Biol 120 Exam 1 part 1

  1. Microbes
    SA/V & Nutrient uptake
    Growth rate is proportional to nutrient uptake
  2. Bacteria Storage Form of Sugar
    • Usually glycogen
    • Sometimes cellulose
    • Never starch
  3. Prokaryote Cell Membrane
    Protein Anchor
    Site of many proteins for transport and bioenergetics
  4. Prokaryote Cell Membrane
    Energy Conservation
    Membrane is used for proton motif force
  5. Triclosan
    Chemical in soap that inhibits enoyl reductase, killing prokaryotes
  6. Chemoorganotroph
    Use organic molecules (glucose, acetate, etc) to affix O2
  7. Chemolithotrophs
    Use inorganic molecules (H2, Fe, NH4+) to affix O2
  8. Hopanoids
    Present instead of sterols in archaea
  9. Ether Linkage
    Used instead of ester linkage for lipid linkage in archaea
  10. Lipid Composition of Bacteria
  11. Lipid Composition of Archaea
    • Sulfolipids
    • Glycolipids
    • Nonpolar isoprenoid lipids
    • Phospholipids
  12. 3 Characteristics of Active Transport
    • 1. Saturation Effect
    • 2. Highly Specific
    • 3. Number of transport proteins is highly regulated
  13. 3 Types of Simple Transport
    • Driven by energy of proton motif force
    • 1. Antiporter
    • 2. Uniporter
    • 3. Symporter
  14. Antiporter
    Transport a molecule across a membrane while simulataneously transporting a second molecule in the opposite direction.
  15. Uniporter
    Transports a molecule in a single direction across the membrane
  16. Symporter
    Cotransporters. Transport one molecule along with another substance, usually a proton.
  17. Group Translocation
    Involves a series of proteins in the transport event. Driven by phosphoenolypyruvate
  18. Phosphoenolpyruvate
    Drives group translocation
  19. ABC System
    • Transport involving three components:
    • 1. A substrate binding protein
    • 2. A membrane-integrated transporter
    • 3. ATP hydrolyzing protein
  20. Membrane Transporters
    (Alpha Helix)
    All membrane transporters contain 12 alpha helix domains that weave back and forth through the membrane to form a channel
  21. Periplasmic Binding Protein
    ATP Binding Protein
    • Involved in ABC transport
    • Periplasmic Binding Protein is on the outside of the membrane while the ATP binding protein is on the inside
  22. Sec System
    Translocase. Used to transport proteins out of cell or into membrane
  23. How do bacteria (and some archaea) maintain shape and rigidity?
    Cell Wall
  24. What acids cause cell wall to be negatively charged?
    • Teichoic acid
    • Lipoteichoic acid
  25. Two Sugar Derivitives of Peptidoglycan
    • N-acetylglucosamine
    • N-acetylmuramic acid
  26. Amino Acids of Peptidoglycan
    • L-alanine
    • D-alanine
    • D-glutamic acid
    • Lysine or DAP
  27. Techoic Acid of Peptidoglycan
    Used to attach bacteria to host cell
  28. Outer membrane of Gram negative bacteria
    Outer membrane are anchored to peptidoglycan via lypoproteins
  29. Paripathis Space
    Area between peptidoglycan and other layers of cell wall
  30. Lipopolysaccharide (LPS) layer
    • Outer membrane of gram negative bacteria.
    • 1. Polysaccharid portion has two components: O antigen and Core Polysaccharide
    • 2. Lipid portion called Lipid A: fatty acids connected to amine group
  31. Lipid A of LPS
    Causes inflamation when immune system kills bacteria
  32. How many carbons are in Core Polysaccharide of LPS?
    7 (this is odd)
  33. Outer membrane has a lot of porins for movement of small hydrophilic molecules
    (2 types)
    • 1. Non-specific: Water filled
    • 2. Specific: Have binding site for specific substance
  34. Slime Layer
    Loosely associated layer
  35. Capsule
    • Tightly associated amino acid polymer.
    • Usually associated with disease causing
    • 1. Protects from dessication
    • 2. Adherence to cells via biofilms
    • 3. Prevention of phagocytosis
  36. Bacterial DNA
    (location and binding proteins)
    Found in nucleoid. No histones, but have binding proteins. Circular chromosome.
  37. Plasmids
    (Shape and function)
    Small circular DNA. Don't usually have necessary genes, but have genes that give selective advantage in various environments.
  38. Drugs ending in -mycin
    Target bacterial ribosomes. Archaeal ribosomes are not effected. They are too similar to eukaryotes.
  39. Thylakoid Membranes
    Phototrophs have these. They are folds in plasma membrane that function in the light reactions of photosynthesis.
  40. Carboxisomes
    Surrounded by a protein membrane. Contain rubisco which is used for affixing CO2
  41. Gas Vessicles
    Protein coat that is permeable to gases, but not liquid. They are used for buoyancy in photosynthetic bacteria
  42. Enterosomes
    • Found in intestinal (enteric) bacteria
    • Metabolize enzymes in the intestine
  43. Pilli
    • Usually found on gram negative bacteria
    • Involved in conjugation
    • Made of pillin
    • Bind viruses
    • Motility
  44. Image Upload 1
    • Composed of flagellin
    • Hook- Wide region at base of filament. Connects filament to motor portion of base.
    • Motor- Central rod that passes through series of rings.
    • L Ring- Gram neg: Anchored to LPS layer
    • P Ring- Peptidoglycan layer
    • MS & C Rings- Cytoplasmic Membrane and cytoplasm
    • Mot Proteins- Generate torque
    • Fli Proteins- Motor switch, reverses direction
  45. How Flagella Works
    • Rotor: Central rod, L, P, C, and MS Rings- together called the Basal Body
    • Stator: Mot Proteins surrounding basal body

    Proton movement through Mot Proteins drives rotation.
  46. Fimbriae
    Shorter than flagella. Used for cell to adhere to surfaces
  47. Vocab:
    1. Single Flagella
    2. Single Flagella at Each Pole
    3. Tuft of Flagella at One or Both Ends
    4. Evenly Distributed Flagella All Over Surface
    • 1. Monotrichous
    • 2. Amphitrouchous
    • 3. Lophotrichous
    • 4. Peritrichous
  48. Chemotaxis
    • Drawn toward chemicals of food or other bacteria
    • 1. Spacial Gradient- Conc. of chem in space
    • 2. Temporal Gradient- Is conc. increasing or decreasing
  49. Phototaxis
    Drawn toward light
  50. Antigens on bacterial surface (3)
    • H Antigen- Flagellar antigen
    • O Antigen- LPS
    • K Antigen- Capsular antigen
  51. Endospores
    • Produced in detrimental environment
    • Resist heat, chemicals, radiation
  52. Cycle of Spore Formation
    Vegetative Cell -> Sporulating Cell -> Mature Spore -> Germination (repeat)
  53. Seven Stages of Endospore Formation
    • 1. DNA becomes dense
    • 2. Asymetric Cell Division
    • 3. Endospore septum grows around protoplast
    • 4. Forespore formation, Primordial cortex formed between two membranes, dehydration
    • 5. Calcium incorporation, dehydration, coat layers formed
    • 6. Maturation (development of heat resistant chemicals)
    • 7. Lysis of cell and release of endospore
  54. 4 Properties of Viruses
    • 1. Infectious
    • 2. Must use host to manufacture components
    • 3. Genome codes for proteins host can't provide
    • 4. Self assemble
  55. Capsid
    Protein case, arranged in precise repetitive order
  56. Capsomer
    Larger capsid. More elaborate with more types of proteins. Smallest thing to be seen with an electron microscope
  57. Nucleocapsid
    Complete package of nucleic acids and proteins
  58. Icosahedron
    • 20 faces, 12 vertices
    • Most efficient arrangement of subunits
  59. Lysozyme
    Enzyme carried by virus to produce hole in cell wall to enter or lyse
  60. Reverse Transcriptase
    Carried by retroviruses to convert RNA into DNA
  61. Titer
    Measure of virus quantity
  62. Plaque Assay
    • Each plaque is from a single virion
    • Plaque- cleared area of plate
  63. 5 Steps of Virus Replication
    • 1. Attachment (Absorption) into host
    • 2. Penetration (entry, injection) of virion or genome
    • 3. Synthesis- of viral nucleic acid and proteins
    • 4. Assembly- of capsids and pachaging of viral genomes (maturation)
    • 5. Release- of mature virions from cell
  64. Latent Period
    Eclipse + Maturation
    • Eclipse- When viruses attach to host and are unable to affect other cells
    • Maturation- Titer increases as new viruses are formed, but they are trapped in host cell
  65. Burst Size
    Number of viruses released from host
  66. Attachment
    Attach to specific receptor of host
  67. What does it mean that a cell is "permissive to a virus"?
    Cell allowed viral genome to enter
  68. Restriction Endonucleases
    How do they defend cell? How do viruses get around this?
    • Destroy double strand viral DNA after it enters.
    • Virus can use glucosylation or methylation to mark DNA for protection from restriction enzymes.
    • Virus can also encode proteins to inhibit restriction system.
  69. Seven Classes of Viruses
    • 1. dsDNA
    • 2. ssDNA
    • 3. dsRNA
    • 4. ssRNA +
    • 5. ssRNA -
    • 6. ssRNA w/ DNA intermediate
    • 7. dsDNA w/ RNA intermediate
  70. Shapes of Viruses & Examples
    • 1. Helical (Tobacco mosaic virus)
    • 2. Polyhedral (Adenoviruses)
    • 3. Spherical (Influenza)
    • 4. Bacteriophage (T4)
  71. Naked Virus vs Enveloped Virus
    • Naked: Nucleocapsid
    • Enveloped: Nucleocapsid inside envelope
  72. Bacteriophage Anatomy
    Image Upload 2
  73. Early Proteins
    • Synthesized soon after infection
    • Necessary for replication of virus nucleic acids (poymerases)
    • Typically act catalytically
    • Synthesized in smaller amounts
  74. Late Proteins
    • Synthesized later in infection
    • Include proteins of virus coat
    • Typically structural components
    • Synthesized in larger amounts
  75. Retrovirus Structure and Function
    Image Upload 3
  76. Retrovirus Genome
    • Two identical ssRNA+ molecules
    • gag gene: structural proteins
    • pol gene: reverse transcriptase and integrase
    • env gene: encode envelope proteins
  77. Animal RNA Viruses
    • Nonenveloped: ssRNA, dsRNA
    • Enveloped: ssRNA only
  78. Effects of Virus on Animal Cell (5)
    • 1. Cell fusion
    • 2. Virus present but not replicating=lysis
    • 3. Slow release of virus w/o cell death
    • 4. Lysis
    • 5. Tumor Cell
  79. Prion
    • abnormal protein with a lot of beta sheets.
    • transmissible spongiform encephatopathies (TSE)
    • Turns other proteins abnormal
    • Mad Cow Disease
  80. Generation Time aka Doubling Time
    Time it takes for bacteria to reproduce
  81. Graph (log of viable cells)
    Lag Phase
    Exponential growth phase
    • Lag Phase- small slow. Bacteria still getting used to medium
    • Exponential growth phase- When generation time is measured. Keep growing until resources run out
    • Downslope- bacteria consume eachother (cell walls)
  82. Spread Plate Method vs Pour Plate Method
    • Spread plate- hockey stick to spread on medium
    • Pour plate- bacteria diluted and poured along with medium
  83. Common errors in viable cell counts
    • 1. Innoculation size
    • 2. Culture medium
    • 3. Incubation conditions and length
  84. Turbidity
    • Cells reflect light
    • turbidity is proportional to the number of cells
  85. Continuous Culture
    Steady state. Cell number and nutrient status remain constant.

    Chemostat adds medium, air, and removes dead cells
  86. Growth Yield
    Concentration of nutrient in limiting amount
  87. Factors Influencing Microbial Growth
    • Macronutrients- Carbon, nitrogen, water, etc. (need a lot)
    • Micronutrients- cofactors and growth factors (need a little)
    • Siderophores excreted to obtain iron
  88. Microbial nutrition chart
    Categorized by energy source and carbon source
    Image Upload 4
  89. Chemicall defined media vs Chemically undefined media
    • Chemically defined- precise amount of purified chemicals and distilled water
    • Chemically undefined- protein and amino acid based (better)
  90. Selective Medium
    Allows growth of some organisms and inhibits others
  91. Differential medium
    Identify organism by biochemical difference between two organisms that grow equally well on certain medium
  92. Enriched Medium
    • Add nutrients that allow organism to grow that wouldn't normally
    • ex. bile and crystal violet- selects for gram negative
    • ex. lactose fermentation- select for organism that ferments lactose. Read with pH meter
  93. Temperature Extremophiles
    • Psychorophile - 4
    • Mesophile- 39
    • Thermophile- 60
    • Hyperthermophile- 106
  94. Obligate Aerobe
    Needs oxygen
  95. Obligate anaerobes
    Die in oxygen environement
  96. Facultative Anaerobes
    Use oxygen and other electron acceptor. Can survive in oxygen but doesn't need it
  97. Microaerophilic
    Require low oxygen levels
  98. Aerotolerant anaerobes
    Don't use oxygen but aren't killed by it
  99. Sodium thioglycolate
    Used to reduce oxygen in lab. Gives layers in broth of varied oxygen concentrations
  100. Aerobes vs Anaerobes in flast
    Lab setting
    • Aerobes:
    • 1. Vigorously shake flask
    • 2. Bubbling sterilized air
    • 3. Large headspace

    • Anaerobes
    • 1. Fill tube so no headspace
    • 2. Reducing agent (reduce O2 to H2O) ex. thiogycolate
  101. Toxic forms of O2
    Image Upload 5
  102. Acidophile Nomenclature

    Adaptations of acidophiles & alkaliphiles
    • Obligate- Needs acidic environment
    • Tolerant- will survive in acid but doesn't prefer

    Acidophiles- adapt membrane stability under high proton concentration

    Alkaliphiles- adapt Na+ gradient instead of H+ gradient
  103. Halophiles
    • Halophiles- salt
    • Osmophiles- sugar
    • Xerophiles- dry environment
  104. To maintain osmolarity in salty environment
    • 1. pump inorganic ions
    • 2. increase synthesis of organic solute (Compatable solutes= don't inhibit biochemistry or cell processes)
  105. Bacteriocidal
    • Bacteriocidal- kill bacteria
    • Bacteriostatic- inhibit growth of bacteria
    • Decontamination- treatment to make inanimate surface safe to handle
    • Disinfection- Eliminate all pathogens, but not all microbes
    • Sterilization- Eliminate all microbes
  106. Physical Antimicrobial Control (3 methods)
    • 1. Heat- high temp for long time to get microbe and endospores
    • 2. Radiation
    • 3. Filtration
  107. Autoclave
    Used to sterilize. use steam heat pressure at temp above boiling point
  108. Thermal Death Times
    Time it takes to kill cells at certain temp
  109. Decimal Reduction Time
    Time required for ten-fold reduction of population density at a given temperature
  110. Electromagnetic Radiation (3 methods to control microbial growth)
    • 1. UV radiation- decontaminate air and water
    • 2. Ionizing radiation- penetrate light absorbing materials and break DNA
    • 3. heat
  111. Best filter size
    • 0.2um filter
    • Used especially for heat sensitive mediums (mediums that can't be heated)
    • HEPA filter traps bacteria
  112. Which of the following statements about the intracellular state of a virus is NOT correct?

    a) The virus particle is referred to as a
    b) New copies of the virus genome are produced.
    c) The virus replicates.
    d)The components that make up the virus coat are synthesized.
    a) The virus particle is referred to as a virion.
  113. The smallest morphological unit of a virus that can be seen with the electron microscope is the:

    A) capsomer.
  114. Which of the following statements does NOT describe a factor affecting the efficiency of plating in quantitative virology?

    A) The virus successfully infects a host cell and causes the formation of a plaque.
  115. During the first few minutes after a virus infects a cell, the virus is said to undergo:

    D) eclipse
  116. Restriction enzymes are specific for:

    C) double-stranded DNA viruses.
  117. What type of virus requires an enzyme known as reverse transcriptase?

    D) retroviruses
  118. T4 DNA is protected from host defenses by glycosylation of:

    C) cytosine.
  119. Which of the following viruses causes a latent infection?

    D) herpes simplex virus
  120. During a retroviral infection, where is the RNA converted into DNA?

    D) in the cytoplasm within an uncoated viral core particle
  121. Viroids possess what type of nucleic acid?

    C) single-stranded RNA
  122. A prion particle contains:

    C) protein.
  123. Which of the following is NOT one of the three distinct mechanisms by which prion disease occurs?

    A) endogenous prion disease
  124. Which statement regarding the cytoplasmic membrane is NOT correct?

    B) The cytoplasmic membrane is a highly fluid structure in which proteins are free to move among the phospholipids.
  125. In a peritrichous arrangement of flagella, how are the flagella distributed over the organism?

    A) Multiple flagella are randomly dispersed over the cell surface.
  126. ABC System refers to:

    A) the ATP-binding cassette.
  127. The outer portion of the outer membrane is, for the most part, composed of:

    A) lipopolysaccharide.
  128. Which cell surface structure can also be used as a receptor by certain viruses?

    D) pili
  129. Which of the following statements regarding the cell wall of bacteria is NOT correct?

    C) It is composed of a repeating framework of lipids.
  130. The outermost layer of the outer membrane is composed of:

    C) lipopolysaccharide.
  131. Species of the Euryarchaeota include all the following EXCEPT:

    D) photoautotrophs.
  132. What is always a product of a methanogenic reaction?

    B) CH4
  133. Where does oxidative phosphorylation take place within an aerobic eukaryote?

    C) the mitochondrion
  134. hloroplasts are found in all the following organisms EXCEPT:

    D) photosynthetic prokaryotes.
  135. Where in a eukaryotic cell are 70S ribosomes found?

    D) They are found within the mitochondria of a eukaryotic cell.
  136. The energy to drive motility in
    motile eukaryotes is derived from a protein called ________, which is
    attached to tubulin and functions as an ATPase.

    A) dynein
  137. Which of the following protists are animal parasites?

    B) apicomplexans
  138. To obtain iron, some bacteria produce phenolic siderophores called:

    C) enterobactin
  139. In oxidative phosphorylation, ATP is produced:
    at the expense of the proton motive force.
  140. Chemolithotrophs use what compound as a carbon source?

    D) carbon dioxide
  141. Under which of the following conditions would a lag phase NOT occur?

    C) An exponentially growing culture is transferred into the same medium under the same conditions of growth.
  142. The most important environmental factor affecting the growth and survival of microorganisms is:

    B) temperature.
  143. Organisms capable of causing disease in humans and animals are of which temperature class?

    B) mesophiles
  144. Which of the following statements about thermophiles/hyperthermophiles is NOT correct?

    produced at high levels and help to stabilize proteins.
    d) Their proteins have an increased number of ionic bonds between basic and acidic amino acids and their often highly hydrophobic interiors.
    • A) The amino acid sequence of their enzymes differ greatly from those
    • of the heat-sensitive forms of the enzymes that catalyze the same
    • reaction in mesophiles.
  145. In which habitat would you expect to find aerobic prokaryotes?

    B) the ocean surfaces
  146. To live in the presence of oxygen, an organism must possess:

    D) superoxide dismutase and either catalase or peroxidase
Card Set
Biol 120 Exam 1 part 1
Exam 1 Flashcards