microbiology

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nloput
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41304
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microbiology
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2010-10-12 03:22:39
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microbiology
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  1. Nutrition
    Chemical substances are acquired from the environment and usedin cellular activities
  2. Essential nutrients
    Must be provided to an organism
  3. Macronutrients
    • • Required in large quantities
    • • Play principal roles in cell structure and metabolism
    • • Proteins, carbohydrates
  4. Micronutrients or trace elements
    • • Required in small amounts
    • • Involved in enzyme function and maintenance of protein structure
    • • Manganese, zinc, nickel2
  5. Organic nutrients
    • Contain carbon and hydrogen atoms and are usually theproducts of living things
    • Methane (CH4), carbohydrates, lipids, proteins, and nucleicacids
  6. Inorganic nutrients
    • Atom or molecule that contains a combination of atoms other than carbon and hydrogen
    • Metals and their salts (magnesium sulfate, ferric nitrate,sodium phosphate), gases (oxygen, carbon dioxide) andwater
  7. Chemical Analysis of Microbial Cytoplasm
    • – 70% water
    • – Proteins
    • – 96% of cell is composed of 6 elements
    • :• Carbon
    • • Hydrogen
    • • Oxygen
    • • Phosphorous
    • • Sulfur
    • • Nitrogen
  8. • Sources of Essential Nutrients
    • – Carbon
    • – Nitrogen
    • – Oxygen
    • – Hydrogen
    • – Phosphorous (Phosphate Sources)
    • – Sulfur
  9. Heterotroph
    • • Must obtain carbon in an organic form made by otherliving organisms
    • • Such as proteins, carbohydrates, lipids, and nucleicacids
  10. Autotroph
    • • An organism that uses CO2 as its carbon source
    • • Not nutritionally dependent on other living things
  11. Nitrogen Sources
    • – Main reservoir is nitrogen gas (N2)
    • • 79% of earth’s atmosphere is N2– Nitrogen is part of the structure of proteins, DNA, RNA andATP
    • • These are the primary source of N for heterotrophs– Some bacteria and algae use inorganic N sources
    • • NO3-, NO2-, or NH3– Some bacteria can fix N2.– Regardless of how N enters the cell, it must be converted toNH3
    • • The only form that can be combined with carbon to synthesize aminoacids, etc.
  12. Oxygen Sources
    • – Major component of carbohydrates, lipids, nucleicacids, and proteins
    • – Plays an important role in structural and enzymaticfunctions of cell
    • – Component of inorganic salts (sulfates,phosphates, nitrates) and water
    • – O2 makes up 20% of atmosphere
    • – Essential to metabolism of many organisms
  13. Hydrogen Sources
    • – Major element in all organic compounds andseveral inorganic ones (water, salts, and gases)
    • – Gases are produced and used by microbes
    • – Roles of hydrogen:
    • • Maintaining pH
    • • Acceptor of oxygen during cell respiration
  14. Phosphorous (Phosphate Sources)
    • – Main inorganic source is phosphate (PO4-3)
    • • Derived from phosphoric acid (H3PO4) found in rocks andoceanic mineral deposits
    • – Key component of nucleic acids, essential togenetics
    • – Serves in energy transfers (ATP)
  15. Sulfur Sources
    • – Widely distributed in environment, rocks;sediments contain sulfate, sulfides, hydrogensulfide gas and sulfur
    • – Essential component of some vitamins and the amino acids: methionine and cysteine
    • – Contributes to stability of proteins by forming disulfide bonds
  16. Other Nutrients Important in MicrobialMetabolism
    • – Potassium – essential to protein synthesis and membrane function
    • – Sodium – important to some types of cell transport
    • – Calcium – cell wall and endospore stabilizer
    • – Magnesium – component of chlorophyll; membraneand ribosome stabilizer
    • – Iron – component of proteins of cell respiration
    • – Zinc, copper, nickel, manganese, etc.
  17. Growth Factors: Essential Organic Nutrients
    • • Organic compounds that cannot be synthesized by an organism because they lack the genetic and metabolic mechanisms to synthesize them
    • • Growth factors must be provided as a nutrient– Essential amino acids, vitamins
  18. Main determinants of nutritional type are
    • – Carbon source – heterotroph, autotroph
    • – Energy source
    • • Chemotroph – gain energy from chemical compounds
    • • Phototrophs – gain energy through photosynthesis
  19. • Autotrophs and Their Energy Sources
    • – Photoautotrophs
    • • Oxygenic photosynthesis
    • • Anoxygenic photosynthesis
    • – Chemoautotrophs
    • • lithoautotrophs
    • • survive totally on inorganic substances
    • – Methanogens
    • • A kind of chemoautotroph
    • • Produce methane gas under anaerobic conditions
  20. • Heterotrophs and Their Energy Sources
    • – Majority are chemoheterotrophs
    • • Aerobic respiration– Two categories
    • • Saprobes– Free-living microorganisms that feed on organic detritusfrom dead organisms
    • – Opportunistic pathogen
    • – Facultative parasite
    • • Parasite– Derive nutrients from host
    • – Pathogens
    • – Some are obligate parasites
  21. • Passive transport
    • – does not require energy; substances exist in a gradient and move from areas of higher concentration toward areas of lower concentration
    • – Diffusion
    • – Osmosis – diffusion of water
    • – Facilitated diffusion – requires a carrier
  22. • Active transport
    • – requires energy and carrier proteins;gradient independent
    • – Active transport
    • – Group translocation – transported molecule chemically altered
    • – Bulk transport – endocytosis, exocytosis, pinocytosis
  23. • Niche
    – Totality of adaptations organisms make to theirhabitat
  24. • Environmental factors affect the function of metabolic enzymes
    • Factors include
    • – Temperature
    • – Oxygen requirements
    • – pH
    • – Osmotic pressure
    • – Barometric pressure
  25. • Three Cardinal Temperatures
    • – Minimum temperature – lowest temperature that permits a microbe’s growth and metabolism
    • – Maximum temperature – highest temperaturethat permits a microbe’s growth and metabolism
    • – Optimum temperature – promotes the fastest rate of growth and metabolism
  26. • Three Temperature Adaptation Groups
    • – Psychrophiles – optimum temperature below15oC; capable of growth at 0oC
    • – Mesophiles – optimum temperature 20o-40oC;most human pathogens
    • – Thermophiles – optimum temperature greater than 45oC
  27. • Gas Requirements
    • – Oxygen– As oxygen is utilized it is transformed into several toxic products:
    • • Singlet oxygen (1O2), superoxide ion (O2-), peroxide (H2O2), and hydroxyl radicals (OH-)
    • – Most cells have developed enzymes that neutralize these chemicals:
    • • Superoxide dismutase, catalase– If a microbe is not capable of dealing with toxic oxygen, it is forced to live in oxygen free habitats
  28. 1 Aerobe
    2 Obligate aerobe
    3 Facultative anaerobe
    4 Microaerophilic
    5 Anaerobe
    6 Obligate anaerobe
    7 Aerotolerant anaerobes
    • 1 utilizes oxygen and can detoxify it
    • 2 cannot grow without oxygen
    • 3 utilizes oxygen but can also growin its absence
    • 4 utilizes oxygen but can also growin its absence
    • 5 does not utilize oxygen
    • 6 lacks the enzymes to detoxify oxygenso cannot survive in an oxygen environment
    • 7 do not utilize oxygen but can survive and grow in its presence
  29. • Carbon Dioxide Requirement
    • – All microbes require some carbon dioxide in their metabolism
    • – Capnophile – grows best at higher CO2 tensions than normally present in the atmosphere
  30. • Effects of pH
    1 Obligate acidophiles
    2 Alkalinophiles
    • Majority of microorganisms grow at a pH between6 and 8
    • 1 grow at extreme acid pH
    • 2 grow at extreme alkaline pH
  31. • Osmotic Pressure
    1 Halophiles
    2 Osmotolerant
    • Most microbes exist under hypotonic or isotonic conditions
    • 1 require a high concentration of salt
    • 2 do not require high concentration of solute but can tolerate it when it occurs
  32. Other Environmental Factors
    • Barophiles
    can survive under extreme pressure and will rupture if exposed to normal atmospheric pressure
  33. • Symbiotic
    1 Mutualism
    2 Commensalism
    3 Parasitism
    • two organisms live together in aclose partnership
    • 1 obligatory, dependent; both members benefit
    • 2 commensal member benefits,other member neither harmed nor benefited
    • 3 parasite is dependent and benefits;host is harmed
  34. Non-symbiotic
    1 Synergism
    2 Antagonism
    • organisms are free-living;relationships not required for survival
    • 1 members cooperate to produce aresult that none of them could do alone
    • 2 actions of one organism affect the success or survival of others in the same community (competition)
    • • Antibiosis
  35. • Interrelationships Between Microbes andHumans
    • Human body is a rich habitat for symbiotic bacteria, fungi, and a few protozoa
    • normal microbial flora
    • Commensal, parasitic, and synergistic relationships
  36. • Biofilms
    • result when organisms attach to a substrate by some form of extracellular matrix that binds them together in complex organized layers
    • • Dominate the structure of most natural environments on earth
    • • Communicate and cooperate in the formation and function of biofilms – quorum sensing
  37. • Microbial growth occurs at two levels
    • Division of bacterial cells occurs mainly throughbinary fission (transverse)
    • – Growth at a cellular level with increase in size
    • – Increase in population
    • – Parent cell enlarges, duplicates its chromosome, and forms a central transverse septum dividing the cell into two daughter cells
  38. • Rate of Population Growth
    • – Time required for a complete fission cycle is called the generation, or doubling time
    • – Each new fission cycle increases the population by a factor of 2
    • – exponential growth– Generation times vary from minutes to days
  39. • The Population Growth Curve
    1 Lag phase
    2 Exponential growth phase
    3 Stationary phase
    4 Death phase
    • 1 “flat” period of adjustment, enlargement; little growth
    • 2 a period of maximum growth will continue as long as cells have adequate nutrients and a favorable environment
    • 3 rate of cell growth equals rate of celldeath caused by depleted nutrients and O2, excretion oforganic acids and pollutants
    • 4 as limiting factors intensify, cells die exponentially
  40. Methods of Analyzing Population Growth
    • • Turbidometry – most simple
    • • Degree of cloudiness, turbidity, reflects the relative population size
    • • Enumeration of bacteria:
    • – Viable colony count
    • – Direct cell count
    • – count all cells present;automated or manual
  41. Metabolism
    1 Catabolism
    2 Anabolism
    • all chemical and physical workings of a cell
    • 1 degradative; breaks the bonds of larger molecules forming smaller molecules; releases energy
    • 2 biosynthesis; process that forms larger macromolecules from smaller molecules; requires energy input
  42. Enzymes
    • are biological catalysts
    • –Lower the energy of activation
    • – The energy of actvation is the resistance to a reaction
    • – The enzyme is not permanently altered in the reaction
    • • Enzymes use a specific lock and key fit with substrate
  43. 1 Simple enzymes
    2 Holoenzymes
    • 1 consist of protein alone
    • 2 contain protein and nonprotein molecules
    • Apoenzyme-protein portion
    • Cofactors–nonprotein portion
    • • Metallic cofactors: iron,copper,magnesium
    • Coenzymes,organicmolecules:vitamins
  44. • Enzyme Specificity and the Active Site
    1 active site,orcatalytic site
    2 induced fit
    • Appropriate reaction occurs;product is formed and released
    • 1 Site for substrate binding
    • 2 A temporary enzyme-­‐substrate union occurs when substrate moves into active site


    • 1. Transported extracellularly
    • They break down large food molecules or harmful chemicals
    • Cellulase, amylase, penicillinase
    • 2. retained intracellularly and function there
    • Most enzymes are endoenzymes
  45. 1. Constitutive enzymes
    2. Regulated enzymes
  46. 1. Always present
    • Always produced in equal amounts or at equal rates
    • Enzymes involved in glucose metabolism
    • 2.Not constantly present
    • Production is turned on (induced) or turned off (repressed) in response to changes in concentration of the substrate
  47. Synthesis or condensation reactions
  48. – Anabolic reactions to form covalent bonds
    • – Between smaller substrate molecules
    • – Require ATP
    • – Release one molecule of water for each bond formed
  49. Hydrolysis reactions
  50. – Catabolic reactions that break down substrates into small molecules
    – Requires the input of water to break bonds
  51. Sensitivity of Enzymes to Their Environment
  52. Activity of an enzyme is influenced by cell’s environment
    • • Temperature
    • – Reduce activity
    • – Denature
    • • pH
    • – Reduce activity
    • – Denature
    • • Substrate concentration
    • – Reaches a saturation point
  53. Direct Controls on the Actions of Enzymes
    1. Competitive inhibition
    2. Noncompetitive inhibition
    3. Enzyme repression
    4. Enzyme induction
    • 1. Competition for the active site
    • 2. Allosteric enzymes
    • The binding by a substance to a site other than the active site
    • 3.Inhibits at the genetic level by controlling synthesis of key enzymes
    • 4. Enzymes are made only when suitable substrates are present
  54. 1.Energy
    2.Forms of energy
  55. 1. The capacity to do work or to cause change
    2. Thermal, radiant, electrical, mechanical, atomic, and chemical
  56. Cell Energetics
    1. Endergonic reactions
    2. Exergonic reactions
  57. Cells manage energy in the form of chemical reactions that make or break bonds and transfer electrons
    • 1. consume energy
    • 2. release energy
  58. Redox reactions
    • Always occur in pairs
    • There is an electron donor and electron acceptor which constitute a redox pair
    • Process salvages electrons and their energy
    • Released energy can be captured to phosphorylate ADP or another compound
  59. Electron and Proton Carriers
    • Repeatedly accept and release electrons and hydrogen to facilitate the transfer of redox energy
    • – Most carriers are coenzymes:
    • • NAD+
    • • FAD
    • • NADP
    • • coenzyme A
    • • Compounds of the respiratory chain
  60. Adenosine Triphosphate: ATP
    • – Metabolic “currency”
    • – Three part molecule consisting of
    • • Adenine
    • – a nitrogenous base
    • • Ribose
    • – a 5--‐carbon sugar
    • • 3 phosphate groups
    • – ATP utilization and replenishment is a constant cycle in active cells
    • – Removal of the terminal phosphate releases energy
  61. ATP can be formed by three different mechanisms
    • 1. Substrate -level phosphorylation
    • – transfer of phosphate group from a phosphorylated compound (substrate) directly to ADP
    • 2. Oxidative phosphorylation – series of redox reactions occurring during respiratory pathway
    • 3. Photophosphorylation – ATP is formed utilizing the energy of sunlight
  62. Primary catabolism of fuels (glucose) proceeds through a series of three coupled pathways
  63. 1. Glycolysis
    • 2. Kreb’s cycle
    • 3. Respiratory chain, electron transport
  64. Nutrient processing is varied, yet in many cases is based on three catabolic pathways that convert glucose to CO2 and gives off energy
    • 1.Aerobic respiration
    • – glycolysis, the Kreb’s cycle, respiratory chain
    • 2.Anaerobic respiration
    • – glycolysis, the TCA cycle, respiratory chain; molecular oxygen is not final electron acceptor
    • 3.Fermentation
    • – glycolysis, organic compounds are the final electron acceptors
  65. Aerobic Respiration
  66. – Series
    • or
    • enzyme--‐catalyzed
    • reac+ons
    • in
    • which
    • electrons
    • are
    • transferred
    • from
    • fuel
    • molecules
    • (glucose)
    • to
    • oxygen
    • as
    • a
    • final
    • electron
    • acceptor
    • Glycolysis – glucose (6C) is oxidized and split into 2 molecules of pyruvic acid (3C), NADH is generated
    • TCA – processes pyruvic acid and generates 3 CO2 molecules , three NADH and one FADH2are generated
    • Electron transport chain – accepts electrons from NADH and FADH; generates energy through sequential redox reactions called oxidative phosphorylation
  67. ATP Totals
    1.Glycolysis
    2.Pyruvate to Acetyl CoA
    3.Kreb’s cycle
    4.Total
    • 1. 2 NADH = 6 ATP
    • Plus 2 ATP
    • 2. 2 NADH=6 ATP
    • 3. 6 NADH= 18 ATP
    • 2 FADH2 = 4 ATP
    • Plus 2 ATP
    • 4. 38 ATP
  68. Anaerobic Respiration
    • Functions like aerobic respiration
    • • Except it utilizes other electron acceptors rather than oxygen
    • • Nitrate (NO3 --‐) and nitrite (NO2 --‐)
    • • Used by anaerobes and facultative anaerobes

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