SBI 4U
Unit: Biochemistry
Name: _______________________
Date: _______________________
An Introduction to Biochemistry
Biochemistry is the study of the activity and properties of biologically important molecules. Many biologically
important molecules are organic molecules. This means they contain carbon atoms nearly always bonded to one
another and usually contain hydrogen atoms. Other common atoms they may contain include oxygen, nitrogen,
phosphorus and/or sulfur. Biochemistry is essential to understanding the functions of such molecules in the cell
and in other living organisms.
The activity and properties of biologically important molecules often rest on two factors:
(1) the atoms present in the molecule
(2) the geometry of the molecule (the shapes formed when the atoms come together to make the molecule)
For the most part we will concentrate on (1) the atoms present in the molecule. We’ll build some models later to
look at molecular shape and if you are taking chemistry, you’ll do some more there.
The Atoms Present in Biologically Important Molecules
Biologically important molecules often contain hydrogen and carbon. When only hydrogen and carbon are
present, the molecule is called a hydrocarbon. Here is some general information about hydrocarbons:
(a) Common hydrocarbons are methane, propane and acetylene.
Methane
Propane
Acetylene
Hydrocarbons are combustible and are often used as fuels because as they are burned, a great deal of
energy is released from the breaking and rearranging of the bonds between their carbon and hydrogen
atoms and atoms of oxygen from air. More specifically - More energy is released in breaking the
bonds of the hydrocarbons then is needed to make the bonds for the products of the reaction. This fact
is important in biological molecules, too, because many biological molecules contain sections that are
all hydrocarbon based. When “burned” within a biological system these hydrocarbon sections release
energy for use in biological mechanisms.
(b) Hydrocarbons are non-polar molecules. This means that hydrocarbons have no net electrical charge
within their molecules. The lack of electrical charge or polarity within the molecule is a huge factor in
determining the activity and properties of the molecule.
When atoms other than just hydrogen and carbon are present in a molecule, that molecule is no longer a
hydrocarbon. Other atoms commonly present in biologically important molecules (often along with carbon and
hydrogen) are oxygen, nitrogen, phosphorus and sulfur. Each of these atoms can form a polar covalent bond
with an atom of hydrogen. Atoms in this kind of bond will have a partial electric charge. This is an important
point because it means that when a bond between any one of oxygen, nitrogen, phosphorus or sulfur occurs with
hydrogen, the polarity of that bond will affect the activity and properties of that molecule.
Polar Covalent Bonds
We know that a covalent bond happens between two non-metal atoms. We represent one covalent bond as a
single stick between the two atoms. That stick is actually a pair of electrons being shared between the two
atoms. When one of those atoms pulls the shared electron pair closer to itself, we say that the bond has some
degree of polarity. The atom that is able to pull the shared pair of electrons closer to itself ends up being a little
bit more negative than the other atom because each electron it pulls closer to itself, carries a negative charge.
The other atom ends up being a little bit positive. Determining which atom in a bond will pull the bonding pair
of electrons closer to itself involves the use of electronegativity values. This is a skill taught in SCH 3U. For our
purposes, remembering that oxygen, nitrogen, phosphorus and sulfur are important atoms that will form polar
covalent bonds with hydrogen in biological systems, will suffice most of the time.
Example:
H
H
H
H
C
C
C
H
H
H
O
Carbon and hydrogen
share the electrons in
their bonds about
equally. Oxygen and
hydrogen do not…
H
H H H
| | |
H–C–C–C–
| | |
H H H
O:
:
H
The oxygen atom is pulling the pair of
electrons it shares with hydrogen closer
to itself. This unequal sharing of
electrons in the bond is called a
polar covalent bond.
H
H
H
H
δ-
C
C
C
O
H
H
H
H
δ+
Because it pulls the electrons in the
bond closer to itself the oxygen
ends up with a slightly negative
charge (δ-) compared to the
hydrogen (δ+). The arrow is called
a bond dipole. The arrowhead
points in the direction the electron
pair is being pulled.
When Will a Polar Covalent Bond Inside a Molecule Result in The Molecule Being Polar?
The presence of an oxygen, nitrogen, phosphorus or sulfur atom bonded to a hydrogen atom will produce a polar
covalent bond. In biologically important molecules, the presence of such a bond will also make the molecule as
a whole, at least a slightly polar molecule. The shorter the hydrocarbon part of the molecule is, the more polar
the molecule will be. The more polar covalent bonds are present, the more polar the molecule will be. (Things
tend to be a bit more complicated than this in a chemistry class, however, biologically important molecules tend
to fall under these guidelines.)
When a Polar Molecule Becomes an Ion
We will come across several ions in this course. In terms of biologically important building block molecules,
here are two common types:
(a) Acid Molecules that form ions
Acids are unique because they react with water to form ions in solution. (This is why the reaction is called
ionization.) During this reaction, a hydrogen atom within the acid, that is in a polar covalent bond with
oxygen, nitrogen, phosphorus or sulfur, leaves the bond. When this happens, the hydrogen atom leaves
without its electron, so it leaves with a full positive charge as a hydrogen ion, H1+(aq). The other atom in
the bond (oxygen, nitrogen, phosphorus or sulfur) is then left with an extra electron so it becomes is a
negative ion. When this occurs, the molecule left behind after the hydrogen ion leaves has a full electrical
charge. This new ion will have many of the same activities and properties as a very polar covalent
molecule.
H1+(aq) ions leave to react
Example
with water molecules to
form H3O1+(aq).
Ionization in Water
This is aspartic acid, an amino acid that is one of the building blocks
for protein.
Once ionization in water occurs, hydrogen atoms leave the the
molecule as H1+(aq) ions (so without their electrons). The presence
of H1+(aq) ions floating in solution makes the solution acidic and
the loss of H1+ ions from the molecule leaves the rest of the
molecule as a negatively charged ion.
(b) Molecules Containing Nitrogen with More Than 3 Bonds (These molecules are bases.)
Some compounds containing nitrogen will react will water to break the water up into H1+(aq) and OH1-(aq)
ions. The H1+(aq) ions join a nitrogen atom and make that area of the molecule an ion with a full 1+ charge.
The presence of the OH1-(aq) ions floating around in the water make the solution basic.
OH1-(aq)
H2O
Ionization in
water
H1+
When in water, the bottom part of the lysine
molecule is called “basic” because it leaves
behind OH1-(aq) ions from water when it
reacts with the water. The nitrogen section
ends up with a full positive charge.
This is lysine, another amino acid.
Other ions important to biological systems include but are not limited to: hydrogen ion, H1+(aq); sodium ion,
Na1+(aq); chloride ion, Cl1-(aq); the bicarbonate ion, HCO31-(aq).
Why is it Important to be Able to Recognize a Polar Covalent Bond, A Polar Molecule and an Ion?
Water contains two oxygen-hydrogen bonds so water is a very polar molecule. The very polar covalent bonds
between oxygen and hydrogen in water allow for a force of attraction between neighboring water molecules.
This force of attraction between molecules is called hydrogen bonding. Hydrogen bonding is a type of
intermolecular force because it happens between molecules. Note that hydrogen bonding is NOT a covalent
bond. A covalent bond is an intramolecular force because it happens within a molecule. Note, too, that
hydrogen bonding can only occur between molecules that contain at least one O – H bond, N – H bond or F – H
bond inside them. So, hydrogen bonding can occur between neighboring water molecules or between water
molecules and a different kind of molecule that also contains at least one of these bonds inside it or between two
non-water molecules that both contain these types of bonds.
Examples
Hydrogen bonding in water
Notice all of the O-H
bonds in this
molecule of glucose.
Hydrogen bonding occurs between the
O-H bonds in glucose and those in
water so the glucose dissolves in water.
Any polar molecule (or ion) will be at least somewhat attracted to water. When the intermolecular force of
attraction between two molecules is not hydrogen bonding, it is often given the broader name of dipole-dipole
attraction.
Example
Dipole-dipole intermolecular force of
attraction between water and a molecule of
HCl. This is not hydrogen bonding because
HCl does not contain an H-O, H-N or H-F
bond. Because water and HCl are attracted
to one another, though, HCl is water
soluble.
Hydrogen bonding and dipole-dipole attractions between water and another substance both result in that other
substance having some degree of water solubility. In biology, water soluble substances are called hydrophilic
substances. Non-polar molecules like hydrocarbons, do not have slight or full electric charges so cannot form
dipole-dipole attractions or hydrogen bonds with water. These substances are not water soluble. In biology,
water insoluble substances are called hydrophobic. When placed in water, hydrophobic substances tend to
clump together. This clumping together of non-polar molecules in water is referred to as the hydrophobic effect
and it is central to explaining how membranes form and determining the 3-D shapes of biological molecules like
proteins.
water molecule
Non-polar molecules will not be attracted to
polar water molecules. Instead, they tend to
clump together away from polar water
molecules. This is the hydrophobic effect.
http://oregonstate.edu/instruct/bb450/fall14/stryer7/1/figure_01_12.jpg
So - The polarity of a molecule (or the presence of an ion) influences the intermolecular interactions that can
occur between it and other molecules in biological systems. One of the most important of these interactions is
the interaction with water because water is the major transport fluid in biological systems.
Practice
Page 17 #1 (make it 6 common elements), 2, 4, 5, 7, 8, 9, 11, 12