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2013-03-13 02:59:39
biochem exam

second exam
Show Answers:

  1. Enzyme Characteristics
    • -specific
    • -regulated in several ways
    • -transform energy
    • -don't move equilibrium
    • -stabilize transition state
    • -active site cleft
    • -change in response to correct substrate
  2. Enzyme Regulation
    • Oxidoreductases
    • Transferases
    • Hydrolases
    • Lyases
    • Isomerases
    • Ligases
  3. oxidoreductases
    oxidation- reduction
  4. transferases
    group transfer
  5. hydrolases
    hydrolysis reactions
  6. lyases
    add/remove bonds to form double bonds
  7. isomerases
    intramolecular group transfer
  8. ligases
    ligation of 2 substrates at the expense of ATP hydrolysis
  9. Gibb's free energy (5 statements)
    • 1. a rxn can only take place spontaneously if changeG<0
    • 2.if changeG=0 system is at equilibrium; no net change
    • 3. if changeG>0 an input of free energy is required to drive the rxn
    • 4.changeG of a rxn is independent of the path of transformation
    • 5.changeG provides no information about the rate of the rxn
  10. Gibb's free energy equation
    • changeG = changeH - TchangeS
    • (not at equilibrium)
    • at equilibrium changeG=0
  11. when standard conditions are applied the value of free energy change will be:
    • Standard free energy change
    • changeG0'
  12. Michaelis Menten Equation

    • S=substrate
    • Vmax=maximal rate
    • V0=slowest rate of reaction
  13. Rate constants
    • lowercase k
    • only look at a rxn in a single direction
  14. equilibrium constants
    • look at rxn in both directions
  15. Michaelis Menten Equation graphs as
    rectangular hyperbola
  16. allosteric enzymes graph
    • sigmoidal curve
    • multiple interacting active sites
  17. lineweaver burk plot aka..
    double reciprocal plot
  18. k2
    • turnover number: duration of contact between enzyme and substrate.
    • high turnover means a fast enzyme and vice versa.
  19. Km
    • Michaelis constant
    • substrate concentration at which the reaction rate is half of its max value.
  20. Vmax
    maximum rate of the reaction
  21. competitive inhibition
    • inhibitor combines with enzyme at the active site
    • Vmax gets lower as if less enzyme were present
  22. noncompetitive inhibition
    • doesn't prevent substrate from binding
    • decrease turnover number
  23. epimers
    sugars that are diastereomers and differ at only one asymmetric center
  24. diastereomers
    isomers that are NOT mirror images
  25. enantiomers
    isomers that are mirror images of each other
  26. constitutional isomers
    differ in order of attachment
  27. ketal
    two alkoxy groups to the same carbon
  28. acetal
    two hydroxyl groups to the same carbon
  29. hemiacetal/hemiketal
    • one hydroxyl
    • one alkoxy
  30. reducing sugar
    sugars that react all called reducing sugars
  31. glycosidic linkage
    • attachment at the anomeric carbon
    • bond formed between the anomeric carbon and the oxygen of an alcohol
  32. lactase digests
  33. starch
    • nutritional resevoir in plants
    • is a storage form of glucose
    • polysaccharide
  34. cellulose
    • major polysaccharide found in plants
    • most abundant
    • structural role
  35. glycogen
    • major polysaccharide found in plants for storage of energy
    • storage form of glucose
  36. alpha and beta anomers
    • alpha: OH group is on opposite side of the ring as the anomeric carbon (CH2OH)
    • beta: OH group is on the same side of the ring as the anomeric carbon
  37. to name the keto form of a sugar
    change the aldo form from -ose to -ulose
  38. mutarotation
    the chemical inversion of alpha and beta anomers
  39. Gluconic acid
    COOH at C-1
  40. Glucoronic
    COOH at C-6
  41. glucaric acid
    COOH at c-1 and c-6
  42. furanose
    5 membered ring
  43. pyranose
    6 membered ring
  44. how do archae membranes differ from eukarya membranes?
    • 1. joined by ETHERS rather than ESTERS (more resistant to hydrolysis and extreme environments)
    • 2. alkyl chains are BRANCHED not linear (resistant to oxidation)
    • 3.central glycerol is INVERTED. Have different lipids (no fatty acids).
  45. membrane properties
    • 1.sheetlike
    • 2.lipids and proteins
    • 3.hydrophilic and hydrophobic
    • 4.specific proteins mediate functions
    • 5.noncovalent assemblies
    • 6.asymmetric
    • 7.fluid structures
    • 8.electrically polarized
  46. peripheral membrane proteins
    • not attached to the membrane itself
    • attached to membrane elements
  47. integral membrane proteins
    • attached permanently to the living cell
    • PART of the membrane
  48. phospholipase B2
    • found in bee and snake venom
    • frees arachonoic acid- causes pain
  49. arachonoic acid
    • 20 carbons and 4 double bonds 5,8,11,16
    • gives rise to inflammation process
    • fatty acids stick together
    • aspirin interferes with the process
    • activated by prostaglandin
  50. aspirin
    • fights pain and inflammation
    • blocks cyclooxygenase which is an enzyme that activates prostaglandin synthesis and cause pain, shock and immobilization
  51. proteins are capable of what kind of diffusion?
    lateral diffusion but not able to flip flop or leave the membrane
  52. prostaglandin
    • promotes inflammation
    • integral protein
    • activated by arachonoic acid
  53. lipid bilayers are highly impermeable to
    ions and most polar molecules
  54. oligosaccharides are located
    outside of the cell
  55. gram positive bacteria
    • "i am positively blue over you"
    • stained blue
    • primitive bacteria; first to exist
    • large cell membrane
    • must stay at source of food to eat
  56. gram negative bacteria
    • have a small cell membrane
    • two cell walls; one for protection one for permeability
    • have prions (stomachs) can take food to go and digest
  57. pumps are used for _________ transport
  58. channels are used for _________ transport
  59. facilitated diffusion / passive transport
    • form of passive transport
    • has a Vmax which means there is a max rate of exit or entry so graph is a rectangular hyperbola
    • uses channels; ligand-gated which means door must be opened by something
  60. primary active transport
    • requires energy to take place
    • moves against the gradient
    • usually involves ions
    • utilizes pumos
  61. secondary transport
    • doesnt require ATP
    • carries molecules uphill
    • associates unfavorable molecules with ones that are more favorable
    • antiporters or symporters
  62. ion channels
    • allows ions to flow across membranes 
    • gated by needing a certain ligand or voltage
    • central to the functioning of our nervous systems
  63. gap junction
    • allows the flow of metabolites or ions between cells
    • made up of 12 molecules of connexin
  64. free energy is MAXIMIZED when
    there is an unequal distribution of molecules
  65. Keq for osmosis?
  66. antiporters
    • 2 different species flowing in opposite directions
    • ex: Na+ can only enter when K+ leaves
  67. symporters
    • use the flow of one species to drive another species into the cell in the same direction
    • "you can only come to the party if you bring a date"
    • ex: glucose usually moves against the gradient but it can go inside the cell if it goes with sodium
  68. digitalis
    inhibits dephosphorylation disrupts Na+ equilibrium and makes there have more INSIDE the cell which leads to a slower extrusion of Ca+ which leads to heart problems (enhanced heart contractions)
  69. MDR multidrug resistant protein
    • removes drugs that enter the cell by pumping them out before it has an effect
    • ex: P-glycoprotein
  70. ABC transporters
    • have an ATP binding cassette (2 ATP binding domains)
    • 1. MDR
    • 2. CFTR
    • are in contact but dont bind strongly without ATP
    • mechanism involves scissoring of 2 subunits
  71. CFTR cystic fibrosis transmembrane regulator
    • transports Na and Cl
    • in cystic fibrosis the Cl- transporter malfunctions which causes  NaCl on the skin which causes problems
  72. patch clamp technique
    • enables ion conductance measurement through the path of a cell membrane
    • pipette with two electrodes and the part of the cell that the electrode is suctioned to will have the same ion conductance read by the electrodes
    • the flow through a single channel can be measured with time resolution in microseconds
  73. excised
    • detachment via pulling in the patch clamp technique
    • dont know how many channels you're getting can see channel opening and find out how many ions go through per second
  74. whole cell mode
    • entire cell and plasma membrane monitored
    • suctioning the whole cell
    • less useful than excised, less precise
  75. acetylcholine receptor
    • best understood ligand-gated channel
    • binding of acetylcholine leads to the opening
    • densely packed receptor (20,000 μm)
  76. acetylcholine process
    • Acetylcholine is released from the pre-synaptic membrane inresponse to depolarization.
    • It travels across the synapse and "pushes a button" on the receptor which opens a ligand gated sodium channel, allowing Na+to flow in.
    • Then potassium channels open, allowing K+ to flow out.
  77. Acetylcholinesterase
    • composed of 5 subunits
    • anchored to post synaptic membrane (glycolipid tethered there)
    • rotation effect; all units break right then opens up
    • turnover 25,000/sec
    • binding two causes receptor to open
  78. nerve gas
    • inhibits acetylcholinesterase
    • will kill you
  79. 7 transmembrane helix receptors 7TM
    • responsible for transmitting information initiated signals such as hormones, smells, taste
    • when ligands bind to this receptor they initiate G-proteins
    • passes through the membrane 7 times
  80. G Proteins
    • activates adenylate cyclase
    • activated by 7TM receptors bind with ligands
  81. adenylate cyclase
    • turns cyclicAMP to ATP
    • increases concentration of cAMP
  82. phospholipase c
    • activated by g proteins
    • cleavage of Phosphatidyl Inositol Bisphosphate into 2 parts
    • 1.IP3
    • 2.DAG
  83. IP3
    opens calcium channels
  84. DAG
    activates protein kinase c
  85. PIP2
    • phosphatidyl inositol bisphosphate
    • cleavage results in release of calcium and activation of protein kinase C
  86. what binds to protein kinase C to help its activation?
  87. calmodulin
    • detects influx of Ca2+
    • binds 4 ions that changes it shape
  88. protein kinase C
    • activated by cleavage of pip2
    • stimulates expression of other genes by phosphorylation of the CREBS transcriptional activation cycle
    • phosphorylates target proteins
  89. RRGSI vs. RRGAI
    • enzyme looks for RRGSI but finds close match, RRGAI, but enzyme cant phosphorylate this so RRGAI acts like a chew toy
    • presence of S is real substrate
  90. endoplasmic reticulum
    calcium resevoir in cell
  91. cofactors
  92. "coupling" ATPhydrolysis with another reaction changes the standard free energy change by
    -7.3 kCal/mol which dramatically changes Keq
  93. coupling reactions
    couple favorable with unfavorable to drive the reaction
  94. 3 stages of catabolism
    • 1. digestion- proteins hydrolyzed to AA, polysaccharides to simple sugars, fats to glycerol & fatty acids. NO USEFUL ENERGY. Prep stage.
    • 2. conversion to acetyl units in acetyl CoA. Some ATP generated but not much compared to 3rd. 2 ATP

    • 3.complete oxidation of acetyl unit in acetyl CoA to ATP
    • . acetyl coa brought into the citric acid cycle where it is completely oxidized proton gradient is created which is used to synthesis ATP. 28-36 ATPS.
  95. ligation reaction
    forms covalent bonds but requires free energy from ATP cleavage
  96. atkin's energy charge
    • energy charge regulates metabolism
    • ATP generating pathways (catabolic) are inhibited by high energy charge whereas ATP utilizing pathways (anabolic) pathways are stimulated by high energy charge