The Chemical Context of
Life
Elements of Life
Atoms, Molecules & Compounds
Chemical Bonds
Structure and Function
Chemical Reactions
Organic Chemistry
Chemistry is fundamental to
understanding life
Reactions at the molecular level based
in rules of bonding and reactions “run”
the machinery of life
Chemicals are required for growth,
defense, development and many other
reactions in living organisms
Figure 2.1 The hierarchy of biological order from atom to organism
Figure 2.0 Bombardier beetle
Organic Chemistry
(Continued)
You must understand the elements
within living things and understand how
they combine to form the four basic
organic compounds
A knowledge of how atoms bond and
atomic structure is crucial
Let’s look at the main elements found in
living things
Table 2.1 Naturally Occurring Elements in the Human Body
Atomic Bonding
Remember that atoms bond based on the
number of unpaired electrons in their valence
or outer shell.
Each filled shell has a specific number of
electrons (1st shell 2, Second shell 8)
There can be two electrons in each orbital.
Each orbital fills one electron at a time.
Carbon has four unpaired electrons, within
four orbitals.This gives it four bonding sites
and makes it a versatile compound for living
things
Valence Numbers
The valence number is the number of
unpaired electrons in the outer shell
You should know at least the first ten most
common elements in living things and their
valence numbers
Normally, unpaired electrons will bond with
electrons of other elements to fill the outer
shell
It is how atoms bond (angles,
electronegativity, types of bonds) that
determine a compound’s characteristics
Figure 2.10 Electron configurations of the first 18 elements
Energy Levels of Electrons
The more distant an electron is from the
nucleus the more potential energy it stores
Energy levels are the different states of
potential energy that electrons have in an
atom
Electrons may absorb energy and move to a
higher level or fall to a lower level and
release energy
This is important in one complex reaction we
will study-photosynthesis
Figure 2.9 Energy levels of an atom’s electrons
Compounds
Remember also that a compound will
usually have emergent or different
properties than the individual properties
of the elements that make it up.
Figure 2.2 The emergent properties of a compound
Sodium +
Chlorine
Emergent Properties in a compound
= Table Salt
Types of Bonds in Living
Things
There a number of strong and weak
bonds in living things
You should be familiar with ionic and
covalent bonds already, but we will
review them.
There are also weak bonds important to
some molecules and solutions in living
things.
Covalent Bonds
Covalent bonds are strong bonds that
occur when electrons are shared.
Examples of covalent bonds are on the
following slides
A type of bond called a polar covalent
bond occurs when an atom that has a
high electronegativity pulls atoms of
other elements closer to itself than is
normal (Example: water)
Figure 2.12 Covalent bonding in four molecules
Figure 2.13 Polar covalent bonds in a water molecule
Ionic Bonds
Ionic bonds occur when electrons are
stripped from one atom and
transferred to another (Sodium and
Chlorine is an example when salt forms)
This causes each atom to become
either a cation (atom with a + charge)
or an anion (atom with a – charge)
Ionic compounds those formed by ionic
bonds
Figure 2.14 Electron transfer and ionic bonding
Important Weak Bonds
Van der Waals interactions form weak
bonds and only occur when the atoms
are very close to one another
They are due to the fact that electrons
are in motion all the time and cause
some charge to occur in even nonpolar
covalent bonds.
Hydrogen Bonds
Hydrogen bonds form between
molecules of polar covalent compounds
when there is a very slight difference in
charge between two of them.
They are a relatively weak bonds, but
give water some of its more unique
properties.
Figure 2.16 A hydrogen bond
Atoms, bonds and Shape
When atoms bond to one another, the
positions of their orbitals determine the
molecular shape
Sometimes orbitals can mix or hybridize
in specific ways to give a molecule a
specific shape
Figure 2.17 Molecular shapes due to hybrid orbitals
The Shapes of Biological
Molecules
The shapes of biological molecules
determine their function
Enzymes and neurotransmitters are
examples of molecules whose shapes
are crucial to their functions
Receptors on the neuronal cell
membrane “fit” specific
neurotransmitters which then cause the
neighboring neurons to fire
Figure 2.18 Molecular shape and brain chemistry
Molecular Mimics
If a particular molecule, say from a drug, is
similar to that of a molecule in the body, it
can occupy receptors for that molecule in the
body and affect it
Example: Endorphins are our brain’s pain and
pleasure chemicals
Drugs like morphine and heroin can occupy
the same receptors as these, causing
powerful reactions in the brain
Figure 2.19 A molecular mimic
Chemical Reactions
Chemical reactions make or break the
bonds between atoms and molecules
If bonds are broken, energy is released
Energy is used to make bonds
Reactants are what go in
Products are what come out
Chemical equilibrium is the point where
relative concentrations of reactants and
products stop changing
Unnumbered Figure (Page 38) Chemical reaction between hydrogen and oxygen