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Organic Compounds
 Carbon
containing compounds
 Form covalent
bonds with
(usually) other
carbon or
hydrogen
atoms
By virtue of its 4 valence
electrons:
 Can form single, double,
or triple covalent bonds
with itself (and other
atoms)
 Can form a variety of
shapes (chains, rings,
branches sheets, etc.)

Carbon Molecules
Aromatics
Buckyball
• Hydrocarbons – Organic
molecules consisting only of
carbon and hydrogen; energyrich
• Functional Groups - Groups of
molecules that have definite
chemical properties they retain
no matter where they occur.
Macromolecules
“large”
molecules
synthesized by living things
Many are “organic” (contain
a carbon core)
Most have “functional
groups” attached to carbon
core (determine function of
molecule)
Biological
Macromolecules
Carbohydrates
Lipids
Proteins
Nucleic Acids
ATP
Building Macromolecules
Most organic
macromolecules are
polymers made by using
enzymes to help link together
smaller monomers. Done in a
process called dehydration
synthesis (or condensation).
This
process removes
+
one H from one molecule
and one OH from another
molecule (H20) and
cause the two to link
together
Diversity in
polymers is
Achieved by
arranging
The same
monomers in
Different ways
These
different
arrangements
Are called
ISOMERS
Breaking
macromolecules
uses the reverse process
called hydrolysis; process
in which water is added to
break apart polymers into
monomers.
Carbohydrates
 Carbohydrates
are a loosely
defined group of
molecules that
contain carbon,
hydrogen, and
oxygen in a 1:2:1
ratio (CH2O)
Serve
as energy storing
molecules and structural
elements
Energy is stored in the C-H
bonds; when the bond is
broken, energy is released.
Named according to size
and structure (triose,
pentose, hexose)
Monosaccharides
–
“simple” sugars;
glucose, fructose,
galactose
3-6 carbon sugar
C6H12O6 is the common
fuel source for cells
Many
monosaccharides
have the same empirical
formula, but different
arrangement of double
bonds &/or OH- groups.
This causes their
properties to be
different.
Sugar
Isomers Alternative forms of the
same chemical formula.
Glucose
Fructose
Galactose
Glyceraldehyde
(building blocks)
(ENERGY)
Ribose
(RNA)
(DNA)
(Plants)
– created
when 2 monosaccharides are
joined by dehydration
synthesis. (C12H22O11)
Purpose: so sugars can be
transported w/i an organism
without being metabolized.
Disaccharides
Ex:
glucose + glucose =
maltose
glucose + fructose =
sucrose
glucose + galactose =
lactose
– formed from
assembled disaccharides into an
insoluble form and then stored.
Storage: starch (plant
polysaccharide), glycogen
(animal starch stored in liver
and muscles)
Structural: pectin and cellulose
(plant polysaccharides used to
make plant cell walls), chitin
(animal structural sugar)
 Polysaccharides
– chains of glucose
produced by plants, coil in
water, are rendered insoluble.
Enzymes can cleave them
randomly into smaller, more
soluble, fragments and then cut
into smaller disaccharides of
maltose and then smaller
monosaccharides of glucose for
cell metabolism.
Starch
– produced by
animals; length and number
of branches are larger than
plant starches.
Glycogen
When
the animal body
needs energy, it looks
to the liver to hydrolize
glycogen and release
the resulting
monosaccharides to
the cells.
From
there, the cells,
through respiration release
the energy stored in the
bonds of the
monosaccharide molecule.
The energy is converted to
another energy compound –
ATP.
Cellulose
and Pectin Chain of glucose
molecules that consists of
all beta-glucose subunits.
Cleavage of subunits
requires an enzyme
most organisms lack
Why Fiber?
 We
can’t break
fiber down but we
need it
 It makes us
salivate
 Feel full
 Go to the
bathroom
 Prevents colon
cancer
Cows,
for example, have
bacteria and protists in their
gut that have the necessary
enzymes for digesting the
cellulose of grasses and
grains. Therefore cows can
get energy from this food –
we cannot. This makes
cellulose a good structural
material.
– branched
polysaccharide produced by
plants (citrus); sugars are
cross-linked to form a mesh
of glucose which can only be
broken down by a specific
enzyme. Different plants have
different mesh sizes. (Used
as gelling agents & diarrhea
management)
Pectin
 Chitin
- Modified form of cellulose
with nitrogen group added to the
glucose units.
 Structural unit in many insects.
carb trivia –
Sugars have either
aldehyde or ketone
functional groups
Sugars can be recognized
by their “ose” endings
Most sugars form rings in
aqueous solutions
More
ARE ALL FATS
BAD?
Lipids
 Monomers
are fatty acids and
glycerol
 Compounds with > 2:1 H:O ratio
and large numbers of C-H
bonds
 C-H bonds are nonpolar and
hydrophobic; fat molecules
tend to cluster and are insoluble
Lipids
store energy well
because of the C-H bonds
Most lipids have more than
40 carbons
9 kcal of energy for fats
compared to 4 kcal of
energy for carbohydrates.
People
gain weight
because their energy
levels drop as they get
older, but their food
intake doesn’t
Types
of lipids:
– used in cell
membranes; one fatty acid is
replaced with a polar
phosphate head.
Phospholipids
Triglycerides
(Fats, Oils)
Fats – composed of a
backbone glycerol
molecule and 3 fatty
acid chains (long
hydrocarbon chains –
triglyceride).
Fatty
acids can be of
varying lengths; 14-20
carbons are average
Saturated fats – all
carbons on the internal
structure have H+
bonded to them
These
fats (which
come mostly from
animals) tend to be
solid at room temp;
ex: Crisco; tropical
oils (palm and
coconut)
Unsaturated
+
H
fats –
some
are
lacking on internal
carbons and
double bonds are
in its place
fats – more
than one missing H+ and
more than one double bond
Tend to have low melting
point because chains bend
at double bonds.
Usually liquid at room
temperature.
Polyunsaturated
Based on the double bonds,
what kind of fat is this?
Saturated Fats
Unsaturated
Fats
Solid at room
temp.
A. Usually liquid
(except palm &
B. One or more
coconut oil)
double bonds
B. All single
C-C=C-C=C-C-C
bonds
C. Found in Artic
C-C-C-C-C-C-C-C
animals
C. Increases
Cholesterol
A.
Hydrogenating
(adding hydrogen)
unsaturated fats to
make them solid
(peanut butter and
margarine) are just as
unhealthy as
saturated fats
Unhydrogenated Peanut Butter
Animal
fats are
saturated, while most
plant fats are
unsaturated.
Can convert oil into
solid fat through
hydrogenation (adding
hydrogen).
– 4 carbon ring
lipid (ex: cholesterol), used
to make hormones like
testosterone and estrogen
Terpenes – long lipid
chains that contain
pigments (ex: chlorophyll,
rhodopsin, rubber)
Steroids
– 5 carbon
ring head and 2 nonpolar
tails; act as chemical
messengers; used in
muscle contractions, blood
vessel dilation, ovulation,
uterine contraction, blood
clotting, inflammatory
responses; aspirin inhibits
prostaglandin production
Prostaglandins
 Men
need 4-7% body fat
 Women need 9-16% body fat
 Going below these
percentages is harmful since
your body can’t perform all its
normal functions
Low Carb Diets?





Carbs are needed to synthesize glycogen which
are needed for effective workouts
Without glycogen, you cannot burn as much fat
Body uses fuel in this order (Glycogen, Fat,
Muscle)
Low calorie diets make your body burn muscle
which causes a loss in total calorie burning
potential – muscle cells have more mitochondria)
Weight comes off because of lost muscle but
comes back as fat (NOT GOOD)
Good Things About Fat
More
energy than carbs or
proteins
Helps absorb Vitamins A, C,
etc.
Healthy skin
Gives us fatty acids for
growth
The Good – Omega-3 Fats
 Lower
blood
pressure
 Decrease risk of
heart attack
 Protect against
irregular
heartbeats
How much should you eat?
YUM!
 You
should consume 20 to
30% of your total calories from
fat
 No more than 10% should be
saturated fats
Too
much or too little
can be a health risk!
Nucleic Acids
(Information Molecules)
Nucleic
acids are
information storage
devices, and serve as
templates to produce
precise copies of
themselves.
 Nucleic
acids are polymers
made of monomers called
“nucleotides”
 Nucleotide consists of
Sugar (deoxyribose or ribose)
Phosphate
Nitrogen containing “base”
(adenine, guanine, cytosine,
thymine)
ATP
 Adenosine
Triphosphate
Nucleotide derivative (adenine)
Cell battery
Manufactured in the mitochondria
of cell as a result of the
breakdown of glucose
Energy of the molecule is stored
in the bonds that hold the
phosphates together
Pop Quiz
1) What does hydrolysis do?
2) What are the building
blocks of lipids?
3) Why is cellulose difficult to
digest?
4) How do animals store
glucose?
5) “Double helix” describes
what?
6) Phospholipids always
orient so their tails face:
7) How is sucrose
(disaccharide) created from
glucose and galactose (both
monosaccharides)
Proteins
 Proteins
are polymers of amino
acids.
Covalent bond linking two amino
acids = peptide bond.
Proteins composed of one or
more long chains =
polypeptides
Polypeptides composed of
amino acids linked by peptide
bonds.
Amino Acid
Can act as base
(Accept H+)
Amino
Acids Build Proteins
acids – molecules that
contain an amino group (-NH2)
or carboxyl group (-COOH), a
H+, and a functional (R) group
all bonded to a central carbon
Amino acids determine the
shape of the protein
Amino
20
common amino acids in
nature (Make tens of
thousands of proteins in
human)
The functional (side) groups
give the amino acid its
unique chemical properties
and thus the protein
properties
20
Common Amino Acids
grouped into five chemical
classes, based on functional (R)
groups:
Nonpolar amino acids
Polar uncharged amino acids
Ionizable amino acids
Aromatic amino acids
Special-function amino acids
– contain –CH2 or
–CH3 (Hydrophobic)
Nonpolar
uncharged – Contain
O or only –H (Hydrophilic)
Polar
– acid (R groups are negative)
or base groups (R groups = +)
 Ionizable
Aromatic
–
contain
rings with
alternating
single and
double
bonds
 Special
functions
– cause
chaining,
linking, or
bending
of protein
molecule
2
categories of proteins:
Structural – fibrous; muscle
hair, cell markers
Functional – globular;
enzymes, antibodies,
venom, peptide
messengers, globulins,
hormones
Protein Functions
Enzyme
Catalysis - catalase
Defense - antibodies
Transport – cell membranes
Support - cytoskeleton
Motion – cilia, flagella
Regulation – receptor
proteins
Proteins
consist of long
amino acid chains folded into
complex shapes.
Primary Structure – 1o Specific amino acid
sequence; chains;
characteristic of structural
proteins
Structure - 2o Folding of amino acid chain
by hydrogen bonding into
coils (alpha) and pleats
(beta); characteristic of
structural proteins
Motif – variations on
secondary structure; ex: b
barrel, Beta-alpha-beta)
Secondary
Motifs
Water
helps to position
motifs and also helps to fold
nonpolar side groups into
the interior.
Stability of a protein is
influenced by how well its
interior fits together.
Spider silk







Bullet-proof clothing
Wear-resistant lightweight clothing
Ropes, nets, seat belts, parachutes
Rust-free panels on motor vehicles or boats
Biodegradable bottles
Bandages, surgical thread
Artificial tendons or ligaments, supports for weak
blood vessels.
Tertiary
o
3
Structure folded shape due to
hydrophobic
Final
interactions with
water
hydrogen and ionic bonding
between R groups
disulfide bridges.
bonding determined by
primary structure (types of
amino acids and side groups)
Quaternary
o
4 –
Structure When 2 or more
polypeptide chains join to
form a functional protein.
Ex: Hemoglobin is
composed of 2 a chains
and 2 b chains.
Tertiary Structure
Substitution
of amino
acids due to mutations,
can interfere with
protein stability
Characteristic of
functional proteins
o
1
o
2
and
are usually
structural proteins
o
o
3 and 4 are usually
functional (globular)
proteins.
How Proteins Fold
 Normal
cells contain special
proteins (chaperonins) that help
new proteins fold correctly.
Exact workings are
controversial.
Chaperonin deficiencies
(and, therefore, improper
protein folding) may play
role in certain diseases.
How Proteins Unfold
Alteration
of a protein’s
environment may cause
denaturation.
Usually renders protein
biologically inactive.
pH
extremes,
temperature, ionic
concentration (salt) of
protein’s environment
Some denaturation is
reversible; most are
not.
Pop Quiz
1) Term for a “large molecule
made of similar subunits”?
2) Building blocks of proteins?
3) Hair is made of protein. What
category of protein?
4) Which protein structure is not
affected by denaturing heat?
5) What are the monomers of
protein?
Helpful Websites
Kinetics Tutorial
MathemoleSite;
Molecules, Mass
Water and pH
Arizona University
Chemistry Review
Covalent Bonds
pH Tutorial
Maricopa Atoms and
Molecules Review
Water Chemistry
Chemistry of pH
Periodic Table
Animated
Water Tutorial
pH Scale
pH/pOH Game
Functional Groups
Amino Acids
Monosaccharide
Resource
Macromolecules
Protein Explorer
Carbon Facts