Water, Weak Bonds, and the Generation of Order out of Chaos Flashcards
What is brownian motion?`
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
H2O and gas molecules of environment bounce randomly at rate determined by
temperature. When they collide, the particles move randomly themselves
Water is called the “solvent of life” because:
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.
The polarity of H2O and its ability to form
H-bonds makes it a solvent for any charged or polar molecules
What is the hydrophobic effect?
When nonpolar/hydrophobic molecules sequester themselves away from water (like oil in vinegar salad dressing)
- Causes formation of cells and organelle membranes
What are the three fundamental noncovalent bonds?
Ionic/electrostatic bonds, hydrogen bonds, and van der Waals interactions.
- All greatly affected in different ways in the presence of H2O
Why does H2O weaken ionic bonds?
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
Why does H2O weaken H-bonding?
H2O disrupts H-bonding by competing for new H-bonds with itself
What is the basis of van der Waals interactions?
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
The asymmetry of charge acts through electrostatic interactions to induce
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
What is the advantage of weak bonds?
Easily broken and put back together = repeated interactions among biomolecules
Nonpolar solute molecules are driven together because
when they associate they release H2O molecules (NOT because they have high affinity for each other)
Hydrophobic interactions form spontaneously because
when they form, the entropy of H2O increases
What is the second law of thermodynamics?
The total entropy (randomness) of a system and its surroundings always increases in a spontaneously process
In liquid water, there are about
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
Molecules are constantly in motion, so
H-bonds are continually changing and forming new bonds
Ionic interactions
- 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
What is a buffer?
An acid/base conjugate pair that is able to resist changes in pH
What is pKa?
Point at which half of the acid is dissociated into conjugate base
Weak acid/base pairs can resist changes in pH by
donating or accepting H+
How to select a buffer?
Select buffer with pKa near the target pH
Why are biological system generally buffered?
Biomolecules are sensitive to changes in pH, pH affects ionization state
What is buffer capacity?
The amount of acid or base a buffer can absorb, may be dependent on concentration of buffer
How does the hydrophobic effect favour protein folding?
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
