Lecture #01: Properties of Water

Question 1

· The remarkable structure and function of the cell are stabilized by weak interactions that have only a fraction of the strength of covalent bonds. How is such stabilization possible and why is it an advantage?

Answer 1

o There is stability in numbers. Many weak bonds can result in large stable structures.

o Weak bonds allow transient interactions. Weak bonds allow for dynamic interactions and permit energy and info to move about the cell and organism. (Like substrate binding to enzyme and product leaving it, a hormone binding to a receptor and then leaving).

Question 2

Why is water the solvent of life?

Answer 2

Greatly effects weak bonds making some weaker and powering the formation of others.

Example, fats cannot interact with water at all. Yet, this chemical antipathy is useful. The formation of membranes and the 3D structure of biochemical, most notably proteins, are powered by an energetic solution to the chemical antipathy between water and hydrophobic molecules.

Question 3

Water’s Polarity

Answer 3

Important properties of water are due to fact that oxygen is an electronegative atom. Although the bonds joining the H atoms to O are covalent, the electrons of the bond spend more time near the O atom. Since the charge distribution is not universal, this molecule is polar.

The partially positively charged H atoms can interact with the partially negatively charged O atoms of another water molecule. This interaction is called a hydrogen bond.

Question 4

Hydrophobic Molecules

Answer 4

The fact that water can’t dissolve other compounds is important too. Specially, nonpolar or hydrophobic molecules. These molecules sequester themselves away from water when in it, called the hydrophobic effect.

Question 5

Covalent Bonds: Stability & Arrangement of Electrons

Answer 5

Covalent bonds are stable. Typically release 50-200 kcal/mol of energy upon breakage.

Shared arrangement of electrons.

• Equal Sharing: Uniform charge distribution, molecule is nopolar.
• Unequal sharing: asymmetrical distribution; molecule is polar because the bond involves an electronegative atom. O>N>S>C>P>H

Question 6

· Types of Noncovalent Interactions

Answer 6

Hydrogen bonds, electrostatic (ionic) interactions, Van der Waals forces, Hydrophobic interactions.

Question 7

Hydrogen Bonds Activity

Answer 7

· Hydrogen bonds are rapidly forming, breaking, and reforming in different orientations.

Question 8

Effect of # of Hydrogen Bonds

Answer 8

of hydrogen bonds contributes to stability of the molecule and can be broken by heat, because the molecules are more susceptible to the vibration caused by heat due to the weak bonds.

Question 9

Electrostatic Interactions

Answer 9

(Ionic bonds or salt bridges) are interactions b/w distinct electrical charges on atoms. The electrostatic interactions between two atoms bearing single opposite charges varies inversely with the square of the distance separating them as well as with the nature of the intervening medium.

Question 10

Electrostatic Interactions: Water’s Effect

Answer 10

Water weakens these interactions. This is because when you put a molecule in water with electrostatic interactions, they will dissociate and the ions will bind with water molecules. Water can dissolve anything that has sufficient partial or complete charges on the molecule to interact with water.

Question 11

Electrostatic Interactions: Organic Solvent’s Effect

Answer 11

If the molecule was put in an organic solvent, the electrostatic interaction is likely to increase because there’s a smaller chance of the charges being like an unlike.

Question 12

van der Waals Interaction

Answer 12

Biomolecules that are neither polar nor charged can interact electrostatically by a van der Waals interaction. The basis of it is that the distribution of electronic charge around an atom changes with time and, at any time, the charge distribution is not perfectly symmetric: there will be regions of partial positive and negative charge. This transient asymmetry in the electronic charge around an atom acts through electrostatic interactions to induce a complementary asymmetry in the electron distribution around its neighboring atoms. This attraction increases as they come closer, til they are separated by the van der Waals contact distance.

Question 13

van der Waals Interaction: Strength

Answer 13

Weakest of noncovalent interactions. However, when the surfaces of two large molecules with complementary shapes come together, a large number of atoms are in van der Waals contact, and the net effect can be large.

Question 14

Why Does DNA Need Weak Bonds?

Answer 14

DNA provides great example of why breakage of weak bonds is needed. Hydrogen bonds b/w base pairs stabilize the double helix and keep the coding info (the base sequence) inside the helix away from potential harmful rxns. However, if the info is to be useful, it must be accessible. So, the double helix can be opened up (strands separated) so that the DNA can be copied or so that the genes on DNA can be expressed. The weak interactions are strong enough to stabilize and protect DNA but weak enough to allow access to info of the base sequences under certain situations.

Question 15

Hydrophobic Interactions: the Hydrophobic Effect

Answer 15

Can’t form H bonds with water, avoids it.

Attraction b/w nonpolar molecules.

Question 16

2nd Law of Thermodynamics

Answer 16

The total entropy of a system and its surroundings always increases in a spontaneous process.

Question 17

Entropy

Answer 17

is a measure of randomness. An ordered state has low entropy, while a disordered state has high entropy.

Question 18

Hydrophobic Effect Mechanics

Answer 18

When you introduce a nonpolar molecule in water, a cavity in the solution is temporarily made, and the water molecules reorient themselves to from max number of new hydrogen bonds. The water molecules around the nonpolar molecule are much more ordered than elsewhere in the solution, a decrease in entropy. When you add another nonpolar molecule, they will eventually come together, because it will distort the water more and increase entropy.

Nonpolar solute molecules are driven together in water not mainly cause they have a high affinity for each other but because, when they do associate, they release water molecules. This entropy driven association is called the hydrophobic effect, and resulting interactions are called hydrophobic interactions. Form spontaneously due to an end increase in entropy.

Question 19

Hydrophobic Effect: Cell Membrane

Answer 19

This effect is responsible for the formation of the cell membrane. The reason why the phospholipids are able to come together and stay close to form their how system of entering and leaving material to and from the cell.