The Chemistry of Life: Atoms, Bonds, and Water

Squeeze any living thing — a leaf, a jellyfish, your own thumb — and you are mostly squeezing water. A human body is roughly 60 percent water by mass, and a cell is essentially a busy droplet in which every reaction of life takes place. Biology, at its most fundamental level, is chemistry that happens in water. To understand cells and genes, we have to begin with the atoms they are built from and the remarkable molecule that hosts them all.

Atoms, elements, and bonds

All matter is built from atoms, and living things use a surprisingly short list of elements. Just four — carbon, hydrogen, oxygen, and nitrogen — make up about 96 percent of the mass of any organism, with phosphorus and sulfur rounding out the essentials, a set biologists remember by the initials CHNOPS. What an atom does chemically depends on its electrons, especially those in its outermost shell. Atoms are most stable with a full outer shell, and they reach that stability by forming bonds.

Two kinds of bond matter right away. In a covalent bond, two atoms share a pair of electrons; this is the strong, stable link that holds biological molecules together. In an ionic bond, one atom transfers an electron to another, and the resulting oppositely charged ions attract. When covalent sharing is unequal — one atom pulling harder on the shared electrons — the bond is polar, leaving one end slightly negative and the other slightly positive. That small imbalance turns out to matter enormously.

Water and the hydrogen bond

A water molecule is a single oxygen atom covalently bonded to two hydrogens and bent into a wide V. Oxygen hogs the shared electrons, so its end carries a partial negative charge and the hydrogen ends carry partial positive charges. Water is therefore polar, and the positive region of one water molecule is attracted to the negative region of its neighbor. This weak attraction is the hydrogen bond. Any single hydrogen bond breaks easily, but in liquid water each molecule is hydrogen-bonded to several neighbors at once, and that constantly re-forming web gives water its extraordinary behavior.

Why water makes life possible

• Cohesion and surface tension. Water molecules cling to one another, letting water climb from a tree's roots to its highest leaves and forming a surface film sturdy enough for a water strider to walk on.

• Temperature stability. Breaking hydrogen bonds absorbs heat, so water resists temperature swings, buffering cells and oceans alike against sudden change.

• Ice floats. In solid ice, hydrogen bonds lock the molecules into an open lattice that is less dense than liquid water, so ice floats and insulates the water below — which is why life survives beneath a frozen pond.

• The universal solvent. Polar water surrounds and dissolves other polar and charged substances, called hydrophilic (water-loving), while nonpolar substances such as oils are excluded, called hydrophobic (water-fearing). This simple split later organizes every cell membrane.

Acids, bases, and pH

Occasionally a water molecule splits into a hydrogen ion and a hydroxide ion. The concentration of hydrogen ions sets a solution's pH, a scale from 0 to 14: low pH is acidic (many hydrogen ions), high pH is basic (few), and pure water sits neutral at 7. The scale is logarithmic, so each unit is a tenfold change. Living systems are exquisitely pH-sensitive — most human cells work near 7.4 — and rely on buffers that absorb or release hydrogen ions to hold pH steady. A blood pH shift of just a few tenths can be life-threatening.

Why this matters

Every later topic in this course rests on this chemistry. Proteins fold because some regions are hydrophilic and some hydrophobic; membranes exist because lipids flee water; DNA's two strands are zipped together by hydrogen bonds gentle enough to unzip for copying. Master the polar water molecule and its flickering hydrogen bonds, and the molecules of life stop being a list to memorize and start being a story that makes sense.

Curriculum aligned with OpenStax's Biology 2e; all lesson text is original to Syllabus.