Building Blocks: Atoms
Material in the world is mostly made up of
combinations of elements, particular substances that each
have a unique set of properties. The smallest bit of an
element is an atom - go to anything smaller, and it isn't
that element anymore. Atoms do have parts, though, and the
parts act to produce the element's properties. Atoms can also
combine in ways that produce whole new properties: atoms in
these relationships are called molecules, which are the
smallest bits of compounds. Water is a compound with
two hydrogen atoms and one oxygen atom in each molecule.
Pictures of gold atoms in a surface.
A water molecule, showing how the atoms "line up."
In the middle of each atom is a nucleus
(which, unfortunately, has the same name as the much-bigger middle
of one type of cell - don't get them confused!), a tiny dense body
of two different types of atomic particles. When people
calculate the mass of an atom, each particle in the nucleus has a
single atomic unit (AU) of mass. The two different types each
"weigh" one unit, and the mass of all of the nuclear particles is
added to get the atomic mass or weight. Mass and
weight are different things, but the difference doesn't mean that
much when atoms are being discussed.
Simplified drawing of an atom, showing the particles.
One type of atomic particle is the proton.
Each carries a single positive electrical charge, giving the nucleus
a charge equal to all of the protons in there. The number of
protons also determines which element the atom belongs to, and that
number is called the atomic number. A special force is
required to keep all of those protons from flying away from each
other, and that force is stabilized by the other atomic particle,
the neutron. Neutrons have no charge, because
they contain a positive proton and a negative
electron kind of "smooshed together." Atoms of one element may
have different numbers of neutrons, different atomic weights, and
different nuclear stabilities; atoms of the same element but
having different weights are called isotopes. Isotopes
may be unstable and can "pop" to a more stable form (called
"decaying") through a loss of energy or of whole pieces of the
nucleus - the lost bits are types of radiation, and those
isotopes are considered to be radioactive.
"tour" of atoms.
More on radioactivity.
Some radioactive isotopes decay more quickly than
others. A way to compare the stability of different
radioactive isotopes is the half-life, which is the
amount of time it takes for an half of an amount of radioactive
material to decay. Really unstable isotopes may have
half-lives of fractions of seconds, but slightly unstable isotopes
may have half-lives of thousands or millions of years.
A graphing application to show half-lives in action.
An element found in all living things is carbon.
An element common in the atmosphere is nitrogen, which
can be destabilized by cosmic ray interactions near space that cause
it to lose a proton and become a radioactive isotope of carbon,
called Carbon-14, which gets combined with oxygen to form
carbon dioxide in the air. This isotope of carbon is always
being formed and decaying, leading to what's thought to be a
constant proportion of C-14 to the stable isotope, Carbon-12 (about
0.0000000000013 of all Carbon atoms are C-14, something like
one-in-every-trillion). C-14 decays when one of its neutrons
"spits out" an electron, turning that neutron into a proton and
changing the atom back to nitrogen. Plants take in
carbon dioxide, with both stable and radioactive carbon and, through
photosynthesis, put the carbon into useful molecules that pass up
the food chain; in a currently-living thing, a predictable
tiny amount of all of their carbon atoms are C-14. Once that
organism dies and takes in no new carbon, the C-14 continues to
decay, changing the proportion of C-12 to C-14, which tells you how
much C-14 has decayed. The half-life of C-14 is about 5730
years: after about that time, only half of the original C-14
is still there. Measurements of the C-12-to-C-14 ratios are
used to determine how long ago an organism lived, a process called
carbon dating. This can tell us the age of a wrecked
wooden ship or a buried bone, up to about 50,000 years. If the
material is too old, there's too little C-14 left to get an accurate
Old fossils may be dated by
using materials from the original surrounding sediments that have
much longer half-lives.
A page that shows the drop-off in C-14 over time.
Other types of dating techniques.
There are tiny particles flying about in the space
around the nucleus. The electrons have almost no mass
(that's why they don't figure into the atomic mass / weight
calculation), but each one has a full negative electric charge.
As atoms get bigger, they have more electrons flying around them,
and interactions among the electrons push them into levels and
sublevels. These were originally thought to be orbits,
like planets around a star, except that more than one electron could
"fit" into each orbit: two for the closest one in, then eight
for the others. It was eventually realized that the orbits
weren't simple planes, but went all around, and they were called
orbitals, and when folks figured out just how fast the electrons
were moving, they often called them shells, as if the
electrons were in every part of the level at once.
For basic chemistry, we can stick to the simple image
of orbits: the closest-in can hold 2 electrons, the next ones
can hold eight, and even bigger ones get complicated sublevels.
The fullness of the outermost orbit of an atom is where that atom's
chemistry comes from: those outermost electrons
interact with the outermost electrons of other atoms to produce
chemical reactions. A simple rule about atom chemistry:
usually, a full outer orbit makes for a chemically stable atom.
An atom with equal numbers of protons in the
nucleus and electrons buzzing around has no overall charge.
However, if the outer orbital is not full, that atom will be
unstable, ready to react in a way that will give it a full outer
shell. These atoms are often called radicals;
sometimes, chemical processes in our cells release oxygen
radicals, which can react with and damage important molecules in
the area. Our cells have whole organizations of molecules that
attempt to prevent such damage.
If an atom with a nearly-full outer orbital can
grab free electrons, it will trap them and fill that layer.
Each extra electron brings in its negative charge, and the atom is
now a negatively-charged ion. If the outer orbital has
only one or two electrons and needs eight to be full, those outer
electrons may be dumped off, leaving unbalanced proton charges and
producing a positively-charged ion. Ions are often much more
stable than radicals: the chloride in table salt is a benign
ion, while the chlorine in bleach is a very reactive radical, but
they are both the same element.
The classic picture.
The more modern understanding, still simplified.
If you really want to know more about orbitals...
Scientists tend to love a concept that can be
represented visually. That might explain the periodic
table, a way to organize the elements (using their one- or
two-letter abbreviations) that shows features, especially shared
chemical features. It is arranged in columns that, in
the first three rows, correspond to the number of electrons in the
outer orbital of the uncharged version of the atom - note that there
are 2 elements in the first row for the small innermost orbital,
then 8. Atoms get bigger as you go down, and the orbitals get
bigger and more complex, producing a second and third set of columns
for the "bridges" in the lower table that repeat the basic numbers,
but where the atoms are a bit less predictable in their activity.
The good news is that for the simple chemistry of basic biology, we
don't need to get into the complexities of sub-orbitals.
The table often includes the atomic weight, which you
would think would be a whole number as a sum of protons and
neutrons, but it's often not. If there is a whole number,
that's the weight of the most common isotope; if it's
fractional, it's figured by factoring the different isotopes'
weights with how common each one is. That means, if it's
fractional, you can usually guess the weight of the most common
isotope by rounding the number off.
Simple periodic table.
periodic table where each box links to an informational video.
informational periodic table.
The elements of Column 8 (sometimes called Column 0)
have full outer layers and have very little chemical activity.
The elements in Column One or Column Two tend to lose those
outermost electrons and exist as positive ions - +1 ions from Column
1, +2 ions from Column 2. Elements in Column 7 often steal one
electron and exist as -1 ions. Elements from Column 3 through
6 are more likely to borrow and share out electrons with other atoms
to fill their outer layers as the electrons move around all of the
Periodic table with
Atoms in Committed
Classic way to show bonds.
Molecules are made up of atoms held together
in various ways. The connections between the atoms are called
bonds, and the new arrangement of electrons changes the
properties that the atoms had by themselves. Molecules have
formulas, which show the atoms (by element abbreviations) and
numbers, such as H2O for
water. There are three types of bonds that figure into
Much more on bonds.
Sometimes when atoms from the early and late columns
come together, it's easy for one to give up electrons to the other.
The bonded atoms will become ions and their opposite charges will
hold them together in an ionic bond. Ionic bonds can be
very strong, but they have trouble sticking together when placed in
water (the reason for this will be explained later). Ions are
important in biological systems, but since the systems are based in
water, ionic compounds don't do much chemistry inside cells.
Transfer of electrons shown.
Atoms can share outer-orbital electrons, producing
"full" orbitals with part-time electrons. This holds the atoms
together in covalent bonds, and it can happen among not just
pairs, but multiple atoms. In water, for example, each
Hydrogen (Column 1, needs 1 electron to fill its small 2-spot
orbital) shares its one electron with Oxygen (Column 6, needs 2
electrons to fill that orbital), which shares single electrons with
each hydrogen. The distribution of electrons push the atoms
into particular angles of connection: with water, the
Hydrogens are both pushed to one side of the Oxygen. In large
molecules, the electrons may spread in unusual ways.
Atoms with multiple electron needs may share multiple
electrons and form multiple bonds. The common free form
of Oxygen is O2, with a
double bond between the atoms; Nitrogen gas takes the
form of N2, with a
triple bond between the atoms.
The four most common atoms in the molecules of
Life are Hydrogen, Carbon, Oxygen, and Nitrogen. Each atom has
a different number of available electron slots, in the order HONC:
Hydrogen has one available bond, Oxygen has two, Nitrogen has three,
and Carbon has four. Carbon and Nitrogen support the complex
inner structures of big molecules, Oxygen commonly forms connecting
"bridges," and Hydrogen is all over the outsides, "capping" the
Form of a water molecule.
Atoms that share electrons may not do so equally -
the electrons may spend more time near one nucleus and less near
another, creating regions that are more negative and areas that are
more positive. Molecules with these partial charges are called
polar. Attractions can form between opposite-charged
regions, holding parts of big molecules together or attracting
separate particles to each other. These Hydrogen bonds
(tiny, weak hydrogen atoms are commonly participants) can be of
wildly different strengths, but they are weaker than covalent bonds.
They are very important in the many unusual properties of water.
Hydrogen bonds (dotted lines).
The Unique Properties of
A similar introduction.
Water molecules aren't just polar, they are
bipolar, with partial charges on opposite ends of each molecule.
These small bipolar molecules have many unusual properties that
contribute strongly to how biology on Earth works.
Video simulation of water molecules.
The chemistry of Life needs a support medium,
something that atoms and molecules can float through so that they
can interact. Water molecules hold on to one another with
hydrogen bonds (this is called cohesion), which makes it take a lot of heat to drive the
molecules apart into gas form. Those bonds hold on to water
molecules at surfaces, producing surface tension, which makes
it hard for stray molecules to shoot through into the air.
This process is evaporation, and only happens to the fastest,
hottest molecules (heat = how fast the particles are moving).
This is why evaporating water is very cooling. The
attraction that water molecules have for each other can be very
important in biological systems: it allows tall plants to draw
water to the leaves against the pull of gravity.
As water cools, it gets hard to crowd the
slower-moving molecules together, because the bipolar
molecules can also repel each other. This gives water a wide
range of temperatures at which it is conveniently liquid. In
fact, if you cool water below 4o Celsius, the crowded
molecules start to spin around into an arrangement that pushes them
apart, and when they eventually lock into a solid crystalline
structure at 0o C, the ice that forms is lighter
than the liquid it formed from. Most solids are denser and
heavier than their liquid form; if water were this way, ice
would sink, and freezing water bodies would freeze completely solid
and be very difficult to thaw. But ice floats, insulating the
liquid water beneath that supports Life.
Surface tension contributes to the formation of water drops.
Insects with water-repellent toes can support themselves on surface
Why salt in the water affects freezing.
Water's bipolar molecules allow it to hold many atoms
and molecules, especially ions, floating among them. Charges
on particles attract the opposite ends of water molecules, which
surround the particles and keep them from settling out - that is,
many things dissolve in water, making it an incredibly good
solvent. A mixture of water and dissolved particles is
called a solution. Charged particles like ions may be
completely surrounded by opposite-charged ends of water molecules, a
layer called a hydration shell. Materials that dissolve
are hydrophilic, materials that don't are hydrophobic.
Hydrophobic molecules are important components in water barriers
and hydrophobic domains can be important inner parts of some large
molecules. When water sticks to large molecules or surfaces,
that's called adhesion.
More on dissolving.
Although molecules seem like stable, solid things,
they are constantly shaking and moving and bumping into other
particles, and they occasionally just fall apart. In any
amount of pure water, about one in every ten million water molecules
have separated into positive Hydrogen ions, H+, and OH-,
negative Hydroxide ions. Another way to represent that
number is to say there's a proportion of Hydrogen of
0.0000001, or 10-7, also known as a pH of 7.
pH follows a scale based on those negative exponents. Below 7,
with a material that releases more H+ into solution, you have an
acid; if more OH- is released into solution, the pH is
above 7, and the solution is a base. Each unit
of the pH scale is a tenfold change of ion concentration;
a change of one spot is a ten-times change, two spots is
one-hundred-times, three spots a thousand, etc.
Both H+ and OH-, released into solutions, can
interfere with the hydrogen bonds that hold large molecules in the
tight formations that are critical to their functions: move
such a molecule from a pH in which it is stable to another pH and it
may stop working. Expose such molecules to powerful acids or
bases and they may completely unravel; this is why our
stomachs start the digestive process with a powerful acid, and
powerful bases are used in drain cleaners to affect biological
materials like hair.
pH in natural water.
pH scale with common materials.
How pH affects soils.
Lots of water links.
Atoms and Molecules in Action
- Chemical Reactions
When atoms and molecules interact, they are said to
react. Reactions involve changes in energy, which will
be a major part of a later chapter. Atoms on molecules may
move or come apart, or may be put together to form larger
molecules. These also will be detailed later. For now,
just get used to how reactions are shown on paper.
A reaction is commonly displayed as an arrow.
The reaction can actually happen in both directions, and sometimes
there will be arrows pointing forward and backward, but commonly a
single arrow shows the "normal" direction. Materials or energy
that are needed to get the reaction working but don't themselves
change are called contributors and may be linked to the arrow
in various ways. The materials in front of the arrow are
called reactants or substrates; the materials
behind the arrow are called products. Here's an example
(this is basic photosynthesis):
CO2 + H2O
----- Light-----> C6H12O6
Carbon dioxide and water are
Light is a necessary
Glucose and oxygen are
reactants or substrates.
Electrons often move around during reactions, and
where they go is important. If an atom or molecule picks up
one or more electrons, it is reduced (extra
negatively-charged electrons make its charge goes down) and the
reaction is a reduction reaction; if electrons are
given up, the reaction is oxidation and the donor is
oxidized. Oxidation was first discovered as something
oxygen radicals do, although other materials can do it as well;
systems that counteract oxygen radical effects are commonly called
Expanded coverage on reactions.
Various reaction types.
A bit more chemistry.