Chemistry Tutorial

Basic Chemistry for Understanding Biology

An example of biochemistry
Biology and medicine have enjoyed enormous benefit from a
biochemical approach to life. One striking example uses the fact
that spinning nuclear protons can be regarded as simple magnets,
and interact with an external magnetic field in a way that depends
on their environment. To the right is an MRI scan of the head of a
human using technology based on these principles. The technology
produced high quality images of soft tissue.
A review of the basic chemistry of small molecules
The names of the elements are abbreviated. Often, the
abbreviation makes perfect sense (C for carbon) and
sometimes it does not (Na for sodium). There is an
abundance of elements on earth and in living systems, but
only 4 elements make up 99% of living organisms. These
elements are hydrogen (H), oxygen (O), nitrogen (N), and
carbon (C), and they are special in that they are 1) available
and 2) suitable.
Terms to know
Element
matter composed of atoms that all have the same atomic number (protons).
Atom
the smallest component of an element that still has properties of the element,
consisting of a positively charged nucleus surrounded by a charged cloud of
electrons.
"+" and "-" charges strongly attract.
Proton
particle in the nucleus with a positive charge of +1 and an atomic mass number of 1
Dalton.
Neutron
a non-charged nuclear particle with the same mass as the proton.
Electron
negatively charged particle (-1) with a mass 1/1837 of that of a proton.
Isotope
atoms with the same number of protons and electrons, but different numbers of
neutrons.
Electrons determine chemical properties of elements

Electrons are outside the nucleus, and determine

properties of the atom. Chemical reactions involve
sharing or exchanging electrons. Electrons move
about the nucleus in atomic orbitals. Absorption of
energy can cause an electron to move up to a higher
energy level. The atom is stable when the outermost
energy level of most atoms has eight electrons.
Electrons can be transferred carrying energy to
another molecule. The H atom can carry electrons
for transferring energy. Oxygen has a strong affinity
for electrons. Redox reaction transfer of electrons
from one molecule (oxidized) to another (reduced).
Stability can be achieved by adding, losing, or
sharing electrons.
Sharing electrons leads to the formation of covalent bonds. In the
table to the right, you'll see the bonding patterns of the primary
biologically important elements. Bonds contain energy, and a require
energy to be broken. Bond energy (expressed as kcal/mole) is the
energy required to break a bond. For example, an H-H bond requires
104 kcal/mole to break.

Bonding Patterns
number
of
covalent
element
bonds
H

Chemical bonds and attractive forces

A molecule is two or more atoms linked by a chemical bond. Molecules can contain
different types of bonds. If atoms are sharing electrons, then the bond between them is
covalent. If an atom gives up an electron to another atom, then they have an ionic bond.
Covalent bonds
Methane has four covalent bonds between carbon (C) and hydrogen (H). The figure below
shows the methane molecule in four different views. Notice how these different views
represent the atoms and their bonds differently. Electronegativity refers to the tendency for
atoms to bind electrons. Oxygen (0) with an electronegativity of 3.5 has a strong affinity.
Hydrogen (H)(2.1) and carbon (C)(2.5) each have lower affinities. A bond between C and H
will have nearly equal sharing of electrons. Oxygen and hydrogen form a highly polar bond
because of the much stronger affinity for electrons by O.

Insulin is a complicated molecule called a protein. We will later

consider simpler ways to consider the complicated molecules of
life.

Ionic bonds

Ions are produced when atoms can obtain a stable number

of electrons by giving up or gaining electrons. For example
Na (sodium) can donate an electron to Cl (chlorine)
generating Na+ and Cl-. The ion pair is held together by
strong electrostatic attractions.

Non-covalent bonds and other weak forces

Linus Pauling, 1946
Chemical reactivity of molecules- tendency to break and form chemical bonds.
Biology of molecules- size and shape of molecules, and the nature of weak
interactions with other molecules.
Non-covalent bonds and other weak forces are important in biological structures.
Electrostatic bonds(ionic)-result from the electrostatic attraction between two
ionized groups of opposite charge, such as carboxyl (-COO-) and amino (-NH3+). In
water, these bonds are very weak.
Hydrogen bonds-result from electrostatic attraction between an electronegative
atom (O or N) and a hydrogen atom that is bonded covalently to a second
electronegative atom.

N-H ----- O=C- -O-H----- O=C-

Van der Waals bonds-are short range attractive forces between chemical groups in
contact. Caused by slight charge displacements.

Hydrophobic attractions-cause non-polar groups such as hydrocarbon chains to

associate with each other in an aqueous environment.

Multiple weak bonds or forces can cause strong interactions

Biological recognition results from a three dimensional structure that allows

multiple weak forces between molecules

The Chemistry of Water

The polarity of water
Water has a simple molecular structure. It is composed of
one oxygen atom and two hydrogen atoms. Each hydrogen
atom is covalently bonded to the oxygen via a shared pair
of electrons. Oxygen also has two unshared pairs of
electrons. Thus there are 4 pairs of electrons surrounding
the oxygen atom, two pairs involved in covalent bonds with
hydrogen, and two unshared pairs on the opposite side of
the oxygen atom. Oxygen is an "electronegative" or
electron "loving" atom compared with hydrogen.
Water is a "polar" molecule, meaning that there is an
uneven distribution of electron density. Water has a partial
negative charge ( ) near the oxygen atom due the unshared
pairs of electrons, and partial positive charges ( ) near the
hydrogen atoms.
An electrostatic attraction between the partial positive
charge near the hydrogen atoms and the partial negative
charge near the oxygen results in the formation of a
hydrogen bond as shown in the illustration.
The ability of ions and other molecules to dissolve in water is due to polarity. For example,
in the illustration below sodium chloride is shown in its crystalline form and dissolved in
water.

Many other unique properties of water are due to the hydrogen bonds. For example, ice
floats because hydrogen bonds hold water molecules further apart in a solid than in a liquid,
where there is one less hydrogen bond per molecule. The unique physical properties,
including a high heat of vaporization, strong surface tension, high specific heat, and nearly
universal solvent properties of water are also due to hydrogen bonding. The hydrophobic
effect, or the exclusion of compounds containing carbon and hydrogen (nonpolar
compounds) is another unique property of water caused by the hydrogen bonds. The
hydrophobic effect is particularly important in the formation of cell membranes. The best
description is to say that water "squeezes" nonpolar molecules together.
Acids and Bases, Ionization of Water

Acid release H+
Bases accept H+

We define the pH of a solution as the negative logarithm of the hydrogen ion concentration.

at pH 7.0, a solution is neutral

at lower pH (1-6), a solution is acidic

at higher pH (8-14), a solution is basic

Introduction to Organic Molecules

Organic molecules contain carbon

Alcohol
hydrocarbon with a hydrogen replaced by "OH".
Acid
hydrocarbon with a hydrogen replaced by a carboxyl "COOH".

COOH -> COO- + H+

Amine
hydrocarbon with a hydrogen replaced by an amine "NH2". Basic- accepts protons.
NH2 + H+ -> NH3+
Phosphate
addition of -PO4= (switch)
Amino Acid
hydrocarbon with amino and carboxyl groups