Organic Chemistry Unit 3Objectives:

• 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 proteins.

• Evaluate the benefits/risks of various nutrients or their deficiencies• Compare/contrast hydrocarbons with carbohydrates

Vocabulary:Functional (R) groups * monomers * alcohol * amine * RNA *

Carboxyl group * 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.Carbon is 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:1 meth -2 eth -3 prop -4 but -

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. For example: 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 carboxylic acid. (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 aketone 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:1) Carbohydrates2) Lipids3) Proteins4) Nucleic Acids

Each of these has single units, or building blocks, called monomers. Monomers may link to form more complex polymers (many units).

Carbohydrates: 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 galactose.

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 polysaccharides.

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 contains sugars/carbohydrates.)

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: 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. Saturated fats tend to be solids at room temperature (Ex: butter). Polyunsaturated fats tend to be liquid at room temperature. (Ex: vegetable

oils) Hydrogenated fats, or trans fats, 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 suspect).

So why are partially hydrogenated oils used? Because polyunsaturated oils tend to oxidize easily which makes them go bad (they become rancid).

Remember: “LEO the lion says GERrrrrrr.”(Loss of electrons is oxidation and Gain of electrons is reduction)“Oil Rig”(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 liver.Other Lipids: 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 littlefat 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

Protein: 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 peptide bonds. There are 20 amino acids used in protein synthesis, each with the

characteristic amine group (NH2) on one end and a carboxyl group (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 amino acids

are present. Note: positive a.a.’s are bases.

NH3+

Nucleic Acids:

There are 2 types of nucleic acids:

1) Deoxyribonucleic acid (DNA)

2) Ribonucleic acid (RNA)

These are polymers of nucleotide monomers.

Nucleotides consist of:

1) a 5 carbon sugar (ribose or deoxyribose)

2) at least one phosphate group (PO4)

3) a nitrogenous base (cytosine, guanine, adenine, thymine OR uracil)

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.