Ch 1 Text 2

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Ch 1 Text 2
2014-08-31 14:32:45
Test One: Properties of Water
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  1.                                                                i.      Water is essential to what two things?
                                                                 ii.      Water is __: bentà __charge distribution; oxygen does what, which leaves the hydrogens with a net positive charge
    formation of macromolecular structures and the progress of chemical reactions


    • asymmetric 
    • pulls electrons away from the two hydrogen nuclei
  2.                                                                i.      Water is highly __: interact strongly with one another through __; networks of H bonds do what; similar interactions __ and __

    1.       Polar nature of water is responsible for its __ 

    H bonds

    hold the structure together

    link molecules in liquid water

    account for the cohesion of liquid water

    high dielectric constant of 80
  3. 1.       Molecules interact with water molecules through the formation of __ and through __

    hydrogen bonds

    ionic interactions

    versatile solvent

    dissolve many species
  4.                                                               i.      The __effect: manifestation of the properties of water
    True or False: Interactions of nonpolar molecules with water molecules are as favorable as are interactions between the water molecules themselves

    False: Interactions of nonpolar molecules with water molecules are NOT as favorable as are interactions between the water molecules themselves
  5. a.       The water molecules in contact with these nonpolar molecules do what?
    b.      However, when two such nonpolar molecules come together, some of the water molecules are __, allowing them to __; the release of water from such cages is __
    form “cages” around them, becoming more well-ordered than water molecules free in solution


    interact freely with bulk water

  6.   i.      The result is that nonpolar molecules show an increased tendency to __

    1.       This tendency is called the __and the associated interactions are called __
    associate with one another in water compared with other, less polar and less self-associating, solvents

    hydrophobic effect 

    hydrophobic interactions
  7. a.       The four noncovalent interactions work together in doing what?
    driving the association of two strands of DNA to form a double helix
  8.                                                               i.      First, each phosphate group in a DNA strand carries a __
    1.       These __ groups interact __with one another over distances. Thus, __ take place when strands come together. These phosphate groups are far apart in the double helix with distances greater than __, but many such interactions take place. 
    negative charge

    negatively charged


    unfavorable electrostatic interactions

    10 angstroms
  9. a.       Thus, electrostatic interactions oppose __, but the strength of these repulsive electrostatic interactions is diminished by what?
    the formation of the double helix

    the high dielectric constant of water and the presence of ionic species such as Na+ or Mg2+ ions in solution. These positively charged species interact with the phosphate groups and partly neutralize their negative charges
  10.                                                               i.      Second, hydrogen bonds are important in determining the formation of __in the double helix, but single stranded DNA has the capability of __
    specific base pairs 

    hydrogen bonding with the solution
  11. 1.       When two single strands come together, these __ are broken and new __are formed. The number of H bonds formed is similar to those broken, so there is no overall drive towards __ , but they do facilitate binding
    • hydrogen bonds with water
    • hydrogen bonds between the bases 
    • double-helix formation
  12.                                                               i.      Third, within a double helix, the base pairs are arranged how? The typical separation between the planes of adjacent base pairs is __, and the distances between the most closely approaching atoms are approximately __, which corresponds to the __.

    1.       Bases tend to __ even in single-stranded DNA molecules. However, the __ and __ are nearly optimal in double-helical structure
    parallel and stacked nearly on top of one another

    3.4 Angstroms

    3.6 Angstroms

    vdW contact distance


    base stacking and associated van der Waals interactions
  13.                                                               i.      Fourth, the hydrophobic effect also contributes to the __. More-complete base stacking does what?
    favorability of base stacking

    moves the nonpolar surfaces of the bases out of water into contact with each other
  14. a.       The principles of double-helix formation between two strands of DNA apply to many other biochemical processes
                                                                  i.      Many weak interactions contribute to the overall __of the process, some __ and some __


  15.                                                               i.      Furthermore, __ is a key feature. 

    Explain what this means. What plays  major role in this?
    surface complementarity

    when complementary surfaces meet, hydrogen-bond donors align with hydrogen-bond acceptors and nonpolar surfaces come together to maximize van der Waals interactions and minimize nonpolar surface area exposed to the aqueous environment

    the properties of water play a major role in determining the importance of these interactions
  16. a.       The laws of thermodynamics distinguish between a __ and __
                                                                  i.      A __refers to the matter within a defined region of space; and, the __are the matter in the rest of the universe
    1.       First Law: __
    system and its surroundings



    the total energy of a system and its surroundings is constant. It can be neither created nor destroyed, but can be converted (ex: kinetic energy, potential energy)
  17. 1.       Second law: 

    a.       Entropy may be __ only if the entropy of other parts of the universe is __

    b.      The local decrease in entropy is often accomplished by a __, which increases the entropy of the surroundings
    the total entropy of a system plus that of its surroundings always increases

    decreased locally in the formation of such ordered structures

    increased by an equal or greater amount

    release of heat
  18. a.       Entropy of a system can change by an amount ΔSsystem
    b.      If heat flows from the system to its surroundings, then the heat content, often referred to as the __, of the system will be reduced by an amount ΔHsystem.
                                                                  i.      For the Second Law, we must determine the __
    enthalpy (H)

    change in entropy of the surroundings
  19. 1.       If heat flows from systemà surroundings, then the entropy of the surroundings will ___
    a.       Precise change in the entropy of the surroundings depends on the __.

    Explain this.


    a.       The change in entropy is greater when heat is added to relatively cold surroundings than when heat is added to surroundings at high temperatures that are already in a high degree of disorder
  20.                                                                                                                                       i.      The change in entropy of the surroundings will be __ and __

    1.       In biological systems, T is usually constant
    proportional to the amount of heat transferred from the system and inversely proportional to the T of the surroundings
  21. The function -T ΔS has units of energy and is referred to as __, which does what?
    Gibbs free energy

    keeps track of both the entropy of the system (directly) and the entropy of the surroundings (in the form of heat released from the system)
  22.                                                               i.      The total entropy will increase if and only if __                                                              
    Entropy will increase if __; it must be negative to be a __reaction
    ΔSsystem > ΔHsystem/T

    ΔG < 0

  23. When is there a negative free-energy change?
    when and only when the overall entropy of the universe is created
  24. a.       Before the double helix forms, how do the strands exist? The formation of the double helix __ and __. This formation should violate the __ unless __
    the strands are free to translate and rotate and can take on more forms than when they are in the double helix.

    increases order

    decreases entropy

    Second Law of Thermodynamics

    • heat is released
  25. Though the formation of the double helix should violate the 2nd Law, why can it still occur?
    Yes, a lot of heat is released; and, the change in enthalpy for the process is large. But, althoguh it was violated by an increase in order, the release of heat counters this, thus insuring the entropy of the universe increases