Elements of Life: Study Guide (Biology 1.2)

Where the atoms in your body come from

Every atom in your body was once somewhere else. The carbon in your muscle protein may have been in the air as carbon dioxide a few months ago. The nitrogen in your DNA may have been in soil as nitrate. Living things cannot create atoms. To grow, repair tissues and reproduce, an organism must take in atoms and molecules from its environment and rearrange them into new molecules.

This topic asks two questions:

1. Which elements are used to build the large molecules of life: carbohydrates, lipids, proteins and nucleic acids?
2. Where do organisms get those elements?

The core elements: carbon, hydrogen and oxygen

Carbon (C), hydrogen (H) and oxygen (O) are the most common elements in biological molecules. All four classes of large biological molecule contain them.

Carbon is the backbone. A carbon atom forms four covalent bonds, so carbon atoms can join into long chains, branched chains and rings. Hydrogen and oxygen attach to this backbone. Oxygen also appears in many polar groups, such as the –OH groups on sugars, which you met in Topic 1.1.

Some molecules contain only these three elements:

• Carbohydrates, such as glucose (C₆H₁₂O₆), starch, glycogen and cellulose.
• Fats (triglycerides) and steroids, such as cholesterol. These lipids are mostly carbon and hydrogen, with a little oxygen.

Three more elements: nitrogen, sulfur and phosphorus

The other classes need extra elements. Learn where each one sits, not just which molecule it is in.

Sulfur: proteins

Proteins are chains of amino acids. Two of the amino acids, cysteine and methionine, have sulfur in their side chains. So most proteins contain sulfur. In later topics you will see that the sulfur atoms of two cysteines can bond to each other (a disulfide bridge) and help hold a protein in its folded shape. Nucleic acids, carbohydrates and lipids do not normally contain sulfur.

Phosphorus: phospholipids and nucleic acids

Phosphorus is found in phosphate groups (one phosphorus atom bonded to four oxygen atoms).

• In a phospholipid, a phosphate group forms part of the polar “head”. This is the one common type of lipid that contains phosphorus. Phospholipids make up cell membranes.
• In a nucleic acid (DNA or RNA), every nucleotide carries a phosphate group. Phosphates link the nucleotides together to form the sugar–phosphate backbone of the strand.

Background beyond this topic: the energy carrier ATP also contains phosphate groups. You will meet it in Unit 3.

Nitrogen: nucleic acids and proteins

• In a nucleic acid, nitrogen is in the nitrogenous bases (adenine, guanine, cytosine, thymine and uracil). These ring-shaped bases carry the genetic code.
• In a protein, every amino acid has an amino group (–NH₂) that contains nitrogen. Some side chains contain extra nitrogen as well.

Many phospholipids also have a small nitrogen-containing group in their head, but the element that defines a phospholipid is phosphorus.

Summary table: elements in each class

Seeing the elements in the building blocks

Figure 2 shows where the “extra” elements sit in two building blocks: the amino acid cysteine and a DNA nucleotide.

Reading the figure. Notice that the sugar in a nucleotide is made of the same three elements as glucose. The elements that make a nucleotide different from a carbohydrate are in the phosphate (P) and the base (N). In cysteine, the sulfur is in the side chain, not in the part shared by all amino acids. That is why only two of the common amino acids contain sulfur, while every amino acid has nitrogen.

How organisms obtain these elements

Matter cycles through ecosystems. Organisms take elements in, use them, and eventually return them when they excrete waste or die and decompose.

Element	How a plant takes it in	How an animal takes it in
Carbon	carbon dioxide from the air, fixed in photosynthesis	carbon compounds in food
Hydrogen and oxygen	water from the soil (and CO₂ for oxygen)	food and water
Nitrogen	nitrate (NO₃⁻) or ammonium (NH₄⁺) ions from soil water, through the roots	proteins and nucleic acids in food
Phosphorus	phosphate ions from soil water, through the roots	food
Sulfur	sulfate (SO₄²⁻) ions from soil water, through the roots	proteins in food

Animals break down the large molecules in their food into small units (by hydrolysis, Topic 1.3), absorb them, then rebuild them into their own proteins, nucleic acids and lipids.

Nitrogen gas (N₂) makes up most of the air, but plants and animals cannot use it directly. Among living things, only some prokaryotes can convert N₂ into compounds that other organisms can use. This is why a shortage of nitrate in soil slows plant growth: without nitrogen, a plant cannot make enough amino acids or nucleotides to build new proteins and DNA. A shortage of phosphate does the same for nucleic acids and membranes.

Using elements as labels: tracer experiments

Because each class has its own elements, scientists can follow atoms into molecules. They give cells a radioactive isotope, such as sulfur-35 (³⁵S) or phosphorus-32 (³²P). An isotope of an element behaves the same way in chemical reactions, so cells use it like the ordinary atom. Its radiation can then be detected in whatever molecules the cell has built.

• ³⁵S ends up mainly in proteins.
• ³²P ends up mainly in nucleic acids and phospholipids.

A famous use of this idea: in 1952, Alfred Hershey and Martha Chase grew viruses that infect bacteria with either ³⁵S (labelling the virus protein) or ³²P (labelling the virus DNA). Most of the ³²P entered the infected bacteria, while most of the ³⁵S stayed outside. This supported the idea that DNA, not protein, is the genetic material. You will return to this in Unit 6.

Worked example 1: identifying molecules from their formulas

Question. Four molecules from a cell are listed with their formulas:

Molecule	Formula
W	C₆H₁₂O₆
X	C₃H₇NO₂S
Y	C₁₀H₁₄N₅O₆P
Z	C₅₁H₉₈O₆

(a) Suggest which class of molecule (or building block) each one is, and justify your choice using the elements present. (b) Calculate the percentage by mass of sulfur in X. (c) Calculate the percentage by mass of nitrogen in Y.

(a) Classify.

1. W contains only C, H and O, in the ratio 1 : 2 : 1. That fits a carbohydrate (it is glucose).
2. X contains N and S. Sulfur points to a protein, and nitrogen to an amino group. X is an amino acid (it is cysteine).
3. Y contains both P and a lot of N (five atoms). Phosphorus with several nitrogen atoms points to a nucleotide, the building block of a nucleic acid.
4. Z contains only C, H and O, but very little oxygen compared with carbon and hydrogen. That fits a lipid, such as a fat (it is a triglyceride). It cannot be a phospholipid, because it has no phosphorus.

(b) Percentage of sulfur in X (C₃H₇NO₂S).

1. Add the atomic masses: C: 3 × 12.01 = 36.03; H: 7 × 1.01 = 7.07; N: 14.01; O: 2 × 16.00 = 32.00; S: 32.06.
2. Molar mass = 36.03 + 7.07 + 14.01 + 32.00 + 32.06 = 121.17 g mol⁻¹.
3. Percentage of S = 32.06 ÷ 121.17 × 100 = 26.5%.

(c) Percentage of nitrogen in Y (C₁₀H₁₄N₅O₆P).

1. C: 10 × 12.01 = 120.10; H: 14 × 1.01 = 14.14; N: 5 × 14.01 = 70.05; O: 6 × 16.00 = 96.00; P: 30.97.
2. Molar mass = 331.26 g mol⁻¹.
3. Percentage of N = 70.05 ÷ 331.26 × 100 = 21.1%.

Check. Each percentage is between 0 and 100, and the units cancel (g mol⁻¹ ÷ g mol⁻¹). A common slip is to count atoms instead of mass: S is 1 of 14 atoms in cysteine (about 7%), but because sulfur atoms are heavy, it is over a quarter of the mass.

Interpretation. Nucleotides are rich in nitrogen. A cell copying its DNA needs a steady supply of nitrogen and phosphorus, which is one reason fast-growing tissues and crops need these elements.

Worked example 2: reading tracer data

Question. A student grows two cultures of the same bacterium (fictional data). Culture 1 is given sulfate containing ³⁵S as its only sulfur source. Culture 2 is given phosphate containing ³²P as its only phosphorus source. After several generations, the cells are broken open and four fractions are separated. Radioactivity is measured in counts per minute (cpm). A background reading, with no sample present, is 80 cpm.

Fraction	Culture 1 (³⁵S) / cpm	Culture 2 (³²P) / cpm
Protein	19 280	680
DNA	140	12 080
Phospholipid	95	6 080
Polysaccharide	85	110

(a) Correct the readings for background and calculate the percentage of each label found in the protein fraction and in the DNA fraction. (b) Explain the distribution of each label. (c) Suggest why a small amount of ³²P appears in the protein fraction.

(a) Correct and calculate.

1. Subtract 80 cpm from every reading. Culture 1: protein 19 200, DNA 60, phospholipid 15, polysaccharide 5. Total = 19 280 cpm.
2. Culture 2: protein 600, DNA 12 000, phospholipid 6 000, polysaccharide 30. Total = 18 630 cpm.
3. ³⁵S in protein = 19 200 ÷ 19 280 × 100 = 99.6%; in DNA = 60 ÷ 19 280 × 100 = 0.3%.
4. ³²P in DNA = 12 000 ÷ 18 630 × 100 = 64.4%; in protein = 600 ÷ 18 630 × 100 = 3.2%. (Phospholipid: 32.2%.)

(b) Explain. Sulfur is built into the amino acids cysteine and methionine, so almost all the ³⁵S ends up in protein. DNA, phospholipids and polysaccharides do not normally contain sulfur; their tiny readings are close to background and could come from small amounts of protein left in those fractions. Phosphorus is built into phosphate groups. Every DNA nucleotide has one, and every phospholipid has one in its head, so ³²P is found in both. Polysaccharides contain no phosphorus, so they have almost none.

(c) Small ³²P signal in protein. Some proteins have phosphate groups attached to them after they are made (you will see this in cell signalling, Unit 4). Some contamination by DNA or phospholipid in the protein fraction is another possible explanation. Either way, 3.2% is small compared with the DNA and phospholipid fractions.

How confident? The pattern is very clear, but this is one culture of each type. Repeating each culture and measuring each fraction more than once would show whether the small signals are real or just variation.

Common misconceptions

• “Proteins contain only C, H, O and N.” Most proteins also contain sulfur, in cysteine and methionine.
• “Phosphorus is found only in DNA.” It is also in RNA, in phospholipids and in ATP.
• “All lipids contain phosphorus.” Only phospholipids do. Fats and steroids contain only C, H and O.
• “Only proteins contain nitrogen.” Nucleic acids contain even more nitrogen, in their bases.
• “DNA contains sulfur.” Its standard building blocks do not. That is why ³⁵S labels protein but not DNA.
• “Plants get their mass from the soil.” Most of a plant’s dry mass comes from carbon dioxide taken from the air. The soil supplies smaller amounts of nitrogen, phosphorus, sulfur and other ions.
• “Organisms make the elements they need.” Atoms are never created by cells; they are taken in and rearranged.
• “A radioactive atom behaves differently in a cell.” An isotope has the same chemistry as the ordinary atom; only its radiation is different, which is why it works as a label.

Where this leads

Next, Topic 1.3, Introduction to Macromolecules, shows how cells join small building blocks into polymers and break them apart again. Topics 1.4 to 1.7 then look at each class of molecule in detail. Before moving on, test yourself with the practice questions, then use the revision notes and the checklist. To review water and hydrogen bonding, return to Topic 1.1.