Water, Weak Bonds, and the Generation of Order out of Chaos

Question 1

What is brownian motion?`

Answer 1

Random movement of particles suspended in H2O due to random fluctuation of energy content of the environment (thermal noise), responsible for initiating many biochemical interactions

Question 2

H2O and gas molecules of environment bounce randomly at rate determined by

Answer 2

temperature. When they collide, the particles move randomly themselves

Question 3

Water is called the “solvent of life” because:

Answer 3

Many biochem molecules dissolve in H2O and it is the lubricant that facilitates the flow of energy and information transformations through Brownian motion, which provides the motive force for biochem interactions.

Question 4

The polarity of H2O and its ability to form

Answer 4

H-bonds makes it a solvent for any charged or polar molecules

Question 5

What is the hydrophobic effect?

Answer 5

When nonpolar/hydrophobic molecules sequester themselves away from water (like oil in vinegar salad dressing)
- Causes formation of cells and organelle membranes

Question 6

What are the three fundamental noncovalent bonds?

Answer 6

Ionic/electrostatic bonds, hydrogen bonds, and van der Waals interactions.
- All greatly affected in different ways in the presence of H2O

Question 7

Why does H2O weaken ionic bonds?

Answer 7

i.e NaCl added to H2O, salt dissolves = ionic bond between Na+ and Cl- destroyed because individual ions now bind to H2O molecules rather than to each other

Question 8

Why does H2O weaken H-bonding?

Answer 8

H2O disrupts H-bonding by competing for new H-bonds with itself

Question 9

What is the basis of van der Waals interactions?

Answer 9

The distribution of charge around an atom changes with time, and at any time, charge distribution is not perfectly symmetric
Can become strong when summed

Question 10

The asymmetry of charge acts through electrostatic interactions to induce

Answer 10

a complementary asymmetry in the electron distribution around its neighbouring atom

• Interaction increases as they get closer to each other until separated by van der Waals contact distance
• At short distance = v strong repulsive forces because the outer electron clouds overlap

Question 11

What is the advantage of weak bonds?

Answer 11

Easily broken and put back together = repeated interactions among biomolecules

Question 12

Nonpolar solute molecules are driven together because

Answer 12

when they associate they release H2O molecules (NOT because they have high affinity for each other)

Question 13

Hydrophobic interactions form spontaneously because

Answer 13

when they form, the entropy of H2O increases

Question 14

What is the second law of thermodynamics?

Answer 14

The total entropy (randomness) of a system and its surroundings always increases in a spontaneously process

Question 15

In liquid water, there are about

Answer 15

3.4 H-bonds forming per H2O molecule, whereas in ice (less dense, further spaced apart) there are about 4 H-bonds per H2O molecule

Question 16

Molecules are constantly in motion, so

Answer 16

H-bonds are continually changing and forming new bonds

Question 17

Ionic interactions

Answer 17

• Interactions between distinct electrical charges on atoms
• Water shields charges (“high dielectric constant”) so H2O can dissolve salts because it weakens electrostatic forces as H2O interacts with the (-) charges

Question 18

What is a buffer?

Answer 18

An acid/base conjugate pair that is able to resist changes in pH

Question 19

What is pKa?

Answer 19

Point at which half of the acid is dissociated into conjugate base

Question 20

Weak acid/base pairs can resist changes in pH by

Answer 20

donating or accepting H+

Question 21

How to select a buffer?

Answer 21

Select buffer with pKa near the target pH

Question 22

Why are biological system generally buffered?

Answer 22

Biomolecules are sensitive to changes in pH, pH affects ionization state

Question 23

What is buffer capacity?

Answer 23

The amount of acid or base a buffer can absorb, may be dependent on concentration of buffer

Question 24

How does the hydrophobic effect favour protein folding?

Answer 24

Protein folding proceeds spontaneously under the appropriate conditions with all molecules assuming the same conformation (decrease in entropy!)

• To avoid violating the second law, entropy must be increasing elsewhere in the system/surroundings
• Some amino acids in proteins have nonpolar groups that have a strong tendency to associate with one another in the interior of folded proteins
• Increased entropy of H2O resulting from interactions of hydrophobic amino acids helps compensate for entropy losses in the folding process
• Many weak bonds are formed in the protein folding process to stabilize the 3D structure and these replace interactions with H2O that take place in unfolded protein

Question 25

Alterations in pH can drastically affect the internal electrostatic environment of an organism, which can alter the

Answer 25

weak bonds that maintain the structure of biomolecules = loss of function