Download Chemistry for Biologists

Chemistry for Biologists
It can be argued that life itself is a spontaneous chemical reaction. From this perspective it is no wonder
that the beginning of our biology course focuses on the fundamental principles of chemistry. As this
course unfolds you will gain an increasingly deeper understanding of the interconnectedness between
biology and chemistry. This link is so strong that an entire subdivision of biology called biochemistry has
emerged to study it. Consequently biochemistry is also the title of our first unit of study. What follows
is a summary of some key principles of chemistry that will lay the foundations for your understanding of
subsequent topics throughout this course.
What are living things made of?
For all of their complexity, 96% of the mass of all living things is composed of just four elements. They
are carbon, oxygen, hydrogen and nitrogen. The atomic structure of these elements is important for
understanding how they form molecules. The valence (outer most) electrons are the most important for
bonding. Using a periodic table, let us analyse the composition of these 4 elements.
Recall how to use the periodic table:
Standard atomic
notation
Lewis Diagram
Protons = 15
Electrons = 15
Neutrons = 31-15 = 16
Element
P
Lewis diagram
able to make
3
Bonds
# of bonds it
can form
Carbon
Nitrogen
Oxygen
Periodic table highlighting the most common elements in the human body
Hydrogen
Radioisotopes
The number of protons determines the characteristics of an atom. By changing the number of neutrons
present, the chemical properties of the atom remain identical, however the atoms mass and/or stability
of the nucleus will be altered. Unstable nuclei decay and produce detectable radiation at a steady rate.
These radioisotopes are used by scientists for a variety of functions including determining the age of
organic material and fossils, as radioactive tracers to map biochemical processes and as part of medical
diagnosis and treatments.
Since organic compounds are mostly composed of carbon and hydrogen, it is their isotopes that are
most commonly used to study biochemical processes.
Chemical Bonds
Atoms often form stable interactions known as chemical bonds by allowing their valence electrons to
interact. Electrons may either be transferred from one element to another (ionic bonding), or shared
between atoms (covalent / molecular bonding).
Between:
Mechanism:
Ionic Bonding
Covalent / Molecular Bonding
Metal and Non-metal
Two or more non-metals
Metal loses e-  cation
Valence electrons are shared
(up to three shared pairs)
-
Non-metal gains e  anion
lithium + chlorine  lithium chloride
Example:
Force of
Attraction:
Li
+
Cl

Li
+
Cl

LiCl
[ Li ]+ + [ Cl ]-
bromine + chlorine  bromine chloride
Br
Br
+
+
Cl

Cl

BrCl
Br Cl
Electrostatic interaction
(attraction between positively
and negatively charged ions)
Physically shared eletron pair(s)
Crystal Lattice
Individual molecules.
Structures vary greatly depending on how
individual molecules interact with each other.
Depends mostly on:
polarity, size and 3D shape
Conceptual
Diagram:
Structure:
Polarity
Not all covalent bonds behave the same way. Every element has its own characteristic
electronegativity. This is an assigned value used to describe an element’s overall pull for electrons.
When one element in a covalent bond has a stronger electronegativity than the other, then the
electrons will not be shared evenly. If one side of a molecule holds electrons closer, it will gain a slight
negative charge. The side with a weaker hold on its electrons will become positively charged. A
molecule with an uneven distribution of charge is referred to as a polar molecule.
Intermolecular Forces
If a molecule is polar, or if it is particularly large, forces between different molecules play an important
role in their behaviour. The most important intermolecular forces in biology are hydrogen bonds.
Hydrogen bonds:
Hydrogen often forms strongly polar bonds with electronegative elements like
oxygen and nitrogen. The positively charge hydrogen atoms in these bonds will
attract any nearby negative charges. These may be charges on a different
molecule or a different region of the same molecule.
van der Waal:
Intermolecular forces are collectively known as van der Waal forces. Most are
extremely weak, however their cumulative effect becomes important for
increasingly larger molecules.
Water
More than 65% of your body is composed of water. Reactions in your body take place in aqueous
solution. This means that in order for a substance to be used by your cells, it must be able to dissolve in
water. Water is a polar solvent.
In the context of dissolving: “LIKES DISSOLVE LIKES”
i.e. Polar solutes dissolve in polar solvents. Nonpolar solutes dissolve in nonpolar solvents
Polar molecules


“water loving”

HYDROPHYLLIC
Non-polar
 does not dissolve in water 
“water fearing”

HYDROPHOBIC
Ionic
 usually dissolve in water to form aqueous ions
dissolve in water
Acids and Bases
Some molecular compounds not only dissolve in water, but they also partially dissociate into ions. If
they produce hydrogen ions (H+), then they are referred to as acidic. An acid can be neutralized using a
base. These are hydrogen acceptors which often produce OH- in solution.
The pH Scale
The concentration of H+ ions (which may also be indicated as the hydronium ion, H3O+) in a solution
determines its level of acidity. Acidity is assigned a numerical value on a 14 point scale. This value is
calculated using the concentration of hydrogen ions [H+] in solution according to the following formula:
pH = − log[H+]
The strength of an acid is independent of its concentration and pH. The strength of an acid refers to the
degree to which it dissociates into ions in water. A strong acid completely dissociates in water (there are
only 6 of them), whereas a weak acid only partially dissociates. Organic acids are weak acids. Another
word for a weak acid is a buffer. This is because solutions containing weak acids are able to resist small
changes in pH by either producing H+ or consuming H+ in response to changes in H+ concentration.
A common buffer (weak acid) in human blood is bicarbonate
H2CO3
HCO3−
+
H+
Types of Reactions
Summarize the four most common types of reactions in biology in the table below.
Dehydration /
Condensation
Hydrolysis
Neutralization
Redox
Practice!
Answer the following questions on a separate page.
1) Living things are made mostly from just 4 elements. Based on the number of bonds each of them is
able to make, propose an explanation for why only these 4 elements are needed to make all of the
molecules necessary for life.
2) a) Describe the differences between stable isotopes and radioisotopes.
b) Explain how isotopes can be used to study biochemical reactions
3) a) Based on the properties of molecular compounds explain why they are the main components of
living things rather than ionic compounds.
b) Why are molecular compounds so much more varied than ionic compounds?
4) The molecules that make up organisms seem to obey the same laws of chemistry and physics as all
other molecules. How do these molecules fold into complex 3D shapes and self assemble into
complex arrangements as is required for living things? In your answer focus on the two most
important intermolecular forces we discussed.
5) Explain what is meant by hydrophilic and hydrophobic molecules. Which type would you expect to
find more of in living cells and why?
6) What is a buffer and how are they helpful to living things?
Textbook Work
Pg 18 # 4-10
Pg. 24 # 4, 8, 10
Sample Communication Answers For Question #1
Example #1
Though living things are complex, they are composed almost entirely of just four elements. It is mostly
the 3D shape a molecule that determines its function and 3D shape depends on the number of bonds
made by the elements in the molecule. Hydrogen, oxygen, nitrogen and carbon represent the full
spectrum of potential bond numbers. The minimum number of bonds that an element can make is one
and the maximum is four. Hydrogen makes one bond, oxygen makes two, nitrogen makes three and
carbon makes four. By combining just these four elements you can make molecules that represent nearly
all of the possible 3D shapes that exist in chemistry. Furthermore, these are the simplest, most abundant
elements that can form their respective number of bonds.
Example #2
It may seem surprising that for all of life’s complexity, organisms are almost exclusively composed of just
four elements. These elements are hydrogen, oxygen, nitrogen and carbon. A likely reason for this is
that these four elements are the simplest elements that can form a full range of bond numbers.
Hydrogen forms just one bond, oxygen forms two, nitrogen forms three and carbon forms the maximum
of 4 bonds. By combining these elements, you can form nearly all possible shapes in chemistry.
Ultimately it is the 3D shape of biological molecules that determines their function.