Biol 251 lecture unit 2

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Biol 251 lecture unit 2
2014-03-12 21:51:20
Microbiology microbial genetics metabolism growth nutrition interactions

Microbiology, microbial genetics, microbial metabolism, microbial growth and nutrition, microbial interactions
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  1. What are the two basic vocabulary terms of genetics?
    Genotype & phenotype
  2. Define genetics
    Information contained in an organism
  3. Define heredity
    The way that genetic information is passed on from one generation to another
  4. Define genotype
    The genetic makeup of the organism
  5. How is genotype different between eukaryotes and prokaryotes?
    • In eukaryotes, genotype is stable through out its life.
    • In prokaryote, genotype often change through out its life as some genes are added on or taken away
  6. Define phenotype
    Physical & metabolic characteristic of the organism (expression of the genotype)
  7. What are the different levels of organization of genetic information?
    • Nucleotides (A, G, c, and T); determine the gene code for the proteins that the organism makes.
    • Gene, a set of nucleotides in the correct order that code for proteins.
    • Chromosome, a structure that contains several genes together.
    • Genome, all the genetic material of an organism (Chromosome & plasmid).
  8. What is the purpose of DNA? How about proteins?
    • DNA tells the cell what it needs to do, how to do it, and when to it.
    • Proteins are molecules (created by the DNA) that carryout the functions and made up the structure of the cell.
  9. Define transcription
    Convert DNA coed into RNA code.
  10. How is a gene copied into a RNA?
    • 1) a specific gene is found on the chromosome (the original copy of a protein code).
    • 2) Then a RNA polymerase attaches the DNA and copy its code into mRNA strand that.
    • 3) once the mRNA is complete, it will continue to be translated into protein.
  11. Define translation
    Convert genetic codes carried by mRNA into protein molecules
  12. Explain the process of translation.
    • mRNA is arranged in groups of 3 nucleotides called codons.
    • tRNA is arranged in groups of 3 nucleotides called anti codons (the opposite match of codons) and attach to certain amino group.
    • In a ribosome, the mRNA is lined up and tRNA is inserted and they gets close to each other.
    • The mRNA runs through the ribosome and when the codons and anti-codons are matched up, the amino groups at the end of the tRNA bound to each other in a covalent bonds forming a protein molecule.
    • The protein molecule then, go under farther modification of folding and shaping.
  13. What happens if something gos wrong along the way during transcription, translation, or gene sequence?
    The amino groups in the protein molecules will be changed. This will altered the protein molecule structure & function
  14. Why do we care about microbial proteins?
    Proteins molecules are responsible to structure and metabolism functions of living organisms
  15. Define gene expression
    Production of proteins from the codes in the DNA
  16. What is the purpose of gene regulation?
    Why is that important for the bacteria/organism?
    • Genes are regulated to produce proteins when they are needed.
    • If the bacteria will produce all the proteins that are coded in its DNA all the time, it will run out of nutrients & energy and die.
  17. What are repressors? 
    How are they work?
    • Repressors are small molecules that keep genes from making proteins when the organism do not need them (gene regulation).
    • They attached to the DNA and blocking RNA polymerase from getting to the code of a certain protein at certain times.
    • When certain nutrient is available and it requires certain protein to break it down, a special molecule attaches to the reprasor of that protein and it removed from the DNA.
  18. How the knowledge of how repressors work can be beneficial to us?
    If we want to stop a bacteria from secreting enzyme that is toxic to us, we can find a way to keep its repressor on the DNA
  19. What is Binary fission?
    What are its steps?
    Binary fission is the way that prokaryotes reproduce themselves.

    • 1. the original cell duplicates its DNA and splits the two copies of the chromosomes to two far ends of the cell by its cytoskeleton.
    • 2. the rest of the cell Materials (ribosome cytoplasm, inclusion bodies, etc.) start to split.
    • 3. the cell itself split into two identical cells
  20. What may be the results of mistakes in DNA replication?
    Even if only one nucleotide is changed it can result with totally different protein
  21. Define mutations
    Changes in the in the genes of the organism (genotype) may effect their function & appearance characteristics (phenotype)
  22. What are the two types of mutations that effect protein production?
    • Point mutation
    • Frameshift mutation
  23. How point mutation will effect proteins structure and function.
    • Point mutation caused by insertion of a nucleotide in the wrong place on the DNA.
    • This will lead to one of the following results:
    • Nonsense mutation: stop the production of the protein before completion (UAG).
    • Missense mutation: change the amino group in the protein molecule.
  24. How frameshift mutation will effect protein production?
    A deletion or addition of nucleotide in the DNA will change the arrangement of the gene that will change the dodons (3 nucleotides) when copied into RNA from the point of the frameshift.
  25. What are the three possible outcomes of cell functions as result of mutation?
    • Harmful (most of the times) Changes in protein or stop their production will cause necessary functions of the cell to stop working and may kill the cell.
    • Harmless (some times) may change the appearance of the organism such as pigment and shape.
    • Very helpful (sometimes) can make a protein that have antibiotic resistance in bacteria for example
  26. What are the four genetic recombinations in prokaryotes?
    • Conjugation: Sharing useful genes between two living cells.
    • Transformation: Uptake of DNA from a dead cell.
    • Transduction: Spread of DNA between cells by bacteriophage.
    • Transposons: Gene that moving from one location to another within the cell.
  27. What are the steps of conjugation?
    • 1. start with two prokaryote cells. The donor has plasmid with special trait (fimbriae for example) and the recipient cell doesn't.
    • 2. The donor cell copy its plasmid, form a pilus, connect the pilus to a special site on the recipient cell, and send a copy of the plasmid to the recipient cell.
    • 3. Once the plasmid is transferred, the recipient cell develops the same trait as the donor.
  28. What happen in transformation?
    • 1. We start with one dead bacteria and one live bacteria.
    • 2. The dead bacteria is falling apart and all its intracellular parts now are out in the extracellular environment.
    • 3. alive bacteria close by attaches to sequences of DNA of the dead bacteria by special receptors on its plasma membrane.
    • 4. then the live bacteria brings these sequences of DNA inside its cytoplasm and either add in its chromosome/plasmid o replace them with some of its own DNA sequences.
  29. Why transformation can be dangerous for us?
    Because if two types of pathogenic bacteria that are treated with two different types of antibiotics infect our body at the same time, may pick up each other DNA sequences that make them resistance to both types of antibiotics as some of them start to die.
  30. How transduction occur?
    • 1. Start with tow living bacteria and a bacteriophage.
    • 2. The bacteriophage infected bacteria A (donor).
    • 3. When the bacteriophage copies its genetic material, some of the bacteria's DNA get mixed with it.
    • 4. As the new bacteriophage leave bacteria A and infect bacteria B (receptor), it transfer the genes from bacteria A to bacteria B.
    • 5. bacteria B cannot tell if these genes are good or bad for it and replace the with its own genes.
  31. Explain how transposons occur?
    • 1. When gene starts to get expressed it cause transposon enzyme to cut the gene out.
    • 2. then this gene is reinserted somewhere else in the chromosome or plasmid.
    • 3. it may inserted in the middle of another gene cause it to stop or alter the protein molecule coded for.
  32. True or false; transposons occur only in prokaryotes.
    • False
    • Also in eukaryotes
  33. Which are the most basic types of molecules that require for metabolic reactions in microorganism?
    Nutrients, enzymes (proteins), and energy molecules
  34. Define metabolism
    • All the chemical & physical reactions that happen in the cell which allow it to stay alive and to change things.
    • These changes are done in two ways: catabolism, breaking down big molecules into smaller ones.
    • Anabolism, building up structures from smaller components.
  35. What role do enzymes play in metabolism?
    Which are the two ways they do it?
    • They help lower the amount of energy that the cell need to start metabolic reaction by the one of following ways.
    • they bring two substrates (reactants) close together.
    • They change the shape of the substrates.
  36. Define catalyst
    Enzyme is a catalyst. A molecule that involve in a chemical/metabolic reaction but does not change itself.
  37. What is the purpose of the active site of an enzyme?
    • A site on the enzyme that reactants will attached to and a chemical reaction will take place.
    • It will either bring two reactants together or split them apart but in both ways it will create a product.
  38. Does any enzyme can work on any random reactant?
    • No.
    • Usually enzymes are specific that can work only on few reactants.
  39. Some bacteria have enzymes that are not very specific. How can we use it for our advantage?
    • If bacteria have a non-specific enzyme and its environment lacks its  preferred nutrient, it will break down other substrates.
    • People use these bacteria in bioremediation to break down  as oil or chemical spills.
  40. Define cofactor
    • Inorganic molecule (ofter metals).
    • Often times activates the enzyme.
    • Many times have an extra or missing electron that use for chemical reaction to take place.
    • Also may help chemical reaction take place by bring substrates close together.
  41. Define coenzyme
    • Most of the time an organic molecule and some type of vitamin.
    • They alter the enzyme shape by fit into their active site. This allow the substrate to fit better and help chemical reaction to take place
  42. What are exoenzymes? what is their purpose?
    • Enzymes that bacteria secreted outside to the extracellular environment.
    • Their purpose is to break down big (nutrients) molecules into smaller ones that can cross the membrane and get inside the cell.
  43. What are endoenzymes? what is their purpose?
    • Enzymes that kept inside the cell.
    • Break down nutrients to make ATP & build up molecules that that are used for structure of the cell.
  44. Which are the two main groups of exoenzymes secreted by pathogens?
    Virulence factors & toxins
  45. What are the two divisions of enzyme regulation? How do they function?
    • Competitive inhibition: Non-reactive molecule that bind to the active site of the enzyme and block the substrate.
    • Noncompetitive inhibition: non-reactive molecule that attached to the enzyme (not to the active site) and changes its shape, so substrate cannot fit in the active site
  46. Define energy
    The ability to do work or to cause changes
  47. Which two environmental sources contain energy that the cell can use? How cells extract energy from the environment?
    • Light energy & Chemical energy.
    • Cells convert light energy to chemical energy and chemical energy to another form of chemical energy by breaking or making molecule bonds (freeing & moving electrons around). the cell will keep do this until it gets the type of energy that it can use (ATP)
  48. Explain oxidation/reduction reaction (redox reaction).
    • Electrons are transferred from one molecule to another (that usually will release H+). Two molecules involve in redox reaction.
    • Electron donor get oxidized
    • Electron acceptor get reduced
  49. Define phosphorylation
    • Process that attach inorganic molecule P(i) to Adenosine diphosphate (ADP) in unstable bond by capturing energy from redox reaction.
    • ADP+P(i)+energy from redox reaction⇨ATP (useable energy)
  50. How catabolic reaction is useful for the cell?
    Allow the cell break big molecules into smaller ones and make ATP in the process.

    EX: Polysaccharide⇨ Monosaccharides
  51. Which two types of molecules a microbe/cell will need in order to go through catabolic reaction?
    what is the purpose of these molecules?
    • An electron donor & electron acceptor. Microbes may use organic or inorganic molecules on both cases.
    • The donor will supply the energy and the acceptor will either store or transfer this energy.
  52. Which are the four ways an organism might generate ATP?
    what type of molecules they will start with what would be the products at the end of each process?
    • Aerobic respiration: starts with e.donor molecule (glucose for example) + O2 e. acceptor ⇨ ATP, H2O (byproduct), and CO2 (waste product)
    • Anaerobic respiration:starts with e.donor molecule + some type of inorganic molecule as e.acceptor (but never O2)⇨ATP, acid (waste), and CO2 (waste).
    • Fermentation:starts with e.donor molecule an organic molecule as e.acceptor⇨some ATP, some CO2 (waste) ethanol, acid or both (waste).
    • Photosynthesis:Sunlight, CO2, and H2O⇨Glucose and O2 (waste)
  53. What happens during glycolysis process?
    What this process start with and what it is going to produce?
    • In glycolysis small amount of energy (2 ATPs) invested to split and rearrange glucose (6 carbon) into small carbon-based molecules.
    •  The products of this process are two ANDH molecules (e.donors) +net gain of 2 ATPs + 2 H+
  54. When does citric acid cycle starts?
    What happen during this process?
    • The citric acid cycle starts when glycolysis ends.
    • 1. it starts with glycolysis products NADH (a small carbon containing molecules that embedded in this cycle.
    • 2. These NADHs attached to another carbon containing molecules and go through a series of changing bonds, rearranging the carbons locations, and moving electrons & H+ around.
    • 3. One of the main products of this process are more NADH, FADH2 (both e. donors), and some ATP.
  55. When and where electron transport chain starts?
    What happens during this process?
    • ETC starts when NADH & FADH2 molecules (products of glycolysis & citric acid cycle) are brought to the cell membrane after citric acid cycle ends.
    • 1. Redox reaction: Electrons and H+ passed from ANDH & FADH2 to carrier molecule #1 and than carrier #1 pass the electron to carrier #2 or 3 and so on. Every time that an electron passed on from one carrier to another, a H+ is released to the extracellular space. at the end of the chain a O2 (aerobic respiration) or some other type of inorganic molecule will be the last e.acceptor that will bind with other molecule and create a byproduct (O2→H2O) or (other inorganic molecule→acid).
    • 2. ATP synthesis: H+ from the extracellular are pushed through a ATP synthase, an enzyme that use H+ to attach P(i) to ADP and produce ATP
  56. What are the different between aerobic respiration and anaerobic respiration?
    • Two things are different between them
    • the last electron acceptor
    • Aerobic respiration O2
    • Anaerobic respiration some type of inorganic molecule most common are CO3, NO3, or SO4.
    • The byproduct/waste product
    • Aerobic respiration H2O byproduct
    • Anaerobic respiration some type of acid
  57. What are the two types of fermentation?
    • Lactic acid fermentation (produces acid as waste product)
    • Alcoholic fermentation (produces alcohol as waste product)
  58. Why is fermentation process produces very little ATP in comparison to aerobic & anaerobic respiration?
    Because fermentation goes only trough glycolysis and not citric acid cycle or electron transport chain.
  59. What happens during lactic acid fermentation?
    • 1. Glycolysis process produces NADH, H+, and pyruvate.
    • 2. the cell combines the NADH, pyruvate, some H+ together and creates lactic acid as waste product.
  60. What happens during alcoholic fermentation?
    • 1. Glycolysis process produces some ATP, pyruvate, and NADH.
    • 2. pyruvate acid is modified (broken down) and produces CO2 and acetaldehyde.
    • 3. NADH donate a H+ to acetaldehyde, so it's break it apart a little and produces ethanol.
  61. What type of enzyme do bacteria secrete to break down lipids?
    Why these bacteria need to break down lipids?
    • Lipases (breaks down lipid into fatty acid & glycerol)
    • Some types of bacteria uses lipids as electron donors (nutrients) to start their metabolism going.
  62. What type of enzyme do bacteria secrete to break down proteins?
    Why these bacteria need to break down proteins?
    • Proteases (breaks down proteins to amino acids)
    • Some types of bacteria uses proteins as electron donors (nutrients) to start their metabolism going.
  63. True or false, some bacteria may be able to use more then one energy strategy (aerobic respiration, anaerobic respiration, and fermentation)
    True, some may have one, two, or all strategies
  64. What will be the results of anabolic reaction?
    What are the minimum requirements for this type of reactions?
    • The cell builds large structures from smaller molecules.
    • At the minimum, anabolic reaction needs energy & SPONCH elements.
  65. Define amphibolic
    • Anabolism and catabolism at the same time.
    • During amphibiolic reaction, the cell not only get to use the ATP that creates during metabolic reaction, but also it has the ability to extract some other molecules from the products of different stages of this process and use them in different cell structures.
  66. Elastase
    • An exoenzyme that secreted by pathogenic bacteria.
    • Breaks down elastin in our body.
  67. Collagenase
    • Exoenzyme secreted by pathogenic bacteria.
    • Breaks down collagen in our body
  68. Define nutrients/nutrition.
    Which are the two broad types of nutrients, microbes need for living?
    • Chemicals that organisms get from their environment that allow them to grow an reproduce.
    • Essential nutrients (SPONCH elaments)
    • Nice to have nutrients but not a must nutrients.
  69. macronutrients
    • Making macromolecules (SPONCH elements)
    • Needed in large amount by organisms
  70. Micronutrients
    • Trace elements  (some type of metal)
    • Needed in small amount by the organism for its metabolism reactions.
    • Used as carrier molecules in the ETC & cofactors.
  71. What is a growth factor?
    Do all bacteria need it?
    • A type of large molecule (heme, vitamins, etc.) that a microbe needs for its survival but it can't make it by itself, so it has to get it from its environment.
    • No, most microbes can make their own macromolecules,
  72. Define heterotroph
    An organism that uses organic carbon as its essential nutrient that usually made by another organism.
  73. Define autotroph
    • An organism that uses inorganic carbon from the environment (EX: CO2 in the air or water) as its essential nutrient.
    • Then it turn it into organic molecule in its body.
  74. How do autotrophs and heterotrops benefit each other?
    • Autotrophs are taking the inorganic carbon from the environment and turn it to an organic carbon in their body. The heterotroph comes along and takes that organic carbon from the autotroph and as it uses this organic carbon, it ends up releasing inorganic carbon (CO2) to the environment. Both making ATP this way.
  75. What is the different between phototrophs and chemotrophs?
    • Phototrophs are organism that use light energy to start their ATP process.
    • Chemotrophs are organism that use chemical energy (EX: glucose) to start their ATP process.
  76. Saperobes
    Chemoheterotrophes organisms that are free living decomposers
  77. What type of organism is a parasite?
    Which are the two categories parasite are divided to?
    Do parasitic organism remain parasite throughout its entire life?
    • Chemoheterotrophs (usually pathogens)
    • Obligated parasite (must live in a host ) & opportunist parasite (live in a host but not must to).
    • No, they are considered parasites as long as they live in/on living organism but once the organism is dead (they killed it), they are considered saperobes (decomposers)
  78. What are obligated aerobes?
    What type of ATP generation they will use?
    • Organisms that must have O2 as their terminal electron acceptor or they will die.
    • Aerobic respiration
  79. What are obligated anaerobes?
    What type of ATP generation they will use?
    • Organisms that will die in the presence of O2.
    • Anaerobic respiration, fermentation, or both
  80. What are facultative anaerobes?
    What type of ATP generation they will use?
    • Organism that will use O2 if available but will use other electron acceptor if there is no O2.
    • Aerobic respiration and anaerobic respiration or/and fermentation.
  81. What are aerotolerant anaerobes?
    What type of ATP generation they will use?
    • Organism that will not use O2 if present but it won't die from O2.
    • Anaerobic respiration or/and fermentation.
  82. What are microaerophile?
    What type of ATP generation they will use?
    • Organisms that must have O2 as their terminal electron acceptor but just in the right amount because too much or too little O2 will kill it.
    • Aerobic respiration and fermentation
  83. Define cardinal temperature.
    • a set of temperatures, minimum, optimum, and maximum, that allow the existence & growth of any microbe.
    • Minimum temperate: the cell will survive but will not be able to grow or metabolize. the cell will die at temperature below the minimum.
    • Optimal temperature: The cell's growth & metabolism are at their top speed.
    • Maximum temperature: the cell will not grow and its enzymes won't be very functional. The cell will die above this temperature
  84. What is a psychrophile?
    What is the special group that relater to psychophile?
    • Microorganism that grow in a cold cardinal temperate.
    • around -5o C to 10o C

    Facultative psychrophiles: can grow in cold temperatures but very slow
  85. What is a mesophile?
    • Microorganism that grow in a moderate cardinal temperate.
    • around 10o C to 45o C
  86. What is a thermophile?
    • Microorganism that grow in a hot cardinal temperate.
    • above 45o C
  87. What are acidophiles?
    How they can be useful for us?
    How can thy be harmful to us?
    • Microbes that live in acidic environment, below 6 pH.
    • They can raise the pH in acid spill when used as bioremediation.
    • As pathogens, they may infect our stomach.
  88. What are alkalinophiles?
    How they can be useful for us?
    • Microbes that live in above 8 pH level environment.
    • We use their enzymes in industrial applications such as oven cleaners & laundry detergent.
  89. What is the pH level range that most microbes can survive?
    • Between 6 pH - 7 pH
    • In this range their enzymes & membrane work the best and their growth is fastest.
  90. What is the osmolarity requirements of  most bacteria?
    • A little more salinity (salty) inside the cell then their environment.
    • That cause water to diffuse inside the cell and push the cell membrane against the cell wall which help to keep the cell's shape and nutrients or waste to cross the membrane.
  91. What are halophiles?
    • Microbes that live in very salty lakes.
    • EX: the ocean water have 3.5% salt. Halophiles live in water with between 9% to 11% and many of them prefer 30%
  92. What is generation/doubling time?
    Do all bacteria have the same
    generation doubling time?
    • The time that takes a bacteria to go through binary fission and make a new cell when all the right conditions are met (pH, temperature, nutrients, etc).
    • No, in some bacteria it can take few minutes and others few weeks.
  93. Which are the different phases of the bacteria growth curve?
    What happens during each phase?
    • Lag phase: The bacteria taking in nutrients and getting ready to grow.
    • Log phase: The bacteria is growing very fast.
    • Stationary phase: The bacteria death rate is equal to its growth rate
    • Death phase: The bacteria death rate is faster then its growth rate.
  94. Microbial growth equation
    • Nf = (Ni)2n
    • Ni = Initial number of cells
    • n = total time / generation time
    • 2n = number of cells in that generation
    • Nf = final number of cells
  95. Infectious dose
    • The minimum number of bacteria that can make us sick.
    • This number is different between one bacteria to another.
    • Can be predicted by knowing growth equation and growth curve
  96. What is symbiotic relationship?
    Which are the different categories of it?
    • A relationship between two or more types of organisms that at least one cannot survive without the other member/s.
    • Mutalism:Both organisms benefit from this relationship.
    • Commenalism: One is benefit and the other is not.
    • Parasitism: One is benefit and the other is harmed
  97. What is non-symbiotic relationship?
    Which are the different categories of it?
    • Neither one of the organism must have this relationship.
    • Synergism: Both organisms are benefit from this relationship.
    • Antegonism: One is benefit and the other is harmed.
  98. Who was the first to look at biofilm?
    Antonie Van Leeuwenhoek
  99. What type of relationships can be between organisms in biofilm?
    • Symbiotic relationship: Either mutualism or commenalism.
    • Non-symbiotic: synergism
  100. Which are the stages of biofilm formation and what happen in each stage?
    • Attachment stage: Planktonic bacteria (free living) attaches to something and produces inducer molecule that signal other bacteria to join.
    • Quorum stage:Is the minimum number of individual bacteria attached together that can start to form a biofilm.
    • Matrix stage: Formation of biofilm. The bacteria characteristics in this stage changed and they all act as a unit.