bio 1 test 2

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bio 1 test 2
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bio 1 test 2
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  1. amphipathic
    both hydrophilic and hydrophobic portions (phospholipid and membrane proteins)
  2. fluid mosaic model
    membrane is a fluid structure with with a "mosaic" of various proteins embedded in or attached to (floating in) a double layer (bilayer) of phospholipids.
  3. membranes are held together by
    hydrophobic interactions. Weak-ish, so phopholipids and some proteins shift about laterally.
  4. do membrane proteins move?
    Yes--drift in the fluid mosaic (red and purple dots figure)
  5. Do all membrane proteins drift?
    No, some are held in place by cytoplasmic attachment or extra cellular matrix attachment and some move along cytoskeletal fibers
  6. temperature membrane solidifies at depends on
    saturation and cholesterol
  7. cholesterol's effect on the membrane at different temperatures.
    Fluiditiy buffer. At high temperatures, makes membrane less fluid, but at low temperatures keeps liquid longer.
  8. How is temperature a challenge for life?
    membranes solidify, become differently permeable, and some proteins can't solidify
  9. integral proteins
    those that penetrate the hydrophobic interior of the phospholipid bilayer. Mostly transmembrane proteins.
  10. Transmembrane proteins
    span the membrane
  11. Peripheral Proteins
    not embedded in bilayer at all
  12. what are proteins attached to?
    When not simply floating, the extracellular matrix outside and the cytoskeleton inside
  13. 6 major functions perfomed by proteins of plasma membrane
    • Transport
    • Enzymatic activity
    • Signal transduction
    • Cell-cell recognition
    • intercellular joining
    • attachment to cytoskeleton and extracellular matrix (maintain shape and stabilize proteins)
  14. cells recognize other cells by
    binding to molecules, often containing carbohydrates, on the surface
  15. glycolipids
    carbohydrates on cell surface bonded to lipids
  16. glycoproteins
    carbohydrates on cell surface bonded to proteins
  17. what goes through the membrane?
    nonpolar molecules, such as hydrocarbons, carbon dioxide and oxygen. Water, glucose and other sugars pass very slowly through.
  18. how to polar molecules get through membrane
    transport proteins
  19. channel proteins
    hydrophilic channel or tunnel through protein
  20. aquaporins
    water channels through membrane, speeding up water intake
  21. carrier proteins
    take on passengers and change shape to shuttle them across membrane. Very selective--glucose but not fructose.
  22. passive transport
    diffusion aross a membrane with no energy investment
  23. diffusion
    the movement of molecules of any substance so that they spread evenly into available space. Substances will move from higher concentration to lower. Spontaneous process of passive transport
  24. Concentration gradient
    the region along which the density of a chemical substance increases or decreases.
  25. what kind of energy is concentration gradient
    potential energy
  26. free water
    unbound water uses osmosis to balance its concentration gradient
  27. osmosis
    diffusion of free water across a selectively permeable membrane
  28. hypertonic solution
    more non-penetrating solutes, so less water, so water from the cell leaves and the cell shrivels or crenelates.
  29. hypotonic solution
    has less solute particles and therefore more free water, so the cell will gain water and eventually lyse.
  30. osmoregulation
    control of solute concentrations and water balance
  31. turgor pressure
    the pressure of water on the cell walls of a plant cell to make the cell turgid
  32. healthy state of a plant cell
    turgid
  33. when a plant cell is flaccid in hypertonic solution it is
    plasmolyzed
  34. facilitated diffusion
    passive diffusion with the help of transport proteins
  35. ion channels
    channel proteins that move ions. Many are gated
  36. gated channels
    open and close in response to a stimulus
  37. active transport
    uses energy to move solutes against their gradients
  38. what type of proteins participate in active transport
    carrier proteins (NOT channel proteins)
  39. sodium-potassium pump
    pumps 3 sodium out of the cell and 2 potassium into the cell with use of ATP
  40. charges of membrane
    cytoplasmic side is negative and the extracellular side is positive.
  41. membrane potential
    voltage across a membrane
  42. electrochemical gradient
    the two forces drving the diffusion of ions across a membrane: chemical (ion concentration gradient) an electrical (membrane potential)
  43. electrogenic pump
    transport protein that generates voltage across a membrane (Na-K pump)
  44. proton pump
    main electrogenic force in plants, fungi and bacteria. makes cytoplasm negative
  45. cotransport
    pump one substance "uphill", and on it's "downhill", it picks up something else and transports it against its gradient. Hydrogen atoms bring sucrose back inside the membrane with them in plant cells
  46. exocytosis
    cell secretes biological molecules by fusing vesicles with the cell membrane
  47. endocytosis
    cell takes in matter by budding vesicles off the plasma membrane. 3 types: phagocytosis, pinocytosis, and receptor-mediated endocytosis
  48. phagocytosis
    cell eating. Food vacuole fuses with lysosome
  49. pinocytosis
    cell drinking. Nonspecific--takes droplets into cell
  50. receptor-mediated endocytosis
    a receptor protein binds to ligands the cell wants, then form a vacuole. After ingestion, the receptors are returned to outside by same vesicle.
  51. ligand
    any molecule that binds specifically to a receptor site on another molecule
  52. catabolic pathways
    break big molecules to small molecules (downhill) (breakdown pathways) (cellular respiration)
  53. anabolic pathways
    consume energy to build small molecules into big (uphill) (biosynthetic pathways) Never spontanious
  54. metabolism
    totality of an organisms chemical reactions. manages material and energy resources. Never at equilibrium
  55. metabolic pathway
    starting molecule--altered in series of steps, each with enzyme--results in product
  56. bioenergetics
    study of how energy flows through living organisms
  57. energy
    capacity to cause change. All work of life includes cells using energy
  58. to speed up chemical reaction
    • add heat (kinetic energy, molecules moving faster)
    • add substrate/enzyme
  59. exergonic
    giving off free energy. Spontanious
  60. endergonic
    free energy going in. Needs energy to happen
  61. negative feedback
    end product inhibits earlier step in synthesis. Maintains constant chemical condition
  62. work
    move matter against opposing forces
  63. chemical energy
    potential energy available for release in a chemical reaction
  64. thermodynamics
    the study of energy transformations that occur in a collection of matter
  65. isolated system
    unable to exchange energy or matter with its surroundings
  66. open system
    energy and matter can be transferred between the system and its surroundings
  67. first law of thermodynamics
    principle of conservation of energy--can be transformed or transferred but cannot be created or destroyed
  68. second law of thermodynamics
    every energy transfer or transformation increases the entropy or disorder of the universe. For a process to occur spontaniously it must increase the disorder of the universe
  69. spontantious and nonspontanious processes
    spontanious is energetically favorable. Nonspontanious will not happen without energy input
  70. free energy
    the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system (delta G=delta H-TdeltaS). Processes with negative deltaG are spontanious. High G wants to be lower G--more stable. A process can perform work and is spontanious only when moving towards equilibrium
  71. 3 types of work of cells
    • chemical (pushing of endergonic)
    • transport (pumping of substances against)
    • mechanical (beating of cilla, muscle cells)
  72. energy coupling
    use of an exergonic process to drive an endergonic one
  73. ATP (adenosine triphosphate) structure and hydrolysis
    sugar ribose with nitrogenous base adenine and 3 phosphate groups (used to make RNA). Hydrolysis makes it P + ADP by breaking off a phosphate. spontanious, releases lots of energy. Couples with endergonics to make exergonic couples
  74. enzyme
    macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by it. Specificity results from shape. Shape is fluid-ish.
  75. activation energy
    initial investment of energy for starting a reaction. Enzymes lower this barrier.
  76. substrate
    the reactant an enzyme works on
  77. enzyme-substrate complex
    when the enzyme binds to its substrate.
  78. active site
    the specific portion of the molecule that binds to the substrate
  79. induced fit
    substrate-enzyme fit that holds substrate in the best possible position for reaction. Substrate is held by hydrogen and ionic bonds, and turned into products by R-group interactions
  80. Enzyme mechanisms to speed reaction
    • hold two molecules in proper orientation
    • stretch or bend molecule into optimal shape
    • provide conducive microenvironment
    • direct participation of active site in reaction. Enzyme is restored afterwards.
  81. saturated enzymatic reaction
    So many substrate molecules exist that all enzyme active sites are busy. Reaction cannot speed up more without more enzymes.
  82. optimal conditions for enzymes
    rection increases with increasing temperature as molecules move faster until heat interferes with bonds and eventually denatures protein. pH is the same.
  83. cofactors
    nonprotein helpers for catalytic activity
  84. coenzyme
    an ORGANIC nonprotein helper for catalytic activity
  85. inhibitors
    chemicals that stop enzymes. Covalent bonds mean irreversable inhibition
  86. competitive inhibitor
    reversable enzyme inhibitor that resembles the substrate and competes for admission to active site. Can be overcome by increasing substrates
  87. noncompetitive inhibitors
    bind to allosteric site
  88. allosteric regulation
    a protein's function at one site is affected by the binding of a regulatory molecule to a separate site.
  89. activator vs inhibitor
    molecule binds to a regulatory or allosteric site in to hold it in active or inactive form. Will affect all subunits on enzyme
  90. cooperativity
    amplifies the response of enzymes to substrates. A substrate bonding to an active site triggers a shape changes, increasing catalytic activity.
  91. feedback inhibition
    a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway
  92. fermentation
    a catabolic process that is a partial degredation of sugars/organic fuels without oxygen. occurs in cytosol. Alcohol and lactic acid types. Produce much less ATP than aerobic
  93. -ase
    enzyme
  94. uses of ATP
    powering NA/K pump, muscle contraction, anabolic reactions, cytoplasmic streaming
  95. cellular respiration formula
    • C6H12O6 + 6O2 ---> 6H2O + 6CO2
    • = -deltaG, so exergonic
  96. Where does glycolyis occur
    cytoplasm
  97. glycolysis Carbon activity
    1 glucose in, 2 pyruvic acid out
  98. Energy product gain of glycolysis
    2 ATP and 2 NADH
  99. Redox reaction
    an oxidation-reduction reaction where there is a transfer of electrons from one reactant to another. Can also work with unequal sharing--oxygen is reduced from O2 to 2H2O because it has closer bonds with the elctrons in a polar setting
  100. Oxidation
    loss of electrons
  101. reduction
    gaining of electrons (O2-H2O)
  102. reducing agent
    electron donor in redox reaction
  103. oxidizing agent
    electron acceptor
  104. O2's role in cellular respiration
    terminal electron acceptor
  105. 4 steps of cellular respiration
    glycolysis, pyruvate oxidation, citric acid cycle, oxidative phosphorylation and chemiosmosis
  106. glycolysis
    cytosol--breaks glucose into 2 molecules of pyruvate
  107. oxidative phosphorylation
    ATP synthesis powered by redox reactions of the electron transport chain.
  108. site of oxidative phosphorylation (electron transport chain and chemiosmosis)
    inner membrane of the mitochondrion
  109. substrate-level phosphorylation
    enzyme transfers a phosphate group from a substrate molecule to ADP. Happens in glycolysis and citric acid cycle
  110. How much ATP per glucose
    32 molecules
  111. aerobic respiration
    oxygen is a reactant
  112. net glycolysis inflow and outcome
    • 1 glucose in, 2 pyruvate and 2 water out
    • 2 ATP in, 4 ATP out= 2 ATP
    • 2NAD+, 4 electrons and 4 protons in, 2 NADH and 2 protons out
  113. where does aerobic or anaerobic respiration begin?
    after pyruvate formation (in the cytosol)
  114. what are the types of fermentation
    alcohol and lactic acid. Ethanol done by some bacteria and plants. All occur in cytosol.
  115. what is champagne an example of
    alcoholic fermentation. The bubbles are carbon dioxide. Must be made without oxygen in a closed container.
  116. what are the products of pyruvate oxidation
    for 2 pyruvate (2 per 1 glucose) 2 CO2 released, 4 NADH are made, 2 Coenzyme A are consumed, 2 Acetyl CoA (exergonic, high potential energy) are produced.
  117. where does pyruvate oxidation/Acetyl CoA formation occur
    Pyruvate begins oxidation in the cytosol and becomes Acetyl CoA in the matrix of the mitochondrion after moving across 2 membranes.
  118. citric acid cycle generates:
    3 NADH, 1 ATP and 1 FADH per turn (so double that b/c 2 pyruvate per glucose) and gives off 2 CO2.
  119. The citric acid cycle has ____ steps
    8
  120. Where does the citric acid cycle occur
    mitochondrial matrix
  121. Where does oxidative phosphorylation occur
    Inner mitochondrial membrane (cristae)
  122. Purpose of electron transport chain
    to pump protons out of the cell to make pH of intermembranal space more acidic. pH gradient is used to make ATP with ATP Synthase (chemiosmosis)
  123. superhighway of metabolism
    carbohydrates
  124. what is the electron transport chain
    a collection of molecules embedded in the inner membrane of the mitochondrion in eukaryotic cells
  125. Where do the first electrons for the electron transport chain come from
    NADH
  126. At the end of the electron transport chain
    Oxygen accepts the two electrons, reducing, and picks up two protons in the solution and forms water
  127. ATP Synthase
    the protein in the inner membrane of the mitochondria that makes ATP from ADP and phosphate.
  128. what is the net product of oxydative phosphorylation
    26-28 ATP
  129. what powers ATP synthase?
    the difference in the concentration of H+ on either side of the inner mitochondrial membrane tries to equalize, spinning the rotor to do work
  130. chemiosmosis
    energy in the form of a hydrogen ion gradient across a membrane drives cellular work such as the synthesis of ATP
  131. what makes the proton gradient in the mitochondria?
    electron transport chain puts more H+ between the inner and outer mitochondrial membrane and less inside the cristae using electrons from NADH and FADH
  132. why does FADH produce less energy than NADH
    enters the electron transport chain at a lower place.
  133. total ATP output from one glucose molecule
    oxidized to 6CO2, 30-32 ATP
  134. difference between anaerobic respiration and fermentation
    an electron transport chain is used in anaerobic respiration but not in fermentation
  135. How does anaerobic respiration differ from aerobic?
    Oxygen is not the electron acceptor at the end. Sulfer can be, or something else
  136. fermentation
    the continuous generation of ATP by the substrate-level phosphorylization of glycolysis.
  137. lactic acid fermentation releases
    lactate No CO2
  138. similarities and differences in respiration types
    All use glycolysis to make pyruvate and use NAD+ as an electron acceptor. They differ in how to oxidize NADH back down.
  139. obligate anaerobes
    cannot carry out aerobic respiration or survive in the presence of oxygen.
  140. facultative anaerobes
    can survive with either fermentation or respiration
  141. deamination
    process during dygestion of proteins where amino groups are removed prior to entering glycolysis
  142. beta oxidation
    breaks down fatty acids into two-carbon fragments which enter the citric acid cycle as acetyl CoA, generating NADH and FADH2
  143. equation for photosynthesis
    • 6CO2 + 6H2O --chll a--> C6H12O6 + 6O2
    • exact opposite of cellular respiration. Endergonic, catabolic.
  144. autotrophs
    self-feeders, like plants. "producers" of the biosphere
  145. heterotrophs
    live on compounds produced by other organisms
  146. site of photosynthesis
    chloroplasts (leaves)
  147. mesophyll
    tissue in the interior of the leaf, where chloroplasts are usually found
  148. stomata
    microscopic pores where CO2 enters and oxygen exits.
  149. chloroplast
    2 membranes surrounding a dense fluid called the stroma. Suspended in the stroma are thylakoids stacked in columns called grana. Inside these is the thylakoid space. The thylakoid membrane has chlorophyll
  150. Thylakoid
    suspended in the stroma, the membrane that holds the chlorophyll and the space inside, called the thylakoid space.
  151. Stroma
    dense fluid inside the membranes of the chloroplast that suspends the thylakoids
  152. direct product of photosynthesis
    oxygen and a 3-carbon sugar that can be used to make glucose. water is on both sides of the equation--12 go in and 6 come out.
  153. redox reaction of photosynthesis
    CO2 reduces to C6H12O6 and H2O oxidizes to O2. Process requires energy and is endergonic
  154. two stages of photosynthesis
    light reactions and calvin cycle
  155. Light reactions
    takes in H2O, light, NADP+, ADP and Phosphate ion and give off NADPH, ATP and O2.
  156. photophosphorylation
    light energy using chemiosmosis to power the addition of a phosphate to ADP
  157. carbon fixation
    initial incorporation of carbon into organic compounds
  158. site of light reactions
    thylakoids of the chloroplast
  159. site of calvin cycle
    stroma
  160. How do protons effect pH
    more protons make pH more acidic (lowers).
  161. wavelength
    distance between the crests of electromagnetic waves
  162. electromagnetic spectrum
    entire range of radiation
  163. visible light
    380-750n. violet is 380-red is 750
  164. photons
    the particles of light. Not really particles, but each has a fixed amount of energy--the shorter the wavelength, the more energy
  165. pigments
    particles that absorb visible light
  166. light absorption versus wavelength graph
    absorption spectrum
  167. chlorophyll a
    participates directly in light reactions
  168. accessory pigments and use
    chlorophyll b and the carotenoids. Photoprotection--sunscreen and sometimes energy transfer
  169. which lights are best for photosynthesis?
    violet-blue and red. Green is the least effective
  170. action spectrum
    profiles the relative effectiveness of different wavelengths of radiation in driving a process. The living version of the absorption spectrum
  171. Englemann 's photosynthesis experiment
    bacteria to measure the rates of photosynthesis in algae. Match to action spectrum.
  172. fluorescence
    when the energy harvested from the sun in chloroplasts has no where to go, it will give off light and heat
  173. carotenoids
    carotene and xanthophyll
  174. chromotology
    separating chemicals but putting them in a nonpolar solution and seeing who travels the furthest (most nonpolar)
  175. reaction center complex
    holds the special chlorophyll molecules (P680 and P700) and the primary electron acceptor.
  176. light harvesting complex
    has the regular chlorophyll a, b and carotenes bound to proteins.
  177. photosystem
    the reaction center complex surrounded by the light-harvesting complexes. There are 2 in photosynthesis, #2 comes first. In the thylakoid membrane
  178. why 680 and 700?
    those are their favorite wavelengths
  179. linear electron flow
    light excites the electrons of P680, so they go to the electron acceptor, down the transport chain, making ATP, falling further to P700, where they get exited again by light and fall down another chain to make NADPH. Photosystem II breaks water to get electrons back
  180. cyclic electron flow
    only uses photosystem I, only makes ATP, does not generate NADPH or oxygen
  181. how are chloroplasts and mitochondria similar?
    Both have double membrane and DNA, both generate ATP with an electron transport chain pumping protons across a membrane then synthesizing ATP with the resulting gradient (chemiosmosis)
  182. where is the proton gradient in photosynthesis
    the thylakoid space functions as the H+ reservoir. ATP is synthesized as hydrogen ions diffuse back to the stroma through ATP synthase, so ATP forms in the stroma where the Calvin cycle is
  183. calvin cycle
    uses the energy of ATP and NADPH to reduce CO2 to sugar
  184. cycle
    starting material is regenerated after molecules enter and leave the cycle (calvin and citric acid)
  185. Differences between Calvin and Citric acid cycles
    citric acid cycle is catabolic and Calvin cycle is anabolic.
  186. three phases of the calvin cycle
    carbon fixation, reduction and regeneration
  187. calvin cycle carbon fixation phase
    incorporates CO2 molecule, attaches it to RuBP (5-C sugar). Enzyme that catalyzes is Rubisco. Product is two molecules of a 3-C sugar
  188. rubisco
    enzyme that fixes carbon into RuBP in the first step of the Calvin Cycle. Most abundant protein in chloroplasts and possibly on earth.
  189. Calvin cycle reduction phase
    3-C sugar gets an extra phosphate from ATP and gets reduced by NADPH to make 3-C sugar. One gets released for use in the plant and 5 go back to regeneration phase
  190. Calvin cycle regeneration phase
    5 2-C sugars are rearranged into 3 5-C RuBPs.
  191. Calvin cycle in and out
    • 3 CO2 in = 1 G3P out
    • 9ATP in = 9 ADP out
    • 6 NADPH in = 6 NADP+ out
  192. photorespiration
    when stomata close to conserve water, oxygen builds up and carbon dioxide runs down, plants use (rubisco fixes) O2 instead of CO2 and produce a 2-C compound instead. Peroxisomes and mitochondria split this compound, releasing CO2. Produces no ATP but uses some, and produces no sugar. Releases CO2 the plant would otherwise use.
  193. Uses of wasteful photorespiration
    protects against excess light. C4 plants and CAM plants have found ways to mostly avoid it
  194. C3 plants
    Rice, wheat and soy.
  195. C4 plants
    sugarcane and con
  196. C4 photosynthesis
    C4 plant leaves have bundle-sheath cells and normal mesophyll cells. Calvin cycle is in chloroplasts of bundle-sheath. PEP carboxylase in mesophyll cells fixes CO2 into a 4-C product and exports through plasmodesmata to bundle-sheath and Calvin.
  197. bundle-sheath cells
    tightly-packed sheaths around veins of leaf in C4 plant. Where Calvin cycle takes place in C4. Also use cyclical electron flow with no photosystem II to generate ATP.
  198. C4 mesophyll cells
    have PEP carboxylase enzyme that fixes CO2. Export CO2 and 4-C compound to bundle-sheaths through plasmodesmata so rubisco will not fix oxygen.
  199. PEP carboxylase
    enzyme in mesophyll cells of C4 plants that makes a 4-C product out of CO2. Higher affinity for CO2 than rubisco and none for O2. Can fix C when stomata are closed. Can be thought of as CO2 pump into bundle-sheath powered by ATP
  200. CAM plant adaptations
    open stomata during night and close during day, storing CO2 products in vacuoles. Have Calvin cycle and carbon fixation in same cell at different times.

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