Biology 121
Lectures 2.1 & 2.2
Organic Molecules
Functional Groups
Chemical Reactions
Organic? That means ‘healthy’, right?
• The term “organic”
has developed a
vernacular meaning in
our language, causing
many people to
associate organic with
the terms “healthy”
and “natural”.
Organic? Aren’t those kind of dangerous?
• In chemistry, the term
organic maintains its
original meaning. As you’ll
find, in the scientific
context, some organics are
healthy, but many are
synthesized in the lab, so
they aren’t “natural” – and
they aren’t necessarily
healthy!
Organic? What does that mean?
• Organic chemistry is the
study of organic
molecules. What
organic molecules all
have in common is…
• Carbon!
• More specifically, C and
H.
Organic means C and H
• So CO2 is generally
not considered an
organic molecule,
but CH4 is.
• CH4 = organic
• CO2 = inorganic
• C6H12O6 = organic
• H2O = inorganic
Categorizing Organic Molecules
• The compounds in the human
body are organic -- we are a
carbon-based organism.
• Organic compounds are the
building blocks of life.
• There are 4 major categories:
– Carbohydrates
– Lipids
– Proteins
– Nucleic acids
Categorizing Organic Molecules
• Keep in mind the nature of C
bonds. C-C and C-H bonds are
very nonpolar.
• H2O is a very polar molecule,
and our bodies are 60-70%
water. We are a very polar
environment, and simple
hydrocarbons would not fare
well in our tissues!
• Biologically important carbon
molecules need other atoms
like O and N that are more
electronegative to add polarity
to the molecules.
Why Carbon?
• C has characteristics which make it a good
choice for this very central role in biology.
Nature of Carbon Bonds - Variety
1. C has 4 valence e– C can form 4 covalent bonds
to satisfy a full valence shell.
– An example of a satisfactory
arrangement is CH4,
commonly known as
methane. Methane is one of
the simplest organic
compounds.
– These 4 covalent bonds yield
lots and lots of possible
combinations
Nature of Carbon Bonds - Variety
2. C’s 4 covalent bonds are
very strong, but are still
breakable by cells
– Normal biological methods
can break and reform these
bonds
3. C bonds allow rotation to
form lots of shapes and
conformations
Nature of Carbon Bonds - Variety
4. C can form single, double
or triple bonds
H H H H
H C C C C H
H H H H
Butane
• Here are 3 similar
molecules, but C is single,
double or triple-bonded.
H H
H C C C C H
H H H H
Butene
H H
H C C C C H
H H
Butyne
Categorizing Organic Molecules
• For any given pair of ions, there
was ONE possible arrangement
to make an ionic compound.
• In covalent bonds, any unpaired
e- in the carbon shell can bond
with ANY other atom with
unpaired e- . The possibilities
are endless, so there are many
more types of organic
molecules, and they can
become incredibly large and
complex, even when there are
only C and H bonding.
Categorizing Organic Molecules
• Simple organic molecules
contain just C and H =
hydrocarbons
• But more complex organic
molecules contain C and H,
but also O, S, P, and N and
other elements
• With all this complexity, we’re
going to need some sort of
system to categorize the
myriad organic compounds
into recognizable groups.
Categorizing Organic Molecules
1. Start simple. Study the bonding
patterns of compounds that
consist of ONLY C and H.
2. Add on polarity with other atoms,
such as O, onto our C framework,
noting how the compound
changes.
– Functional groups
3. With that system in place, we’ll go
on to consider carbohydrates,
lipids, proteins and nucleic acids
IUPAC Nomenclature
• As we scrutinize and categorize
organic compounds, we’ll name
them based on their bonding.
Naming is also referred to as
“nomenclature”.
• Naming compounds allows us to
develop a common language, so that
we can discuss compounds easily.
• It’s helpful if we all use the same
naming system. IUPAC is the
chemistry organization responsible
for setting naming rules. Even in
biology, we follow their guidelines.
Start With the Simplest Carbons
• To begin, we’ll
consider molecules
that ONLY contain C
and H.
– Hydrocarbons
• First, we’ll consider
only hydrocarbons
that have all single
bonds.
– Alkanes
Start With the Simplest Carbons
• Start with 8 alkanes, listing C
number, name, and
structure.
• Each compound has an ”ane” ending, because they
are alkanes.
• The prefix for each
compound is assigned based
on its C number.
– 1 C is meth– 8 Cs is oct-
• have formula CnH2n+2
“Straight” carbon chains
• We call hydrocarbons that have
all the Cs arranged linearly (in a
straight line) “straight chain”
hydrocarbons.
• As the ball and stick models to
the right indicate, they actually
aren’t “straight” at all, that’s
because of the tetrahedral
shape of the individual C
atoms. They aren’t straight for
the same reason water isn’t
straight.
• Flexible, can bend and rotate
Double Bond  Alkene
• Cs can bond through more complex
patterns than just single bonds,
forming double and even triple bonds
with one another.
• If there is at least one double bond in a
hydrocarbon, we call it an alkene. Its
prefix stays the same, but the ending is
now –ene.
• All have formula CnH2n
• Must lose 2 H to form a double bond
• Double bond is more rigid, no rotating
around double bond
ethane
ethene
Triple Bond  Alkyne
• If there is at least one triple
bond in a hydrocarbon, we
call it an alkyne. Its prefix
stays the same, but the
ending is now –yne.
• All have formula CnH2n-2
• Lose 2 more H to form a triple
bond.
• Triple bond is also rigid, no
rotating around triple bond
ethane
ethene
ethyne
Double and Triple Bonds – fewer Hs
• Ethane = C2H6
• Add a double bond,
remove two Hs. Ethene
= C2H4.
• Add a triple bond,
remove two more Hs
Ethyne = C2H2
ethane
ethene
ethyne
Double and Triple Bonds
• C-C single bonds in
alkanes are movable. The
Cs can spin with respect to
one another, causing the
Hs to spiral like spokes on
a wheel.
• In ethene and ethyne the
C-C double and triple
bonds cannot move, so
the Hs are stuck in one
place.
ethane
ethene
ethyne
Start With the Simplest Carbons
• Learning Goal: Be
able to name
molecules based on
the IUPAC guidelines
for C1 through C8
compounds
Name That Molecule
Name That Molecule
3 C, one triple bond = propyne C3H4
5 C, all single bonds = pentane C5H12
6 C, all single bonds = hexane C6H14
8 C, one double bond = octene C8H16
Hydrocarbons can have many structures
1. Straight chain
– All Cs bonded together in
one line (even if bent due
to rotation around bonds)
– Can be very long (25+ Cs)
H H H H H
H H
H C C C C C C C C C H
H H H H H H H H H
Hydrocarbons can have many structures
2. Branched chain
– Main chain has one or
more Cs attached as a side
chain
– Named according to the
longest continuous chain
• Branched propane
• Branched heptane
• Branched decene
H H H H H H H H H H
H C C C C C C C C C C H
H H H
H H
H H
H C H
H C H
H
Naming Branched Chains
• The trick for branches, is to name the molecule based
on the number of the longest C chain, and treat the
branch as an “accessory”. So the bottom compound is
a “heptane”, with a 3C branch off of the middle C.
Naming Branched Chains
• The real name of this compound is 4-propyl-heptane.
We will not be covering IUPAC rules of naming such
complicated molecules, you simply need to know this
as a branched heptane for now.
3. Ring Structures
• It is also possible for a chain of C to
bend around so that the end C bonds
with the first C, forming a ring.
– Rings can be as small as 3 C, but 5
and 6 C rings are the common sizes
we’ll see in biology.
• To name such compounds, add
“cyclo” to the front. So a 6C ring with
all single bonds is called cyclohexane.
• Lose 2 H to make the C-C bond to
close the ring.
• Some rotation around bonds, but less
flexible than chains.
Rings
• Notice that when a
hydrocarbon turns into a ring,
you need to remove two Hs to
accommodate the extra C-C
bond - just like adding a double
bond.
• Notice, also, that the ring
structure holds the Hs rather
rigidly in place, they aren’t free
to spiral anymore - just like
adding a double bond.
• Can have single, double, triple
bonds, branches, more rings,
etc.
Benzene – a special ring
• Benzene, C6H6 is a very special
molecule in chemistry. It has an
unusual bonding arrangement
which puzzled chemists for years.
A rather simple representation
(which suits us just fine) is to think
of benzene as a 6-cabon ring with
alternating single and double
bonds.
• Benzene is not found in the human
body (it is actually a carcinogen),
but there are many derivatives of
benzene -- compounds which
contain a benzene ring -- found in
nature. They are called
“aromatics” because they have
pleasant aromas, you’d find them
in rose oil, for example.
Chain, Branched and Ring Hydrocarbons
• Learning Goal: For
carbon chains between 1
and 8 carbons long,
including straight-chain,
branched and rings, be
able to name molecules
based on the IUPAC
guidelines
What’s missing from these structures?
• Now that we’re such good
chemists, we’re going to
need to understand some
common shortcuts
– Leave Hs off, assume
maximum Hs whenever
they’re omitted
– C at every corner unless
something else is indicated
cyclopentane
heptane
More Name That Molecule!
4 C, ring, only single
bonds
= cyclobutane
2 C, straight chain, only
single bonds
= ethane
5 C, branched chain,
only single bonds
= branched butane
5 C, straight chain, only
single bonds
= pentane
More Name That Molecule!
4 C, ring, only single
bonds
= cyclobutane
2 C, straight chain, only
single bonds
= ethane
4 C, branched chain,
only single bonds
= branched butane
5 C, straight chain, only
single bonds
= pentane
More Name That Molecule!
7 C, branched chain,
only single bonds
= branched heptane
8 C, straight chain,
double bond
= octene
5 C, ring, single bonds
= cyclopentane
4 C, straight chain,
double bond
= butene
More Name That Molecule!
7 C, branched chain,
only single bonds
= branched heptane
8 C, straight chain,
double bond
= octene
5 C, ring, single bonds
= cyclopentane
4 C, straight chain,
double bond
= butene
Isomers – same formula, different structure
• Because C is such a ‘flexible’ atom it
can bond in many different
arrangements.
• Even for simple hydrocarbons, you can
have two different molecules with the
same molecular formula
– different spatial arrangements in
space
• For example, C4H10 can be a straight
chain OR branched.
• If we needed to distinguish which of
these two isomers we wanted, we
would need to expand the molecular
formula, as in the figures to the right.
• Important because different structures
have different functions
Isomers – same formula, different structure
3 types of isomers –
1. Structural – same formula,
different bond arrangement
2. Geometric – same formula and
bonds, but held in different
positions
– Requires a double bond
3. Enantiomers – same formula,
same bonds, but held in different
arrangement around a central C.
– Requires 4 different groups on
C (chiral)
– Non-superimposable mirror
image
How Many Structural Isomers are Possible
for the Alkanes?
No. of C Atoms
Molecular
Formula
1-3
Possible Isomers
1
4
C4H10
2
5
C5H12
3
6
C6H14
5
7
C7H16
9
8
C8H18
18
No memorization necessary!
Drawing Structural Isomers
• Different isomers often have different names –
don’t worry about this in Biol 121
• Learning Goal: For a given molecular formula
of a hydrocarbon, be able to draw a stated
number of different structural isomers
Sample Problems
• Draw 2 structural isomers of C4H10.
1. Any rings, double or triple bonds?
– Compare no. of Cs and Hs
2. Draw straight chain
3. Reduce chain by 1C and add 1C branch(es)
– Move branch around first half of chain
4. Reduce chain by 2C and add 2 1C branch(es)
– Move branch around first half of chain
5. Reduce chain by 2C and add 2C branch(es)
– Move branch around first half of chain
6. Draw rings, rings with branches, etc.
Sample Problems
• Draw 2 structural isomers of C4H10.
H H H H
H C C C C H
H H H H
H
HCH
H
H
HC C CH
H H H
Sample Problems
• Draw 6 structural isomers of C7H16.
• Draw 4 structural isomers of C7H14.
Two More Types of Isomers
• In addition to the structural
isomers we have already
discussed, there are two more
special situations where we need
to be able to distinguish between
similar, but different, molecules.
– Geometric isomers occur around
double bonds
– Enantiomers occur every time a
carbon has 4 different atoms
attached to it
2. Geometric Isomers
• A special type of situation exists around double
bonds. Remember that single bonds can rotate
like wheel spokes. But double bonds are held
firmly in space.
• In the example molecule on this page, dichloro-ethene, the green chlorine atoms can
either be attached to the same sides of the
double bond, or to opposite sides.
• When atoms are on the same side, they are cis.
When they are on different sides, they are
trans. These are different geometric isomers,
because the chlorines cannot rotate around the
double bond from one side to another.
• For di-chloro-ethane, the chlorine atoms are
free to rotate from one side to another, there
are no geometric isomers to worry about for
that molecule.
2. Geometric Isomers
• Need to have a double
bond so no rotation
• Groups held in
different positions
• Each C must have 2
different groups
attached.
• If one C has 2 of same
group, not isomers
H3 C
H
C
H
H3C
CH3
C
C
H
H
Not geometric isomers
C
CH3
3. Enantiomers
• Enantiomers have same bonds, but 4 different
groups arranged differently around a central C.
• C in middle, hold one atom at top & rotate to
make match. No match  enantiomers
3. Enantiomers
• If can rotate to match  not
enantiomers
• If no possible match 
enantiomers
• If enantiomers, central C is a
chiral C.
not enantiomers
– 4 different groups attached to C
– Black sphere is a chiral C in
bottom enantiomer pair
enantiomers
Biology 121
Lectures 2.1 & 2.2
Organic Molecules
Functional Groups
Chemical Reactions
Functional Groups add Flavor
• Remember that hydrocarbons
(organic molecules with only Cs
and Hs) are
– Nonpolar covalent and are not
soluble in H2O
– Undergo combustion, but are
otherwise fairly unreactive.
• In contrast, the biologically
significant organic molecules we
need to study are generally
– polar covalent and
– more reactive.
– contain O, N and other atoms.
Functional Groups add Flavor
• Functional group = atom or
group of atoms added to
hydrocarbons that change
their properties
• Each functional group
– Name
– Formula
– Function
• Good charts and descriptions
in book
• R always indicates “rest of
the molecule,” anything
No functional group
• Hydrocarbon only
– C-H
– Non-polar, do not interact with
H2O
– Interact weakly with each
other
• Hydrocarbon branches
– R-CH3
– R-CH2-CH2
methyl group
ethyl group
H
H
│
│
H – C – C – H
│
│
H
H
ethane
5 ways to add O
1. Hydroxyl
R-OH
– Polar bond, makes molecule polar and hydrophilic
– Family = alcohols
– Increases cohesion by allowing interaction of molecules
(ethanol is liquid at RT whearas ethane is a gas)
H
H
│
│
H – C – C – OH
│
│
H
H
ethyl alcohol,
ethanol
5 ways to add O
2. Oxyl
R-O-R
– formed when molecules w/ -OH join together
– Family = ethers
– provides place to break larger molecules apart
CH3CH2-O-CH2CH3
diethyl ether
5 ways to add O
3. Carbonyl
R=O
– polar bond, make molecule
hydrophilic
– 2 kinds of carbonyl groups
a. Aldehyde
• carbonyl at the end of the
molecule
• Family = Aldehydes
b. Ketone
• carbonyl in the middle of the
molecule
• Family = ketones
O
║
R–C–H
O
║
R–C–R
O
║
H – C – H
formaldehyde
H O H
│ ║ │
H–C–C–C–H
│
│
H
H
acetone
5 ways to add O
4. Carboxyl
R-COOH
– very polar, two O have very strong pull, can take electron
from H, creates ions
– Family = carboxylic acids
– R – COO- + H+ = weakly acidic
– important in amino acids to make proteins
O
║
R – C – OH
H
O
│
║
H – C – C – OH
│
H
acetic acid
5 ways to add O
5. Ester
R-COO-R
– formed when molecule w/ -OH joins carboxyl from
H, creating ions: R – COO- + H+
– Family = esters
– can donate H+ so weakly acidic (- charge)
– important in amino acids to make proteins
O
║
R – C – OR
O
║
CH3–C–O–CH3
Other Atoms - Add an N
6. Amino
R-NH2
– can accept a H+ to become R – NH3+
– Family = amines
– weakly basic (+ charged)
– important in amino acids and nucleic acids
H
│
H – C – NH2
│
H
Other Atoms - Add a P
7. Phosphate
R-H2PO3
– very polar, strong pull of O can take electrons from one
or both H, creating ions R – PO42- + 2H+
– Family = organic phosphates
– weakly acidic (- charge)
– found in nucleic acids
O
║
R – P – OH
│
OH
Other Atoms - Add an S
8. Sulfhydryl
R-SH
– polar due to electronegativity of S
– Family = thiols
– found in amino acid cysteine
SH
│
H – C –
│
H
NH2
│
C –
│
H
O
║
C – OH
cysteine (amino acid)
Other Atoms - Add 2 S
9. Disulfide
R-S-S-R
– formed when two sulfhydryls join
– Family = disulfides
– disulfide bonds between amino acids stabilizes
protein structure
Name the Family!
Name the Family!
aldehyde
aldehyde
alcohol
alcohol
ketone
Name that Functional Group!!
Name that Functional Group!!
alcohol
amine
Carboxylic acid
amine
aldehyde
ketone
Morphine
Morphine
hydroxyl
oxyl
amine
hydroxyl
Epinephrine
Epinephrine
hydroxyl
hydroxyl
amine
hydroxyl
Maitotoxin
(toxin discovered in contaminated reef fishes)
Maitotoxin
(toxin discovered in contaminated reef fishes)
hydroxyl
Maitotoxin
(toxin discovered in contaminated reef fishes)
hydroxyl
oxyl
Maitotoxin
(toxin discovered in contaminated reef fishes)
hydroxyl
oxyl
others
Summary of Functional Groups
• Functional Groups are
specific arrangements of
atoms that are attached to
C chains.
• Look for the nonhydrocarbon parts of the
molecule
• Learning goal: be able to
recognize and name these
9 functional groups on
organic molecules
Biology 121
Lectures 2.1 & 2.2
Organic Molecules
Functional Groups
Chemical Reactions
What is a Chemical Reaction?
• Remember our concept
of the hierarchal
organization of life
• Subatomic particles
atoms molecules…
• The next step in our
understanding of
molecules, we can add
that… molecules undergo
chemical changes.
Chemical Reactions Rearrange Bonds
• Sometimes when molecules come into contact with
one another, the conditions dictate that the bonds
holding those molecules together are replaced by new
bonding interactions.
• Simple example of a chemical reaction:
Chemical Reactions Rearrange Bonds
• A reaction = breaking and/or forming bonds to create
different molecules
• Reactants (what you start with)  Products (what you
end with)
• Show reactions in the form of an equation A + B  C + D
Chemical Reactions
• Later in this course, we’ll
discuss specific
categories of chemical
reactions.
• For now, it is sufficient
to set the groundwork
by learning how to
diagram chemical
reactions, and how
reactions can be placed
in categories based on
similarities in their
outcome.
Diagramming Reactions
• Here is a specific example of a simple chemical
reaction, burning methane (CH4). CH4 is the primary
component of natural gas, so this reaction is one that
takes place in many furnaces.
• Notice there are two reactants, they are separated with
a “+”
• There are two products, they are also separated with a
“+”
CH4 + O2 → CO2 + H2O
Diagramming Reactions
• There is a number “2” in front of O2 and in front of
H2O, because there are two of them. For every single
CH4 that burns, 2 O2molecules are needed.
• Chemical reactions, written properly, have the same
number of each atom on each side of the arrow.
CH4+2O2→CO2+2H2O
5 Important Types of Reactions
1. Bond Rearrangement – changing the bonds
within a molecule to form a new molecule
– No addition or loss of atoms, just changes form
one structural isomer to another
2. Functional Group Transfer – moves a
functional group from one molecule to
another
– Phosphate groups are frequently transferred from
one molecule to another
5 Important Types of Reactions
3. Dehydration/Condensation – joining two
molecules by removing a water molecule
– Allows creation of big macro molecules from subunits
– One molecule donates an H+, one donates an OH-, and
they bond to each other
– CH3–CH2–OH + HO–CH2–CH3 
CH3–CH2–O–CH2–CH3 + H20
– Anabolic reaction (building up molecules), takes
energy
• Simple sugars  complex carbohydrates
• Amino acids  proteins
3. Dehydration/Condensation
• Sugar
monosaccharides are
joined via
dehydration/
condensation during
starch synthesis
• Amino acids joined
this way during
protein synthesis
5 Important Types of Reactions
4. Cleavage – breaking a bond to make smaller
molecule
– Hydrolysis – breaking a molecule into two smaller
molecules using H2O
– CH3–CH2–O–CH2–CH3 + H20 
CH3–CH2–OH + HO–CH2–CH3
– Opposite of dehydration, catabolic reaction (breaking
down molecules), released energy
5. Oxidation/Reduction – transfer of electrons
between molecules
– Will deal with these in detail in section 4
Enzymes assist most reactions
• Reactions can happen on their own, but
enzymes make them react more quickly and
efficiently
– Hold reactants in place in the right orientation so
the reaction can occur
– Almost every reaction in the body requires its own
specific enzyme
Learning Goals:
• Describe the 4 types of reactions discussed in
class and given an equation or diagram,
determine which type of reaction is depicted
• For dehydration and hydrolysis reactions, know if
the reaction is anabolic or catabolic and whether
it requires or releases energy
• Understand that dehydration synthesis is the
reaction that joins subunits to make complex
carbohydrates, lipids, proteins, and nucleic acids