Atoms, Bonds and the Chemistry of Water
General Biology · Section 1.2 · 18 study cards
Atomic structure, isotopes, the four bond types, electronegativity, the emergent properties of water, and pH with buffers.
Practice this set → Spaced repetition, card by card. No account needed.
Method
Work outwards from the valence shell
Almost every chemistry question in this unit can be answered from the number of valence electrons. Count them, decide how many the atom needs to complete its shell, and the bonding behaviour follows: hydrogen forms one bond, oxygen two, nitrogen three, carbon four. Do not memorise bond counts as separate facts when they fall out of one rule.
Rank bond strength and know where each type is used
- Covalent bonds, strongest, build molecular skeletons and are broken only by enzymes or harsh conditions.
- Ionic bonds, strong when dry but weak in water, appear in salt bridges within proteins.
- Hydrogen bonds, weak individually but numerous, set the structure of water, of the DNA double helix and of protein secondary structure.
- Van der Waals interactions, weakest, matter only when surfaces fit closely.
When an exam question asks what breaks first under heating, answer in this order from the bottom up.
Derive water's properties, never list them
Every property of water traces to one cause: a bent, polar molecule that forms up to four hydrogen bonds. Cohesion, adhesion and surface tension are the network holding together. High specific heat and high heat of vaporisation are the energy needed to disrupt the network. Ice floating is the network becoming rigid and open. Solvent power is the network reorganising around a solute. If you can recite the cause, you can reconstruct all four consequences under exam pressure.
Treat pH as a logarithm, always
Convert between pH and concentration before comparing solutions. A solution at pH 4 has 10⁻⁴ M H⁺; at pH 6 it has 10⁻⁶ M, a hundredfold less. Buffers work because a weak acid and its conjugate base coexist, so the system can absorb additions in either direction; state both directions when asked to explain one.
Definitions and theorems
Worked example
Solution A has a pH of 3 and solution B has a pH of 6. (i) State the hydrogen ion concentration of each. (ii) How many times more concentrated in H⁺ is A than B? (iii) A student adds a small volume of strong acid to solution B, which contains a carbonic acid bicarbonate buffer, and finds the pH falls only to 5.9. Explain.
pH is the negative base-ten logarithm of the H⁺ concentration, so H⁺ concentration equals 10 raised to the power of minus pH.
Solution A: 10-3 M H⁺. Solution B: 10-6 M H⁺.
The ratio is 10-3 divided by 10-6, which is 103, so A is 1000 times more concentrated in H⁺ than B.
Adding strong acid adds free H⁺, which without a buffer would produce a large drop in pH.
The buffer contains bicarbonate, the conjugate base, which accepts the added H⁺: HCO₃⁻ + H⁺ → H₂CO₃.
Most of the added H⁺ is therefore removed from solution, and the free H⁺ concentration rises only slightly, so the measured pH falls only from 6 to 5.9.
Note the limit: once the bicarbonate is consumed the buffering capacity is exhausted and further acid causes a steep fall.
Common mistakes
- Reading the pH scale linearly. Students describe pH 5 as slightly more acidic than pH 6. It is ten times more acidic in H⁺ concentration. Convert to a power of ten before comparing, and remember that a lower pH means a higher H⁺ concentration, which reverses the direction people expect.
- Claiming hydrophobic molecules repel water. There is no repulsive force. Nonpolar molecules simply cannot form hydrogen bonds, so water excludes them to preserve its own network. Phrasing this as an active repulsion loses the mark on any question about why bilayers form.
- Forgetting that geometry decides molecular polarity. Polar bonds do not guarantee a polar molecule. CO₂ is linear and symmetric so its dipoles cancel, while water is bent so they do not. Always check the shape before declaring a molecule polar.
- Explaining ice floating by saying there are more hydrogen bonds in ice. The number per molecule is higher, but the point is that they are held at fixed angles in an open crystal lattice, so the molecules are spaced further apart than in the liquid. Density comes from spacing, not from bond count alone.
- Saying a buffer prevents pH change. A buffer resists change and has a finite capacity. Write that it minimises the change while its weak acid and conjugate base remain available, and note that the capacity can be exceeded.
Practice it
Reading the method is not the same as being able to recall it under pressure. This set drills 18 cards one at a time and schedules each card separately, so the ones you keep missing come back sooner.