Chapters 2-5 and 8:

Chemistry of Life
Atoms: smallest unit of matter that still
maintains the characteristics of the matter.
Contains nucleus with protons (+) and
neutrons (neutral = 0). Electrons (-) are
arranged outside of the nucleus.

Molecules: 2 or more atoms held together
by chemical bonds sharing or
transferring of e
-
by atoms.

I. Atoms/Molecules
Electronegativity: how well an atoms attracts
electrons. Certain bonds form as a result of the
property of electronegativity.

1. Ionic Bond: formed by TRANSFERRING
electrons. The result of 2 atoms having very
different electronegativities. One high and one
low. The atom with the higher electronegativity
has a stronger pull on the e
-
, gains the e
-
and has
a negative charge. The atom with the lower
electronegativity has a weaker pull on the e
-
, loses
the e
-
and has a positive charge results in
formation of ions = charged particles.
ex. NaCl [Na]
+
[Cl]
-
Lewis Dot:


2. Covalent Bond: formed by SHARING
electrons. The result of 2 atoms having similar
electronegativities. There are two types:

a. Nonpolar Covalent: e
-
are shared equally
because electronegativites are virtually
identical no partial charges.
ex. O
2
Lewis Dot:

b. Polar Covalent: e
-
are shared unequally because
the electronegativities are different enough
that one atom has more pull on the e
-
than the
other results in partial charges.
ex. H
2
O Lewis Dot:
2 e
-
shared 4 e
-
shared 6 e
-
shared
Electronegativity Spectrum & Bonding
Hydrogen Bonds: WEAK bonds between
molecules not single atoms. Formed when the
positive pole around one H
+
in a molecule is
attracted to the negative pole around another
covalently bonded molecule the O
2-
of
another water molecule, for example.


1. Universal Solvent: ionic substances are very
soluble in water because the partial + & -
charges of H
2
O molecules interact with the - &
+ poles of ionic substances, respectively and
separate them into their ions this is
dissolving. The same holds true for polar
covalent substances (their partial charges are
attracted to those of the water molecule).
Nonpolar covalent substances do not dissolve
in H
2
O because they lack + and poles.
Hydrophilic (polar/ionic) dissolves in H
2
O
(salt)
Hydrophobic (nonpolar) does not dissolve in
H
2
O (oil)
II. Properties of H
2
O:results of H
2
bonding
2. High Heat Capacity: heat capacity is the amount of
heat energy needed to change the temperature of 1g of
a substance 1
o
C (heat loss and heat gain). It takes a
large amount of heat to change the temperature of
H
2
O because of the hydrogen bonds. Therefore large
bodies of H
2
O remain at relatively stable temperatures
coastal areas remain cooler in the summer than
those inland and warmer in the winter (it takes more
heat to change the temperature of water than
Earth/rock). It is also why the ocean temperature
take so long to increase in the summer.


3. Ice Floats: H
2
O expands as it freezes
becoming less dense than its liquid
form and floating. In its solid form,
the weak hydrogen bonds of H
2
O
become rigid and crystallize keeping
the molecules separated from each
other and resulting in a decrease in
density Bonds cannot break and
reform allowing the molecules to
approach each other as they do in its
liquid form.



4. Strong Cohesion: the attraction between like
molecules, i.e., hydrogen bonding in between
H
2
O molecules. Strong cohesion = high
surface tension, resulting in a water surface
that is firm bugs can walk on H
2
O w/o
sinking and water can be pulled up a plants
stem against gravity.
5. Adhesion: the attraction between unlike
molecules. When H
2
O adheres to the walls
of narrow tubing or absorbent solids like
paper = capillary action water moves up
plants and through materials.

III. Organic Molecules
Molecules that contain carbon with the exception
of CO
2
and molecules with -CO
3
e.g., H
2
CO
3
.
Organic molecules are called macromolecules which
are polymers molecules that are made up of
repeating single units called monomers.
Carbon can form up to 4 bonds with itself N, O, H
or other elements in long branched chains or rings.
Macromolecules with similar properties share
similar functional groups = clusters/groups of
atoms w/in a macromolecule.
There are four major classes of macromolecules:

1. Carbohydrates
Classified based on the # of sugar/saccharide molecules
present
a. Monosaccharide = single sugar molecule. Most common
examples are glucose and fructose all sugars have the
same formula (CH
2
O)
n
as the ratio of C : H : O is 1 : 2 : 1.
glucose, n = 6 C
6
H
12
O
6
fructose, n = 6 C
6
H
12
O
6
but the structure is different.
Most carbohydrates end with the suffix -ose.
b. Disaccharide = 2 sugar molecules joined by a glycosidic
linkage. This is formed by a dehydration synthesis
reaction: an H
2
O molecule is lost during the formation of
the bond.
ex. sucrose, lactose (glucose + galactose), and maltose
(glucose + glucose).
Dehydration Synthesis:
water is lost & a bond
is formed.
Hydrolysis:
water is added & a
bond is broken.
c. Polysaccharide: 3 or more monosaccharides
linked. Considered a polymer because it consists
of repeating units of monosaccharides
(monomers). Common polysaccharides include:
i. Starch principle energy storage molecule in plant
cells (polymer of -glucose molecules).
ii. Glycogen principle energy storage molecule in
animal cells (polymer of -glucose molecules
different branching).
iii. Cellulose structural molecule in plant cells; only
broken down by specialized organisms (polymer
of -glucose molecules).
iv. Chitin structural molecule in fungi cells, and
exoskeletons of insects, arthropods and mollusks
(similar to cellulose with addition of N- groups).



2. Lipids
Macromolecules that are insoluble in H
2
O
(hydrophobic) but are soluble in nonpolar
substances like chloroform. There are 3 classes
of lipids:
a. Triglycerides fats, oils,
and waxes. Consist of 3 fatty
acid chains (CH
2
hydrocarbons) with a carboxyl
group (COOH) at one end,
attached to a glycerol molecule
Fatty acid chains vary based on the
number of hydrogens attached and the
types of bonds:
i. Saturated fatty acid: each C has the
maximum number of hydrogen attached (all
single-bonded).
ii. Monounsaturated fatty acid: each C does
NOT have maximum number of hydrogen
attached because there is one (mono-) double bond
C=C.
iii. Polyunsaturated fatty acid: each C does
NOT have maximum number of hydrogen
attached because there are many (poly-) double
bonds.

b. Phospholipids a lipid that looks just like a
triglyceride except that one of the fatty acid
chains is replaced by a phosphate group
(PO
3
). This phosphate group makes up the
head of the phospholipid which is hydrophilic.
The 2 fatty acid chains make up the tails of
the phospholipids which are hydrophobic.
Phospholipids orient themselves with the
hydrophobic tails facing each other & the
hydrophilic heads facing outside towards an
aqueous solution. This orientation provides the
structural foundation of cell membranes
referred to as amphipathic = molecules with
both hydrophobic and hydrophilic regions.
c. Steriods: characterized by a backbone of 4 linked C
rings cholesterol is in cell membranes, testosterone &
estrogen).
3. Proteins
Proteins are the polymers of amino acids
(monomers). The bonds between amino acids are
called peptide bonds & the chain formed is called a
polypeptide or peptide.
There are 20 amino acids each consisting of a
central C bonded to an H, a COOH & an NH
2
. The
4
th
bond is the radical (R) & this bond is what
makes one amino acid different from the other 19.
Peptide bonds are similar to the glycosidic linkages
in that they formed via dehydration synthesis
reactions.

Amino acids and dehydration synthesis:
There are four levels of protein structure:
a. Primary Structure
b. Secondary Structure
c. Tertiary Structure
d. Quaternary Structure
a. Primary Structure (1
o
)
The order of
amino acids.
(amino acids have
3 letter
abbreviations &
the primary
structure of a
protein can be
written as such).
b. Secondary Structure (2
o
)
When the chain of amino acids takes on a 3D shape by
producing a spiral (-helix) or a folded sheet (-pleated
sheet). This occurs due to hydrogen bonding between
the NH
2
& the COOH of adjacent amino acids.
c. Tertiary Structure (3
o
)
When the -helix or -pleated sheet folds up on
itself.
This occurs as a result of any of the following:
Hydrogen bonding between R groups.
Ionic bonding between R groups.
Hydrophobic interactions between R groups that
move away from the aqueous solution towards the
center of the protein.
Disulfide bridges between the sulfurs in the R group
of the amino acid CYSTEINE. (Remember the R
group of the cysteine is CH
2
-S-H.

d. Quaternary Structure (4
o
)
When 2+ polypeptide chains come together.
Protein can all be grouped according to their
functions:
i. Structural Proteins: keratin (hair, horns),
collagen in the connective tissue & silk in
spider webs.
ii. Storage Proteins: casein (milk), ovalbumin
(egg whites), & zein (corn seeds).
iii. Transport Proteins: located in the membrane
proteins that make-up transport channels &
O
2
carrying hemoglobin molecules in RBC
s
(red blood cells).
iv. Defensive Proteins: antibodies
v. Enzymes: regulate rates of chemical reactions.
4. Nucleic Acids
The genetic information of a cell that is
stored in the molecular structure of
deoxyribonucleic acid (DNA) & depending
on the cell, ribonucleic acid (RNA).
DNA is a polymer made up of nucleotides
(monomers).
A nucleotide is made up of 3 parts:
Nitrogen base
Deoxyribose sugar (5 carbons)
Phosphate groups.
There are five different nucleotides each
with one of the following nitrogen bases:
a. Adenine (A): purine (double C ring)
b. Thymine (T): pyrimidine (single C ring)
c. Cytosine (C): pyrimidine (single C ring)
d. Guanine (G): purine (double C ring)
e. Uracil (U): pyrimidine (single C ring)

A pairs with T (DNA) or U (RNA)
C pairs with G
***Purine is a pet food. Cats have nine lives. Adenine +
Guanine.***
DNA:
Double-stranded molecule that forms when
nucleotides bond (A with T & C with G) via weak
hydrogen bonds. Once the nucleotide are paired,
the molecule also spirals forming the well
known double-helix shape.
The two strands of DNA are antiparallel the
two strands run in opposite directions. One
strand is arranged 5 to 3 while the other is
arranged 3 to 5.
How many bonds between A & T? Between C & G?
RNA:
RNA differs from DNA in the following ways:
i. It has ribose sugar as opposed to the
deoxyribose sugar in DNA which has one less
O atom.
ii. RNA is single-stranded NOT double-stranded
like DNA.
iii. Instead of thymine, RNA has uracil which
pairs with the adenine in DNA.
iv. There are at least three types of RNA in the
body (rRNA, mRNA, and tRNA)
v. RNA can leave the nucleus of a cell, not DNA.
IV. Chemical Reactions in
Metabolic Processes:
In order for a chemical reaction to occur the
activation energy (E
A
) of the reaction must first be
reached. Activation energy = the amount of energy
needed to trigger the formation of new bonds. This
energy is established by the collisions of the
reacting molecules/atoms.
Most reactions occurs spontaneously however the
presence of a catalyst will speed up the rate of the
chemical reaction by lowering the activation energy,
i.e. the amount of energy needed for the reaction to
begin.
During the reaction, the catalyst is not chemically
changed and can thus be reused.
1. Metabolism: the sum of all chemical reactions in
a biological system organism including
catabolism = the breaking down of substances,
and anabolism = the formation of new products
and the transferring of energy from one
substance to another.
Whether or not a reaction proceeds in the
forward or reverse direction depends solely upon
the [reactants] & [end products]. Chemical
Equilibrium = the condition when the rate of the
reaction in the forward direction equals the rate
of reaction in the reverse direction. As products
are made, they are immediately consumed no
NET production of reactants or products.
Remember, AB + CD AD + CB. AB and CD
are rectants. AD and CB are products.
Or, AB + CD AD + CB. Now AD and CB are
reactants and AB and CD are products.

2. Enzymes: catalysts for metabolic reactions:
The substrate is the substance upon which the enzyme
acts (salivary amylase catalyzes the breakdown of the
substrate starch in the mouth).
Enzymes are substrate-specific (amylase breaks down
the -glycosidic linkage in starch but not the -
glycosidic linkage in cellulose).
Enzymes work by way of the induced-fit model a
substrate readily interacts with an enzyme due to the
shape & polarity of the enzymes active site = the point
of attachment between enzymes & substrates. Once
attached, the substrate causes the enzymes active site
to change shape allowing the reaction to take place.
This process has HIGH SPECIFICITY 1 enzyme, 1
substrate.
Enzymes are unchanged as result of a reaction & can
be reused repeatedly.
Enzymes are affected by temperature & pH (all
enzymes function at an optimal temperature & pH).
Should the temperature or pH exceed optimum range
the enzyme (protein) will begin to denature i.e. lose its
4
o
-2
o
structure. An enzyme is only denatured beyond
repair if its primary structure is destroyed).
Most enzymes end with the suffix -ase.

3. Cofactors: non-protein molecules that assist enzymes.
When an enzyme & cofactor unite, a holoenzyme is
formed, and the enzyme is now referred to as an
apoenzyme.
Organic cofactors: also known as coenzymes. Function
to donate or accept some component of a reaction
(usually e
-
). Vitamins are often coenzymes.
Inorganic cofactors: metal ions like Fe
2+
.


4. ATP: adenosine triphosphate is a common source of energy. ATP is
essentially an RNA adenine nucleotide with 2 additional phosphate
groups. In the processes of giving up its energy for a reaction, the
last high energy phosphate bond is broken & the ATP is converted
into ADP (adenosine diphosphate) + P
i
. On the other hand, ATP is
assembled by phospharylation which is when ADP is bonded to P
i

creating ATP (an energy-rich molecule like glucose is needed).
To regulate chemical reactions, biological
systems must regulate enzymes in the
following 4 ways:
a. Allosteric Enzymes: enzymes with 2 active sites. One
is for the substrate & the other is for either an allosteric
activator = a molecule that binds to the enzyme &
induces the enzymes ACTIVE form, OR an allosteric
inhibitors = a molecule that binds to the enzyme &
induces its INACTIVE form. In Feedback Inhibition
the end product of the reaction acts as an allosteric inhibitor
shutting down one of the enzymes reaction series.
negative feedback (insulin and glucagon).
b. Competitive Inhibition: a molecule that mimics the
substrate & occupies the active site so the substrate
cannot bind. The reaction DOES NOT proceed.
c. Noncompetitive Inhibitor: a molecule that binds
to the enzyme at a site other than the active or
allosteric sites, however it still succeeds at
changing the shape of the enzyme & preventing
the substrate from binding. Again the reaction
DOES NOT proceed.
d. Cooperativity: the process by which an enzyme
becomes more receptive to additional substrate
molecules after the 1
st
substrate molecule attaches
to an active site. (This can only occur if the
enzyme consists of 2+ subunits each with its own
active site O
2
binding to hemoglobin is an
example of this). It is similar to positive feedback
(milk production in female mammals).