ATOMS AND MOLECULES SUMMARY
Atoms contain positively charged protons in the nucleus and negatively charged electrons in their
energy levels. The energy levels want to be full. If they are not already full, they can get full by sharing
electrons (A) equally in a covalent bond or (B) unequally in a polar covalent bond. A polar covalent bond
causes the electrons to stay more towards one side, giving it a partial negative (-) charge. The other
side then becomes partially positive (+).
Water is an example of a molecule with polar covalent bonds because the oxygen atom has 8
protons and the hydrogen only one. Note that water does not have a full charge, just a lopsidedness. The
eight protons pull harder on the shared electrons, so they spend more time with the oxygen, making that
end - and the hydrogen ends +. The - and + ends attract each other, forming hydrogen bonds
between oxygen of one molecule and hydrogen of another molecule. These partial charges are attracted
to any other atoms or ions that have a charge or partial charge, so the water surrounds them, thus
dissolving them. Since most molecules and all ionic compounds have some sort of charge, water
dissolves all the molecules (hydrophilic molecules) except non-polar ones (hydrophobic molecules).
Example: the hydrogen ends of water (+) will be attracted to the Cl- ions of table salt, and the oxygen
ends of water (-) will be attracted to the Na+ ions of table salt, dissolving the NaCl crystal. The water
(solvent) dissolves the salt (solute).
At temperatures over 100OC water molecules are bumping each other so hard that they move far
apart, thus forming a gas. At room temperature, water molecules move around quite a bit and hydrogen
bonds constantly form and reform, and water is in its liquid state. These hydrogen bonds give water
“surface tension” which is so strong that water beads up on surfaces and water skippers can be
supported by it. Non-polar molecules (like ethane) do not have hydrogen bonds, so they don’t attract
each other. A water skipper would drown in pure alcohol! If you put a non-polar solution (like oil) in water,
the water will prefer to form hydrogen bonds and “squish” the non-polar molecules out of the way. If the
temperature gets too cold, the molecules of water aren’t moving enough for the hydrogen bonds to
break. The hydrogen bonds make the molecules line up in a crystalline pattern, causing them to take up
more space. Liquid water is thus more dense than ice, and ice floats on liquid water.
Another way the energy levels can become full is if an atom that has just one or two extra
electrons gives them away to an atom or atoms that WANT another electron. One atom becomes
positively charged (a positive ion), the other negatively charged (a negative ion), which results in them
attracting each other (kind of like magnets). We call this an ionic bond. Atoms joined by ionic bonds form
ionic compounds (versus molecules). Of the three kinds of bonds just described, covalent are the
strongest and hydrogen are the weakest.
Of all the molecules that form, many contain hydrogen in a covalent bond, which means they are
both sharing one electron with the other. Depending on the kind of molecule, sometimes the other atom
wants the electrons so much more than hydrogen does, that it rips the hydrogen’s one electron away.
The hydrogen gladly gives it up, because then it is left as a bare-naked proton with NO energy levels,
which is stable. Bare-naked hydrogen ions in a solution make the solution acidic (0-7 on the pH scale;
how acidic depends on the concentration of H+). Likewise, some molecules do the same thing with –OH
groups (alcohol or hydroxyl groups). If –OH is let go of, it forms OH- ions, causing the solution to become
more basic (7-14 on the pH scale). If you add acids and bases to certain very special chemicals, those
chemicals can absorb either of them (up to a certain “breaking point” when they are too full). This causes
the pH to remain stable. We call these chemicals buffers. NOTE: a buffer resists a change in pH, but that
does not mean the pH is 7! Water is a terrible buffer. It cannot absorb either (in fact, if you split water up
you get one H+ and one OH-. We say that water has a pH of 7). Living tissues contain buffers so that the
products of metabolism don’t change the pH of their environment. They cannot afford to have the pH
change because the chemical reactions that occur in cells require enzymes to make them occur at body
temperature. Enzymes are made of proteins and proteins are denatured (uncoiled and broken) by high or
low pH levels. If enzymes are denatured, chemical reactions don’t happen, and the tissue dies.
There are 92 naturally occurring elements. Of these Carbon (C), Hyddrogen (H), Oxygen (O),
Nitrogen (N), Phosphorus (P) and Sulfur (S) are used to make up 92% of life. Carbon forms the
backbone of all organic molecules (since it needs four electrons it can join with many different kinds of
atoms), but to be an organic molecule there must be H atoms attached to C atoms (so CO 2 would not be
classified as an organic molecule, and neither would H2O). All organic molecules are big
(macromolecules); they include four groups: proteins, carbohydrates, lipids, and nucleic acids.
Proteins make up muscles and do lots of things in the body, but the most important thing they
make up are globular proteins called enzymes. Normally chemical reactions occur when two molecules
come close enough together at the right angle and with enough force that they can react. This usually
requires that they are moving very fast (are hot) which is a problem for living things. An enzyme can
lower the amount of heat energy needed by pulling molecules into their active sites, “hugging” them,
causing them to react, then releasing them. Thus the enzyme can be reused. Enzyme function can be
reduced by cooling, but that function can be “brought back” by warming. Enzymes that get oo hot are
denatured and can no longer function, even when brought back to normal temperature.
Proteins are made of chains of amino acids, hooked together by the process of dehydration
synthesis. Dehydration synthesis [to form by removing water] removes the H+ of an amine group of one
amino acid and the OH- of an acid group of a different amino acid and joins them at those spots. The
ions that are removed combine to form water. Some organisms are so good at saving water that they can
use this “metabolic water” as their ONLY source of water! (The reverse of this process, hydrolysis [to
break using water] puts the water back in and breaks up the amino acids.)
Amino acids have a central carbon surrounded by a –H, an amine group (-NH2), an organic acid
group (-COOH) and an R group. Note that in the acid group there are two oxygen atoms, which pull hard
on the electron of the hydrogen, often pulling it off the hydrogen. The hydrogen gives up its electron and
leaves as a H+, or free proton. That is, the –COOH group acts as an acid, which is why it is called an acid
group! Also note that the amine group has nitrogen, an atom that carbohydrates do not have. There are
20 different kinds of R groups, so there are 20 different kinds of amino acids. How these amino acids line
up is determined by the DNA code. Proteins can vary in the number, kind, and order of amino acids. This
order determines how the protein will fold because the R groups can be positively or negatively charged
(and will attract each other), polar (will be on the outside facing water), or non-polar (be facing inside
away from water). How a protein folds determines if it will be a linear protein (found in muscles) or a
globular protein (like an enzyme) and therefore what kind of chemical reactions will occur in a cell. Shape
is extremely important to enzyme function!
Carbohydrates are made of sugars (which always end in “–ose”). “Carbohydrate” means “carbon
– water.” All carbohydrates have approximately one H2O for every carbon atom (although they are
arranged H-C-OH). Sugars can be single sugars (like glucose and fructose). We call these simple sugars
or “monosaccharides.” If you put glucose and fructose together via dehydration synthesis, you get the
dissacharide called sucrose (table sugar). Both mono- and disaccharides are used for energy by cells.
The energy is stored in the C-H bonds. If we make a long chain of sugars via dehydration synthesis we
get complex carbohydrates or “polysaccharides.” Polysaccharides include starch (plant starch), glycogen
(animal starch, stored in your muscles and liver), cellulose (plant fiber, or wood), and chitin (stuff that
makes exoskeletons of insects and crustaceans [crabs, lobsters, shrimp, etc.]). Starch and glycogen are
used for energy, but cellulose and chiton are used to build body structures. Humans can digest starch
but not cellulose, even though they are both made of chains of sugars. It’s HOW the chains are bonded
together that make the difference.
Lipids include fats & oils (used for energy), waxes (used for structure, like in bee hives),
cholesterol (which makes hormones, the chemical messengers of the body) and phospholipids (which
make up the majority of cell membranes). We are concerned here with fats and phospholipids. Fats are
made by the dehydration synthesis of one glycerol molecule (it looks like three alcohol groups stuck
together) and three fatty acids. The fatty acids have an acid group at one end and hanging off that acid is
a long chain of carbon atoms to which just hydrogen is attached. If there are only single bonds between
the carbons, then all other carbon bonds are full of hydrogen. We say that the fat is “saturated.” These
fatty acid tails pack well together, so the fat is dense and solid at room temperature. If there are double
bonds between some carbons, the fatty acid tails are “unsaturated” and they “kink,” taking up more
space, causing the fat to be less dense at room temperature: it is a liquid (oil). Fats are hydrophobic.
They are also better at storing energy than carbohydrates because of all the C-H bonds where energy is
stored.
Phospholipids are hydrophilic because one of the three fatty acids is replaced by a phosphate
group (PO4). With all that oxygen, it pulls very hard on electrons, making it very negative. That end of the
molecule is hydrophilic, while the fatty acid end is hydrophobic.