Lecture 2: Water and Buffers

Question 1

Reactions take place in aqueous environments

Answer 1

• Biological molecules assume their shape and function in response to the physical and chemical properties of the surrounding water
• Water is the medium for the majority of biochemical reactions
• Water actively participates in many biochemical reactions – particularly H+ and OH-

Question 2

Water is a tetrahedral polar molecule

Answer 2

• it can form hydrogen bonds
• Oxygen has a partial charge of -0.66 e
• hydrogen partial charge of 0.33 e
• a single water molecule can donate two hydrogens and accept two hydrogens (energy ~ 20 kJ mol-1)

Question 3

Hydrogen bonds are constantly switching

Answer 3

Networks of water molecules are constantly breaking and re-forming every 2*10^-11 seconds. Water’s boiling point is 100 C; this means it takes more energy for water to switch phases than methane (BP -164 C)

Question 4

Many molecules can form hydrogen bonds

Answer 4

Hydroxyl, carbonyl, carboxylate (acceptors), and ammonium groups can form hydrogen bonds.
The strength of a hydrogen bond depends on the orientation of the donor and acceptor (desire to form strong hydrogen bonds).
Straight conformation of the hydrogen bond is stronger than a bent conformation

Question 5

Hydrophilic substances

Answer 5

They dissolve in water. Ions surrounded by water molecules are solvated by ordered waters of hydration. Ex. salts
Dissolving salt in water is a spontaneous process

Question 6

Hydrophobic substances

Answer 6

They tend not to dissolve in water. Ex. olive oil

Question 7

Hydrophobic effect

Answer 7

Tendency of water to minimize its contacts with hydrophobic groups (ex. olive oil clumps together when coming into contact with water).
Dissolving non-polar substances in non-polar solvents is entropically driven.

Question 8

Experiment with non-polar molecules

Answer 8

We can take non-polar molecules that are dissolved in an aqueous solution and move them into a non-polar solvent. ΔG is negative so this is an exergonic reaction. All reactions have a positive change in enthalpy, so it is an endothermic reaction (requires heat from the surroundings). The change in enthalpy is driving the reaction to be non-spontaneous, but the reaction is actually SPONTANEOUS. This is because the ΔS for the reaction is a large positive value, so it is entropically favored. Therefore, dissolving non-polar substances in non-polar solvents is entropically driven.

Question 9

Aggregation

Answer 9

Seeks to minimize the surface area of the non-polar substance and maximize entropy of the water molecules.
Less water molecules are pulled out of bulk solvent (minimized contact, therefore, minimized entropic cost). This maximizes the total entropy of the water molecules

Question 10

Water ionizes to form H+ and OH-

Answer 10

Water can dissociate into a free ion and a hydroxide ion (which can participate in acid-base reactions; these are very quick)

Question 11

Proton hopping/jumping

Answer 11

When hydrogens can quickly move from one water molecule to the next. It is caused by the ability of water to quickly accept/donate protons

Question 12

Dissociation constant for water

Answer 12

Concentrations of H+ and OH- are reciprocally related. If you increase the number of protons in a solution, that will decrease the number of hydroxide ions in that same solution. When there is an equal amount of H+ and OH- ions in a solution, the pH will be 7

Question 13

Bronsted and Lowry acids and bases

Answer 13

Acid: substance that can donate a proton
Base: substance that can accept a proton
Water can act as both an acid and a base
Strong acids will have equilibrium to the right of the equation (produce more of the acid and less of the weak conjugate base) whereas weak acids have equilibrium pushed to the left (produce less of the acid and more of the strong conjugate base)

Question 14

Dissociation constants

Answer 14

It is what determines the strength of an acid (ex. Ka = 10^-5). They are also typically written as pKa values (ex. pka = 5)

Question 15

Determining pH of a solution

Answer 15

Can be determined by looking at the relative concentrations of acids and bases

Question 16

Henderson-Hasselbach (H-H) equation

Answer 16

Can be used to calculate the pH of weak acids

Question 17

Monoprotic acids

Answer 17

Can donate one proton when dissolved in aqueous solutions (ex. acetic acid, ammonium ion)

Question 18

Diprotic acids

Answer 18

Can donate two protons when dissolved in aqueous solutions (ex. carbonic acid, glycine carboxyl, glycine amino)

Question 19

Triprotic acids

Answer 19

Can donate three protons when dissolved in aqueous solution (ex. phosphoric acid, dihydrogen phosphate, monohydrogen phosphate)

Question 20

Weak acids

Answer 20

K < 1

Weak acids with pKs close to 7 can be used as biological buffers (they resist changes in pH very well)

Question 21

Strong acids

Answer 21

K&raquo_space; 1

Question 22

Buffers

Answer 22

Resist changes in pH. They have relatively equal amounts of acid and conjugate base ions.

Question 23

Biological molecules contain ionizable groups

Answer 23

A large protein molecule may have hundreds of ionizable groups. Enzymes (used to catalyze reactions) have defined pH optima. This means if a pH is too low or too high, the enzyme may be non-functional.

Question 24

Protonation vs deprotonation states

Answer 24

If the pH < pKa, the ionizable group will favor the protonated state.
If the pH > pKa, the ionizable group will favor the deprotonated state.