Biochemical Foundations of Physiology -2

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Biochemical Foundations of Physiology -2
2014-08-31 23:31:06

Biochem lecture 2
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  1. What are enzymes ?
    • Enzymes are protein catalysts that increase
    • the rate of reactions without being changed in the overall process.
  2. What are RNAs with catalytic activity called ? Are they (more or less) encountered than protein catalysts ?
    RNAs with catalytic activity are called ribozymes

    • Much less encountered than
    • protein catalysts.
  3. What are the 6 classes of enzymes ?
    • Oxidoreductase 
    • Transferase
    • Hydrolase 
    • Lyase
    • Isomerase
    • Ligase
  4. What reaction does Oxidoreductase catalyze ?
  5. What reaction does Transferase catalyze ?
  6. What reaction does Hydrolase catalyze ?
  7. What reaction does Lyase catalyze ?
  8. What reaction does Isomerase catalyze ?
  9. What reaction does Ligase catalyze ?
  10. How does  Synthetase perform ?
    It requires ATP
  11. How does Synthase perform ?
    Does not require ATP
  12. How does Phosphatase perform ?
    removes phosphate group
  13. How does phosphorylase perform ?
    adds a phosphate group using Pi
  14. How does Kinase perform ?
    adds a phosphate group using ATP
  15. What does oxidase perform ?
    Oxidase – catalyze oxidation-reduction reactions using O2 as the electron acceptor but oxygen atoms are not incorporated into substrate
  16. What does Oxygenase perform ?
    oxidize a substrate by transferring oxygen atoms to it
  17. Explain the following properties of enzymes ?

    Active Site :
    Efficient :
    Specific :
    Regulated :
    • Active site: It contains AA side chains that
    • participate in substrate binding and catalysis

    Efficient: 103-108 times faster than uncatalyzed reactions.

    • Specific: Interacts with one or a few substrates and catalyzing only
    • one type of reaction

    • Regulated: Enzyme activity can be regulated, that is, increased or
    • decreased so that the rate of product formation responds to cellular needs

    • Location: Most enzymes are located in specific organelles within the
    • cell.
  18. What is a Holoenzyme ?

    What is a Apoenzyme ?
    Enzyme with its nonprotein component (active)

    Enzyme without its nonprotein component (inactive)
  19. What is a Cofactor ?

    What is a Coenzyme ?
    Nonprotein moeity (inorganic or organic) of the enzyme

    • Nonprotein moeity (small organic molecule). Frequently derived from vitamins. 
    • Example: NAD+ from niacin and FAD from riboflavin
  20. What is a Prosthetic group ?
    Refers to coenzymes that are permanently associated with the enzyme.
  21. What is a Cosubstrate ? refers to coenzymes
    that only transiently associate with the enzyme
    refers to coenzymes that only transiently associate with the enzyme
  22. What is an Allosteric Enzyme ?
    refers to enzymes that change their conformation when bound by an effector at a site other than the active site. Enzyme can then become activated or inhibited.
  23. What is free energy of activation ?
    A reaction barrier , it is the energy difference between that of the reactants and a high-energy intermediate that occurs during the formation of product

  24. For molecules to react they must contain sufficient energy to overcome what ? 

    An enzyme allows a rxn to proceed rapidly
    by lowering the ?
    the energy barrier of the transition state.

    free energy of activation.

  25. What happens when you increase the substrate concentration in a reaction ?
    The rate of an enzyme catalyzed rxn increases with increased substrate concentration until a maximal velocity (Vmax) is reached.

  26. How does temperature affect the reaction velocity ?
    Increase of velocity with temperature due to increased number of molecules having sufficient energy to pass over the energy barrier and form the products of the rxn.

    • Decrease of velocity with higher
    • temperature due to temperature induced denaturation

  27. How does pH affect enzyme activity ?
    Optimum varies for different enzymes

    Extremes of pH can lead to denaturation of the enzyme because the structure of the catalytic activeprotein molecule depends on the ionic character of the AA side chains

  28. Describe the reaction rate equation ?
    Enzyme (E) reversibly combines with its substrate (S) to form an ES complex that subsequently yields product (P), regenerating the free enzyme

    k1, k-1, and k2 are rate constants
  29. Describe Michaelis-Menten equation ?
    What does a large km mean vs a small km ?

    V0 = initial velocity
    Vmax= maximum velocity
    Km= Michaelis constant = (k-1+ k2)/k1
    [S] = substrate concentration
    • Large km = low affinity for substrate 
    • Small km = high affinity for substrate

  30. "Orders of Reaction "

    Explain the First order with respect to substrate ?

    Explain the Zero
    order with respect to substrate ?
    • - When [S] is much less than Km
    • -V is proportional to [S]

    • -When [S] is greater than Km
    • -V is constant and independent of [S]

  31. In reference to a Line weaver-burk plot.When vo is plotted against [S], it is not always possible to determine when Vmax has been achieved,because of the ?
    gradual upward slope of the hyperbolic curve

  32. If  1/vo is plotted against 1/[S], a straight line is obtained , what is this called ?
    Lineweaver-Burk plot or a double reciprocal plot.

  33. What can a Lineweaver-burk plot or double reciprocal plot be used to determine ?
    • This plot can be used to calculate Km and Vmax, as well as determine the mechanism of action of the enzyme
    • inhibitors.
  34. What is an inhibitor ?

    What type of bonds do reversible inhibitors make ?

    What type of bonds do Irreversible inhibitors make ?
    Any substance that can diminish the velocity of an enzyme-catalyzed reaction is called an inhibitor.

    • Reversible inhibitors typically bind to
    • enzymes through noncovalent bonds

    • Irreversible inhibitors bind to enzymes
    • through covalent bonds
  35. Explain competitive inhibition ?
    • Inhibitor binds reversibly to the same
    • site that the substrate would normally occupy and, therefore, competes with the
    • substrate for that site.

    Higher -1/Km = Higher Km = less affinity
  36. Explain Non competitive inhibition ?
    Higher 1/Vmax = Lower Vmax

    Occurs when the inhibitor and substrate bind at different sites on the enzyme

    The noncompetitiveinhibitor can bind either free E or the ES complex, thereby preventing thereaction from occurring
  37. The widely prescribed β–lactam antibiotics, such as penicillin and amoxicillin, act by activating enzymes involved in bacterial cell wall
    synthesis ? T or F

    The widely prescribed β–lactam antibiotics, such as penicillin and amoxicillin, act by inhibiting enzymes involved in bacterial cell wall synthesis
  38. What are Allosteric enzymes ?
    Theyare ezymes regulated by molecules called effectors (or modifiers) that bind noncovalently at a site other than the active site
  39. Explain Negative effectors ?

    Explain Positive effectors ?
    Inhibit enzyme activity

    Increase enzyme activity
  40. Explain Homotropic effectors ?

    Explain Heterotropic effectors?
    -When the substrate itself serves as an effector

    -Has effectors that are different from the substrate
  41. What is Phosphorylation ? What family of enzymes performs this function ?
    The addition of a phosphate group to a molecule

    Phosphorylation reactions are catalyzed by a family of enzymes called protein kinases.
  42. What is Dephosphorylation ? What family of enzymes perform this function ?
    Dephosphorylation reactions are catalyzed by a family of enzymes called phosphoprotein phosphatases.
  43. How do enzymes react to phosphorylation ?
    Depending on the specific enzyme, the phosphorylated form may be more or less active than the unphosphorylated enzyme.
  44. Cells can regulate the amount of enzyme present by altering the rate of enzyme degradation or more typically the rate of enzyme synthesis ? T or F
  45. The increase(_____) or decrease (_____) of enzyme synthesis leads to an alteration
    in the total population of active sites
    The increase(induction) or decrease (repression) of enzyme synthesis leads to an alteration in the total population of active sites
  46. Explain E = mc2 ?
    • E = Energy (Joules)
    • m = mass (kg)
    • c = speed of light (3 x 108 m/s)

    • The ability to do work
    • Anything that has the ability to cause a physical effect on another entity  

      is said to contain energy

     Results in a physical change on matter
  47. What is Bioenergetics ?

    Where do Cells obtain energy ? from chemical reactions

    What does Bioenergetics predict ?
    It is the study of energy transformations in biological systems.

    Chemical reactions

     if a process is possible
  48. What are the three factors that effect bioenergetics ?
    • Enthalpy (H)
    • Entropy (S)
    • Free energy (G)
  49. Explain these three things and how they fnction in this equation ? Enthalpy (H)Entropy (S)Free energy (G)

    ∆G = ∆H  -  T∆S
  50. - ∆G = 
    + ∆G = 
    ∆G = 0

    spontaneous or exergonic reaction
    nonspontaneous or endergonic reaction
    process at equilibrium
    • - ∆G = spontaneous or exergonic reaction
    • + ∆G = nonspontaneous or endergonic reaction
    • ∆G = 0, process at equilibrium

  51. ∆G = free energy
    ∆Go = standard free energy

    ∆G = free energy change

    • ∆Go = standard free energy change (1 mol/L, 298K and 1
    • atm.)
    • R = gas constant (1.987 cal/mol x oK)
    • T = absolute temperature (oK)
    • ln = natural logarithm
  52. ATP hydrolysis (endergonic) is coupled to exergonic reactions due to ATP’s large negative ∆G ? T or F
    ATP hydrolysis (exergonic) is coupled to endergonic reactions due to ATP’s large negative ∆G ?
  53. The standard free energy of hydrolysis of ATP, ∆Go, is approximately ____ kcal/mol for each
    of the 2 terminal phosphate groups.

  54. 1. Energy rich molecules
    such as ____ are metabolized by a series of oxidation rxns ultimately leading to CO2 and water.

    2.The metabolic intermediates of these reactions donate electrons to specific coenzymes- NAD+ and FAD to form the energy rich reduced coenzymes NADH and FADH2 ? T or F

    3. NADH and FADH2 each donate a pair of electrons to a specialized set of electron carriers, collectively called the ETC. ? T or F


  55. The process whereby the energy generated by the ETC is conserved by ADP phosphorylation to ATP is ?

    The remainder of energy not trapped as ATP  is used to ?
    Oxidative Phosphorylation

    • 1) drive ancillary rxns such as Ca2+       transport into the mitochondria and
    • 2) generate heat.
  56. ETC is present in the what layer of the mitochondrial membrane and is the final common pathway by which electrons
    derived from different fuels of the body flow to oxygen ?

    Is the inner membrane impermeable to most small ions and small molecules such as ATP. ?
    Inner membrane

  57. Does the Matrix contain NAD+ and FAD, as well as ADP and Pi ?
  58. How many protein complexes are there in the electron transport chain ?
    5 protein complexes, I,II, III, IV and V
  59. In the electron transport chain FMNH2 then transfers the hydrogen atoms to ?
    CoQ (ubiquinone)
  60. Which is closer to the inner membrane Complex I or Complex II ?

    What are two major mobile electron carriers ?

    Is Free energy is released as electrons are transferred along the ETC from an electron donor to an electron acceptor ?
    Complex I

    Coenzyme Q and cytochrome c.

  61. CoQ (ubiquinone) transfers electrons to which complex ?
    Complex III (cytochrome bc1)
  62. Site-specific inhibitors of the ETC prevent the passage of electrons by binding to a component of the chain, blocking the oxidation/reduction reaction ? T or F

    Inhibition of the ETC does not inhibit ATP synthesis because these processes are tightly coupled

    Incomplete reduction of oxygen to water produces reactive oxygen species such as superoxide and hydroxyl radical which can damage biomolecules such as DNA,  proteins and lipids ? T of F

    F - Inhibition of the ETC inhibits ATP synthesis because these processes are tightly coupled

  63. What determines direction of electron flow in
    the ETC?
    Electrons flow from the pair with the more negative E0 to the more positive E0

  64. Passage of a pair of electrons from NADH through the ETC to O2 generates about __ ATP

    Passage of a pair of electrons from FADH2 to O2, which bypassescomplex I, generates about ___ ATP

  65. H+ then moves back into the matrix at which complex that results in ATP synthesis ?
    complex V
  66. In reference to oxidative phosphorylation , what are Uncoupling proteins ?

    The energy is released as heat and the process is called ?
    These carrier proteins allow protons to re-enter the mitochondrial matrix without energy being captured as ATP

    • Nonshivering thermogenesis. 
    • 1) Thermogenin in brown fat in hibernating animals
    • 2) Dinitrophenol (synthetic chemical)
    • 3)High dose aspirin
  67. Monosaccharide = 
    Disaccharides =
    Oligosaccharides =
    Polysaccharides =
    • 1 sugar 
    • 2 sugars
    • 3-10 sugars
    • >10 sugars
  68. What are aldoses and ketoses ?
    Aldoses - Carbohydrates with aldehyde as their most oxidized functional group

    • ketoses -Carbohydrates with keto as their most
    • oxidized group are called
  69. What are isomers ?

    What are epimers ?
    • Isomers are compounds that have the same
    • chemical formula but different structures. 

    • Epimers are carbohydrate isomers that differ
    • in configuration around only one specific carbon atom (with the exception
    • of the carbonyl carbon). 

  70. What are enatiomers ?

    They are designated D- and L-
    sugar. Are most sugars  (D-sugars or L sugars)?

    What are Racemases ?
    Isomers that are mirror images of each other

    D sugars

    They are are enzymes that can interconvert D- and L-isomers
  71. Monosaccharides are predominantly found in what form ?

    Pyranose is a ?

    Furanose is a ?
    the ring(cyclic) form 

    6 membered ring consisting of 5 carbon and 1 oxygen

    5 membered ring with 4 carbons and 1 oxygen
  72. As cyclization occurs, the carbonyl carbon becomes a new ? Which is also called a ?
    Chiral center

    Anomeric carbon
  73. Diastereomers (not mirror images) that may form during the cyclization reaction are called ?

    How many anomers can there be in a single molecule ? what are they named ?

    a-anomer (alpha) and b-anomer (beta)
  74. In the Fisher projection the α-anomeric hydroxyl occurs on the (right or left) while the β–hydroxyl occurs on the (right or left ) ?
    • a =right
    • b=left
  75. In the Haworth projection the α-anomeric hydroxyl occurs trans to the CH2OH group ? T or F

  76. What are reducing sugars ?

    These sugars can react with chromogenic agents such as Benedict’s reagent or Fehling’s solution causing what to happen ?
    If the hydroxyl group on the anomeric carbon of the cyclized sugar is not linked to another compound by a glycosidic bond, the ring can open.The sugar can then act as a reducing agent and is termed a reducing sugar.

    The reagent to be reduced and colored, with the aldehyde group of the acyclic sugar becomingoxidized
  77. What is the bond called that links sugars ?

    How is the linkage named based upon the alpha and beta method ?
    glycosidic bond

    If the anomeric hydroxyl group is in the α-configuration, the linkage is an α-bond 

    If the anomeric hydroxyl group is in the β-configuration, the linkage is an β-bond.

  78. The joining of monossaccharides is done by what enzymes ?
  79. Explain what an N-glycosidic bond and
    O-glycosidic bond are ?
    Carbohydrates can be attached by glycosidic bonds to non-carbohydrate structures, including purine and pyrimidine bases, aromatic rings, proteins and lipids

  80. Where are the principal sites for digestion ?

    What enzymes perform this action ?
    • Mouth and Intestinal lumen
    • Glycosidases

  81. During mastication, salivary amylase acts briefly on dietary starch and glycogen, hydrolyzing random ____(what type of bonds) ?
    α(1>4) bonds.
  82. If starches are partially digested in the mouth and halted in the stomach , where is the digestion process completed ? by what ?
    pancreatic α-amylase continues the process of starch digestion

    final digestive processoccur primarily at the mucosal lining of the upper jejunum
  83. If you are lactose deficient /intolerant what sugar can you not breakdown ? (Very easy question)
    are less able to metabolize lactose
  84. Metabolism is the sum of all the chemical changes occurring in a cell
    a tissue or the body ? T or F

    Most pathways can be classified as either catabolic (degradative) or anabolic (synthetic) ? T or F


  85. The glycolytic pathway is employed
    by some tissues for the breakdown of
    glucose to provide energy (in the form of ATP) and intermediates for other metabolic
    pathways ? T or F 

    Glycolysis is at the hub of carbohydrate metabolism because virtually all sugars can ultimately be converted to glucose ? T or F

    Pyruvate is the end product of glycolysis in cells with mitochondria and an adequate supply of oxygen ? T or F
    F -The glycolytic pathway is employed by ALL tissues for the breakdown ofglucose to provide energy (in the form of ATP) and intermediates for other metabolicpathways 


  86. Can Glucose diffuse directly into cells ? If not , then how ?

    State systems 1 and 2 ?
    No , it utilizes a transport mechanism

    • 1. Na+-independent, facilitated diffusion
    • transport system

    • 2. Na+-monosaccharide
    • co-transporter system
  87. Match the following ?
    GLUT-1 =

    is abundant in erythrocytes and blood brain barrier

    is abundant in pancreatic β-cells, liver and

    is abundant in neurons

    is abundant in adipose tissue and
    skeletal muscle
    • GLUT-1 is
    • abundant in erythrocytes and
    • blood brain barrier

    • GLUT-2 is
    • abundant in pancreatic β-cells, liver and
    • kidney

    • GLUT-3 is
    • abundant in neurons

    • GLUT-4 is
    • abundant in adipose tissue and
    • skeletal muscle
  88. Which of the GLUT transporters are the most important ?
    GLUT-2 is abundant in pancreaticβ-cells, liver and kidney

    GLUT-4 is abundant in adipose tissue and skeletal muscle
  89. Draw out the sequence in which Glucose , Galactose , and Fructose enter the lumen ?
    Galactose > SGLT  >Glut 2

    Fructose > Glut 5 > Glut 2