Table of Contents
Overview: Why Carbon Forms So Many Compounds
Carbon is exceptional because it can form an enormous variety of stable compounds, far more than any other element. This diversity stems mainly from:
- Its four valence electrons (tetravalency), allowing four covalent bonds.
- Its ability to bond strongly with itself (C–C) and with other elements.
- The possibility of single, double, and triple bonds.
- The formation of long chains and rings (catenation).
In this chapter, the focus is not on how carbon bonds (that belongs to earlier sections), but on the kinds of compounds that result from these possibilities and why they are relevant for life.
Chains, Branches, and Rings
Straight and Branched Chains
Carbon atoms can link together into:
- Straight (unbranched) chains: e.g.,
–C–C–C–C– - Branched chains: where side chains split off from a main chain.
Even with the same number of carbon atoms, different arrangements are possible:
- Example with 4 carbon atoms:
- Straight chain:
CH₃–CH₂–CH₂–CH₃ - Branched chain:
CH₃–CH(CH₃)–CH₃
These are different compounds (isomers) with different physical properties (such as boiling point), even though they have the same molecular formula.
Rings (Cyclic Compounds)
Carbon chains can also close to form rings:
- Cycloalkanes: single-bonded rings, e.g. cyclohexane (6-membered ring).
- Aromatic rings: special stable ring systems with alternating single and double bonds (e.g. benzene ring).
Rings are widespread in biology:
- Many vitamins and hormones contain ring structures.
- Nucleotides (building blocks of DNA and RNA) include sugar rings and nitrogen-containing rings.
- Some amino acids (like phenylalanine, tryptophan) contain aromatic rings.
Different Bond Types Between Carbon Atoms
Carbon atoms can connect via:
- Single bonds (
C–C): allow free rotation, give flexible chains. - Double bonds (
C=C): more rigid; restrict rotation. - Triple bonds (
C≡C): very short and strong; give straight, rigid segments.
These bond types affect:
- The shape of molecules (flexible vs rigid).
- The reactivity: double and triple bonds are often more chemically reactive than single bonds.
An important consequence of double bonds:
- Geometric isomerism (cis-trans isomers): For a
C=Cbond with different groups attached, the groups can be: - On the same side of the double bond (cis).
- On opposite sides (trans).
Cis-trans isomers can have very different biological effects; for example, naturally occurring unsaturated fatty acids in cell membranes are often cis-configured, which keeps membranes fluid.
Open-Chain (Acyclic) vs Cyclic Carbon Compounds
Carbon compounds are often classified as:
- Acyclic (open-chain): straight or branched, but not closed into a ring.
- Cyclic: forming one or more rings.
Many biologically important molecules combine both features:
- A ring as a “core” with open chains attached.
- Multiple fused rings (e.g. steroid nucleus in cholesterol and many hormones).
These overall shapes are crucial for how molecules fit into enzymes or receptors (like keys into locks).
Broad Classes of Carbon Compounds
Inorganic vs Organic Carbon Compounds
Not all carbon compounds are considered organic. Some important exceptions:
- Carbon dioxide $(\mathrm{CO_2})$
- Carbon monoxide $(\mathrm{CO})$
- Carbonates (e.g. calcium carbonate, $\mathrm{CaCO_3}$)
- Bicarbonate (hydrogen carbonate, $\mathrm{HCO_3^-}$)
- Cyanides (e.g. $\mathrm{HCN}$, $\mathrm{CN^-}$)
These are usually classified as inorganic. They are still extremely important in biology (for example, $\mathrm{CO_2}$ in photosynthesis, carbonates in shells and bones), but the huge variety of life’s molecules belongs to organic chemistry.
Organic compounds are broadly grouped by the types of atoms and bonding patterns in their carbon skeletons and the functional groups attached.
Hydrocarbons: Carbon + Hydrogen Only
Hydrocarbons are the simplest organic compounds: they contain only carbon and hydrogen.
Main types:
- Alkanes (saturated): only single bonds, formula roughly $\mathrm{C_nH_{2n+2}}$ for straight chains.
- Alkenes (unsaturated): at least one C=C double bond.
- Alkynes: at least one C≡C triple bond.
- Aromatic hydrocarbons: contain benzene-like ring structures.
In living systems, pure hydrocarbons rarely act directly as biomolecules, but:
- Long-chain hydrocarbon segments occur in fatty acids and lipids.
- Hydrophobic (water-repelling) hydrocarbon regions are vital for forming cell membranes and waterproof coatings (e.g. waxes).
Functionalized Carbon Compounds
Most biologically important carbon compounds carry additional atoms or groups (oxygen, nitrogen, phosphorus, sulfur, etc.). These groups are called functional groups, and they define the molecule’s chemical behavior.
Common families (without going into their detailed chemistry here):
- Alcohols: contain hydroxyl groups (
–OH). - Aldehydes and ketones: contain carbonyl groups (
C=O). - Carboxylic acids: contain carboxyl groups (
–COOH). - Amines: contain amino groups (
–NH₂or related forms). - Amides: link of a carboxyl group with an amino group (peptide bond in proteins).
- Esters: formed from an acid and an alcohol, important in fats.
- Phosphates: phosphorus-containing groups (e.g. in ATP, DNA backbone).
Each type of functional group makes the carbon compound:
- More or less polar (water-soluble or water-insoluble).
- Acidic or basic.
- More or less reactive.
The same carbon skeleton with different functional groups can behave completely differently in biological systems.
Structural and Stereoisomerism
Many carbon compounds can exist in different isomeric forms:
- Same molecular formula, but different structure or spatial arrangement.
- Isomers often have very different properties and biological roles.
Key types:
Structural (Constitutional) Isomers
These differ in how atoms are connected:
- Different branching patterns.
- Different positions of functional groups.
- Different ring vs chain structures.
Example: two compounds with formula $\mathrm{C_3H_8O}$ could be:
- An alcohol on the end carbon.
- An alcohol on the middle carbon.
- An ether with two shorter chains.
In biology, structural isomers may be metabolized differently or may bind to different enzymes.
Stereoisomers
Stereoisomers have the same connectivity but differ in the 3D arrangement of atoms.
Important types in biology:
- Geometric isomers (cis/trans) at double bonds (already mentioned).
- Optical isomers (enantiomers): mirror-image forms around asymmetric (chiral) carbon atoms.
Chiral carbons are bonded to four different substituents; they create “left-handed” and “right-handed” forms of a molecule.
Biology often uses only one of these mirror forms:
- Natural amino acids (except glycine) are of the L-form.
- Natural sugars in nucleic acids and metabolism are mostly of the D-form.
The “wrong” enantiomer can be less active or completely inactive, or even harmful, because it does not fit correctly into biological binding sites.
Small vs Large Carbon Compounds
Carbon compounds range in size from very small to extremely large:
- Small molecules: e.g. methane, ethanol, acetic acid, simple sugars.
- Often used as fuels, signaling molecules, or metabolic intermediates.
- Medium-sized molecules: e.g. fatty acids, simple vitamins, some hormones.
- Frequently have both hydrophilic and hydrophobic regions.
- Macromolecules (large molecules built from many smaller units):
- Proteins (from amino acids),
- Polysaccharides (from monosaccharides),
- Nucleic acids (from nucleotides),
- Certain lipids (complex assemblies).
The ability of carbon to form repeating units (monomers) that link into long chains (polymers) is central for life’s macromolecules.
Heteroatoms: More Than Just Carbon and Hydrogen
In many biologically relevant carbon compounds, some positions in the carbon framework are occupied by other elements, or such elements are attached to the carbon skeleton:
- Oxygen (O): in alcohols, acids, esters, carbonyls; affects polarity and hydrogen bonding.
- Nitrogen (N): in amines, amides, nucleobases; essential for proteins and nucleic acids.
- Sulfur (S): in some amino acids, coenzymes; can form disulfide bonds stabilizing protein structure.
- Phosphorus (P): in phosphates; crucial for energy transfer (ATP) and nucleic acids.
- Halogens (Cl, Br, I, F): in some natural products and many synthetic compounds.
Such elements are often called heteroatoms when they are part of an organic structure. They strongly influence:
- Solubility in water vs lipids,
- Chemical reactivity,
- Ability to form hydrogen bonds,
- Role in metabolism and signaling.
Summary: The Space of Possible Carbon Compounds
Because carbon:
- Forms stable C–C bonds,
- Allows single, double, and triple bonds,
- Builds chains and rings,
- Combines with many different elements,
- Supports multiple isomeric forms,
the space of possible carbon compounds is essentially limitless. Life exploits only a small fraction of this space, but:
- All major classes of biomolecules (carbohydrates, lipids, proteins, nucleic acids, many vitamins and hormones) are based on carbon.
- Subtle differences in carbon skeletons and their functional groups lead to enormous diversity of structure and function.
Later chapters will examine specific groups of carbon-based biomolecules in detail and show how their structures relate to their biological roles.