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2011-09-08 14:04:13
amino acid protein nucleic lipid DNA RNA biomolecules water enzymes

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  1. What are the 4 classes of biomolecules?
    Proteins, Nucleic acids, Carbohydrates, Lipids
  2. What are nucleic acids?
    -"informational biomolecules"
  3. What are nucleotides?
    Polymers of 3 components:

    • 1) nitrogenous base (purine or pyrimidine)
    • 2) pentose sugar (deoxyribose or ribose)
    • 3) phosphate groups (1, 2, or 3)
  4. Why is the polymerization of carbon possible in living systems and not silicon?
    • -carbon is smaller in size
    • -the byproduct of the combustion of our fuel is CO2 which is soluble in water at normal temps
  5. Name some functions of proteins with examples
    • -signalling: hormones like insulin
    • -structural: muscle proteins
    • -defense: immunoglobulins
    • -catalysts: enzymes
  6. What are the 2 types of bases in nucleic acids?
    Purines and Pyrimidines
  7. Name the 3 purines
    1) Purine 2) Adenine 3) Guanine
  8. Name the 4 pyrimidines
    • 1) Pyrimidine
    • 2) Cytosine
    • 3) Uracil [[RNA only]]
    • 4) Thymine [[DNA only]]
  9. What are the 2 pentose sugars in nucleic acids and what is the main difference between them?
    • -ribose [4 OH groups]
    • -deoxyribose [3 OH groups] has 1 less oxygen
  10. nucleoside = ________ + _________
    nucleoside = nitrogenous base + sugar
  11. Nucleic acids have a ________ backbone
    Nucleic acids have a sugar-phosphate backbone
  12. Explain the process of creating a protein from DNA
    1 ) ________(DNA=>DNA) via _____________
    2 ) ________(DNA=>RNA) via _____________
    3 )________(RNA=>protein) via ____________
    • 1 ) replication (DNA=>DNA) via DNA polymerase
    • 2 ) transcription (DNA=>RNA) via RNA polymerase
    • 3 ) translation (RNA=>protein) via ribosome
  13. mRNA :
    tRNA :
    rRNA :
    • mRNA : code for proteins
    • tRNA : brings AA's to ribosomes
    • rRNA : builds AA chain
  14. What do membrane bound organelles do?
    • transmit signals in / out of the cell
    • allow for the passage of molecules in / out of the cell
    • are molecule specific
  15. What 3 protein filaments give the cell shape and structure while helping organelles move around safely?
    microtubules, microfilaments, intermediate filaments
  16. TEST ? #3 - What organelle(s) have a double membrane?
    nucleus and mitochondria
  17. TEST ? #4 - __________ is a membrane bound organelle filled with digestive enzymes present in eukaryotic cells
  18. TEST ? #5 - What property of water is important for biological interactions?
  19. TEST ? #6 - What happens to nonpolar molecules in water?
    they aggregate together
  20. TEST ? #1 - What biomolecules present in all living organisms play a role in signalling?
    proteins and lipids
  21. TEST ? #2 - Thymidine is a component of RNA (T/F)
    False - Thymidine is a component of DNA
  22. A water molecule has _______ geometry
  23. Special property of water:

    #1 - Water is a __________
    Water is a DIPOLE

    Polarity makes water a good solvent for ions
  24. Special property of water:

    #2 - Hydrogen-bonds btw adjacent water molecules are _______ and _________ .
    Hydrogen-bonds btw adjacent water molecules are LABILE and TRANSIENT.

    Bonds are made and broken in a fraction of a second and these loose bonds give water unusually high surface tension and cohesiveness.
  25. Special property of water:

    #3 - Water is a great solvent for _____.
    • Water is a great solvent for IONS.
    • (i.e. - NaCl)

    *remember "like dissolves like"
  26. Special property of water:

    #4 - _________ dissolving
    SELECTIVE dissolving

    • Water dissolves certain organomolecules that do not dissociate into ions but do have polar properties.
    • (i.e. - alcohols, sugars, hormones)
  27. Special property of water:

    #5 - High ____ capacity.
    High HEAT capacity

    This means water is difficult to heat and, since the body is mostly water, body temp remains relatively constant.
  28. Special property of water:

    #6 - High latent heat of _________.
    High latent heat of EVAPORATION

    It takes a lot of energy to heat liquid water into vapor. This is why we sweat to lose heat and cool down.
  29. Special property of water:

    #7 - Relatively __________ .

    When a force is applied to it, it exerts nearly the same force.

    This makes blood pressure possible.
  30. Water disrupts ______ bonds
    • Water disrupts hydrogen bonds
    • H-bonds longer (weaker) than covalent bond and are easier to break
  31. Hydrogen bonds are _________ and therefore _________ than covalent bonds
    Hydrogen bonds are longer and therefore weaker than covalent bonds
  32. Name the 4 noncovalent bonds discussed in class
    • ionic bonds (aka electrostatic intrx)
    • hydrogen bonds
    • Van der Waals intrx
    • hydrophobic intrx
  33. Ionic or electrostatic interactions take place between atoms with _________________ and ____________________
    Ionic or electrostatic interactions take place between atoms with completely positive charge and completely negative charge
  34. What are Van der Waals interactions?
    The interaction of neutral atoms via electron shuttling of their electron clouds causing attraction/repulsion
  35. Define entropy
    • The measure of randomness...
    • More energy=less randomness=less entropy
    • Less energy=more randomness=more entropy
  36. ________________ drives protein folding
    Hydrophobic intrx
  37. What does water ionization mean?
    • Water molcs exhibit a slight but important tendency to dissociate into H+ and -OH
    • ***Water acts both as an acid (proton donor) and as a base (proton acceptor)
  38. Kw = [H+] [OH-] = ________(mol/L)2
    Kw = [H+] [OH-] = 10 -14 (mol/L)2
  39. pH = _____ [H+]
    pH = -log [H+]
  40. HA <=> H+ + A-
    Ka= ???
    • Ka=[H+][A-] / [HA]
    • (products over reactants)
  41. pH= ?????
    • pH= pKa + log ( [A-]/[HA] )
    • pKa is the pH when the acid is halfway dissociated
  42. Funtional groups only ionize at ________
    • Functional groups only ionize at certain pH
    • COO-....COO-....COOH
    • NH3+......NH2........NH2
    • pH>9.....pH2-9.....pH<2
  43. Weak acids buffer __________
    • Weak acids buffer strong acids
    • buffer needs to be +/- 1 pH of what it is trying to buffer
  44. What is the Bicarbonate Buffer System?
    H+ + HCO3- <=> H2CO3 <=> H2O + CO2
  45. TEST ? #7 -The Henderson-Hasselback equation is pH=pKa + log ( [A-] / [HA] ) . What is the base to acid ration if the equation is simplified to pH=pKa+1?
    10 to 1
  46. TEST ? #8 - What is an alpha-carbon.
    • Alpha-carbon is the carbon containing the R-group, COO- group, and the NH3+ group.
    • ***be able to identify for exam***
  47. Of the ~300 amino acids in nature, how many are in living systems?
  48. The _____ is distinctive for each amino acid
    side chain off the alpha carbon
  49. Only ___ amino acids are present in eukaryotes
    L-amino acids
  50. What is the amino acid called when it is carrying 2 ions, but has no net charge?
    the Zwitterionic form
  51. Where does the Zwitterionic form occur?
    at iso-electric pH
  52. Disulphide bonding occurs between _________
    Cystine - Cystine
  53. Hydroxyl and amide groups serve as ______
    site of attachment of sugars, phosphates, etc
  54. Tryptophan is the precursor of what?
  55. Tyrosine is the precursor of what?
  56. Arginine is the precursor of what?
    Nitric oxide
  57. The "typical pKa" or "isoelectric point" of an amino acid represents what?
    The point when half of the total number of molecules has dissociated
  58. What disease is due to inadequate protein intake and includes stunted growth, weakness, and distended belly?
  59. Methionine contains what?
  60. Aspartic acid has what kind of charge at cellular pH?
  61. Threonine carries a ________ group
  62. Lysine has what kind of charge at cellular pH?
  63. TEST ? #10 - What charged group(s) are present in glycine at a pH of 7?
    both A and B
  64. What are the 2 types of classes of proteins?
    • Fibrous-exist as long strings, tough, water insoluble
    • Globular-spherical, highly folded, water soluble
  65. What kind of structural levels can individual proteins reach?
    • primary, secondary, and tertiary
    • quarternary structures are formed by multiple proteins
  66. How many bonds does a Dipeptide have?
    How many does a Tripeptide have?
    • Dipeptide = 2 AA joined by ONE peptide bond
    • Tripeptide = 3 AA with TWO peptide bonds
  67. Carbonyl groups are H-bond _________
    Amino groups are H-bond _______
    These are essential for ___________ formation
    • Carbonyl groups are H-bond acceptors
    • Amino groups are H-bond donors
    • These are essential for secondary structure formation
  68. What is the mean molecular weight of an AA?
    How much does a protein with 5 AA's weigh?
    • 110 DALTONS
    • 5 AA x 110 Daltons = 550 daltons
  69. How many AA's are there in 360o rotation of an alpha-helix?
  70. What is the degree of rotation between each AA in an alpha-helix?
  71. What kind of AA hate alpha-helix structures?
    branched AA and charged groups
  72. How is the geometric structure of a peptide bond oriented?
    Peptide bonds are planar from alpha-carbon to alpha-carbon
  73. Electron resonance gives peptide bonds a _______________ characteristic.
    Electron resonance gives peptide bonds a partial bond characteristic. *rotation isn't possible
  74. Are peptide bonds in a Cis or Tans configuration?
    All peptide bonds in proteins are in Trans config
  75. What "handedness" is an alpha-helix structure?
  76. What are beta-strands and what types are there?
    Beta-strands are slightly stretched alpha-strands that exist in parallel (both N-->C) , anti-parallel (N--->C vs C--->N) , mixed (both parallel and anti-parallel) , and pleated sheets
  77. TEST ?# 11 - Which isnt true for the 2o protein structure alpha-helix
    a) right handed
    b) H-bond btw carbonyl oxygen of nth AA and amino group of (n+4) AA
    c) Proline is typically not found in an alpha-helix
    d) There are 3.6 AA per turn
    e) There is a requirement for glycine every 3rd AA
    E isnt correct
  78. TEST ?# 12 - What is the appoximate mass of a protein with 200 AA's?
    100 x 200 DALTONS = 22,000 DALTONS
  79. What stabilizes primary protein structures?
    Peptide bonds
  80. What stabilizes secondary protein structures?
    Hydrogen bonds
  81. What is an alpha-coiled-coil?
    A left handed superhelix
  82. What kind of proteins form super-secondary structures and what forces stabilize them?
    Super-secondary structures are only found in fibrous proteins and are stabilized by H-bonds, ionic intrx, Van der Waal forces, and hydrophobic intrx
  83. What forces stabilize a triple helix structure like collagen?
    • Ionic intrx, Van der Waals forces, and Hydrophobic intrx
    • * - no H-bonds
  84. What do "chperones" do?
    They bind to unfolded proteins to prevent misfolding
  85. What is the danger of misfolded proteins?
    They aggregate and deposit in the CNS (mostly brain) and cause neuron disruption
  86. TEST ? #13 - Key properties of proteins include:
    a) wide range of funtional groups
    b) ability to possess either rigid or flexible structures as dictated by functional requirements
    c) ability to interact with other proteins
    d) A&B
    e) All above
  87. TEST ? #14 - Which AA would be most likely to be buried within the interior of a molecule?
    A) Asp
    B) Gln
    C) Phe
    D) Lys
    E) Ser
    C) Phe
    (this multiple choice question has been scrambled)
  88. What is a catalyst?
    A molecule that enhances the rate of a reaction without being consumed in that reaction
  89. T/F - Most enzymes are proteins
    True - (except for catalytic RNAs)
  90. What are the 3 types of specificity exhibited by enzymes?
    • Absolute
    • Relative
    • Stereo
  91. What are the 6 enzyme classifications in order?
    • 1) Oxidoreductases - redox rxns
    • 2) Transferases - xfer functional groups
    • 3) Hydrolases - hydrolysis rxns
    • 4) Lyases - group elim. to form double bonds
    • 5) Isomerases - isomerization rxns
    • 6) Ligases - bond formation with ATP hydrolysis
  92. Enzyme + Prosthetic group = ?
  93. When:
    Enzyme + Prosthetic group = Holoenzyme
    what can the enzyme and prosthetic group also be known as?
    • Enzyme = apoenzyme
    • Prosthetic group = coenzyme
  94. What are prosthetic groups?
    Coenzymes tightly bound to the enzyme
  95. What does deltaG represent?
    Free energy change (free energy difference between products and reactants)
  96. What does it mean when:
    deltaG is negative
    deltaG is positive
    deltaG is zero
    • deltaG is negative: rxn can occur spontaneously & rxn releases energy (exergonic)
    • deltaG is positive: rxn cannot occur spontaneously & requires energy input (endergonic)
    • deltaG is zero: the rxn is at equilibrium
  97. deltaG (does or does not) determine the rate of the reaction?
    Does NOT - deltaG is independent of the path of transformation
  98. How do enzymes accelerate reactions?
    Enzymes decrease the energy of activation needed to reach the transition state
  99. How is it possible to convert substrate to product without enzymes?
    Increase the concentration of the substate
  100. Enzymes alter the rate of the reaction, but not the __________
    but not the reaction equilibrium
  101. What are the 5 feature of the active site of an enzyme?
    • 1) 3D structure (cleft/crevice)
    • 2) takes up small part of total enzyme
    • 3) unique microenvironment
    • 4) multiple weak bonds stabilize ES complex
    • 5) atoms in active site determines specificity
  102. TEST ? #15 - The enzyme Alcohol Dehydrogenase (ADH) requires NAD+ for catalytic activity. In the rxn catalyzed by ADH, an alcohol is oxidized to an aldehyde and the NAD+ is reduced to NADH and dissociates from the enzyme. NAD+ functions as what?
    A Cofactor
  103. TEST ? #16 - Which one of the following is not among the 6 internationally accepted classes of enzymes?
    A) Polymerases
    B) Transferases
    C) hydrolases
    D) Ligases
    E) Oxidoreducatases
    A) Polymerases
    (this multiple choice question has been scrambled)
  104. What is the Lock & Key Model of ES binding?
    The active site of the enzyme is shaped in order to accept one specific substrate
  105. What is the Induced Fit Model of ES binding?
    The substrate changes the active site of the enzyme in order to form the ES complex
  106. What are antibodies?
    Proteins that bind to an antigen
  107. Which are more present in the body, Michaelis-Menten enzymes or Allosteric enzymes
    M-M enzymes
  108. Define the "rate" of the enzyme catalyzed reaction
    • -the amount of substrate disappearance in a given time
    • or
    • -the amount of product formed in a given time
  109. What does the rate of a First Order Reaction depend on?
    First Order Reaction rate depends on the concentration of one substrate
  110. What does the rate of a Second Order Reaction depend on?
    The concentration of two substances
  111. What does the rate of a Pseudo-First-Order Reaction depend on?
    The rate depends on the concentration of the lesser substrate
  112. Define the VMAX of a reaction
    • The maximum velocity that an enzyme can catalyze a reaction.
    • VMAX is when all enzymes are in ES format
    • (*if substrates outnumber enzymes, the rate/velocity is limited by the number of enzymes)
  113. E + S < = > ES < = > E + P
    What does the left-hand side show?
    What does the right-hand side show?
    • Left = affinity of enzyme for substrate
    • Right = actual rate of the reaction
  114. What does KM indicate?
    • KM is the substrate concentration at which Vo is one-half VMAX
    • KM indicates how fast the ES complex forms
  115. Low Km = ?
    High Km = ?
    • Low Km = high affinity of enzyme for substrate
    • High Km = low affinity of enzyme for substrate
  116. TEST ? #17 - The Km is
    a) = to the [P] at initial reaction conditions
    b) = to the [S] when the rxn rate is 1/2 its max
    c) proportional to the standard free energy
    d) all above
    e) none above
    B - The Km is equal to substrate concentration when the reaction rate is 1/2 its max value
  117. TEST ? #18 - Straight-line enzyme-kinetic plot of 1/V0 versus 1/[S] is called a _________.
    Lineweaver-Burk Plot (double-reciprocal plot)
  118. Any protein with multiple active sites will show _________ curves
  119. What are the 2 main categories of enzyme inhibition?
    • irreversible - causes enzyme damage
    • reversible
  120. What are the 3 subclasses of reversible inhibitors?
    • competitive
    • uncompetitive
    • noncompetitive
  121. Define competitive inhibition
    Inhibitor looks similar to substrate and competes for the active site on an enzyme ; only binds to free enzymes ; raises Km & Vmax unchanged
  122. Define uncompetitive inhibition
    Inhibitor prevents product formation ; only binds to ES complex ; lowers Km & Vmax
  123. Define noncompetitive inhibition
    Inhibitor binds to a site on the enzyme other than the active site that alters the active site ; can bind to free enzyme or ES complex ; Km unchanged & lowers Vmax
  124. What are the 4 subclasses of irreversible inhibitors?
    • group-specific reagents
    • affinity labels (substrate analogs)
    • suicide inhibitors
    • transition-state analogs
  125. Define group-specific reagents
    An irreversible inhibitor that covalently bonds to an open site on an enzyme
  126. Define affinity labels
    aka Substrate analogs - inhibitor has similar binding sites as substrate and covalently bonds to enzyme active site
  127. Define suicide inhibitors
    Mechanism based inhibitor where the enzyme creates something from the inhibitor that then destroys the enzyme