Atoms & Molecules

All Matter, Including Biological Matter, is Made of Atoms

Nucleus: _________ (+) charge and neutrons ( ) charge: most of mass

In orbit: ___________ (-) charge: very small mass
Charges must balance (electrons = protons)
Isotopes: have same number of protons, but different numbers of _______; some,
but not all radioactive (see 3 isotopes of carbon below)

The number of protons (6 in the case of carbon) determines the chemical

properties of the element: all 3 of these isotopes will have (almost) the same
chemical properties
Adding the number of protons and neutrons gives the mass number of the
element: these atoms are, from L to R, carbon-14 (radioactive), carbon-13 and
carbon-12 (the most abundant isotope).

There are About 110 Different Types of Atoms (Elements)

About 30 required for life. Each has a 1 or 2 letter symbol. The most important
are:
C

Carbon

Hydrogen

Oxygen

Nitrogen

Phosphorus

Sulfur

Na

Sodium

Potassium

Ca

Calcium

Cl

Chlorine

Mg Magnesium
Fe

Iron

I
Iodine
Mn Manganese Zn
Zinc
Roughly speaking, the top 6 elements (C, H, O, N, P and S) are involved in
organic compounds (carbon compounds), while the others are involved in
inorganic compounds.

97.6% of your body weight is made up of C, H, O, N, P and S.

The atoms on the left make up two important classes of molecules
o Water: the most abundant compound in your body
o The structures of the giant molecules (macromolecules) of biology.
o These atoms make up about 97.5% of your body weight
o Carbon is the central atom of organic chemistry and biochemistry
The atoms on the right usually form small, water-soluble molecules which tend to
form ions in solution (see next lecture).
o They make up almost 2.5% of the body weight
There is some overlap: occassionally the atoms on the right are found in
macromolecules, and sometimes the atoms on the left produce small, water
soluble compounds

Atoms Combine to Make Molecules

All interactions between atoms are electrical attractions between opposite charges
Ionic bonds: one atom __________ ____________ to another
opposite charges they attract each other and form a chemical bond
(they form NaCl, common table salt)
Positively charged ions = cations (i.e., Na+)
Negatively charged ions = anions (i.e., Cl-)
o Loss of an electron = __________
o Gain of electron = reduction

Covalent bonds: ____________ ______________ between 2 atoms

o Most stable arrangement is 8 electrons in outer orbit
o Carbon (see diagram above) has 4 outer shell electrons- will react with
other atoms to get 4 more -> stable arrangement
o Outer shell electrons are called valence electrons
o Each atom donates 1 or more electrons to the bond
o The bonding electrons spend most of their time between the 2 atoms,
attracting both nuclei and pulling them together
o If each atom donates 2 electrons to a bond a double bond is formed
double bonds are stronger and more rigid than single bonds
o A triple bond is formed when each atom donates 3 electrons to the bond
o Biological macromolecules held together by covalent bonds

Hydrogen bonds: weaker than ionic & covalent

o Occur when a hydrogen ion is sandwiched between 2 atoms, usually
nitrogen and oxygen
o H bonds require a H ________ (an H attached to N, P or O) and a H
acceptor (another N or O usually)
o Occur between molecular groups with permanent dipoles (see below)
o H bonds very important in biology:

Responsible for unusual properties of water

Hold protein molecules in correct shapes
In DNA hold the double helix together- act as a "zipper" allowing
replication and transcription

Van der Waals & other weak bonds:

o Weak forces that can bond like atoms together
o Especially important between chains of carbon atoms
Although weak, numerous bonds between the chains can add up to
produce significant cohesion
o Determine physical state of compounds: gas, liquid or solid
o Occur when one atom induces a temporary dipole in another atom
Type of
Bond

Characteristics

Biological Importance

This type of bond holds together the long

chains of macromolecules. These
molecules do not split apart in water.
Complete transfer of electron
Compounds with ionic bonds split into
from one atom to another.
ions in water. Ions conduct electricity.
Ionic
Oppositely charged atoms attract Gives specialized cells (nerve, muscle)
one another.
excitable properties.
Weaker than covalent or ionic
Water: makes water molecules stick
bonds. Formed between a
together. Responsible for many of the
hydrogen covalently bonded to O strange properties of water.
or N and a second O or N. The Proteins: cause protein chains to spiral
second O or N may be on the
and bend, giving unique shapes.
Hydrogen
same molecule or on another
nearby molecule. Occur because DNA: hold together the 2 chains to form
H, O and N atoms in molecules the double helix. Allow chains to "unzip"
usually have partial charges on for replication and transcription.
them, forming dipoles.
Important in holding like molecules
together. Often determine the solid,
Weak bonds that can form where liquid or gas state of a compound.
Van der
one atom induces a temporary Saturated fats are solid at room
Waals
dipole in another atom.
temperature because the have more van
der Waals attractions than unsaturated
fats, which are liquid.
Other
Attractions between permanent Help to determine the shapes of
Weak
dipoles of molecules
molecules.
Bonds
Covalent

Bonding electrons shared

between 2 atoms.

Multiple Bonds Can Form Between Atoms

If an atom can form a ________ bond with another atom it can form a simple
molecule
If an atom can form 2 bonds it can link 2 atoms together and form a long chain
If an atom can form 3 or more bonds it can make branched molecules of many
shapes
Carbon can make up to 4 bonds -> millions of different types of molecules
Physiological chemistry is the chemistry of shapes: example- enzyme and
substrate fit together like a lock and key. Similar "lock & key" fits between
antibodies & antigens, hormones & receptors, etc.

Biological Molecules Interact with Those of Opposite Shape: Complementarity

Complementarity: frequently biological molecules that interact have opposite

shapes so that they fit tightly together
In the diagram below small molecule A is complementary to large molecule C,
and B is complementary to D (note how well they fit together); there is a poor
match between A & D and between B & C- these pairs are not complementary

Enzymes and substrates fit together like a lock and key

Hormones bind to specific receptor molecules with the right shape
Two DNA molecules fit together precisely to make a double helix: the
genetic code is based upon complementarity between nucleotide bases
o In immune reactions antibodies have shapes that exactly match the
antigens that they bind
o In medicine therapeutic drugs are often designed to be complementary to a
biological molecule such as an enzyme or receptor
In a reaction between 2 complementary molecules the molecules are not rigid, but
bend to the shape of their partner (induced fit). Christian de Duve expresses it this
way:
o "The two partners are not rigid. When they embrace, they mold
themselves to each other to some extent. Furthermore, the embrace leads
to binding. Its degree of intimacy is such that electrostatic interactions and
other short-range physical forces act strongly enough to prevent the
association from being disrupted by thermal jostling." (from Vital Dust.
Life as a Cosmic Imperative, NY: HarperCollins, 1995)
Because of the tight fit, complementary molecules form very strong bonds of high
selectivity
o
o
o

Numbers of Atoms & Molecules Measured in Terms of Moles

Mole is convenient number for doing chemistry

Convenient Number

Unit
eggs

dozen

12

paper

ream

500

mole

6x
10^23

chemicals

Mole = 6 x 10^23 atoms.

1 mole of N (14 protons and neutrons) weighs 14 grams
In physiology it is often convenient to speak of millimoles- a millimole is
mole/1000
o 1000 millimoles = 1 mole

Two Chemical Reactions U Should Know:

Respiration:

In our cells we burn the sugar produced by plants to produce energy to run our
bodies. To do this we require oxygen and produce carbon dioxide as a waste
product

Reaction of Carbon Dioxide and Water:

The carbon dioxide that we produce in respiration reacts with water in our cells
and blood to produce carbonic acid (the acid found in soft drinks and beer). This
would produce serious acidosis but the lungs prevent the problem by removing
CO2.
Rates of and Equilibrium States of Chemical Reactions are Determined by
Concentrations of the Reactants

Consider a simple reaction in which 2 substances, A & B, react to form a third

substance, C:
o A + B <-> C
o The rate at which C is formed (in moles/second) will be proportional to
the concentrations of A, B and C
Rate = Kf{A}{B} - Kb{C}

{A}, {B} and {C} = concentrations of A, B and C, respectively; Kf

= rate constant of forward reaction, Kb = rate constant of backward
reaction
Forward reaction rate = Kf{A}{B}
Backward reaction rate = Kb{C}
This relationship is a fundamental law of chemistry, called the Law
of Mass Action
Note that if you double the concentration of either A or B, the rate
of the forward reaction will double
Concentrations are the number of molecules or moles per unit of
volume
Usually concentrations are given in moles/liter
Example: if you have 3 moles of NaCl dissolved in 6 liters of
water the concentration is:
3moles/6liters = 0.5 moles/liter = 500 mM/liter
Why are chemical reaction rates proportional to concentration?
o Molecules must collide to react & number of collisions per second is
proportional to the concentration
o Other factors affect reaction rates by changing the rate constants:
Temperature: affects rates in 2 ways:
High temperature causes molecules to move faster
producing more collisions
At high temperature molecules have more energy and are
more likely to react with other molecules
Catalysis: reaction rates can be greatly accelerated by certain types
of molecules- this will be discussed in lecture 4 when we consider
enzymes
A chemical reaction proceeds until forward and backward reactions are equal
o At this point the reaction is at equilibrium and concentrations do not
change
o At equilibrium:
Kf{A}{B} = Kb{C}
Ke = Kf/Kb = {A}{B}/{C}
The equilibrium constant (Ke) is the forward rate constant (Kf)
divided by the backward rate constant (Kb)
Note: at equilibrium {C} = {B}/{C}/Ke; thus, both the rates of
reaction and equilibrium concentrations are determined by
concentrations of reactants