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Biology · The Chemistry of Life

Atoms, chemical bonds and interactions in biological systems

The oxygen in a water molecule and the oxygen in a sugar belong to the same chemical element, yet they occupy different surroundings. An atom's identity is not the identity of the whole molecule. Start by following what stays the same and what changes when atoms join or separate.

You can begin without a completed chemistry course. Each lesson introduces its essential symbols. The earlier chapter's distinction between a system and its surroundings is useful background. The Chemistry map offers optional depth on atoms, bonding and solutions; those links are support rather than a requirement to finish another subject first.

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By the end, you can

Distinguish an atom's identity, an ion's charge, covalent connections and interactions between molecules.

01

An element is an atomic identity

An atom has a nucleus containing protons and, usually, neutrons, with electrons distributed around it. Proton number identifies the element. Isotopes of an element differ in neutron number; changing electron number instead can produce an ion. These are different kinds of change.

An electron carries negative charge and a proton positive charge. Equal numbers give a neutral atom. A sodium ion, Na⁺, is still sodium: its nucleus has not become a different element. The superscript tells us about net charge; it does not count sodium atoms.

Compare H₂O with 2 H₂O. The small subscript says each water molecule contains two hydrogen atoms. The coefficient says there are two water molecules. Together, those two molecules contain four hydrogen atoms and two oxygen atoms. Keeping these two jobs separate makes later reaction inventories readable.

02

A line within a molecule differs from a link between molecules

A covalent bond involves shared electrons and helps establish which atoms belong to a molecular structure. Sharing need not be even. In an O–H bond, the electron distribution favours oxygen; a water molecule therefore has partial charges, although the whole molecule is neutral.

A hydrogen bond is a different interaction: a suitable hydrogen already covalently attached to an electronegative atom can interact with another suitable atom. In the pictured water pair, the dotted link joins one molecule's hydrogen to the other molecule's oxygen. It is not a third O–H covalent bond.

Many individually modest interactions can matter together. A folded molecule may depend on several contacts, while a binding partner can attach and later leave. Do not infer that an interaction is biologically unimportant merely because it is easier to disrupt than a typical covalent connection.

Distinguish the connections in a water pair

Distinguish the connections in a water pairTwo bent water molecules show solid O–H connections within each molecule and one dotted O···H interaction between molecules. Oxygen is labelled δ− and hydrogen δ+. The whole water molecule remains neutral. The geometry and sizes are schematic.Hδ+Hδ+Oδ−Hδ+Hδ+Oδ−Covalent O–H bondHydrogen-bond interaction
Line styles distinguish connection types. Neither line length nor circle size is quantitative.
Read the diagram in words

Within each water molecule, oxygen is covalently connected to two hydrogens. The dotted line links the oxygen of one molecule with a suitably oriented hydrogen of the other. Partial charges do not make each water molecule a full ion.

Covalent O–H bond
O–H
Hydrogen-bond interaction
O···H
H₂O
O δ− · H δ+
H₂O
O δ− · H δ+
03

Charges act in a surrounding medium

Opposite charges attract, but the effect of a charge also depends on nearby water, ions and the geometry of the system. A sodium chloride crystal is an extended arrangement of ions. Its formula describes their ratio; it is not a picture of isolated NaCl molecules throughout the solid.

When that salt dissolves, the ions become surrounded by water. Dissolving and reacting are distinct questions: ask which particles remain, whether new substances form, and what interactions have changed.

Worked example

Read a charge without changing the element

A neutral sodium atom has eleven protons and eleven electrons. A Na⁺ ion has eleven protons and ten electrons: eleven positive charges minus ten negative charges gives a net charge of +1. Sodium identity follows the eleven protons. By contrast, two Na⁺ ions have twice as many sodium nuclei; the coefficient changes the number of entities, while the superscript describes each entity.

Check your understanding

  1. Does the 2 in H₂O mean two water molecules?

    Show reasoning

    No. It counts hydrogen atoms in one water molecule. Two water molecules are written 2 H₂O.

  2. What changes when a neutral sodium atom becomes Na⁺?

    Show reasoning

    Its electron count changes. The proton count, and therefore its identity as sodium, stays the same.

  3. If a dotted hydrogen-bond link between two water molecules disappears, must both molecules have been split into hydrogen and oxygen?

    Show reasoning

    No. The intermolecular link can change while the covalent O–H connections within each molecule remain.

What to carry forward

Read identity, number, charge and connection as distinct information.

References

Resources supporting this lesson’s explanations and examples.

  1. Mary Ann Clark, Matthew Douglas and Jung Choi · OpenStax2 sources
    1. Biology 2e — Atoms, Isotopes, Ions, and Molecules: The Building Blocks (2018)Mary Ann Clark, Matthew Douglas and Jung Choi · OpenStaxTextbook chapteropenstax.orgRead source
    2. Biology 2e — Water (2018)Mary Ann Clark, Matthew Douglas and Jung Choi · OpenStaxTextbook chapteropenstax.orgRead source
  2. Chemistry 2e — Strengths of Ionic and Covalent Bonds (2019)Paul Flowers, Klaus Theopold, Richard Langley and William R. Robinson · OpenStaxTextbook chapteropenstax.orgRead source