Bio 40 Lec 2: Bonds, properties of water, buffers

How many covalent bonds do C, O, H, N, S, and P typically form?

C4, O2, H1, N3, S2, P5 — the standard bonding numbers for biological atoms.

What is electronegativity?

The tendency of an atom to attract electrons toward its own nucleus. It varies by element.

What electronegativity difference between two bonded atoms is generally needed to produce a meaningful dipole?

≥ 0.5. A difference of 0.5 or greater is the rule of thumb for a reasonably strong dipole; smaller differences (like C-H at ~0.4) don't produce much of a dipole.

Why is a C-H bond considered essentially non-polar, while an O-H bond is strongly polar?

C and H have similar electronegativity (diff ≈ 0.4); O and H differ by 1.4, well above the 0.5 threshold. Electronegativity: O=3.5, H=2.1 (diff=1.4, polar); C=2.5, H=2.1 (diff=0.4, non-polar).

CO2 has two polar C=O bonds. Why is the CO2 molecule as a whole non-polar?

The molecule is linear, so the two bond-dipole vectors point in opposite directions and cancel. Polar bonds can still yield a non-polar molecule if their dipole vectors sum to zero due to molecular geometry — true for linear CO2.

Define cation and anion.

Cation = lost electron(s), positive charge (e.g. Na+, Ca2+); anion = gained electron(s), negative charge (e.g. Cl-).

What makes an atom an H-bond 'donor' versus an 'acceptor'?

Donor = H covalently bonded to an electronegative atom (partial + charge); acceptor = an electronegative atom with a nonbonding (lone pair) of electrons. The H-donor is the H attached to an electronegative atom; the H-acceptor is the electronegative atom (on another molecule/group) offering a lone pair to interact with that H.

Give 3 biological examples where hydrogen bonds are structurally important.

DNA double helix (base pairing), tRNA structure, protein alpha-helices/beta-sheets. H-bonds hold DNA's two strands together, stabilize tRNA folding, and define the alpha-helix and beta-sheet secondary structures of proteins.

What are the two components of van der Waals interactions?

Permanent dipoles (vector sum of bond dipoles) and London dispersion forces (transient dipoles from electron cloud fluctuations). Van der Waals = permanent-dipole interactions + London dispersion forces (very weak, transient, short-range, from momentary electron cloud fluctuations).

Rank bond types from strongest to weakest.

Covalent > ionic > hydrogen bonds > van der Waals. Covalent bonds are strongest (electron sharing); among non-covalent bonds, ionic > hydrogen bonds > van der Waals (weakest, most transient).

Why is water's bond angle about 105° instead of the ideal 109.5° tetrahedral angle?

Oxygen's 2 lone pairs repel the bonding electrons more than bonding pairs repel each other, compressing the angle. Oxygen has 4 sp3 orbitals (2 bonded to H, 2 lone pairs); the extra lone-pair repulsion compresses the H-O-H angle to ~105°.

How many hydrogen bonds can one water molecule form, and how are they split between donor/acceptor roles?

4 total: 2 as donor (its H atoms), 2 as acceptor (its lone pairs). Each water molecule has 2 H's (2 donor sites) and 2 lone pairs on O (2 acceptor sites) = 4 H-bonds max.

How does H-bonding differ between liquid water and ice?

In liquid water, H-bonds flicker on/off in picoseconds; in ice, all 4 H-bonds per molecule are stable in a fixed 3-D matrix. Liquid water's H-bonds are transient (picosecond timescale); ice locks every molecule into the full 4-bond 3-D lattice.

Rank H2O, NH3, and CH4 by dipole moment/H-bonding strength, and explain the consequence.

H2O > NH3 > CH4 — this explains water's unusually high boiling and melting points compared to the other two. Water's strong H-bonding network (from its large dipole) gives it a much higher boiling point than NH3 (-33°C) or CH4 (-161°C).

How does water dissolve ions (e.g. NaCl) versus polar molecules (e.g. glucose)?

For ions, water orients around them and screens/shields their charge; for polar molecules, water forms direct hydrogen bonds with functional groups like -OH. Water's dipole lets it screen ionic charges (hydration shells) and hydrogen bond directly to polar groups such as sugar hydroxyls.

What is the basis for the hydrophobic effect, in terms of entropy?

Isolated non-polar solutes force water into ordered 'cages'; when non-polar groups cluster together, less total surface needs caging, releasing ordered water and increasing overall system entropy. Clustering non-polar groups minimizes the total surface area requiring ordered water 'cages,' freeing water molecules to bulk solvent and raising total entropy — this net entropy gain drives hydrophobic clustering.

Give 3 biological processes where the hydrophobic effect is important.

Protein folding, enzyme-substrate interactions, and membrane (micelle/bilayer) formation. The hydrophobic effect drives non-polar residues into a protein's interior during folding, shapes enzyme-substrate binding pockets, and drives amphipathic lipids to form micelles/bilayers.

What is Kw, and what is its value?

The ion product constant of water: Kw = [H+][OH-] = 10^-14. In pure water, [H+] = [OH-] = 10^-7 M, giving pH 7.

What is the formula for pH, and why is pH described as an exponential/logarithmic measure?

pH = -log[H+]; because [H+] changes by powers of 10, a linear pH scale represents exponential concentration changes. Each 1-unit pH change reflects a 10-fold change in [H+].

Distinguish a strong acid from a weak acid, and state how Ka and pKa relate to acid strength.

Strong acids fully dissociate (large Ka, low/negative pKa); weak acids partially dissociate (smaller Ka, higher pKa) — the stronger the acid, the larger the Ka and the lower the pKa. Ka = [H+][A-]/[HA].

State the Henderson-Hasselbalch equation and what happens when pH = pKa.

pH = pKa + log([A-]/[HA]); when pH = pKa, [A-] = [HA] (50% dissociated), since log(1) = 0.

Why does a mixture of a weak acid and its conjugate base buffer pH, while a strong acid solution does not?

The weak acid/base pair has a reservoir of both HA and A- to absorb added H+ or OH-; a strong acid is always fully dissociated, so there's no undissociated HA reservoir to respond with.

Over what pH range is a buffer's capacity greatest?

From about 1 pH unit below to 1 pH unit above its pKa. The titration curve is flattest (best buffering) in that range; capacity also scales with total buffer concentration.

Name the 3 biologically important buffers discussed, their approximate pKa's, and where each acts.

Phosphate (pKa ~7.2, intracellular fluid); histidine side chains in proteins (pKa ~6.0); bicarbonate/carbonic acid (pKa ~6.35, blood).

In the bicarbonate buffer system, what organ controls CO2, and what organ controls H+/HCO3-? Why is bicarbonate used in blood instead of phosphate?

Lungs control CO2; kidneys control H+ and HCO3-. Bicarbonate is used because blood's phosphate concentration is too low to buffer effectively. CO2 + H2O ⇌ H2CO3 ⇌ H+ + HCO3-.

What causes acidosis versus alkalosis, in terms of CO2 and breathing?

Acidosis: hypoventilation/lung blockage raises CO2, lowering pH. Alkalosis: hyperventilation blows off CO2, raising pH. This is the mechanism behind the opening aspirin case study.