Organic Chemistry Unit 3 Objectives : Identify the monomers that form each of the major macromolecules. Compare and contrast dehydration synthesis (or a condensation reaction) to hydrolysis. Investigate (research) and explain the role of nutrients in health.
Organic Chemistry Unit 3
Identify the monomers that form each of the major macromolecules.
Compare and contrast dehydration synthesis (or a condensation
reaction) to hydrolysis.
Investigate (research) and explain the role of nutrients in health.
Differentiate between the major types of organic compounds.
Describe Carbon’s unique qualities and bonding patterns.
Describe the types, purpose and function of carbohydrates, lipids,
proteins, and nucleic acids in the body
Explain how organic substances are named
Research and report on various amino acids, etc.
Explain how heat, pH, etc. can affect the structure and function of
Evaluate the benefits/risks of various nutrients or their deficiencies
Compare/contrast hydrocarbons with carbohydrates
Functional (R) groups * monomers * alcohol * amine * RNA *
Carboxylgroup * polymer * macromolecule * nucleotide *
Hydrolysis * isomer * monosaccharide * fatty acid *
Disaccharide * polysaccharide * peptide bond * inorganic *
condensation reaction or dehydration synthesis * lipid *
Carbohydrate * protein * amino acid * saturated fat * DNA *
Unsaturated fat * steroids/sterols* cholesterol *wax*
Triglyceride * phospholipid * nucleic acid * organic chemistry*
simple sugar * complex sugar * glycogen* starch *
Enzyme * Sickle cell anemia * polypeptide * gene * inorganic *
Conformation * denaturation * pH * organic * hydrocarbons *
Glycolipid * glycoprotein * diabetes * hypoglycemia *
Hydrogenated or “trans” fats * omega-3 and omega-6 fatty acids *
adipose * catalyst* arteriosclerosis * prostaglandins * synthetic
A whole area of scientific study surrounds the study of carbon.
Carbonis unique in that it has 4 valence electrons that allow it to bond
singly with 4 other elements or form DOUBLE or even TRIPLE bonds. Although many molecules are bent, like the approx. 104.5 degree
bend of a water molecule, carbon compounds can form chains,
branched chains, or even carbon rings.
Carbon can be surrounded by 4 hydrogen atoms to form methane.
Two carbons singly bonded together and surrounded by hydrogen
atoms form ethane. Notice the “- ane” ending? This signifies that only
SINGLE bonding is occurring between carbon atoms. When ANY
double bond occurs anywhere between carbons in a carbon compound,
an “- ene” suffix is usually added. Triple bonded compounds receive a
“- yne” suffix.
Common prefixes by number of carbons in a compound:
Carbohydrates, lipids, proteins, etc. often have specific carbon
combinations referred to as “R”-groups. These “R”-groups are also
known as “functional groups” or reactive groups. The differences in the
various “R”-groups is often what makes one carbon compound different
from the next. Note: “R” groups are not always carbon combinations.
Some “hints” are given as to what is present in an organic compound
by its name.
If “NH2” is present, it’s an amine. If “OH” is bonded to C, it’s an alcohol.
If there is a double bonded “O” and an “OH” bonded to a C, it’s a
carboxylicacid. (Amino acids have an amine and a carboxylic acid.)
Amides have a dbl. bonded O and NH2 bound to a C.
If there is a benzene ring (a 6 carbon ring with every other carbon in a
double bond to the next), it’s a phenyl group.
If a group 7 halogen (F, Cl, Br, I), replaces an “H”, it’s an alkyl halide.
An “O” between 2 “C”s is an ether.
A single “C” with a dbl. bonded “O” and an “H” is an aldehyde. It’s a
ketone if the C has a double bonded “O” and joins to 2 other “C”s.
Esters have a C with a single bond to 1 “O” and a dbl. bond to another
“Organic” refers to something living or once living (“organisms”).
Although, in everyday life, “organic” can mean “grown naturally”, without
synthetic (man-made) chemicals. “Inorganic” refers to a never living
substance, like a mineral or a synthetic substance.
Because living things are made primarily of compounds containing
carbon, organic chemistry is also referred to as the chemistry of carbon
The 4 major organic compounds are:
Each of these has single units, or building blocks, called monomers.
Monomers may link to form more complex polymers (many units).
Carbohydrates get their name from the fact that they are composed
of Carbon, Hydrogen, and Oxygen. These usually exist in a 1:2:1 ratio,
also written as CnH2nOn or Cx(H2O)y. On the other hand, things made
primarily of just hydrogen and carbon are called hydrocarbons. Ex:
petroleum oil, natural gas, and coal (All of these developed after
organic materials were subjected to heat and pressure for long time
periods so they lost most of their oxygen atoms.)
The monomer of a carbohydrate is a monosaccharide. (“Saccharum”
means “sweet” in Latin.) These units usually consist of 3 to 7 carbons.
These are often referred to as “simple sugars’.
There are 3 monosaccharide isomers with the formula C6H12O6.
They are: glucose (blood sugar, etc.), fructose (fruit sugar), and
Glucose: Fructose: Galactose:
Simple carbohydrates, such as these, are usually referred to as
Sugars or saccharides. Notice that most sugars have an “-ose” ending
to their names.
Two monosaccharides can join to form disaccharides via a dehydration
reaction (water is removed, an “H” from 1 monosaccharide joins with an “OH” of
another). If 2 to 10 monosaccharides join, they are often referred to as
oligosaccharides. More than 10 monosaccharides join to form
Hydrolysis (breaking of water) can add a water molecule to a disaccharide or
larger group to split off a monosaccharide.
Maltose (grain sugar) and sucrose (table sugar) are both disaccharides.
Hydrolysis breaks maltose into 2 glucose monomers and sucrose
into glucose and fructose.
Animals produce the disaccharide, lactose, in their milk. The enzyme
lactase allows us to digest milk. However, if the tips of intestinal villi
have been irritated or damaged, the cells that make lactase may not
function. This frequently happens with hidden food allergies, like
gluten intolerance. Occasionally, if the hidden allergen is strictly
avoided, these cells heal and milk can be better tolerated in the diet.
Polysaccharides are often used to store carbohydrates for later energy
use. Starch (a glucose polymer) is an energy storage form for plants.
Glycogen, in our muscles and liver, is a storage form of carbohydrates
used by animals. (Anything with a “glyco-” means the substance
Cellulose is a polysaccharide that forms the cell walls of plants but is
not used for energy. It is part of wood, paper, cotton, etc. Cows and
termites can digest cellulose due to bacteria specific to their intestines,
we cannot. Cellulose acts as roughage, or fiber, in our diets.
In general, carbohydrates are the most abundant organic
components of plants. And plants, at least indirectly, are the main
source of carbohydrates in our diets.
Carbohydrates can form complexes with proteins, such as
glucosamine, which is needed for joint health and is a component of
heparin, which prevents blood from clotting.
Carbohydrates can form complexes with lipids. Glycolipids, along
with glycoproteins, are associated with the cell membrane and its ability
to interact with other cells and invading viruses or bacteria. These
glycolipids and glycoproteins are part of the cell determinants that give
you your “A”, “B”, “AB”, or “O” blood type.
Some antibiotics (anti - against, bio - life), such as streptomycin,
neomycin, and gentamicin are amino (protein related) sugars that
usually work even against bacteria resistant to penicillin.
It is also interesting that the commercial synthesis of vitamin C starts
with a sugar, L- sorbose (L and R are used to indicate left and right
“handed” or “rotary” molecules). Vitamin C appears very similar to
glucose. In fact, restricting carbohydrates in cancer patients’ diets
while administering high doses of vitamin C can trick cancer cells into
absorbing vitamin C instead of glucose. Cancer feeds on glucose but
can not use vitamin C which then helps destroy these cells. (Note:
Cancer cells have 24x more glucose receptors than normal cells.)
Vitamin C also blocks an enzyme from turning glucose into sorbitol in
the body. Sorbitol is also in many diet foods. It accumulates in the
nerves, eyes, and kidneys possibly causing the damage found there in
diabetics. Many disorders can occur if the body does not regulate
sugar properly. These include diabetes (high blood sugar) and
hypoglycemia (low blood sugar), also referred to as hyperinsulinemia
Lipids (Greek “lipos” means fat) are very similar to carbohydrates but
tend to have fewer oxygen molecules in proportion to carbon and hydrogen
molecules. This is also why fats tend to release 9 Kilocalories per gram of
energy versus 4 Kcal per gram from carbohydrates. (Fats are more energy
dense.) While simple sugars usually dissolve readily in water, complex
carbohydrates and most fats do not.
Fatty acids are “sort of” the monomers for lipids. Fatty acids can have 100%
single bonds between carbons to form saturated fats. If there are any double
bonds, the fat is unsaturated. A single double-bonded fat is sometimes called
monounsaturated (“mono-” = one). Whereas fats with more than 1 double bond
are called polyunsaturated (poly = many). Double bonds usually only occur
after the 9th C.
Saturatedfats tend to be solids at room temperature (Ex: butter).
Polyunsaturated fats tend to be liquid at room temperature. (Ex: vegetable oils)
Hydrogenatedfats, or transfats, are polyunsaturated fats that are
heated to high temperatures and forced to link to hydrogens to saturate
them to a point that they are usually semisolid or solid at room temperature.
An example of a hydrogenated fat is margarine, made from corn oil.
Unfortunately, forced hydrogenation changes cis - form double bonds
to an unnatural trans – form (hence “trans” fats) in those double bonds
that did not react during the hydrogenation process. (Only partial
hydrogenation is performed because total hydrogenation makes foods
hard and brittle.) These are suspected culprits in cell membrane
(bi-lipid layer) problems and heart disease (carbohydrates are also
So why are partially hydrogenated oils used? Because
polyunsaturated oils tend to oxidize easily which makes them go bad
(they become rancid).
“LEO the lion says GERrrrrrr.”
(Loss of electrons is oxidation and Gain of electrons is reduction)
(Oxidation is loss and reduction is gain of an electron)
Omega-3 fatty acids have a double bond at the third to last Carbon.
They are found in cold water fish and certain plants. These are
believed to be important for heart health, autoimmune diseases, skin
disorders, attention deficit disorder, and rheumatoid arthritis.
DHA (docosahexaenoic acid) is an omega-3 fatty acid EXTREMELY
important to brain health. It is part of the gray matter of the brain and
retinal tissue of the eye. It is found in breast milk but was only fairly
recently added to baby formulas when it was found that breast-fed
babies tended to have higher IQs than bottle-fed babies.
Omega-6 fatty acids are also important to life but are usually in too
high of a ratio to omega-3’s in the American diet. Many common
vegetable oils contain omega-6’s. Corn oil is an excellent example. It
is pervasive in processed food.
Triglycerides, more recently referred to as triacylglycerols, consist of
a 3 carbon alcohol (an alcohol is an “OH” group), known as glycerol,
with 3 long chain fatty acids attached. Triglycerides are a natural
part of our body’s chemistry, but like cholesterol, people worry about
their heart health when they get to too high of levels. Although these
are fats, their blood levels seem to rise more when our diets are high
in carbohydrates rather than fats. Decreasing carbohydrates seems to
reduce triglyceride levels.
Sterols (the “-ol” suffix indicates an alcohol is present) have 4 linked
carbon rings. These include some very important biological
substances, such as: Vitamin D (essential to bone development and
maintenance), cortisol (our body’s natural pain killer, but harmful at
high levels for longer periods of time), bile acids, and cholesterol.
Cholesterol isn’t such a bad guy. It is needed to produce
testosterone, estrogen, etc. It acts as a band-aid when tiny tears occur
in blood vessels. So why the bad reputation?
High cholesterol has been linked to arteriosclerosis (hardening of the arteries)
and atherosclerosis (plaque build-up) and to heart attacks and strokes when
build-ups of cholesterol (plaque) break away and plug a blood vessel to the
heart or head. Gallstones can also form due to cholesterol deposits in the liver
and gall bladder. Our liver makes cholesterol but we also eat it in our diets.
Cholesterol is often referred to as HDL (high density lipoproteins), LDL,
(low density lipoproteins) and VLDL (very low density lipoproteins).
HDL is considered “good” cholesterol because it carries lipids from the
tissues to the liver where it is excreted from the body. LDL (bad
cholesterol) has large and small molecules. We now know only one of
these tends to carry lipids from the liver to the tissues or blood vessels
where it can be deposited. The other is more like HDL. High blood sugar binds
to LDL and prevents it from binding to liver sites that would normally shut down
cholesterol production (biofeedback)2. VLDL is considered “bad”.
Although high cholesterol levels can be associated with heart
attacks, many studies now show that LOW cholesterol may be a more
serious health problem. And, C– reactive protein and homocysteine
(take B6, B12, and folic acid) are better indicators of impending heart
attack or stroke.
2 Energy Times, July/Aug. 2006, p.34 “Trouble From Head to Toe”, by Karyn Maier
It makes sense that if CRP (C – reactive protein) is high, cholesterol
(our plaque forming band-aid) will also be high. Cholesterol is part of
our body’s response to inflammation and/or illness. CRP indicates
inflammation is in the body. The cause of high cholesterol is NOT a
deficiency of lipitor or other cholesterol drugs (which carry warnings
that they may cause liver problems – the very organ that needs to be in
good health in order to properly control cholesterol). So, we need to
look for the cause of inflammation in the body or poor function of the
Waxes are fatty acids that form a relatively hard, water repellant
covering on feathers, leaves, skin, etc.
Prostaglandins are a group of lipids that can affect: heart rate, blood
pressure and clotting, allergic responses, fertility, fever, inflammation.
While some prostaglandins reduce inflammation, others cause it.
Aspirin blocks the formation of pain inducing prostaglandins from
arachidonic acid (some foods are high in this). This is probably how it
also reduces fever.
Phospholipids, or phosphatides, include lecithin (important for
cholesterol control due to its choline content and for blood sugar control
due to its inositol content), phosphatidylserine (needed for brain
health/memory), and cephalins. Phospholipids are an extremely
important part of cell membranes (the lipid bi-layers). (Note: saturated
fat is low in choline which allows an increase in fat in the liver.
Increasing choline helps the liver.)
Soaps, ironically, are fat based. But “like dissolves like”, so a non-
polar substance is needed to dissolve fats, which are non-polar.
Extremely low fat diets can be dangerous. Fat is required in the diet
to absorb vitamins A (skin and eye health), D (bone and teeth health),
E (great anti-oxidant), and K (important for normal blood clotting). Fat
makes up the myelin sheath around our nerves. Disorders such as
multiple sclerosis occur if myelin is damaged or destroyed. Too little
fat in the diet of very restricted caloric diets can also affect the female
hormonal cycles. And, don’t forget, our brains are mostly fat!
Certain fatty acids, like caprylic acid and lauric acid (coconut oil)
have anti-fungal (Candida) properties. Linoleic and linolenic acids are
needed to prevent scaliness of the skin.
You are what you eat. The types of fat in our diets affect how supple
our cell membranes are, how healthy our brain is, and even our fat
stores (adipose) themselves. For example, the melting point of dog fat
(pretty gross, isn’t it) can be raised from 20 degrees Celsius to 40 deg. C.
by feeding them mutton tallow or it can be lowered from 20 degrees
Celsius to 0 deg. C. by feeding them linseed oil. Hog producers don’t
like to feed the swine too much liquid fat (oil) because their fat becomes
too soft to make lard. But beware! “A diet high in carbohydrate has a
‘hardening’ effect… 1 ” forming fats with a higher melting point. This
can have the same impact as large amounts of “bad” fats with the
additional side effect of higher insulin levels disturbing our health.
Carbs. are readily converted to fat in the body. Think: triglycerol)
People storing fat in their mid-section tend to have high insulin levels
due to higher carb. intake.
1 Practical Physiological Chemistry by Hawk and Bergeim, eleventh addition, p.783
The monomers of proteins are amino acids. Like carbohydrates and
lipids, they are primarily composed of C. H. O, but also contain nitrogen
and occasionally sulfur.
Amino acids link via dehydration synthesis (removal of 2 H’s and an
Oxygen) a.k.a. a condensation reaction to form dipeptides (2 amino
acids) or polypeptides. Proteins consist of 1 or more polypeptides.
The bonds between amino acids are called peptidebonds.
There are 20 amino acids used in protein synthesis, each with the
characteristic amine group (NH2) on one end and a carboxylgroup
(COOH, a carboxylic acid) on the other. Of these 20 amino acids, some
can be made by the body and are considered “nonessential” in the diet,
but the rest are “essential” and must be gotten from our food.
While most of the amino acids are neutral, some are charged. It is
the sequence of amino acids that makes each protein unique. And it is
the proteins we make that give us our characteristics.
Proteins fold into specific shapes called conformations. The protein
must be in its correct shape in order to function properly in the body. A
protein can be unfolded, or denatured by temperature changes (Ex:
excess heat), pH changes, or certain chemical treatments (such as
formaldehyde). A protein can also take on the wrong shape if an
incorrect amino acid is substituted. In sickle cell anemia, a charged
amino acid is substituted for a neutral a.a. and this causes the protein
to fold incorrectly on itself. This “sickles” the cells which then get stuck
in blood vessels/capillaries in the organs. Areas suffer from lack of
oxygen and that causes damage, pain, and a shorter life span.
Proteins not only form most of the structures of the body, but also
form hair, nails, antibodies for our immune system, etc. They also form
enzymes of many types (enzyme names usually have an –ase ending),
hormones, and catalysts (enzymes that speed up or lower the energy
needed for a reaction without becoming part of the reaction itself).
Again, pH (acidity) and temp. can affect the function of enzymes.
Essential Amino Acids include:
Isoleucine, leucine, lysine (this has a positively charged R group),
methionine, phenylalanine, threonine, tryptophan, and valine
(Children also require arginine and histidine)
“Nonessential” Amino Acids include:
Alanine, arginine (positive charge), asparagine, aspartic acid
(negative charge), cysteine, glutamine, glutamic acid (negative charge),
glycine, histidine (positive charge), proline, serine, tyrosine
Glycine is the most fundamental in structure:
H The “H” on the left is replaced by different “R” groups for other amino acids. On dietary
H – C – COO – proteins, “complete” means all aminoacids
are present. Note: positive a.a.’s are bases.
There are 2 types of nucleic acids:
These are polymers of nucleotidemonomers.
Nucleotides consist of:
DNA forms a double helix with hydrogen bonds holding bases together
(C to G and A to T) as the “rungs” of the twisted ladder. Deoxyribose
and phosphate make the “ladder” rails. Nucleotide triplets code for
amino acids. A sequence coding for a polypeptide is a gene.
RNA is single stranded, uses ribose as its sugar, and comes in several
shapes and forms. RNA can even act as an enzyme.