molecules found in living things fall into four major classes.
Each class of molecule has features that determine its use in living
The first class of molecules are called
The simplest type of these, monosaccharide simple sugars,
have a basic formula: for every carbon atom, there are two
hydrogens and one oxygen, or one water for each carbon. Carbo
- hydrate. Glucose is a common carbohydrate that will
show up again and again as we discuss cell chemistry: its
formula is C6H12O6.
Table sugar, sucrose, is two single sugars bound together:
a disaccharide simple sugar. Sugars can be anything
from a single sugar molecule up to several bound together.
When organic molecules are bound together, a bonding
site must be freed up on each participant. This happens by
clipping a single hydrogen from one participant, and an
oxygen-hydrogen piece (hydroxide) off of the other. Where each
bit used to be become the new bond, and the two freed pieces stick
together as H2O.
This building process where water comes out is called dehydration
synthesis, and is used whenever we build molecule from
components. When molecule chains need to be broken apart, such
as happens in digestion, the opposite reaction happens:
the bond breaks, and one spot gets a hydrogen while the other gets
hydroxide. A water molecule breaks apart - in Latin, that's
hydrolysis, and that's what this process is called.
Sugars can be bound together in long chains, which
may form branches and even networks: these huge carbohydrates
are called starches. Both sugars and starches are
commonly used as sources of energy in cells: sugars are
broken apart for the bond energy, and starches are a way to store
lots of sugars in a fairly inactive form. Large, stiff
starches can also be used as structural molecules:
cellulose is what hold most plants up. That "-ose" ending
is a giveaway that something is a carbohydrate, although they don't
all end that way.
When the same type of molecule component is used
over and over in a much bigger molecule, the bigger molecules are
called polymers. Starches, proteins, and nucleic acids
are all different types of polymers.
There are other uses for carbohydrates in living
systems, but energy and structure are by far the most common ones.
Monosaccharides, showing how they bond typically into a ring with an
Formation of sucrose, showing dehydration synthesis.
More on carbs, showing some bits of starch chains.
bit of artwork based on polymer molecules.
The second class of organic molecules are
Fats and oils are included in this class of molecules. These
have a fairly simple structure, starting with the 3-carbon
glycerol molecule. Each carbon picks up a bit called a
fatty acid, which can be short or fairly long, and then it's a
lipid molecule. A pair of terms that can applied to other
types of molecules often shows up in descriptions of lipids: a
saturated molecule has all of the atoms its carbons could
possibly hold, and has only single bonds in the fatty acid chains;
an unsaturated molecule has at least one double bond between
carbons, and so could hold at least one more hydrogen. Not
surprisingly, this alters the chemistry of the molecules.
Lipid molecules are usually hydrophobic:
they won't dissolve in water and tend to separate out from it
(materials that will dissolve in water are hydrophilic).
Vegetable oil is a lipid - what happens when you mix them?
This makes them useful as water barriers, and they are found
in cell membranes as well as such things as waxes and
waterproofing oils. Not mixing with water also reduces their
chemistry, and lipid molecules can be a nice, nonreactive place to
store extra energy: the lipids in fat are constructed
for longterm energy storage. When energy is really
needed, the fat molecules are broken apart and "fed" into the middle
of the same process that gets energy from sugar molecules.
Some lipid molecules can dissolve well enough in
water to move around, but also can dissolve through other lipids
like those in cell membranes; this makes lipids good
signaling molecules. Included in this group are steroid
Lipids also has other, varied uses, including
insulation in organisms that need to hold onto heat in unusual
conditions, like deep underwater. Lipids are also commonly a
holding point for lipid-soluble toxins, which can accumulate
there to dangerous levels. Many manufactured toxins,
like pesticides, are lipid soluble: it helps get them into the
target organisms, but gets them into others as well.
Basic lipid molecule - note the main glycerol connecting the 3 fatty
Saturated and unsaturated.
Fat molecules - each carbon bond holds a bit of usable energy.
Steroids get pretty complicated.
Technical abstract about the action of some lipid-soluble toxins.
Article on how pesticides may disrupt female reproductive function.
The last two classes of molecules are
Proteins are long chains of components
called amino acids and have three to four levels of
structure. The first level of structure, called primary
structure, is just the order of amino acids in each chain.
At the secondary structure level, amino acids in a particular
region connect to each other and produce local formations, like
pleated sheets of coils. At the tertiary structure
level, the entire molecule is pulled together into a particular
three-dimensional shape, often through hydrogen bonds but
sometimes through cross-connecting covalent bonds. Only
some proteins have a quaternary structure, where the molecule
has more than a single chain of amino acids, but again the overall
three-dimensional structure is critical, because the function of
proteins is connected to their shapes. When these shapes
are changed, the functions may change or disappear; this can
happen when other molecules attach to them, when the proportion of
ions around them changes (such as in pH shifts), or when a change in
temperature shakes or compresses the shape.
The possible shapes that proteins can take is virtually infinite, so
they have a broad array of possible functions. What follows is
just a partial list, some of the major things that proteins do in
Tertiary and quaternary structure.
All the levels covered.
Structure. Most cells have
particular shapes, and those shapes are commonly held together by
proteins that connect to the outer membrane and often to each other.
Cells are often held together with protein-based structures. Protein
is an important component to structure in fungi, in animals in
exoskeletons, and in things like tendons, ligaments, and cartilage.
Movement. A single cell moves, or swims,
using a protein-based movement system. Animal muscle depends
upon two proteins, actin and myosin, contracting
cells. Membranes have proteins that help move things through
Communication. Cells often send
signals to each other using various types of proteins. Many
hormones are proteins, as well as pheromones
(signals-by-scent) and alarmones (signals that alert other
individuals). Protein neurotransmitters carry signals
between nerve cells. Receptors may be at the target
cell that will attach to the signal molecule, and there are
receptors that pick up other things, such as the light receptors in
visual systems. Antibodies are proteins made
specifically to attach to "foreign" molecules (the foreign molecules
are called antigens); once attached, the molecule
changes to a shape that attaches to receptors on immune cells and
activates them to attack whatever the antibody is attached to (in an
autoimmune disease, a system makes antibodies to molecules on
its own cells and calls attacks on them).
Chemistry. The reactions that happen
in cells often need a boost to get going, and that boost is supplied
by enzymes, most of which are proteins. Enzymes are
catalysts, chemicals that activate and speed along reactions.
They typically are named to give some indication of the reaction
they aid, and commonly have the ending -ase on their names. Almost every bit of chemistry done in cells is aided by enzymes.
Cell junctions with several proteins labeled.
Proteins in cilia, which help cells swim.
Activity of actin and myosin
A bit about pheromones in a book synopsis.
How neurotransmitters work.
How enzymes work.
The last class of organic molecules are
the nucleic acids.
There are two varieties: ribonucleic acid, or
RNA, and deoxyribonucleic acid, or DNA.
These polymers are long chains of components called bases, of
which there are only five types. RNA is a single-strand
molecule; DNA is a spiral of two cross-connected strands.
DNA carries information. Part of the DNA in a
cell is genes, which code for protein molecules. Each
type of receptor, or enzyme, or neurotransmitter, has a stretch of
DNA in which its sequence of amino acids is coded. The
code-to-primary-structure ratio is three-to-one: three bases
(called a codon) per amino acid. The codes proteins can
vary, and code variations for a single type of protein are called
alleles. Different alleles can produce proteins that have
the exact same amino acid sequence, have different sequences but no
difference in activity, have different sequences that produce
different levels of activity (including no activity at all), or
produce a new type of activity. These will be returned to in
the chapter on genetics.
DNA is the code from which living things are made,
since the DNA codes for proteins and the proteins are the foundation
of cellular chemistry. Carbohydrates, lipids, and nucleic
acids are made by enzyme-driven systems.
A huge proportion of
the DNA on many chromosomes is not used for protein production.
This non-coding DNA is made up of many different types of DNA
stretches: some are critical to interacting with the proteins
that hold chromosomes together; some are codes that aren't
used, either old sequences or dangerously mutated sequences or
foreign sequences (invaders from disease organisms); some are
non-gene codes that work to get genes processed; some produce
functional stretches of RNA (see below); some are short
stretches that exists to propagate themselves, a kind of molecular
parasite; and a lot of what's there, no one knows what the
origin or possible purpose is. All of this used to be called
junk DNA, but that term is going away as functions are
discovered for these bits.
The other nucleic acid form, RNA, is used in
getting DNA code to protein sequence. RNA moves the code from
where it is stored to where it is executed. RNA is a critical
component of the cell parts that takes the codes and makes the
protein. Small RNA molecules do all sorts of things in and
around the genes; some are ribozymes, having similar
activity to enzymes.
More on nucleic acids.
Nucleic acid roles in images.
and DNA structures.
More on RNA functions.
More on non-coding DNA.