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2012-11-30 16:49:17
Sunday Week

Sunday Week 1
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  1. Cellular metabolism
    refers to all of the chemical processes that occur inside living cells.
  2. All biological processes require ?
  3. Catalysts
    are not used up or changed in any way during the reaction
  4. What do Enzymes consist of
    may be pure proteins or proteins  plus cofactors such as metallic ions or coenzymes, organic group that contain groups derived from vitamins
  5. Enzyme + Substrate = 
    ES complex
  6. The active site is the location on the enzyme where 
    the substrate fits
  7. An enzyme works by
    binding with its substrate, the molecule whose reaction is catalyzed
  8. How are Enzymes are highly specific
    There is an exact molecular fit between enzyme and substrate.

    Some enzymes work with only one substrate, others work with a group of molecules
  9. Catabolic (degradation) reaction catalyzed by 
    enzyme A
  10. Anabolic (synthesis) reaction catalyzed by 
    enzyme B
  11. Biological reactions require_______to proceed
  12. molecule with stored energy 
  13. See Page 16 sunday week 1
  14. ATP consists of 
    adenosine (adenine + ribose) and a triphosphate group
  15. The bonds between the phosphate groups are
    high energy bonds
  16. An atom that gains an electron has been 
    reduced. Higher energy.
  17. An atom that loses an electron has been 
    oxidized. Oxygen is a common electron acceptor.
  18. Redox reactions always occur in pairs
    –One atom loses the electron, the other gains the electron.
  19. Energy is transferred from one atom to another via 
    redox reactions
  20. Describe cellular respiration
    the oxidation of food molecules to obtain energy
  21. Cellular respiration has two stages what are they
    • 1st: Glycolysis
    • 2nd: Aerobic or anaerobic respiration 
  22. Aerobic respiration 
    in the presence of oxygen
  23. A large amount of ATP is made during 
    aerobic   respiration. 
  24. Anaerobic respiration
    in the absence of oxygen
  25. NAD+ is recycled during the 
    anaerobic process of fermentation.
  26. see page 25 sunday week 1
  27. In aerobic respiration, ATP forms as electrons are
    • harvested, transferred along the electron transport chain
    • and eventually donated to O2 gas.
  28. –Oxygen is required & Glucose is completely broken-down during ?
    aerobic respiration
  29. Glycolysis – coupled reactions used to make 
    • •ATP.
    • –Occurs in cytoplasm
    • –Doesn’t require O2
  30. Oxidation – harvests electrons and uses their energy to power 
    • ATP production.
    • –Only in mitochondria
    • –More powerful
  31. Electron transport chain (ETC) occures
    •Occurs in the mitochondria of eukaryotes and cell membrane of bacteria
  32. Different electron acceptors are used instead of oxygen (sulfur, or nitrate) in
    A. Aerobic Metabolism
    B. Anaerobic Metabolism
    B. Anaerobic Metabolism
  33. Start of Anaerobic respiration is 
    • Glycolisis
    • This means that glycolysis is part of aerobic and anaerobic respiration

  34. Two steps in anaerobic respiration:

    • Glycolysis
    • Fermentation
  35. In the absence of oxygen, the end-product of glycolysis is
    pyruvate, is used in fermentation.
  36. Fermentation replenishes more 
    NAD+  and allows glycolysis to start again
  37. During glycolysis, NAD+ gets used up
    When this happens ________will stop.
  38. Yeasts, single-celled fungi, produce 
    • alcohol
    • Present in wine & beer.
    • Alcoholic fermentation
  39. The term microbial growth refers to the 
    growth of a population (or an increase in the number of cells), not to an increase in the size of the individual cell.
  40. Cell division leads to 
    the growth of cells in the population 
  41. Microbial control of growth is important for
    • –infection control
    • –growth of industrial and biotech organisms
  42. Factors Regulating Microbial Growth
    • •Nutrients
    • •Environmental conditions: temperature, pH, osmotic pressure
    • •Generation time
  43. Saprobe – lives on 
    organic matter of dead organisms
  44. Parasite – lives on 
     organic matter of living host = pathogens
  45. Environmental Factors Influencing Growth
    • •Temperature
    • •O2
    • •pH
    • •Osmotic Pressure (tonicity)
    • •Moisture
    • •Hydrostatic pressure
    • •Radiation
    • •Nutrients
  46. most common group of organisms
  47. Top influencing factor in growth range
    Optimum growth temperature is usually near the top of the growth range
  48. Death above the maximum temp. comes from 
    enzyme inactivation 
  49. Thermophiles used in 
    • Many industrial processes involve high heat
    • –450C (113F) is a problem for most enzymes
    • –First Extremophile found in 1972
  50. Psychrophiles functions
    • •Efficient enzymes to work in the cold
    • –Enzymes to work on foods that need to be refrigerated
    • –Perfumes - most don’t tolerate high temperatures
    • –Cold-wash detergents
  51. Oxygen Requirements
    Strict or obligate anaerobes 
    oxygen kills the bacteria; ex. Clostridium tetani
  52. Oxygen Requirements
    Strict or obligate aerobes
    lack of oxygen kills the bacteria; ex. Pserdomonas
  53. Oxygen Requirements
    Facultative anaerobes
    •can shift their metabolism (anaerobic if oxygen is absent or aerobic if oxygen is present); ex. E.coli, Staphylococcus
  54. Oxygen Requirements
    the bacteria don’t use oxygen, but oxygen doesn’t harm them; ex. Lactobacillus
  55. Oxygen Requirements
    •like low oxygen concentrations and higher carbon dioxide concentrations; ex. Campylobacter
  56. See pg 55
  57. acidophiles
    (acid-loving) – grow best at a  pH of 1 to 5.4; Ex. Lactobacilllus (ferments milk)
  58. Neutrophiles
    exist from pH to 5.4 to 8.5; most bacteria that cause human disease are in this category.
  59. Alkaliphiles
    •(base loving) – exist from pH to 7.0 to 11.5; ex. Vibrio cholerae (causes cholera)
  60. •Enzymes used to increase efficiency of animal feeds
    –enzymes help animals extract nutrients from feed
    –more efficient and less expensive
  61. “Stonewashed” pants
    –Alkaliphilic enzymes soften fabric and release some of the dyes, giving worn look & feel
  62. •Detergents
    • –Enzymes dissolve proteins or fats
    • –Detergents do not inhibit alkaliphilic enzymes
  63. Halophiles
    salt lovers inhabit the oceans.
  64. Acidophiles and Alkaliphiles sometimes excrete 
    protective substances and enzymes
  65. Acidophiles often lack 
    cell wall
  66. used as food additives or as food-coloring agents
    The extraction of carotene from carotene rich halobacteria and halophilic algae 
  67. bacteria that can exist in a dormant state in a dry environment
    Spores of sport-forming bacteria 
  68. Hydrostatic pressure
    •Pressure exerted by standing water (ex. lakes, oceans, etc.)
  69. Some bacteria have enzyme systems that can repair some mutations
  70. Asexual two types 
    • Binary fission 
    • Budding
    • see pg 69
  71. Budding
    bacteria and some eukaryotes (including yeasts) may also replicate by budding, forming a bubble-like growth that enlarges and separates from the parent cell
  72. Name A microbial lab culture typically passes through 4 distinct, sequential phases of growth that form the standard bacterial growth curve
    • A.    Lag Phase
    • B.    Log Phase
    • C.   Stationary Phase
    • D.   Death Phase 
  73. Lag Phase
    • •The number of cells doesn't increase.
    • •However, considerable metabolic activity is occurring as the cells prepare to grow.   
    • •This phase may not occur, if the cells used to inoculate a new culture are in the log phase & provided conditions are the same.
  74. Lag Phase
    • •Cell numbers increase exponentially
    • •During each generation time, the number of cells in the population increases by a factor of two. 
    • •The number of microbes in an exponentially increasing population increases slowly at first, then extremely rapidly. 
    • •Organisms in a tube of culture medium can maintain log growth for only a limited time, as nutrients are used up, metabolic wastes accumulate, microobes suffer from oxygen depletion.
  75. Stationary Phase
    • •The number of cells doesn't increase, but changes in cells occur
    • •Cell become smaller and synthesize components to help them survive longer periods without growing (some may even produce endospores)
    • •The signal to enter this phase may have to do with overcrowding (accumulation of metabolic byproducts, depletion of nutrients, etc.).
  76. Death Phase
    • •In this phase, cells begin to die out. 
    • •Death occurs exponentially, but at a low rate. 
    • •Death occurs because cell have depleted intracellular ATP reserves. 
    • •Not all cells necessarily die during this phase!
  77. Summary of Phase of Growth

    –Adapt to nutrients
  78. Summary of Phase of Growth
    Active Growth 
  79. Summary of Phase of Growth
    Death = Growth rate
  80. Summary of Phase of Growth
    • Nutrients consumed 
    • ph too low
  81. Indirect Measurement
    Measures a property of the mass of cells and then ESTIMATE the number of microbes
  82. A spectrophotometer can measure how 
    much light a solution of microbial cell transmits; the greater the mass of cells in the culture, the greater its turbidity (cloudiness) and the less light that will be transmitted.
  83. Metabolic Activity
    • •The rate of utilization of a substrate, such as oxygen or glucose.
    • •The rate of formation of metabolic products, such as gases or acids, that a culture produces.
  84. Metabolic Activity
    •The rate of reduction of certain dyes.
  85. Direct Measurements 
    Give more accurate measurements of numbers of microbes.
  86. Direct Culture Counts
    • •electronic counter
    • • rapid & accurate only if bacterial cells are the only particles present in the solution.
    • •[gives a total count - live & dead cells].
  87. Plate Count
    Bacterial colonies are viewed through the magnifying glass against a colony-counting grid; called a
    • Quebec colony counter 
    • [gives a viable count]
  88. Liquid medium is best when you want to 
    rapidly increase the concentration of the organism or when you want to grow motile cells
  89. Culture plates are used when you want to test 
    • (1) antibiotic sensitivity
    • (2) estimate culture concentrations from environmental samples
    • (3) isolate individual colonies from environmental
    • samples. 
  90. Liquid medium is solidified by using
    agar (agarose) and poured as a thin layer in the bottom of a culture dish (also sometimes called petri plate)
  91. Discribe Differential Media
    has an ingredient that causes an observable change in the medium when a particular biochemical reaction occurs (ex. a color or pH change).
  92. Thioglycollate medium
    •oxygen-binding agent added to the medium to prevent oxygen from exerting toxic effects on anaerobes
  93. Actions of Microbial Control Agents
    • •Alteration of membrane permeability
    • •Damage to proteins and nucleic acids
    • •Mutation
  94. Physical Control Methods
    • •Temperature
    • •Desiccation
    • •Osmotic pressure
    • •Radiation
  95. Desiccation =
    The removal of water
  96. Moist Heat
    • •Coagulates proteins by breaking hydrogenbonds
    • •Boiling: 10 minutes kills most pathogens (hepatitis
    • virus needs 30 minutes and spores need 20 hours!)
    • •Autoclave: 15 psi for 15 minutes (121° C)
  97. Pasteurization
    • •Used when taste of product would be damaged by longer heating: lowers numbers of pathogens (63°C for 30 minutes)
    • •High-temperature short-term (HTST) pasteurization (72°C for 15 seconds)
  98. lyophilization =
    frezze druing
  99. Types of Ionizing radiation: 
    • gamma rays,
    • X rays,
    • high energy electron beams – most energetic
  100. Describe UV Radiation
    • •Thymine dimers in DNA
    • •Germicidal lamps, vaccine disinfection
    • •Not penetrating
    • •Can damage eyes
  101. Microwaves
    • •Very little effect on microbes
    • •Microwave ovens kill vegetative pathogens by heating
    • •Solid foods heat unevenly
  102. Chemical Methods
    • •Disinfectants and antiseptics
    • •Surface-active agents (surfactants)
    • •Chemical food preservatives
    • •Aldehydes
    • •Gas sterilization
    • •Oxidizing agents
    • •[Antibiotics]
  103. Disinfectants
    • •Kill/inhibit growth of  microbes on surfaces
    • •Phenols and phenolics: damage lipid membranes
    • –Active in presence of organic matter
    • –Stable
    • –Persist for long periods after application
  104. Phenol =
    OH also called carbolic acid
  105. Antiseptic Alcohol
    • •protein denaturation and membrane damage
    • – evaporate quickly
    • – ethanol and isopropanol
    • – [not effective if taken internally]
  106. Heavy Metals
    •Denature proteins
    • silver nitrate (topical cream)
    • mercuric chloride (paint)
    • copper sulfate (algaecide)
    • zinc (mouthwash, paints
  107. Surfactants
    • •Decrease surface tension
    • •Soaps and detergents
    • – Quaternary ammonium compounds : microbicidal
  108. Aldehydes
    • •Formaldehyde (formalin) and glutaraldehyde
    • –Disinfect instruments
    • –Used to preserve tissues for pathology
    • –Cross-link protein molecules
  109. Oxidizing Agents
    • •Ozone
    • •Hydrogen peroxide
    • •Benzoyl peroxide
    • •Peracetic acid
    • – Interfere with metabolism (especially of
    • anaerobes)
  110. Types Bacterial Genetics
    • •Genetic recombination
    • •Genetic engineering
    • •Microbial genomics
  111. Genotype =
    • •The genetic compliment of an organism
    • •Types of genotypic changes
    • –Mutation
    • –Conjugation
    • –Transduction
    • –Transformation
  112. Phenotype=
    • •The genetic expression of an organism
    • •Types of phenotypic expressions
    • –Morphology
    • –Cultural
    • –Physiological
  113. The Bacterial Chromosome
    •DNA is arranged as a single molecule with no histones present, and with no dominance or recessiveness in the genes.
  114. histones
    are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes
  115. Plasmids
    • •Fragments of DNA in the cytoplasm
    • •R Factors - confer drug resistance
    • •Bacteriocins -proteins toxic to other bacteria and human cell
    • •Many plasmids are found in Gram-Negative bacteria
  116. Bacterial Mutation
    • Spontaneous mutations = Example: Salmonella
    • strains antibiotic resistance
    • Induced mutations = Chemical
    • or Physical agents enhance mutation rate
  117. Repair Mechanisms
    • –Mismatch repair “proofreads”
    • –Damage repair
    • »Excision repair
    • »Dimer repair (UV light)
  118. Transformation (Griffith's experiments)
    DNA transformation involves the transfer of naked DNA into a recipient cell
  119. Conjugation
    Thetransfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells
  120. Transduction
    Is the process by which DNA is transferred from one bacterium to another by a virus.
  121. The lytic cycle is typically considered the 
    main method of viral replication, since it results in the destruction of the infected cell. 
  122. A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA exists as a 
    separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA
  123. Operons
    Genetic regulatory system found in bacteria and their viruses
  124. Genetic Engineering
    • •Genetic engineering involves changing the genetic material in an organism to alter its traits or products
    • •A recombinant DNA molecule contains DNA fragments spliced together from 2 or more organisms 
  125. Genetic Engineering Modern applications
    • •Pharmaceutical production
    • –Insulin, interferon, hormones, vaccines etc.
    • •Genetically engineered plants 
    • •Animal gene alterations
    • •Gene probes
    • •DNA fingerprinting
    • •The human genome initiative
  126. Energy in the form of ATP is produced via 
  127. Growth of microbes depend on the 
    physical and chemical environment
  128. We can utilize microbes for our benefit by altering their 
    •DNA to produce what we want