Difficulty: Introductory | Prerequisites: Basic understanding of atoms and bonding (covered in the Water, Bonding, and pH notes).
Carbon is the element that makes biology possible. Its ability to form four stable bonds and link into long chains, rings, and branching structures gives rise to the enormous variety of molecules found in living things. This section of Unit 1 introduces carbon's bonding behaviour and the small clusters of atoms, called functional groups, that attach to carbon skeletons and determine how each molecule behaves. If you understand functional groups, you will have a much easier time with proteins, lipids, carbohydrates, and nucleic acids later in the course.
Carbon forms four covalent bonds and can chain with itself indefinitely, which is why it is the structural backbone of every major biological molecule. Functional groups (hydroxyl, carboxyl, amino, phosphate, and others) snap onto carbon skeletons and give each molecule its chemical personality: whether it acts as an acid, a base, stores energy, or signals other molecules.
Hydrocarbon
A molecule made entirely of carbon and hydrogen atoms. Hydrocarbons are non-polar and store energy in their C–H bonds. Think of it as the simplest possible carbon skeleton, before any functional groups are added.
Functional group
A specific cluster of atoms that replaces one or more hydrogens on a carbon skeleton and determines the molecule's chemical behaviour. In simple terms, functional groups are the "accessories" that give a carbon chain its job.
Methyl group (–CH₃)
A carbon bonded to three hydrogens. When attached to DNA, methyl groups regulate gene expression (turning genes on or off). Think of it as a molecular switch.
Hydroxyl group (–OH)
An oxygen bonded to a hydrogen. It is polar, forms hydrogen bonds with water, and makes molecules hydrophilic. Alcohols carry hydroxyl groups, which is why ethanol mixes with water.
Carbonyl group (C=O)
A carbon double-bonded to an oxygen. Found in sugars (aldehydes and ketones). Whether the carbonyl sits at the end of the chain (aldehyde) or in the middle (ketone) changes the molecule's identity.
Carboxyl group (–COOH)
A carbon double-bonded to one oxygen and single-bonded to a hydroxyl. It donates H⁺, so it behaves as an acid. Amino acids all carry a carboxyl group at one end.
Amino group (–NH₂)
A nitrogen bonded to two hydrogens. It accepts H⁺, so it behaves as a base. Amino acids carry an amino group at the opposite end from the carboxyl group.
Phosphate group (–PO₄)
A phosphorus bonded to four oxygens, usually ionised and carrying a negative charge. Phosphate groups are central to energy transfer: ATP (adenosine triphosphate) stores energy in the bonds between its phosphate groups.
Living matter is composed primarily of four elements: carbon, hydrogen, oxygen, and nitrogen
Carbon has four valence electrons, so it can form four stable covalent bonds with other atoms, including other carbons
This lets carbon build chains, branching structures, and rings of virtually any length
Chains of carbon and hydrogen alone are called hydrocarbons
Hydrocarbons are non-polar and hydrophobic
They store a great deal of energy in their C–H bonds, which is why fats (lipids) are energy-dense
The diversity of carbon-based molecules is what makes biological complexity possible: by rearranging how carbons connect and which functional groups attach, cells produce thousands of distinct molecules from the same handful of elements
Functional groups replace one or more hydrogens on a hydrocarbon skeleton. Each group brings a distinct chemical behaviour, so recognising them tells you what a molecule can do.
Methyl (–CH₃) – non-polar, does not participate in chemical reactions on its own
Its biological role is regulatory: methyl groups added to DNA silence genes, and methyl groups on histone proteins affect how tightly DNA is packed
Hydroxyl (–OH) – polar, makes molecules soluble in water
Forms hydrogen bonds with surrounding water molecules
Found in sugars and alcohols
Carbonyl (C=O) – polar, found in aldehydes (carbonyl at the end of the chain) and ketones (carbonyl in the middle)
Commonly seen in sugar molecules (glucose is an aldehyde sugar; fructose is a ketone sugar)
Carboxyl (–COOH) – acts as an acid by donating H⁺
Present in all amino acids and in fatty acids
When it loses its H⁺, the group carries a negative charge (–COO⁻)
Amino (–NH₂) – acts as a base by accepting H⁺
Present in all amino acids (the name "amino acid" comes from this group)
When it picks up an H⁺, the group carries a positive charge (–NH₃⁺)
Phosphate (–PO₄) – ionised, carries negative charge, highly polar
Central to energy transfer: ATP releases energy when a phosphate group is cleaved off
Also forms the backbone of DNA and RNA (phosphodiester bonds link nucleotides through phosphate groups)
Biological vocabulary is built from Greek and Latin prefixes, roots, and suffixes. Learning a handful of them lets you decode unfamiliar terms on sight.
Hydro- = water (hydrophilic, hydrocarbon, hydrolysis)
-philic = loving / attracted to (hydrophilic = water-loving)
-phobic = fearing / repelled by (hydrophobic = water-fearing)
-lysis = breaking apart (hydrolysis = breaking with water)
-ase = enzyme (lipase, protease, polymerase)
Poly- = many (polymer, polysaccharide)
Mono- = one (monomer, monosaccharide)
-mer = part / unit (monomer = one unit, polymer = many units)
When you encounter a new term, split it at its prefix and suffix. Nine times out of ten, you can work out the meaning without looking it up.
Functional Group | Formula | Charge behaviour | Where you will see it |
|---|---|---|---|
Methyl | –CH₃ | Non-polar, neutral | DNA methylation, histone modification |
Hydroxyl | –OH | Polar, neutral | Sugars, alcohols |
Carbonyl | C=O | Polar, neutral | Aldehydes (glucose), ketones (fructose) |
Carboxyl | –COOH | Acidic, donates H⁺ | Amino acids, fatty acids |
Amino | –NH₂ | Basic, accepts H⁺ | Amino acids |
Phosphate | –PO₄ | Ionised, negative charge | ATP, DNA/RNA backbone |
The energy density of hydrocarbons is the reason fossil fuels (oil, natural gas) and dietary fats store so much energy per gram: both are carbon-hydrogen chains releasing energy when their C–H bonds are broken.
DNA methylation (methyl groups attaching to DNA) is a major area of epigenetics research, with implications for cancer biology, ageing, and developmental disorders.
ATP, the cell's energy currency, works by releasing a phosphate group. This same principle is harnessed in laboratory assays that measure cellular energy use.
Students often think "organic" means "healthy" or "natural." In chemistry, organic simply means carbon-based. Plastics are organic molecules.
A hydroxyl group (–OH) is not the same as a hydroxide ion (OH⁻). The hydroxyl group is covalently bonded to a carbon and does not float free in solution.
Students sometimes assume that all functional groups make a molecule polar. Methyl groups (–CH₃) are non-polar and do not increase solubility in water.
Carboxyl and amino groups are often confused. Remember: carboxyl donates H⁺ (acid), amino accepts H⁺ (base). The two sit at opposite ends of every amino acid.
⚠️ Be able to identify each functional group by its structure and predict its behaviour (acidic, basic, polar, non-polar).
⚠️ Know why carbon is uniquely suited to be the backbone of biological molecules (four bonds, self-chaining, structural diversity).
⚠️ Understand the role of phosphate groups in ATP and energy transfer. This comes back in cellular respiration and photosynthesis.
⚠️ Recognise that the same carbon skeleton can produce entirely different molecules depending on which functional groups are attached.
True or false: Carbon can form a maximum of two covalent bonds. (False. Carbon forms four.)
Fill in the blank: A chain of carbon and hydrogen atoms with no functional groups is called a ______. (hydrocarbon)
True or false: The carboxyl group behaves as a base. (False. It donates H⁺ and behaves as an acid.)
Fill in the blank: The functional group –NH₂ is called the ______ group, and it acts as a ______. (amino; base)
True or false: ATP stores energy in the bonds between its phosphate groups. (True.)
Q: Explain why carbon is described as the "backbone" of biological molecules.
A: Carbon has four valence electrons, allowing it to form four covalent bonds simultaneously. It can bond to other carbon atoms to create long chains, branched structures, and rings, providing a versatile and stable scaffold on which functional groups attach to produce the full range of biological molecules.
Q: A molecule contains both a carboxyl group and an amino group. At physiological pH, what charges would each group carry?
A: The carboxyl group loses its H⁺ and carries a negative charge (–COO⁻). The amino group picks up an H⁺ and carries a positive charge (–NH₃⁺). This is the typical zwitterion form of an amino acid at physiological pH (~7.4).
Q: How does the addition of a methyl group to DNA affect gene expression?
A: Methylation of DNA typically silences gene expression. The methyl group does not change the DNA sequence itself but alters how accessible the gene is to the cell's transcription machinery, reducing or preventing transcription.
Q: Compare the hydroxyl group and the carboxyl group. How are they structurally similar, and how do they differ in chemical behaviour?
A: Both contain an oxygen bonded to a hydrogen (–OH). In a hydroxyl group, the –OH is bonded directly to a carbon and is polar but neutral. In a carboxyl group, the –OH is bonded to a carbon that is also double-bonded to a second oxygen (C=O), and this arrangement makes the hydrogen much easier to donate, so the carboxyl group acts as an acid.
Q: Why are hydrocarbons good energy-storage molecules?
A: Hydrocarbons contain many C–H bonds, each of which stores energy. When these bonds are broken (oxidised), a large amount of energy is released. This is why fats, which have long hydrocarbon tails, store roughly twice the energy per gram compared with carbohydrates.
Functional groups reappear throughout AP Biology. Carbohydrates (Unit 1 continued) are built from carbon skeletons studded with hydroxyl and carbonyl groups. Proteins fold and function based on the R-group chemistry of their amino acids, which is just functional-group chemistry on a larger scale. Nucleic acids (DNA and RNA) rely on phosphate groups to link nucleotides together and on hydrogen bonding between bases to hold the double helix in shape. If you master functional groups now, every macromolecule chapter will feel like a natural extension.
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