are Gram negative & live in legume root nodules

  • 80% of atmosphere is N2, but plants can’t use nitrogen gas
  • Nitrogen-fixing bacteria change N2 into usable ammonia (NH3)
  • Important part of the Earth’s nitrogen cycle

Methods of Nutrition

  •  Saprobes feed on dead organic matter
  •  Parasites feed on a host cell
  •  Photoautotrophs use sunlight for energy, but get carbon from organic compounds (not CO2) to make their own food  
  • Chemoautotrophs obtain food by oxidizing inorganic substances like sulfur, instead of using sunlight

Methods of Respiration

  •   Obligate aerobic bacteria can’t live without oxygen; (tuberculosis bacteria)
  •  Obligate anaerobes die if oxygen is present; (tetanus bacteria that causes lockjaw)
  • Facultative anaerobes do not need oxygen, but don’t die if oxygen is present; (E. coli)
  • Anaerobes carry on fermentation, while aerobes carry on cellular respiration 

Bacterial Reproduction & Genetic Recombination

  • Most bacteria reproduce asexually by binary fission (chromosome replicates & then the cell divides)  
  •   Bacteria replicate (double in number) every 20 minutes under ideal conditions  
  • Bacteria contain much less DNA than eukaryotes
  • Bacterial plasmids are used in genetic engineering to carry new genes into other organisms  
  • Bacteria recombine genetic material in 3 ways — transformation, conjugation, & transduction

Conjugation

  • Sexual reproductive method
  • Two bacteria form a conjugation bridge or tube between them

  •   Pili hold the bacteria together
  •   DNA is transferred from one bacteria to the other       

Transformation

  • Bacteria pick up pieces of DNA from other dead bacterial cells
  • New bacterium is genetically different from original

Transduction

  • A bacteriophages (virus) carries a piece of DNA from one bacteria to another

  • Human insulin is produced in the lab by this method

Pathogenic bacteria

  •   Known as germs or pathogens
  • Cause disease
  • Can produce poisonous toxins
  • Endotoxins are made of lipids & carbohydrates by Gram – bacteria & released after the bacteria die (cause high fever, circulatory vessel damage…)
  • E. coli  produce endotoxins
  • Exotoxins are made of protein by Gram + bacteria 
  • Clostridium tetani produce exotoxins
  • Antibiotics interfere with cellular functions (Penicillin interferes with synthesis of the cell wall; tetracycline interferes with protein synthesis)
  • Some antibiotics are made by bacteria or fungi
  • Broad-spectrum antibiotics affect a wide variety of organisms
  • Bacteria can mutate and become antibiotic resistant (often results from overuse of antibiotics)
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