Biochemistry Study Guide BI

 

Biochemistry Study Guide
A molecule that has a partial negative charge on one side and a partial positive charge on the other would be what type of molecule?
Give several reasons why water is so important to life.
Does a molecule of water have a charge? Explain.
Explain why water is a polar molecule.
What element do all organic compounds contain?
Name the 3 elements most often found in organic compounds.
What organic molecules are considered to be carbohydrates?
Animals store glucose in their liver in what form?
What type of macromolecule would polysaccharides be?
Amino acids are the monomers for what polymers??
Proteins are made of long chains of what molecules?
Sketch a fatty acid.
Sketch a molecule of glucose.
Give several examples of lipids.
Long carbon-hydrogen chains linked by double covalent bonds make up what type of fats?
Name the 4 main types of macromolecules found in living thins.
What are the monomers of nucleic acids called?
Name 2 nucleic acids.
Explain why water’s polarity makes it useful for living things.
If an atom has four outermost electrons, how many covalent bonds can it form?
What type of molecule has a carboxyl “head” and makes up cell membranes?
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Bacteria & Virus Study Guide B1

 

 

Bacteria & Virus Study Guide

What color do Gram + bacteria stain?   Gram-?

How do bacterial cells differ from other types of cells?

How are chickenpox & shingles alike?

Why do people get the flu more than once?

What scientist discovered that viruses aren’t cellular?

Name several things used to classify viruses.

What are the 3 shapes for bacteria & give the name for each shape?

Can bacteria survive without oxygen? with oxygen?

How does the size of bacterial cells compare to the size of eukaryotic cells?

If a virus enters the Lysogenic cycle, can it change to the lytic cycle? Explain.

What 2 things make up a virus?

Why don’t antibiotics kill some bacteria?

What is necessary for a virus to reproduce?

Are viruses cellular?

Which bacteria are least responsive to antibiotics — Gram+ or Gram-?

What are prions?

What is a capsid?

How does forming an endospore help bacteria?

Describe the DNA of a bacterium.

What are pili?

What whiplike projections do some bacteria for movement use?

What occurs during conjugation?

What are retroviruses & what enzyme do they contain?

What is a viroid?

A protein coat & a nucleic acid core make up what typical structure?

In what cycle(s) does viral DNA get injected into host cells?

Is the Ebola virus linked to cancer?

Where would you find RNA in retroviruses?

 

Notes Study Guides

 

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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Bacteria PPT Questions

Bacteria
ppt Q’s

Prokaryote & Eukaryote Evolution

1. What does our current evidence tell us about the evolution of prokaryotes and eukaryotes?

 

2. About how long ago did eukaryotes evolve from prokaryotes?

3. Name the 2 theories of cellular evolution.

 

4. Explain the infolding theory.

 

 

5. What does endosymbiosis mean?

 

6. Explain the endosymbiotic theory of cell organelle formation.

 

 

 

7. Name 2 organelles thought to have arisen in this way.

 

Prokaryotic & Eukaryotic Cells

8. Label the parts of this prokaryotic cell.

9. Name several structures that are found in eukaryotic, but NOT prokaryotic cells.

 

 

10. What type of cells are the most numerous on Earth?

11. What are the most common type of prokaryotic cells?

12. How old are the earliest prokaryotic fossils?

Classification of Life

13. Name the 3 domains and the organisms found in each.

     a.

     b.

     c.

14. ______________ are found in harsh environments.

15. Give 3 examples of harsh environments in which Archaebacteria can be found.

 

16. What group is referred to as the true bacteria?

17. What photosynthetic member is in this group?

Characteristics of Bacteria 

18. What must be used to view prokaryotic cells?

19.What cell structures are lacking in prokaryotes?

20. Do bacteria have ribosomes like other types of cells?

21. Describe the genetic material of the bacteria.  be sure to tell where it is found.

 

22. What surrounds the cytoplasm of bacterial cells?

23.What surrounds the outside of all bacterial cells?

24. Cell walls of true bacteria contain ____________________.

25. Some bacteria have a sticky ____________ around the cell wall to attach to __________ or other bacteria.

26. Besides the circular chromosome, where else can DNA be found inside a bacterial cell?

27. What is the size of most bacterial cells?

28. Compare the size of bacteria to the tip of a pin.

 

29. ____________ of the bacterial cell membrane are called _______________.

30. What two cellular processes can take place in mesosomes?

 

31. At what pH do bacteria do best?

32. Most bacteria act as ________________. Why is this so important?

 

33. How can some bacterial be harmful?  Give an example.

 

34. name two other important uses for bacteria.

 

35. What does motile mean?

36. Motile bacteria may have one or more ______________ for movement.

37. Flagella attach to the bacteria by the ___________ ___________.

38. The basal body attaches to the cell through both the cell _________and the cell ___________.

39. What protein makes up bacterial flagella?

40. Tell how these types of bacteria differ from each other:

     a. Monotrichous

     b. Lophotrichous

     c. Amphitrichous

     d. Peritrichous

41. What type of bacteria is this?

42. What are bacterial pili?

 

43. How do pili compare to flagella in size?

44. Give three functions of pili.

     a.

     b.

     c.

 

Bacterial Shapes

45. Name and describe 5 shapes used to classify bacteria. 

     a.

     b.

     c.

     d.

     e.

46. What does each of these prefixes tell you about the bacteria’s shape:

     a. Diplo-

     b. Strepto-

     c. Staphylo-

47. Sketch the shape of these bacteria:

     a. Coccus

     b. Bacillus

     c. Spirillium

     d. Diplococcus

     e. Streptococcus

     f. Staphylococcus

     g. Diplobacillus

48. E. coli is classified as what shape bacteria?

Bacterial Kingdoms

49. How do the cell walls of Archaebacteria differ from the true bacteria?

50. How do the cell membranes differ?

51. Are the ribosomes the same?

52. Are the gene sequences the same?

53. Do Archaebacteria require oxygen?

54. How is there environment different from true bacteria?

 

55. What are they commonly called?

56. How many groups make up the ancient bacteria and name them?

 

57. Methanogens live in _____________ environments. What is lacking in this environment?

58. How do methanogens get their energy?

 

59. Name 3 environments in which methanogens are found.

 

 

60. How do methanogens help cows?

 

61. How did the methanogens get their name?

 

62. The __________ ___________ live in very salty environments.

63. How do they get their energy?

 

64. Name two bodies of water in which halophiles are found.

 

65. ______________ live in extremely hot environments.

66. Thermophiles that also live in acidic conditions are called _____________________.

67. Name 3 habitats in which thermophiles are found.

 

Kingdom Eubacteria

68.  Most true bacteria are ____________ and come in ________ basic shapes. Name the shapes.

 

69. Do eubacteria require oxygen?

70. How are they identified?

71. When was gram staining developed?

72. Describe Gram staining.

 

73. What colors do bacterial cell walls stain?

74. Describe the cell wall of Gram positive bacteria.

 

 

75. What color do they stain?

76. Can Gram positive bacteria be treated with antibiotics?

77.Name 5 Gram positive bacteria and tell how they’re used or what they may cause.

     a.

     b.

     c.

     d.

     e.

78. Describe the cell walls of Gram negative bacteria.

 

79. Are antibiotics effective against Gram negative bacteria?

80. Some photosynthetic Gram negative bacteria make ___________ instead of oxygen.

81. How do some Gram negative bacteria help plants?

82. Where can Rhizobacteria be found and what is their job?

 

83. _____________ are parasitic bacteria carried by ticks that may cause ___________ disease or _____________ _______________ _____________ fever.

84. Cyanobacteria are Gram ____________ and carry on ______________ to make food.

85. What is the common name for cyanobacteria?

86. What two main pigments do cyanobacteria contain?

87. What colors are cyanobacteria?

 

88. _______________ is a cyanobacterium that grows in chains.

89. Name the specialized structures on cyanobacteria that help fix nitrogen.

90. How do cyanobacteria cause eutrophication?

 

91. Spirochetes are Gram __________ bacteria that move by ___________.

92. Describe the motion of spirochetes.

93. Do all spirochetes need oxygen?

94. Spirochetes may be _______________, _______________, or symbiotic.

95. What are enteric bacteria? Give an example.

 

96. _______________ is an enteric bacterium that causes food poisoning.

97. How do chemoautotrophic bacteria get their energy?

 

Nutrition, Respiration, and Reproduction

98. Name and describe 4 modes of nutrition in bacteria.

     a.

     b.

     c.

     d.

99. Explain each of the following methods of respiration in bacteria.

     a. Obligate Aerobes-

 

     b. Obligate Anaerobes-

 

     c. Facultative Anaerobes-

 

100. Anaerobes carry on ______________ to release energy from food, while aerobes carry on ____________ _______________.

101. Bacteria reproduce asexually by what method?

102. Before the cell can divide, what must happen?

103. Is binary fission a slow or fast process?

104. How do the new cells compare with each other after binary fission? What are they called?

 

105. Bacteria can reproduce sexually by ________________.

106. Describe how conjugation occurs.

 

107. What is the function of pili in conjugation?

108. How do the new cells compare to each other after conjugation?

109. When can bacteria produce spores and why?

 

110. What are the spores called?

111. How long can an endospore survive?

112. Why are endospores such a problem in health care facilities and in the canning industry?

 

113. Bacteria can genetically change by _________________ and ____________________.

114. Disease-causing bacteria may become ______________ _____________ when they genetically change.

115. How do bacteria transform?

 

116. Describe transduction in bacteria and give an example of a product made by bacteria using this method.

 

Pathenogenic Bacteria

117. What are pathogens?

 

118. Pathogens may cause ____________.

119. What are toxins?

 

120. What is the difference between endotoxins and exotoxins?

 

121. Name a bacterium that produces each type of toxin.

     a. Endotoxin?

     b. Exotoxin?