Unit 1: Macromolecules

The great tragedy of science the slaying of a beautiful hypothesis by an ugly fact.

--Thomas Huxley

All living organisms (everything from humans, to bacteria, to trees) are made out of
chemicals. Chemicals are made from atoms. There are many important atoms for living
organisms. One of these atoms is Carbon. Carbon makes up the backbone for all organic
molecules. Therefore, most of the important compounds of life are carbon based. The 4
most important compounds for life are: carbohydrates, lipids, proteins, and nucleic acids.
We will discuss these shortly. Another important chemical for life is water. Water is not
organic because it does not contain carbon. We will discuss water first.
Much of this information is also found in the textbook, so be sure to read those relevant
sections as well. We are focusing on the macromolecules chapter, and that is the one
assigned for this unit. However, there is a chemistry chapter just prior that will help you
understand macromolecules. I would recommend you read the chemistry chapter to get a
good foundation for understanding macromolecules. Part A of this introduction covers the
chemistry basics that you will need.

Part A: Chemistry Basics

All things are made of matter. Matter is anything that takes up space and has mass. You are
made of matter, the computer is made of matter, the earth is made of matter. All matter is
made of atoms.
At the center of the atom is a nucleus. The nucleus contains positively
charged protons, and neutrally charged neutrons. The image on the right
is a helium atom. The protons are red circles with a + and the neutrons
are green circles with no +. The neutrons add mass to the atom; but
they are not part of our current discussion, so we will not include them
further.
The number of protons tells us the type of atom. Helium always has 2 protons, hydrogen
always has 1 proton, carbon always has 6 protons, oxygen always has 6, etc. The periodic
table of elements lists elements in order of their proton number (call atomic number). How
many atoms does Neon (abbreviated Ne) have? [Answer: 10]

Look back at the helium atom, notice the yellow circles with a - sign on the outside of the
atom. These are electrons; they are negatively charged and reside in zones (called shells)
outside the nucleus. Atoms can have different numbers of electrons, but they are most stable
when the electron numbers fill the shells in which they reside.

Atoms that have the same number of positively charged protons and negatively charged
electrons have no net charge (that is they are neutral because the proton charges cancel out
the electron charges). For example, the helium atom has 2 protons and 2 electrons; therefore
it is not charged.
Other atoms tend to have unequal numbers of protons
and electrons; these are called ions. Sodium (Na) has
11 protons but it tends to only have 10 electrons;
therefore it has a net charge of +1. Chlorine (Cl) has
17 protons but it tends to have 18 electrons; therefore
it has a net charge of -1. Positive ions and negative
ions are attracted to each other and will form an ionic
bond. This type of bond is similar to 2 magnets where
the positive and negative ions are attracted but they do
not fuse to each other. The image to the right is of
NaCl (table salt) which is made of many sodium ions
attracted to many chloride ions. Notice that although
these ions are attracted to each other they do not fuse with each other.
Other elements stabilize their electron numbers by sharing electrons. These bonds are called
covalent bonds. In the molecule of methane (CH4) to the right you can see that 1 carbon atom
is sharing electrons with 4 hydrogen atoms. Each covalent bond is a sharing of a pair of
electrons (one electron from each atom).
Carbon (C) forms 4 covalent bonds, while hydrogen (H) only forms
1. Elements tend to form the same number of covalent bonds all the
time. So, Hydrogen will always form 1 covalent bond, and Carbon
will always form 4. There are exceptions, but this is a good general
rule.
The 4 atoms in the image are attached to each other. A covalent
bond builds molecules. Methane is a molecule made of 1 carbon
atom covalently bound to 4 hydrogen atoms.
Another way to draw atoms is using lines to
indicate covalent bonds. This is much simpler to
draw, as you can see with the image to the left
which is also of methane.

Part B: Water
Water is made of 1 oxygen and 2 hydrogen atoms that bound with a covalent bond.
However, oxygen and hydrogen do not share their electrons equally oxygen is electron
greedy and holds on to the electron stronger than the hydrogen. (This is kind of like
someone hogging the sheets. You are both covered, but the sheet hog is covered a little bit
better. Similarly, the electron spends a little more time near the oxygen than near the
hydrogen).
Therefore, the oxygen has a slight negative charge and the hydrogen has a
slight positive charge. This makes the water molecule polar. Polar
molecules have one region (pole) that is slightly negative (shown as a - next
to the O), and one region (pole) that is slightly positive (shows as a + next to
each H). The polarity of water gives it many important characteristics because
the negative pole of one molecule is attracted to the positive pole of another.
Hydrogen Bonds
Because water is polar, each water molecule is able to form weak bonds (called hydrogen
bonds) with 3 other water molecules. Although each of these bonds is relatively weak, many
of them acting together are quite strong. (A good analogy to think of there is a twig. One
twig is easy to break, but a handful of twigs can be rather challenging.) In fact, these
hydrogen bonds are strong enough to pull water up the tallest tree! Trees dont have to work
to bring water up to their leaves, it does so naturally because of the shape of the cells of the
tree and the physical forces of the water. The image below shows water molecules bound to
each other with hydrogen bonds. (The red and white spheres are het another way to draw
molecules). Hydrogen bonds are drawn as dotted lines between the molecules.

The Nearly Universal Solvent

Water can form hydrogen bonds with any polar or charged chemical. These types of
chemicals are called hydrophilic. Hydro refers to water and philic refers to loving (so water
loving molecules). Therefore, water is able to dissolve most chemicals (such as sugar, salt,
Kool-Aid, etc.)
However some chemicals have no charge (these are called non-polar). These chemicals
(like oil) do not dissolve in water. These are called hydrophobic. Hydro refers to water and
phobic refers to fearing. (Although Im not sure fear is an emotion that chemicals can feel
).
Some molecules are amphipathic. This term means that they have a region
that is polar and a region that is non-polar. These chemicals form droplets in
water (shown in the picture to the right). The circles represent the polar region
of the amphipathic molecule; these would be in contact with the water.
The lines represent the non-polar regions of the molecule; these would
be tucked into the center, away from the water.
These chemicals are important because they can interact with both polar
and non-polar substances. Dish soap is one example of an amphipathic
chemical. Soap forms droplets around the oil. These droplets can then be washed away
with excess water. The figure to the right shows the oil (represented by Ms) in the center of
the droplet of soap.
Surface tension & Capillary action
As mentioned earlier, the hydrogen bonds of water are strong enough to pull a stream of
water up a tall tree. The strength of the hydrogen bonds also makes the surface of the water
relatively difficult to break. You have felt the effect of this if youve ever done a belly-flop into
a pool. Breaking the surface tension of the water is what hurts! This surface tension is also
what allows leaves (and other things) to float on water.
Other characteristics
Water has many other important characteristics. For example, water is able to maintain its
temperature. This is why temperatures near large bodies of water are generally more stable
throughout the year. Also, water becomes less dense when it freezes. This is why ice floats.
This is important for living organisms because the layer of ice on the top of a lake protects the
fish below it and allows them to live through the winter. These are characteristics that other
liquids simply dont have.

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pH scale
Pure water has a pH of 7 because some water
molecules dissociate (breaks apart). In a container
of pure water there is a concentration 10-7 M of H+.
This correlates to a pH of 7; pH is a measure of
concentration.
However, keep in mind that lower pH numbers
indicate a higher concentration of H+. This is
because a pH of 1 is a concentration of 10-1 which
is a higher number than a pH of 2 which is a
concentration of 10-2. It is not essential that you
understand the details of the calculations, but you
should know that lower pH numbers indicate more
protons (H+) and that each step in the pH reading is
a multiple of 10. This means that a pH of 1 is 10
times more acidic than a pH of 2; and a pH of 1 is
100 times more acidic than a pH of 3.
Maintaining homeostasis of pH is essential for
living organisms. For example, blood must maintain
a pH of 7.4 an increase or decrease of just 0.3 is
a life threatening situation. Buffers are chemicals
that help maintain particular pH levels. Buffers
work by donating protons if the solution becomes
too basic, and binding protons if the solution
becomes too acidic.

Part C: Macromolecules
We will discuss 4 important macromolecules for living organisms: carbohydrates, lipids,
proteins, and nucleic acids.
Carbohydrates
Carbohydrates (sugars) are a common source of energy and structural support for living
organisms.
The basic structure of a carbohydrate is a carbon ring. Carbohydrates with a
single carbon ring are called monosaccharides. mono means one and
saccharide means sugar. Glucose is a common monosaccharide. This is the
blood sugar that diabetics measure. Fructose, the sugar commonly found in
fruit, is also a monosaccharide.
When 2 monosaccharides are linked together the chemical is called a disaccharide. Di
means 2 and saccharide means sugar. Sucrose, table sugar, is a common disaccharide.
Lactose, milk sugar, is also a disaccharide. People that are lactose intolerant dont have the
enzyme needed to break the covalent bond between the two monosaccharides that make up
lactose. Therefore, they have difficulty digesting the lactose unless they take something like
Lactaid which contains the enzyme.
Polysaccharides are chains of many
monosaccharides linked together. Poly means
many and saccharide means sugar. Starch is a
common polysaccharide. Plants use starch as a
way to store energy. Cellulose is also a
polysaccharide made by plants, but this is used
for structure rather than energy storage.
Cellulose is what makes up the stringy part of
celery and the wood of trees. Humans cannot
digest cellulose (we lack the enzyme needed to
break the bonds between the monosaccharides).
However, cellulose is important in the human diet because it provides bulk. Fiber, or
roughage, is cellulose. Humans store excess glucose as glycogen which is a polysaccharide
very similar to starch.
Carbohydrate names often end in -ose. So, when you are reading food labels, any
unfamiliar term that ends in a ose (such as xylose) is likely to be a sugar. Chemically,
sugars have one or more carbon rings in a chain.

Nucleic Acids
Nucleic acids are used to store information. DNA (deoxyribonucleic acid) is the nucleic acid
that stores the information necessary for living organisms. We will discuss DNA in more
detail in Unit 5 when we discuss how DNA is used to make proteins.
A single nucleotide is made of a sugar, a base, and a phosphate
group. The sugar is used for structure, the base is what carries the
information, and the phosphate group is able to hold energy. There
are 4 different types of bases: adenine (A), thymine (T), Cytosine
(C), and Guanine (G).
One of the most common nucleotides is ATP (Adenosine
triphosphate). This is how living organisms store energy that
is going to be used in a short time. ATP is a useful way to
store energy because it has 3 phosphate groups (tri means
3). We will discuss ATP in more detail when we discuss
metabolism in Unit 7.

DNA is made of two long chains of

nucleotides. When the two strands of
DNA bind to each other A is always
across from T and C is always across
from G. DNA is the blueprint of the
cell. The sequence on the DNA
strands determine what proteins your
cells make. The proteins, in turn, are
responsible for most of the major
functions of a cell. Therefore, the
information carried on the DNA is
essential for life. To keep this
information safe, your cells store the
DNA inside a protective structure in the
cell. You will learn more about this
structure, the nucleus, in the next unit.
The nucleus keeps the DNA protected,
but the information from the DNA
molecule needs to get out to the rest of

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the cell. Therefore, your cells copy the DNA into RNA. You can think of the RNA as a
photocopy of a very valuable book. Your cells make many of these photocopies which are
sent out to the cell and contain the instructions for building proteins. These photocopies are
often damaged while they are out and about in the cell, but that isnt a problem because the
original (the DNA) is still safely stored in the nucleus.
Chemic ally, the main difference between DNA and RNA is which sugar is used in the
nucleotide. The letters DNA stand for deoxyribonucleic acid and the letters RNA stand for
ribose nucleic acid. The first word in the name tells you which sugar is being used.
(remember, sugars often end in ose). So, RNA uses ribose and DNA uses deoxyribose.
The difference between these sugars is that DNA has one less oxygen (de-oxy).
The other main difference between DNA and RNA is that DNA tends to be double stranded.
It forms a double helix two strands wound around each other. RNA tends to be single
stranded.

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Proteins
Proteins are the work horses of living organisms. Almost everything your body does is done
by proteins. For example: your muscles move because of proteins, you grow because of
proteins, you are able to digest because of enzymes (a type of protein), and your brain is able
to read this information because proteins are translating electrical signals.
Proteins are very important for living organisms, so you have to be sure that they are working
properly. High temperatures or a pH that is too acidic or too basic can cause proteins to stop
working. Therefore, your body has to maintain homeostasis (balance) that is optimal for
your proteins. Your blood contains buffers that keep the ph stable, and you maintain a
constant temperature. One of the reasons a fever can be dangerous is that if your core
temperature gets too high, your proteins stop working.
Proteins are long chains of amino acids that are folded into a variety of different 3D
structures. There are about 20 different amino acids. A typical amino acid is shown below.
Almost all amino acids have the
same amine (NH3), Carboxyl
(COOH), and H groups. However,
Each amino acid has a different R
group this is what makes amino
acids different from each other. The specific R group of
each amino acid gives it particular chemical abilities
and will determine the function of the protein.
The particular sequence of amino acids is different for
each protein. The image to the right shows how a single
long chain of amino acids can be folded into complex
shapes. (The quaternary structure is actually multiple
strands of amino acids, but not all proteins use this level
of structure).
Proteins have a wide variety of complex shapes
because of their varied functions. Proteins that are
used to build your body (such as keratin) are long
chains, but enzymes tend to be more globular.
(Globular means they have the shape of a glob (blob)
I know, very scientific!).

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Lipids
Lipids are the best way to store energy for long periods of time. This is why your body stores
excess energy as fats rather than glycogen or ATP. Lipids are also important for making cell
membranes (we will discuss this more later). Lastly, many hormones are lipids. In this unit
we will focus on lipids as a way to store energy.
Energy storing lipids are called triglycerides
because there are 3 (tri) carbon chains attached
to a glycerol (glyceride). The image to the right is
of a standard triglyceride
Triglycerides are all non-polar. Therefore, lipids do
not dissolve in water.
The carbon chains of the triglycerides can be saturated with hydrogens; these are
also called fats. Saturated means full, and in this case it means that each carbon
is bound to as many hydrogens as it can hold. On the image above, each corner
point is a carbon atom; hydrogens are not drawn because they are very common.
The way to know that these carbons are attached to as many hydrogens as possible
is because they dont form any double bonds. This may be clearer in the picture to
the right. The carbons are black circles, the hydrogens are white circles, and the
oxygens are red circles. The linear shape of saturated fatty acids makes them solid
at room temperature (think of bacon grease).
The carbon chains of the triglycerides can also be unsaturated; these
are also called oils. Unsaturated means not full, and in this case it
means that some carbons are not bound to as many hydrogens as
possible. These carbons end up forming a double bond between them
which creates a bend in the chain. You can see the double bonds in the
top picture as 2 lines (there are a total of 4 double bonds in the 2
unsaturated fatty acids in the top image). You can see the bend these
double bonds create in the image to the right. The bends of unsaturated
fatty acids makes them liquid at room temperature (think of vegetable
oil).

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Image Sources
Helium Atom
By Svdmolen/Jeanot (converted by King of Hearts) (Image:Atom.png) [GFDL
(http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via
Wikimedia Commons
Periodic Table
http://commons.wikimedia.org/wiki/Periodic_Table_of_Elements
Covalent Bond
By DynaBlast (Created with Inkscape) [CC-BY-SA-2.5 (http://creativecommons.org/licenses/by-sa/2.5)], via
Wikimedia Commons
Methane
http://commons.wikimedia.org/wiki/File:Methane-2D-square.png
Water molecule
http://commons.wikimedia.org/wiki/File:Wasser.png
Hydrogen bonds
By translated by Michal Maas (User:snek01) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0
(http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons
Nucleotide
By Frank Boumphrey (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0-2.5-2.0-1.0
(http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
ATP
By User:Mysid (Self-made in bkchem; edited in perl.) [Public domain], via Wikimedia Commons
DNA
http://commons.wikimedia.org/wiki/File:DNA_chemical_structure.svg
DNA v. RNA
By Difference_DNA_RNA-DE.svg: Sponk (talk) translation: Sponk [CC-BY-SA-3.0
(http://creativecommons.org/licenses/by-sa/3.0), CC-BY-SA-3.0-2.5-2.0-1.0
(http://creativecommons.org/licenses/by-sa/3.0), GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0
(http://creativecommons.org/licenses/by-sa/3.0), CC-BY-SA-3.0-2.5-2.0-1.0
(http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia
Commons
Triglyceride
By Wolfgang Schaefer (author) [Public domain], via Wikimedia Commons
Saturated Fatty Acid
By Jynto and Ben Mills (Derived from File:Valeric-acid-3D-balls-B.png.) [Public domain], via Wikimedia
Commons
Unsaturated Fatty Acid
By Jynto [CC0], via Wikimedia Commons
Amino Acid
By User:Ppfk (Original File) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0
(http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons