Atoms, bonding, gases, balanced equations, moles, solutions, pH, buffers, equilibrium and an organic and biochemistry preview, with short fill-in-the-blank Python calculators.

Chemistry Fundamentals

## Why this matters

Organic chemistry, the chemistry of carbon compounds, covers fuels, plastics, medicines, solvents and every molecule in a living cell. There are millions of organic compounds, but you do not need to memorise them. Chemists sort them by **functional groups**: small arrangements of atoms that react the same way wherever they appear. Spot the group and you can predict how a molecule behaves, how it might be named, and how it will show up on an instrument.

## Carbon's backbone

Carbon forms **four bonds**. It bonds readily to other carbons, making chains and rings, and to hydrogen, oxygen and nitrogen. A molecule made only of carbon and hydrogen is a **hydrocarbon**:

| family | bonds between carbons | example |
|---|---|---|
| alkane | single only (C–C) | ethane, CH₃CH₃ |
| alkene | at least one double (C=C) | ethene, CH₂=CH₂ |
| alkyne | at least one triple (C≡C) | ethyne (acetylene), HC≡CH |
| aromatic | a benzene ring | benzene, C₆H₆ |

The C–H backbone is nonpolar and fairly unreactive. The interesting chemistry happens at the functional groups attached to it.

## The groups to know

Chemists write **R** for "the rest of the molecule" (a carbon chain).

| group | structure | name ending | example |
|---|---|---|---|
| alcohol | R–OH | -ol | ethanol, CH₃CH₂OH (drinks, hand sanitiser) |
| ether | R–O–R | ether | diethyl ether, CH₃CH₂OCH₂CH₃ |
| aldehyde | R–CHO (C=O at the end of a chain) | -al | methanal (formaldehyde), HCHO |
| ketone | R–CO–R (C=O inside a chain) | -one | propanone (acetone), CH₃COCH₃ |
| carboxylic acid | R–COOH | -oic acid | ethanoic (acetic) acid, CH₃COOH |
| ester | R–COO–R | -oate | ethyl ethanoate (ethyl acetate), CH₃COOCH₂CH₃ |
| amine | R–NH₂ | -amine | methylamine, CH₃NH₂ |
| amide | R–CONH₂ | -amide | ethanamide (acetamide), CH₃CONH₂ |
| haloalkane | R–X (X = F, Cl, Br, I) | chloro-, bromo- | chloromethane, CH₃Cl |

The **carbonyl** group, C=O, appears in aldehydes, ketones, acids, esters and amides. What is attached to the carbonyl carbon decides which one it is:

```text
H on the carbonyl carbon         -> aldehyde   R-CHO
two carbons on it                -> ketone     R-CO-R
an -OH on it                     -> carboxylic acid  R-COOH
an -O-R on it                    -> ester      R-COO-R
an -N on it                      -> amide      R-CONH2
```

## Worked examples: name the group

1. **CH₃CH₂CH₂OH**. An –OH on a carbon chain: **alcohol** (propan-1-ol).
2. **CH₃COCH₂CH₃**. A C=O with carbon on both sides: **ketone** (butanone).
3. **CH₃CH₂COOH**. –COOH at the end: **carboxylic acid** (propanoic acid).
4. **HCOOCH₃**. C=O bonded to an O that leads to another carbon: **ester** (methyl methanoate).
5. **CH₃CH₂NH₂**. Nitrogen bonded to carbon and hydrogens: **amine** (ethylamine).
6. **Aspirin** contains a benzene ring, a carboxylic acid and an ester, all in one molecule. Real molecules often have several groups.

## What groups tell you about properties

- **–OH, –COOH, –NH₂** can hydrogen-bond, so small alcohols, acids and amines mix with water and have higher boiling points than hydrocarbons of similar size. Ethanol boils at 78 °C; propane, of similar mass, boils at −42 °C.
- **Carboxylic acids** are weak acids (vinegar is about 4–8% acetic acid in water). **Amines** are weak bases, like ammonia.
- **Esters** often smell fruity and are used in flavourings and solvents. Many nail-polish removers are acetone, a ketone.
- An acid plus an alcohol can form an ester and water (esterification); an acid plus an amine can form an amide. The amide link is the **peptide bond** that joins amino acids in proteins, which you will see in the next lesson.

## Where you will see this at work

Functional groups are how chemists read infrared spectra (a C=O shows a strong peak near 1700 cm⁻¹), how pharmacologists think about how a drug behaves in the body, and how materials scientists describe polymers (polyesters, polyamides such as nylon). Lab and instrument work is learned in supervised lab courses; this lesson is the vocabulary.

## Common mistakes

- **Mixing up aldehyde and ketone.** Aldehyde: the C=O carbon carries a hydrogen (chain end). Ketone: C=O between two carbons.
- **Calling an ester an ether.** An ester has a C=O next to the O; an ether has only C–O–C.
- **Calling every –OH an alcohol.** In –COOH the –OH is part of a carboxylic acid, which behaves very differently.
- **Amine vs amide.** Amide has a C=O attached to the nitrogen; amine does not.

## Quick recap

- Carbon makes four bonds and forms chains and rings; hydrocarbons are the backbone.
- Functional groups set the chemistry: alcohol, ether, aldehyde, ketone, acid, ester, amine, amide.
- Look at what is attached to a C=O to tell its group apart.
- Polar groups raise boiling points and water solubility.

## Try it

Open the **Do** tab and take the quiz: you will identify the functional group in several formulas.


Recognise the common functional groups in organic molecules (alcohol, aldehyde, ketone, carboxylic acid, ester, amine, amide) and what each one tells you.

Functional groups

Functional Groups

Identifying functional groups | Organic chemistry | Khan Academy

## Why this matters

Biochemists, biological technicians and medical laboratory scientists spend their days measuring biomolecules: glucose and cholesterol in blood, proteins on a gel, DNA in a PCR tube. Materials scientists increasingly work with bio-based polymers too. Every one of these molecules belongs to one of four classes, and each class is built by the same chemistry you have already met: functional groups joined into bigger molecules.

## The big idea: monomers, polymers and water

Most large biological molecules are **polymers**: long chains of small repeating units called **monomers**.

- **Condensation (dehydration synthesis)** joins two monomers and releases a water molecule.
- **Hydrolysis** breaks the link by adding water back. Digestion is mostly hydrolysis, sped up by enzymes.

```text
monomer–OH + H–monomer  ->  monomer–monomer + H2O     (condensation)
monomer–monomer + H2O   ->  monomer–OH + H–monomer    (hydrolysis)
```

## The four classes

| class | elements | building block | link between units | main jobs |
|---|---|---|---|---|
| carbohydrates | C, H, O | monosaccharides (glucose) | glycosidic bond | fast energy, structure (cellulose) |
| lipids | mostly C, H, a little O | fatty acids + glycerol (not a true polymer) | ester bond | long-term energy, membranes, hormones |
| proteins | C, H, O, N (often S) | amino acids (20 standard) | peptide (amide) bond | enzymes, structure, transport, signals |
| nucleic acids | C, H, O, N, P | nucleotides | phosphodiester bond | store and express genetic information |

### Carbohydrates

Formula often close to (CH₂O)ₙ. **Glucose** (C₆H₁₂O₆) is the main fuel for cells.

- **Monosaccharides**: glucose, fructose, galactose.
- **Disaccharides**: two joined, such as sucrose (table sugar = glucose + fructose) and lactose.
- **Polysaccharides**: starch and glycogen (energy storage in plants and animals) and cellulose (plant cell walls, the most abundant organic polymer on Earth). Starch and cellulose are both made of glucose, but the links differ, which is why you can digest one and not the other.

### Lipids

Lipids are grouped by being **hydrophobic** (they do not dissolve well in water), not by a single repeating unit.

- **Triglycerides** (fats and oils): one glycerol joined by **ester** bonds to three fatty acids. Saturated fatty acids have no C=C double bonds and pack tightly (solid butter); unsaturated ones have C=C kinks (liquid olive oil).
- **Phospholipids**: a water-loving phosphate head and two water-fearing tails. They form the **bilayer** of every cell membrane.
- **Steroids**: four fused rings. Cholesterol and hormones such as testosterone and oestradiol.

### Proteins

Proteins are chains of **amino acids**. Each amino acid has an amine group, a carboxylic acid group and a side chain (R group) that gives it its character. The acid of one joins the amine of the next by a **peptide bond** (an amide), releasing water.

A protein's function depends on its **shape**, built up in levels: the sequence (primary), local folds such as helices and sheets (secondary), the full 3-D fold (tertiary), and sometimes several chains together (quaternary, as in haemoglobin). Heat, extreme pH or some chemicals can **denature** a protein, unfolding it so it stops working: that is what happens to egg white when you cook it. This is also why buffers matter in biology.

**Enzymes** are protein catalysts: they lower activation energy for specific reactions, exactly the idea from the rates lesson.

### Nucleic acids

**DNA** and **RNA** are chains of **nucleotides**. Each nucleotide has a sugar (deoxyribose in DNA, ribose in RNA), a phosphate and a base.

- DNA bases: A, T, G, C. RNA uses U instead of T.
- Sugars and phosphates alternate along the backbone, joined by **phosphodiester** bonds.
- In DNA's double helix, A pairs with T and G pairs with C by hydrogen bonds.

DNA stores the instructions; RNA carries them out to build proteins. Lab methods such as PCR and sequencing all rely on this chemistry, and they are taught in supervised lab courses.

## Worked example: classify the molecule

1. **Contains C, H, O in roughly a 1 : 2 : 1 ratio, tastes sweet.** Carbohydrate.
2. **Contains nitrogen and sulfur, made of 300 linked units with peptide bonds.** Protein.
3. **Contains phosphorus, has a sugar–phosphate backbone and bases A, T, G, C.** Nucleic acid (DNA).
4. **Does not dissolve in water; glycerol plus three long chains joined by ester bonds.** Lipid (a triglyceride).

## Common mistakes

- **Calling fats polymers.** Triglycerides are assembled from parts but are not long repeating chains.
- **Assuming only proteins contain nitrogen.** Nucleic acids contain nitrogen too (in the bases), and phosphorus.
- **Forgetting the water.** Condensation releases water; hydrolysis uses it.
- **Thinking denatured means broken into amino acids.** Denaturing unfolds the shape; the peptide bonds usually stay intact.

## Quick recap

- Four classes: carbohydrates, lipids, proteins, nucleic acids.
- Monomers join by condensation and split by hydrolysis.
- Bonds: glycosidic (sugars), ester (fats), peptide (proteins), phosphodiester (DNA/RNA).
- Shape determines protein function; DNA stores information in base sequence.

## Try it

Open the **Do** tab and take the quiz: you will match biomolecules to their building blocks, bonds and jobs.


Name the four classes of biomolecules, their building blocks and the bonds that join them, and say what each class does in a cell.

Biomolecules

Biological Molecules - You Are What You Eat: Crash Course Biology #3

Biomolecules (Updated 2023)

## Why this matters

A name in chemistry is a precise instruction. On a reagent bottle, a safety data sheet or a lab request, "iron(II) chloride" and "iron(III) chloride" are different substances with different hazards and amounts. Chemists, lab technicians and engineers must be able to go from a name to a formula and back without guessing. The rules are systematic (set by IUPAC, the International Union of Pure and Applied Chemistry), so a handful of patterns cover most of what you will see.

## Step 1: decide what kind of compound it is

- **Metal + nonmetal** (or a polyatomic ion such as NH₄⁺): **ionic** naming.
- **Two nonmetals**: **molecular** naming with prefixes.
- **Carbon chains with hydrogen**: **organic** naming.

## Ionic compounds

Name the **cation** (positive ion) first, then the **anion** (negative ion). A single-element anion ends in **-ide**.

```text
NaCl    sodium chloride
MgO     magnesium oxide
CaCl2   calcium chloride
Al2O3   aluminium oxide
K2S     potassium sulfide
```

Ionic names do **not** use prefixes: CaCl₂ is calcium chloride, not calcium dichloride. The charges decide the ratio: Ca²⁺ needs two Cl⁻ to balance.

### Metals with more than one charge

Many transition metals form more than one ion. Put the charge in **Roman numerals** after the metal (the Stock system):

```text
FeCl2   iron(II) chloride       Fe2+ with two Cl-
FeCl3   iron(III) chloride      Fe3+ with three Cl-
CuO     copper(II) oxide
Cu2O    copper(I) oxide
```

To find the numeral from a formula, work out what the metal's charge must be to cancel the anions: in Fe₂O₃, three O²⁻ give −6, so each of the two irons is +3: iron(III) oxide.

### Polyatomic ions

Some ions are groups of atoms that stay together. Learn the common ones:

| ion | name | ion | name |
|---|---|---|---|
| NH₄⁺ | ammonium | OH⁻ | hydroxide |
| NO₃⁻ | nitrate | SO₄²⁻ | sulfate |
| CO₃²⁻ | carbonate | HCO₃⁻ | hydrogen carbonate (bicarbonate) |
| PO₄³⁻ | phosphate | CH₃COO⁻ | acetate (ethanoate) |

```text
NaOH      sodium hydroxide
CaCO3     calcium carbonate
NaHCO3    sodium hydrogen carbonate (baking soda)
NH4NO3    ammonium nitrate
Na2SO4    sodium sulfate
Ca3(PO4)2 calcium phosphate
```

Use brackets when you need more than one polyatomic ion: Ca₃(PO₄)₂ has two phosphate groups.

## Molecular (covalent) compounds of two nonmetals

Use Greek **prefixes** to give the number of each atom, and end the second element in **-ide**. Drop "mono-" on the first element.

| prefix | number | prefix | number |
|---|---|---|---|
| mono- | 1 | tetra- | 4 |
| di- | 2 | penta- | 5 |
| tri- | 3 | hexa- | 6 |

```text
CO      carbon monoxide
CO2     carbon dioxide
N2O4    dinitrogen tetroxide
PCl5    phosphorus pentachloride
SF6     sulfur hexafluoride
```

Some molecules keep common names you are expected to know: H₂O is water, NH₃ is ammonia, CH₄ is methane.

## Simple organic names

Organic names are built from parts: **prefix (branches) + root (chain length) + ending (functional group)**.

### The root: the longest carbon chain

| carbons | root | alkane |
|---|---|---|
| 1 | meth- | methane CH₄ |
| 2 | eth- | ethane C₂H₆ |
| 3 | prop- | propane C₃H₈ |
| 4 | but- | butane C₄H₁₀ |
| 5 | pent- | pentane C₅H₁₂ |
| 6 | hex- | hexane C₆H₁₄ |

Alkanes follow CₙH₂ₙ₊₂, which is a quick way to check a formula.

### The ending: the functional group

```text
-ane   alkane            propane       CH3CH2CH3
-ene   alkene (C=C)      propene       CH2=CHCH3
-ol    alcohol           propan-1-ol   CH3CH2CH2OH
-al    aldehyde          propanal      CH3CH2CHO
-one   ketone            propanone     CH3COCH3 (acetone)
-oic acid                propanoic acid CH3CH2COOH
```

### Numbers and branches

Number the main chain from the end that gives the functional group (or the first branch) the **lowest number**. Branches are named as **alkyl** groups (methyl, ethyl) with their position:

```text
CH3CH(OH)CH3         propan-2-ol (isopropyl alcohol)
CH3CH(CH3)CH3        2-methylpropane
CH3CH(CH3)CH2CH3     2-methylbutane (not 3-methylbutane)
```

## Common mistakes

- **Prefixes on ionic compounds.** MgCl₂ is magnesium chloride, not magnesium dichloride.
- **Leaving out the Roman numeral** for iron, copper and other variable-charge metals.
- **Confusing sulfide (S²⁻), sulfite (SO₃²⁻) and sulfate (SO₄²⁻).**
- **Numbering from the wrong end** of a chain; pick the end that gives the lowest numbers.
- **Counting branch carbons in the root.** The root is the longest continuous chain only.

## Quick recap

- Ionic: cation + anion (-ide), Roman numerals for variable-charge metals, no prefixes.
- Molecular: prefixes for atom counts, second element ends in -ide.
- Organic: chain length root + functional-group ending + numbered branches.

## Try it

Open the **Do** tab and take the quiz: you will name compounds and turn names back into formulas.


Name simple ionic compounds (including transition metals and polyatomic ions), binary molecular compounds with prefixes, and short-chain organic molecules.

Naming compounds

Naming ions and ionic compounds | Chemistry | Khan Academy

The Basics of Organic Nomenclature: Crash Course Organic Chemistry #2

Functional groups, the four classes of biomolecules, and naming simple ionic, molecular and organic compounds.