1Atoms come from the environment

An organism cannot make atoms; it can only take them in and rearrange them. Think about where a growing plant gets each element:

• Carbon and oxygen from carbon dioxide in the air, which photosynthesis builds into sugars (Unit 3).
• Hydrogen (and more oxygen) from water.
• Nitrogen from the soil, absorbed by the roots as dissolved ions such as nitrate or ammonium.
• Phosphorus from the soil, as phosphate ions.
• Sulfur from the soil, as sulfate ions.

An animal gets the same elements secondhand, by eating plants or other animals and breaking their molecules down into smaller ones (topic 1.3), which it then rebuilds into its own. When organisms die, decomposers break their molecules down again and the atoms return to the soil, air and water to be used once more. In Unit 8 you meet those journeys as the carbon, nitrogen and phosphorus cycles.

Organisms build new molecules only from atoms they take in from their environment; a molecule that needs an element the organism cannot get cannot be made.

2Carbon, hydrogen and oxygen: the common core

Carbon, hydrogen and oxygen are the most common elements in biological molecules. Carbon is the backbone. Each carbon atom forms four covalent bonds, so carbon atoms can link to each other in long chains, branched chains and rings, with hydrogen and oxygen attached around them. That one property is why there are so many different biological molecules and why they can be so large.

A useful picture: carbohydrates are almost entirely C, H and O, roughly one carbon to two hydrogens to one oxygen (glucose is C₆H₁₂O₆). Fats are almost all C and H with very little O, which is why they are nonpolar (topic 1.5).

3Which element goes where

This table is the heart of the topic. Learn it as a pattern rather than as a list.

Three short rules come out of it.

• Sulfur means protein. Of the four classes, only proteins contain sulfur, in the R groups of a few amino acids. Topic 1.7 shows why it matters: sulfur atoms in two R groups can bond covalently to each other and hold a folded protein in shape.
• Phosphorus means nucleic acid or phospholipid. Every nucleotide carries a phosphate group (topic 1.6), and every phospholipid has a phosphate in its head (topic 1.5). ATP, the cell's energy carrier, is a nucleotide too, so it also contains phosphorus.
• Nitrogen means nucleic acid or protein. Every nucleotide has a nitrogenous base, and every amino acid has an amine group.

So if a label turns up in DNA but not in protein, it was phosphorus. If it turns up in protein but not DNA, it was sulfur. If it turns up in both, it was nitrogen (or carbon, hydrogen or oxygen, which are everywhere).

4Following atoms with tracers: a worked example

Biologists track elements by giving cells a tracer: a form of an element that can be detected, such as radioactive sulfur (³⁵S) or radioactive phosphorus (³²P). The cells cannot tell the tracer from the ordinary element, so they build it into molecules in the usual way. The cells are then broken open, the classes of molecule separated, and the radioactivity in each measured.

An invented experiment. Two cultures of bacteria were grown for one hour, one with ³⁵S-labelled sulfate and one with ³²P-labelled phosphate. The radioactivity in each fraction was measured in counts per minute (cpm).

The percentage of the label in one fraction is the counts in that fraction divided by the total, times 100.

Now the claim, evidence and reasoning. Claim: sulfur is used to build proteins, and phosphorus to build nucleic acids and some lipids. Evidence: 98.9% of the ³⁵S was in protein; 84.4% of the ³²P was in nucleic acid and 14.4% in lipid. Reasoning: amino acids with sulfur in their R groups are built into proteins, while every nucleotide and every phospholipid contains a phosphate group. The tiny counts elsewhere (60 cpm, 40 cpm) are background: the counter always picks up a little radiation, and a few labelled molecules stick to the wrong fraction during separation. Treat very small numbers as zero, and say so.

5Rates: how fast an element is taken up

The formula sheet's rate is the change in a quantity divided by the change in time, dY ÷ dt. Suppose (invented data) roots take up phosphate from a solution, and the phosphate inside the roots rises from 0.14 to 0.62 µmol per gram of root over 40 minutes.

Always give the unit: amount per gram per minute here. A question might then ask you to predict the effect of a soil with less phosphate: a lower rate of uptake, so less phosphorus available to build nucleic acids and phospholipids, so slower growth.

6Predicting the effect of a shortage

The CED's argument skill is predicting what happens when one part of a system changes. With elements, the logic always runs the same way: missing element, so the molecules that need it cannot be made, so the jobs those molecules do suffer.

• Nitrogen shortage. A plant cannot build enough amino acids and nucleotides, so it makes less protein (including enzymes) and less DNA and RNA. Growth is slow and stunted. This is why farmers add nitrogen fertiliser.
• Phosphorus shortage. Less DNA and RNA can be made, so cell division and protein synthesis slow; fewer phospholipids, so less new membrane; less ATP. Growth slows.
• Sulfur shortage. Proteins that need sulfur-containing amino acids cannot be completed.

A shortage of carbon, hydrogen or oxygen would stop the building of every class of molecule, but in practice organisms rarely run short of these.