Microbiology exam 3

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  1. genetics
    - study of function and transfer of genes
  2. genome
    all genetic information in a cell
  3. chromosome
    part of the genome, cluster of DNA, contains genes
  4. genes
    segments of DNA
  5. characteristics of DNA
    • deoxyribonucleic acid
    • 3 nucleotide components: sugar (5 carbon deoxyribose), phosphate and nitrogenous base-
    • hydrogen bonds between nitrogenous bases
    • double helix, antiparallel, runs 5' → 3' and 3' → 5' (new always made 5' → 3
  6. which nucleotides complementary base pair with each other?
    • A and T
    • C and G
  7. genotype
    genetic makeup, represents only potential charecteristics
  8. phenotype
    expression of genotype, the actual observable characteristic
  9. what is the leading strand? how is it formed?
    continuous strand that is made in 5' → 3' direction
  10. what is the lagging strand? how is it formed?
    synthesized in pieces because there is no free 3' end
  11. components of DNA replication: helicase
    enzyme that unwinds the double helix
  12. components of DNA replication: template
    original DNA strand
  13. components of DNA replication: replication fork
    where 2 strands are separated and new nucleotides are added
  14. components of DNA replication: DNA polymerase
    enzyme that adds new nucleotides and proofreads
  15. components of DNA replication:RNA primer
    small pieces of RNA where DNA polymerase can attach (only on lagging strand)
  16. components of DNA replication: DNA ligase
    enzyme that joins fragments of DNA (glue) on the lagging strand
  17. DNA vs. RNA
    • DNA: deoxyribose, thymine, double stranded
    • RNA: ribose, uracil, single-stranded
  18. transcription
    process of making mRNA from a DNA template
  19. what does RNA polymerase do in transcription?
    enzyme that makes a new strand of mRNA
  20. what does the promoter do in transcription?
    site on DNA template where RNA polymerase binds (start)
  21. what does the terminator do in transcription?
    site on DNA template that ends transcription (stop)
  22. steps of transcription
    • 1. RNA polymerase binds to promoter site on DNA template
    • 2. RNA polymerase synthesizes a complementary base strand of the DNA template working in a 5' → 3' direction.
    • 3. transcription continues until a terminator is reached
    • 4. RNA polymerase and a new mRNA are release from DNA template
  23. translation
    process of protein synthesis
  24. components in translation: mRNA
    messenger RNA, carries info transcribed from DNA, specifies the amino acid sequence of the protein products
  25. components in translation: tRNA
    carries amino acids, contains anticodons which pair with the codons on mRNA
  26. components in translation: ribosomes (structure)
    • site of translation, attaches to mRNA, small and large subunits
    • A site (acceptor), holds tRNA carrying next amino acid
    • P site (peptide), holds tRNA with growing peptide chain
    • E site (exit), where tRNA leaves ribosome
  27. components in translation: rRNA
    ribosomal RNA, part of the ribosome
  28. steps in translation: initiation
    • 1. start codon, AUG signals mRNA to bind to small subunit of ribosome
    • 2. initiator tRNA (with the amino acid methionine) attaches its anticodon (UAC) to mRNA in P SITE!!!!!!
    • 3. large and small subunits join
  29. steps in translation: elongation
    • 1. mRNA is threaded through ribosome
    • 2. 2nd tRNA (with amino acid) binds its anticodon with mRNA's codon in the A SITE! of the ribosome
    • 3. peptide bond forms between amino acids
    • 4. polypeptide chain is transferred to tRNA in A site and 1st moves to E site and is released
    • 5. tRNA with growing polypeptide chain moves from A to P site.
  30. steps in translation: termination
    • 1. elongation continues until a stop codon reaches the A site
    • 2. ribosome splits apart and polypeptide chain is released 
  31. codons
    • set of three nucleotides bases on mRNA that encode for a specific amino acid
    • 64 codons, 20 amino acids
    • 61 sense, 3 nonsense
  32. how do codons code for amino acids to form proteins?
    the nucleotides (3) on the mRNA code for a specific amino acid that together build up to create proteins.
  33. sense codons
    code for amino acids
  34. nonsense codons
    • stop codons
    • UAA, UAG, UGA
  35. how is bacterial gene expression regulated and why?
    • using feedback inhibition (inhibit enzyme reactions when unnecessary) regulated if only needed at certain times
    • making enzymes is controlled by genetics, transcription and translation
  36. how are genes repressed?
    • by a process that turns off transcription, repressor block RNA polymerase at the promoter
    • caused by overproduction of end products
  37. induction
    turned on (induced) by substrate of enzyme
  38. operon
    • system of gene regulation
    • includes genes promoter and operator
  39. operator
    starts/ stops transcription of (lac) gene
  40. promoter
    where RNA polymerase initiates transcription
  41. E. coli and the lac operon
    • lac operon ON: lactose → allolactose → binds to tell ribosomes get rid of repressor and to make beta-galactosidase
    • lac operon OFF: repressor bound to operator, nothing happens
  42. mutation
    • a change in a base sequence of DNA, permanent and passed on
    • ex. antibiotic resistance
  43. base substitution
    a single base is replaced with another base
  44. missense mutation
    base substitution results in amino acid substitution
  45. nonsense mutation
    base substitution codes for a stop/nonsense codon
  46. frameshift mutation
    one or more bases are deleted or inserted
  47. mutagen
    a substance that causes mutations
  48. what are the different types of mutagens?
    • chemicals (nitrates/nitrites, household cleaners)
    • radiation (UV light, xrays. causes thymine dimers to form)
  49. genetic transfer
    exchange of genes between 2 DNA molecules to form new combinations of genes
  50. what is crossing over?
    2 chromosomes break apart and rejoin, resulting in 2 original chromosomes having a combination of eachother
  51. why is it important for genes to transfer?
    contributes to genetic diversity, genes for resistance to drugs develop, new nutritional and metabolic capacities develop, increases virulence
  52. plasmid
    circular pieces of DNA, replicate separately from chromosomal DNA
  53. 3 types of genetic transfer
    • transformation
    • conjugation
    • transduction
  54. what is transformation and how does it work?
    process of genetic transfer when a cell lyses and naked DNA is transferred to another bacteria, donor combines with recipient DNA to form a new recombinant
  55. what is the significance of plasmids?
    can enhance pathogenicity (disease causability)
  56. F factor
    fertility, used in conjugation, carries genes for a sex pilus
  57. R factor
    resistance, transfers antibiotic resistance, can transfer resistance to heavy metals, synthesize factors such as toxins, enzymes and adhesion
  58. what is conjugation and what components are involved?
    • sex pilus: connection between 2 cells
    • donor has F+ plasmid
    • recipient has no plasmid, F-
  59. what are the steps in conjugation?
    • 1. sex pilus grows out of F+ call and attaches to F- cell 
    • 2. copy of F+ is transferred to F--results in two F+
  60. transduction
    process of genetic transfer in which DNA is passed from one bacterium to another by a bacteriophage (virus)
  61. transposons (also advantages and disadvantages)
    • segments of DNA tht move from 1 region to another, "jumping genes"
    • advantages: genetic diversity, change in morphology and pigmentation traits, replaces damaged DNA
    • disadavantages: mutations, cell dysfunction
  62. genetic engineering/ recombinant DNA technology
    techniques in microbiology that manipulate DNA
  63. benefits of biotechnology
    use of microbes to produce food antibiotics, vitamins, and enzymes
  64. basics of restriction enzymes/ endonucleases
    enzymes from bacteria, recognize foreign DNA and can break bonds when adjacent nucleotides, used in recombinant DNA technology
  65. gel electrophoresis
    technique that produces readable patterns of DNA fragments, uses a soft agar gel and electrical current to separate fragments based on SIZE
  66. purpose of DNA sequenceing
    used to determine the exact genetic code (order of bases), Sanger method
  67. why is polymerase chain reaction used?
    makes multiple copies of a piece of DNA enzymatically (Taq polymerase from T. aquaticus)
  68. basics of DNA profiling/ fingerprinting and uses-
    DNA profiling, forensic tool, uses restriction enzymes to cut DNA at specific parts and separate with gel electrophoresis
  69. Taxonomy
    idea of classifying organisms
  70. 3 domain system
    • 2 are prokaryotic cells- archea and bacteria
    • Eukarya is other domain
  71. What is the only domain that has kingdoms?
  72. What is the endosimbiom theory?
    Chroloplasts in past were prokaryotic cell. Then they were endocitosed and evolved into organelle. Same is true with mitochondria.
  73. Is archea more closely related to eukara or bacteria?
  74. What are three major groups of archea domain?
    • 1. hypothermophiles (like to grow in hot environment)
    • 2. extreme halophiles- like to grow in salty enviroment
    • 3. methanogens- like to produce methanin
  75. What does bacteria contain in cell walls?
  76. What is found in arches walls?
  77. What is found in plant cell walls?
  78. What is found in fungi cell walls?
  79. Phylogenetics
    • each species retains some characteristic from ancestor(idea behind taxonomy)
    • look at: anatomy, fossils, and rRNA
  80. What do we use to name species?
    Binomial Nomenclature (genus + specific epithet)
  81. Why are viruses excluded from the 3 domains?
    They are not made of cells. This system divides organisms into eukaryotic and prokaryotic cells.... Can't put them in either.
  82. Which phylum does staph lacoccus belong to? Micrococcus?
    Fermacutes, Atino bacteria
  83. ranking order
    Kingdom, Phylum, Class, Order, Family, Genus, Species
  84. Culture
    Grown in laboratory media
  85. Clone
    • population of cells derived from a single cell
    • Ex: streak out plate and get a colony... all came from one cell.
  86. Strain
    • genetically different cells within a clone
    • Ex: streak out plate and get a mutation... it starts to reproduce within colony
  87. What do orders end in?
  88. What do families end in?
  89. What order and family does pseudomonas aeruginosa belong to?
    pseudomonales and psedomonaceae.
  90. Main characteristic used in putting organisms in phylum
    how much G + C they had (high G + C) (low G + C)
  91. 4 basic classifications in eukara domain
    • 1. animalia 
    • 2. plantae:
    • 3. fungi:
    • 4. protista:
  92. Animalia
    • multi-cellular, no cell wall, chemoheterotrophic (organic carbon, energy source)
    • ex: worms
  93. Plantae
    multicellular, cellulose cell wall, usually photoautotrophic
  94. Fungi
    Chemoheterotrophic (just like you and i), unicellular or multicellular, cell walls of chitin, have sexual and asexual reproduction
  95. Protists
    Most people don't consider this a kingdom anymoreA catchall kingdom of eukaryotic organisms that so not fit in any other kingdoms(Grouped into clades based on rRNA)
  96. What do we call unicellular fungi?
    yeast and molds.
  97. Viruses orders
  98. Viruses families
  99. How do all herpes viruses end?
  100. Virus Genus endings
  101. Virus Species
    • Common, everyday name.
    • Example: HIV
  102. Virus Sub Species
    • end in number.
    • ex: HIV 1 or HIV 2
  103. Classification vs identification
    • Classification- looking at how they are related to one another
    • Identification- looking more at what we do in the lab and see how we can identify them
  104. What 3 things to you need to know to identify your unknown
    • 1. Morphological characteristics- cocci, balicilli, presence and endospores, capsules, flagella
    • 2. Differential staining (gram stain, acid fast)
    • 3. Biochemical tests- determines presence of bacterial enzymes (catalase)
  105. Whats the first thing we do in identification?
    Gram stain
  106. What do all differential stains have in common?
    Give you information about cell wall.
  107. What are dichotomous key
    always used for identification of bacteria, series of yes or no question... "Is it gram positive" Y or N... not "gram positive"
  108. Enterotube
    you don't have to inoculate anything, scoring with 5 digit number... look up number in book. (no critical thinking)
  109. serology test
    • 3 tests based on same principle: antibody (proteins)- antigen binding
    • **bc the bonding of antibodies and antigens is so specific... great for IDing
  110. 3 types of serology tests
    • 1. Slide agglutination test: bacteria clumps together if positive test
    • 2. ELIZA test- attach an enzyme to antibody... if antibody binds to antigen we can tell by adding a substrate and see if it attaches to the enzyme or not
    • 3. Western blot- put proteins on gel and they'll be separated by size using gelophoreeses... transfer it to filter paper. antibodies will stick.
  111. Phage typing
    • Always uses lytic phage. 
    • Primarily used for tracing outbreaks, see where original source was... look at patternsPlate bacteria out, Put it on grid, if phage infect bacteria... it is gonna replicate cause cell too lyse and create clearing called a plaque
  112. What is a phage?
    • Virus that invades bacteria
    • Part of Transduction
  113. DNA chips
    use glass slide and spot DNA on slides. one slide can have 10,000 different sequences of DNADNA on slide is SINGLE stranded! (its hybridization)take DNA sample from patient, put florescent label on it.. which dot lights up
  114. Nucleic Acid Hybridization
    • Southern blotting
    • Probes
    • DNA chips
    • FISH
  115. iRNA
    drug to knock out expression of specific gene
  116. FISH
    used for identification
  117. cladograms
    used to try and see what organisms are related.. classification
  118. how do we define a node?
    similarity in rRNA
  119. Protozoa
    Eukaryotic, unicellular, classified by motility, some parasitic, heterotrophic (get food from outside of body by vacuoles/cell membrane absorbtion)
  120. Protozoa Habitat
    Moisture, water and soil, some can live in extreme environments
  121. Protozoa Trophozoite Life Cycle
    Motile feedingstage, requires water and food
  122. Protozoa Cyst Life Cycle
    Dormant stage, conditions unfavorable
  123. Protozoa Asexual Reproduction: Binary Fission
    Division of 1 cell into 2 identical cells
  124. Protozoa Asexual Reproduction: Budding
    Protrusion off of parent cell
  125. Protozoa Asexual Reproduction: Schizogony
    Nucleus undergoes multiple divisions before the cell divides (plasmodium)
  126. Protozoa Sexual Reproduction: Conjugation
    Genetic exchange between 2 mating pairs that requires cell to cell contact
  127. Protozoa Classification
    Domain: eukarya, kingdom: protista, subkingdom: protozoa
  128. Phyla of Protozoa: Amoebozoa
    Move by pseudopods, example amoeba
  129. Phyla of Protozoa: Euglenozoa
    Flagellated, example euglena or trypanosoma
  130. Phyla of Protozoa: Ciliophora
    Move by cilia, example stentor or paramecuim
  131. Phyla of Protozoa: Apicomplexa
    nonmotile, most parasitic, example plasmodium causes malaria or toxoplasma can harm babies transmitted by cat poop
  132. Algae
    Eukaryotic, uni or multi cellular, classified by color/pigment, contain chloroplasts, photoautotrophic (make food from the sun)
  133. Algae: Thallus
    Body, performs photosynthesis
  134. Algae: Holdfast
    Root-like anchors
  135. Algae: Stipe
  136. Algae: Blade
  137. Algae Habitat
    Aquatic, soil, rocks, cool water often near surface
  138. Algae Reproduction
    Asexually by binary fission, sexual not very frequent
  139. Algae Classification
    • Domain: eukarya
    • kingdom: protista
    • subkingdom: algae
  140. Phyla of Algae: Phaeophyta
    Brown algae, kelp, big, can get to 50 meters, found in coastal waters, used in ice cream/ toothpaste/ soap/ lotion
  141. Phyla of Algae: Rhodophyta
    Red algae, deeper in ocean, used to make agar
  142. Phyla of Algae: Chlorophyta
    Green algae, contain chlorophyll, most microscopic, example volvox or spirogyra
  143. Diatoms
    Most numerous unicellular algae, important in food chain, have shells
  144. Dinoflagellates
    Plankton, cause red tide, photosynthetic, have shells
  145. Cyanobacteria
    Blue-green, domain bacteria, prokaryotic, example oscillatoria and anabaena
  146. Mycology
    Study of fungi
  147. Fungi
    Eukaryotic, multicellular (except yeast), classified by spores, some parasitic, macrofungi (mushrooms), microfungi (molds & yeast), cell walls made of chitin
  148. Fungi Nutrition
    Heterotrophs, absorb or decompose animal and plant debris
  149. Fungi Habitat
    Low moisture, pH 5, can grow in high salt and sugar concentations
  150. Fungi: Hyphae
    Filaments of cells, develop from spores, grow by elongating at tips, each part can form a new mold
  151. Fungi: Mycelium
    Group of hyphae
  152. Fungi: Septae
    Cross-walls in hyphae
  153. Fungi: Nonseptae
    No crosswalls
  154. Fungi Asexual Reproduction: Conidiospore
    Fragmentation of hyphae, produced in chains
  155. Fungi Asexual Reproduction: Sporangiospore
    Fragmentation of hyphae, produced in sacs
  156. Fungi Sexual Reproduction: Zygospore
    Union of 2 nuclei of 2 morphologically similar cells, (+) and (-) come together
  157. Fungi Sexual Reproduction: Ascospore
    Union of 2 nuclei of 2 morohologically similar or not similar cells, produced in ascus (sac-like structure)
  158. Fungi Sexual Reproduction: Basidiospore
    Union of 2 mating strains that bud off of parent cells, produced in club shaped structure
  159. Fungi Classification
    • Domain: eukarya
    • kingdom: fungi
  160. Phyla of Fungi: Zygomycota
    Nonseptate hyphae, asexual sporangiospores, sexual zygospores, example rhizopus or phycomyces
  161. Phyla of Fungi: Ascomycota
    Septate hyphae, asexual conidiospores, sexual ascospores, example aspergillus or penicillium or yeast
  162. Phyla of Fungi: Basidiomycota
    Septate hyphae, sexual basidospores, asexual conidiospores, example club fungi or mushrooms or puff balls
  163. Yeast
    unicellular, nonfilimentous, spherical or oval, can grow with or without oxygen, can ferment carbs to create carbon dioxide and alcohol, make bread/ beer/ wine (cereviseae), yeast infections (candida albicans)
  164. Yeast Reproduction
    Budding example cereviseae and fission (2 new cells) example longname octosporous
  165. Fungi Uses
    Food chain, mushroms for food, bread/ beer/ wine, drugs (penicillin), anticancer drugs
Card Set
Microbiology exam 3
microbiology exam for chapter 8,9,10,12
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