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Water is essential to what two things?
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
- pulls electrons away from the two hydrogen nuclei
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 __
hold the structure together
link molecules in liquid water
account for the cohesion of liquid water
high dielectric constant of 80
Molecules interact with water molecules through the formation of __ and through __
dissolve many species
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
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
The result is that nonpolar molecules show an increased tendency to __
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
The four noncovalent interactions work together in doing what?
driving the association of two strands of DNA to form a double helix
First, each phosphate group in a DNA strand carries a __
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.
unfavorable electrostatic interactions
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
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
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
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
vdW contact distance
base stacking and associated van der Waals interactions
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
The principles of double-helix formation between two strands of DNA apply to many other biochemical processes
Many weak interactions contribute to the overall __of the process, some __ and some __
i. Furthermore, __ is a key feature.
Explain what this means. What plays major role in this?
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
The laws of thermodynamics distinguish between a __ and __
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)
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
Entropy of a system can change by an amount ΔSsystem
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
For the Second Law, we must determine the __
change in entropy of the surroundings
If heat flows from systemà
surroundings, then the entropy of the surroundings will ___
Precise change in the entropy of the surroundings depends on the __.
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
The change in entropy of the surroundings will be __ and __
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
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)
The total entropy will increase if and only if __
i. Entropy will increase if __; it must be negative to be a __reaction
ΔSsystem > ΔHsystem/T
ΔG < 0
When is there a negative free-energy change?
when and only when the overall entropy of the universe is created
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.
Second Law of Thermodynamics
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