STANDARD SET 6. Chemistry of Living Systems

6. Principles of chemistry underlie the functioning of biological systems.

a. Carbon, because of its ability to combine in many ways with itself and other elements, has a central role in the chemistry of living organisms

CARBON

Of the naturally occurring elements, carbon is probably the most important organic element. On the Periodic Table, carbon is the first member of Group IV. Group IV members have four valence electrons, so they can become stable by either losing or gaining four electrons. Other groups will either lose or gain electrons, but with Group IV's flexibility, these atoms, particularly carbon, tend to share electrons.

Sharing electrons forms strong covalent bonds between atoms. Group IV atoms can form four covalent bonds, one for each electron. Remember that electrons have a negative charge. So these electrons repel each other. For the bonds to become stable, they must lie equal distance from each other. This arrangement forms a tetrahedron. A tetrahedron is like a camera tripod, with the legs and camera stand having equal lengths. Of the Group IV atoms, carbon forms the most stable covalent bonds.

Carbon is also unique in that it can form very stable bonds with other carbon atoms. It is this nature that forms the foundation for organic molecules. Proteins, sugars, fats and genetic material is made with a carbon backbone, upon which other elements are attached.

Because carbon has four valence electrons, one in each of the four pairs, it is more willing to share electrons with another atom (rather than grabbing them or giving them up). For example, methane is one atom of carbon bonded to four atoms of hydrogen. This would have the chemical formula, CH₄. When atoms share electrons as they bond together, this is called a covalent bond. Many compounds with covalent (co- = with, together; valent = strength) bonds are not water soluble. Carbon can also form covalent bonds with other atoms of carbon, thus making long, stable chains possible. These are very important to living organisms.

The shape of a molecule of methane is a tetrahedron. The hydrogen nuclei (one proton each) are all “trying” to get as close as possible to all the electrons around the carbon, yet keep as far away as possible from each other (like + and – poles on a magnet). In a tetrahedron, there are four sides, all of which are triangles (in a pyramid, the bottom is square and there are five sides). The hydrogen protons are equally spaced in three dimensions around the carbon.

b. Living organisms are made of molecules consisting largely of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.

Naturally Occurring Elements in the Human Body

Symbol	Element	Atomic Number	% Human Body Weight
O	Oxygen	8	65.0
C	Carbon	6	18.5
H	Hydrogen	1	9.5
N	Nitrogen	7	3.3
Ca	Calcium	20	1.5
P	Phosphorus	15	1.0
K	Potassium	19	0.4
S	Sulfur	16	0.3
Na	Sodium	11	0.2
Cl	Chlorine	17	0.2
Mg	Magnesium	12	0.1

From Cummings et al. Table 2.1, Biology. 2001.

The elements in your body. (Adapted From Cummings et al. Table 2.1, Biology. 2001.)

More than a hundred different elements have been discovered so far. The elements that occur in nature are called the natural elements. Some natural elements are oxygen, calcium, nitrogen, and zinc. Synthetic elements have been made by scientists in the laboratory. When scientists discovered a synthetic element, they had the privilege of naming it. Californium was discovered at the University of Berkeley in California. Plutonium was named after the planet Pluto.

Organic Elements

The organic elements are those elements commonly found in living organisms. They compose the building blocks for our organic molecules, like proteins, sugars, fats, and genetic material. These elements also consist of ions needed for common organic processes, like nerve cells communicating with each other, moving muscles, or releasing adrenaline. The most common organic elements are oxygen, carbon, hydrogen and nitrogen. Together, these atoms form 96.3% of the Human body by weight. The following table shows the most commonly occurring natural elements found in the Human Body.

Organic building blocks
Organic Group	Formula	Compounds
Methyl	—CH3 and —CH2	proteins, carbohydrates, lipids, nucleic acids, etc.
Hydroxyl	—OH	alcohol
Carboxyl	—COOH and —COO^–	proteins, lipids
Amino	—NH2	proteins, amino acids, nucleic acids
Sulfydrl	—SH	some amino acids, Thiols
Phosphate	—PO4	organic phosphates like ATP, DNA, RNA

c. Living organisms have many different kinds of molecules, including small ones, such as water and salt, and very large ones, such as carbohydrates, fats, proteins, and DNA.

water	salt
Carbohydrates	Lipids(fats)
Proteins - Hemoglobin	Nucleic Acids

Organic Groups

As they form organic molecules, elements are commonly arranged in organic groups. There are six common organic groups that for smaller units of organic molecules. These are methyl, hydroxyl, carboxyl, amino, sulfydrl, and phosphate groups. By combing these groups in particular arrangements, common organic molecules are formed.

Organic Molecules

There are four basic groups of organic molecules:

Proteins, Carbohydrates, Lipids, and Nucleic Acids.

These molecules are made by bonding different organic groups to each other in differing orders.

All organic molecules contains methyl groups, and most contain hydroxyl groups.

For example, you can describe the basic amino acid, the molecule that makes proteins, as a molecule that contains a methyl group, an amine group, and a carboxyl group, plus one R-group that varies from amino acid to amino acid. Carbohydrates have 3-6 methyl groups, with about the same number of hydroxyl groups, and maybe containing a carboxyl group. Lipids are strings of methyl groups, with one carboxyl group at one end. Nucleic Acids have alternating methyl and amine groups.

Proteins:

Elements: C, H, O, N, and sometimes S.

Function: Enzymes, structural proteins, storage proteins, transport proteins, hormones, proteins for movement, protection, and toxins.

General Structure

Proteins are made from several amino acids, bonded together. It is the arrangement of the amino acid that forms the primary structure of proteins. The basic amino acid form has a carboxyl group on one end, a methyl group that only has one hydrogen in the middle, and a amino group on the other end. Attached to the methyl group is a R group.

There are 20+ amino acids, each differing only in the composition of the R groups. An R group could be a sulfydrl, another methyl, a string a methyls, rings of carbons, and several other organic groups. Proteins can be either acidic or basic, hydrophilic or hydrophobic. The following table shows 20 amino acids that common in proteins.

Carbohydrates:
Elements: C, H, and O.
Function: Energy, structure
Carbohydrates are sugars and starches. The most basic structure consist of 3-6 carbons, but we are going to concentrate upon sugars that form a either a pentagon ring (5-carbon sugars) or a hexagon ring (6-carbon sugars). These sugars are named pentoses and hexoses respectively. The sufix –oses refers to sugar, and prefix refers to the number of carbons. One corner of the ring has an oxygen, so that one carbon group lies outside of the ring. Attached to each carbon is a hydroxyl group, and a hydrogen. If you said that carbohydrates had a primary structure, akin to proteins, it would be the order of the sugars, the pentoses and the hexoses. The simplest sugars are monosaccharides (mono–: one; –saccaharides: sugar). Among the hexoses, sugars having six carbons, there are glucose, galactose, and fructose. Both glucose and galactose have very similar structures, and only differ in the arrangement of on hydroxyl group on the 4^th carbon. Fructose looks more like glucose than galactose, but it differs from glucose by having a hydroxyl group on the 1^st carbon, with its 2^nd carbon having the double bond with oxygen
Glucose	Galactose	Fructose
Above: Simple diagrams of glucose, galactose, and fructose not showing the hexagon shape.

Lipids:

Elements: C, H, and O.

Function: Storage, cushion, hormones.

Fatty Acids:

Fatty acids are lipids that are made from long chains of methyls. Fatty acids can be either saturated, where the chain only has groups of CH₂, or fatty acids can be unsaturated, where there are one or more CH = CH groups, carbons attached with a double bond to another carbon. Think of the fatty acids as being unsaturated with H, since to form a double bond, two carbons must lose H. So saturated fatty acids are saturated with H, and unsaturated fatty acids have room for more H atoms. At room temperature, saturated fatty acids are waxy solids, and unsaturated fatty acids are liquid. Below are two 18C fatty acids, stearic acid and oleic acid. They differ only in that stearic acid is saturated with H, while oleic acid is an unsaturated fatty acid.

Stearic acid

Common Fatty Acids

Name(Carbon Atoms)	Formula
Saturated
Butyric (4)	CH3(CH2)2COOH
Palmitic (16)	CH3(CH2)14COOH
Stearic (18)	CH3(CH2)16COOH
Unsaturated
Oleic (18)	CH3(CH2)7CH=CH(CH2)7COOH
Linoleic (18)	CH3(CH2)4CH=CHCH2CH=CH (CH2)7COOH

Triglycerides:

Triglycerides, or fats, have the simplest form of all lipids. In plants, triglycerides form the major proportion of lipids in plants. In animal, adipose cells (fat cells) stores triglycerides for future use as energy. Triglycerides are made from three chains of fatty acids, bonded to a pole of glycerol. In the molecular formula below, the R-group represents fatty acids, where they can either be all different, be the same, or only two fatty acids be the same.

Triglyceride

Essential Fatty Acids:

Just as there are essential amino acids that our bodies can not synthesis, there are also essential fatty acids, like linoleic acid, that our body has to get our from food. We can easily make saturated fatty acids and unsaturated fatty acids that have one double bond, but we do not have the proper enzymes to synthesis unsaturated fatty acids that have more than one double bond. These fatty acids are very important to our immune system and to help us regulate our blood pressure, for they are used to make essential compounds, such as prostaglandins. Prostaglandins are a group of organic molecular messengers that changes our blood pressure, open air passages, and cause uterine contraction.

Nucleic Acids:

Elements: C, H, O, and N.

Function: Blueprint for protein synthesis in cells, heredity.

Of the organic molecules, there are fewer nucleic acids, yet they the most unique parts among the organic molecules. Nucleic acids are made from three organic groups, a phosphate group, a pentose sugar, and nitrogen bases. One nucleic acid is bound to another through the phosphate group. Nucleic acids can be divided into two groups, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

There are only three differences between these two nucleic acids. First, RNA is made with the pentose sugar ribose, and DNA is made with the pentose sugar deoxyribose. Second, RNA contains the nitrogen base uracil, and DNA contains the nitrogen base thymine. Third, RNA has only one strand of nucleic acids, while DNA is made from a double strand, wrapping around each other in a double helix. Beyond the pentose sugar, nucleic acids differ in the nitrogen base that they contain. The nitrogen bases can be divided into two groups based upon the shape of the nitrogen base, pyrimidines and purines. The pyrimidines have a hexagon shape, generally made with four carbons and two nitrogens. The pyrimidine cytosine has an amine group attached to the first carbon. Both thymine and uracil has an oxygen in place of the amine group. But thymine has a methyl group attached to the second carbon, where uracil does not. The pyrimidines are bonded to the pentose sugar by the nitrogen that lies at the third position, between the CH and C=O, on the hexagon ring.

The purines have a double-ring shape, with a pentagon attached to one side of a hexagon. Adenine , similar to cytosine, has an amine group attached to the first carbon of the hexagon ring. Guanine, similar to thymine and uracil, has an oxygen in place of the amine group. The purines are bonded to the pentose sugar by the nitrogen on the pentagon ring.

On DNA, and when RNA is being made, RNA synthesis, pyrimidines attach to purines by hydrogen bonds between the nitrogens of the purines, as well as the double-bonded oxygen and the nitrogen on the pyrimidine.

It is the arrangement of the nucleic acids on these large genetic molecules that form the genetic code for living organisms.

Bd glucose

Cholesterol

4 types of Bio-Chemicals

Carbs – Glucose (the sugar in your blood, sucrose (granulated sugar), fructose (in honey, fruits)

Lipids(Fats/Oils) –

Nucleic Acids – DNA/RNA

Proteins -

Note the arrangement of the periodic table: elements are organized into columns by how many electrons they have in their outermost energy levels (for example, H, Li, and Na each have one electron in whichever energy level is “outermost”), and organized into rows by which energy level (1^st, 2^nd, etc.) they’re filling (for example, Li, C, and N all have their first energy level full and are in various stages/numbers of electrons of filling their second level).

For any element, the electrons in the outermost energy level/shell are the most important. These determine an element’s chemical properties – how it will react in a chemical reaction. These important electrons are known as the valence electrons. Know how many valence electrons carbon, oxygen, hydrogen, nitrogen, sodium, and chlorine have.

Consider sodium and chlorine. Sodium is in column I so it has one valence electron. If it could get rid of that one, lonely electron from level 3, then its outer level would be level 2 which is nice and full. Chlorine is in column VII, so it has seven valence electrons, one short of a full outer shell. Thus, it would be more stable if it could grab an electron from somewhere to fill up that one, last spot.

Thus, when sodium and chlorine come together, in an explosive reaction, chlorine grabs sodium’s “unwanted” electron. This forms sodium ions with a +1 electrical charge (extra proton because it lost an electron) and chloride ions with a –1 charge. Chemists would write this as Na + Cl Na⁺ + Cl^–. These positive and negative ions are still strongly attracted to each other, forming ionic bonds, bonds in which one atom grabs electrons from another. When compounds with ionic bonds are put into water, the ions come apart and dissolve in the water.

Water

The shape of a water molecule is also a tetrahedron. Oxygen has six valence electrons and two “holes,” thus can bond with two hydrogens. Therefore, the chemical formula for water is H₂O. Oxygen’s other four valence electrons, in two pairs, are not bonded to any other atoms, thus these are referred to as unshared pairs of electrons. Oxygen shares electrons with hydrogen, but pulls just a little harder on the electrons. The electrons are just a little closer to the oxygen than the hydrogens, so this is called a polar covalent bond. Note that even though the molecule as a whole is electrically neutral (the + and – charges balance), the ends of the molecule where the hydrogen nuclei are (which contain only a proton) have a sort-of positive charge, and the ends of the molecule by the unshared pairs of electrons are sort-of negative. The sort-of positive ends on one water molecule are attracted to the sort-of negative ends on another water molecule. This is called hydrogen bonding. Actually, hydrogen bonding can happen with other molecules besides water as we will see later.

Water is a key ingredient in all life. Cells are 70 to 95% water. About 75% of the Earth's surface is covered with water. Water is the only common substance existing naturally in all three forms: solid, liquid, gas. Water has many unique properties due, in great part, to its hydrogen bonding.

 Water sticks to itself. It forms droplets. It acts like it has a film on top.

 Water sticks to other things; well, at least some other things. Hydrophilic substances like glass, paper, and sugar can mix with or stick to water (yes, on very clean glass, water “sheets” and flows over the glass without beading up). On the other hand, hydrophobic substances like teflon, salad oil, and car wax will not mix with water, and water placed on those surfaces will bead up.

 Water can absorb a lot of heat without changing temperature very much. No, “heat” and “temperature” are not the same thing! For example, suppose you have a Corningware^® or glass pot and an aluminum pot that weigh the same amount (contain the same amount of material). If you would place these two pots on equal burners on the stove, which would get hot faster? Aluminum, right? The Corningware pot can absorb more of the heat from the burner without changing temperature as much. In the summer, in the daytime, lakes and oceans can absorb a lot of heat from the sun, keeping the surrounding air much cooler. At night and/or in the winter, bodies of water will gradually give up their heat, warming the surrounding air. That’s why costal areas tend to have more mild seasonal changes. In deserts, where there is very little water to absorb and retain heat, summer daytime temperatures can be extremely high, yet at night, a person would need a warm jacket, campfire, and/or sleeping bag to keep warm in the 40 to 50° F (5 to 10° C) weather. This property of water is also useful in our bodies: in the summer we can absorb a lot of heat from the sun without overheating too much, and in the winter we don’t immediately freeze when we go outside.

 Ice floats. For most substances, the solid form is more dense than the liquid form and would sink to the bottom of any mixture of the two, but for water, the solid (ice) is less dense. If ice sank, in winter as water froze, it would sink to the bottom of ponds and lakes, thus they would freeze from the bottom up. In spring/summer, only the top few inches would thaw because the solid ice on the bottom would never rise high enough to be warmed by the sun. Thus, it would be impossible for any organisms to live in water.

pH

Even in plain, distilled water, because of the hydrogen bonding, sometimes one of the hydrogen protons from one water molecule “jumps over” to one of the pairs of unshared electrons in another water molecule (leaving its electron behind). Thus ions of H₃O⁺ (hydronium ion) and OH^– (hydroxide ion) are formed. This reaction would be written as 2H₂O  H₃O⁺ + OH^–. Somebody figured out that in one liter of pure, distilled water, there will be 0.0000001 M each of H₃O⁺ (often written as H⁺) and of OH^– present.

Rather than having to write out all that, chemists came up with the concept of pH as a shorthand way to keep track of how much H₃O⁺ is present in a solution. First, the 0.0000001 M is converted to scientific notation, so becomes 1 × 10^–7. Next the exponent or logarithm of that number is found: the logarithm of 1 × 10^–7 is simply –7. Then, since scientists, like other people, don’t like to have to do any more writing than necessary, the negative (–) sign is removed. Based on all of this, pH = –log[H⁺], or pH is equal to the negative logarithm of the hydrogen (hydronium) ion concentration (“[ ]” means “the concentration of”).

f other substances are added, the concentrations of hydrogen (hydronium) and hydroxide ions (notated as [H⁺] and [OH^–]) may change, but pH is always based on the hydrogen ion concentration, [H⁺]. If [H⁺] is greater than 0.0000001 M, (like 0.0001 or 10^–4 so pH = 4), that solution is an acid, and if [H⁺] is less than 0.0000001 M, (like 0.0000000001 or 10^–10 so pH = 10) the solution is a base. Somebody figured out that [H⁺] × [OH^–] always equals 10^–14, so if one increases, the other decreases, proportionately, such that the product of the two will always be 10^–14.

ACIDS & BASES

An acid is a substance which adds H⁺ to a solution. A base is a substance which subtracts H⁺ from or adds OH^– to a solution. A neutral solution has a pH of 7. If the pH of a solution is less than 7 (because [H⁺] is greater than 10^–7) the solution is an acid, and if the pH is greater than 7 (because [H⁺] is less than 10^–7) the solution is a base. Biological substances like lemon juice and vinegar are acids, and both of these have pH values around 3. The hydrochloric acid (HCl) in toilet bowl cleaner and in our stomachs is a strong acid — the pH of stomach acid is between 1 and 3. Lye (NaOH), the main ingredient in many drain-openers, is a strong base, with a pH of 12 to 14, depending on the concentration of the solution. I have heard that the typical pH of our scalp and skin is around 5, slightly acidic, and that pH is best for skin and scalp health and resistance to infection and diseases. Soap and many shampoos are made via a chemical reaction involving lye, and since there is typically a bit of unreacted lye left in them, they are bases (some quite strong bases). Thus, while our skin can secrete chemicals to recover its pH balance following occasional, reasonable use of these products, too-frequent use of these products (shampooing one’s hair on a daily basis, daily showers using soap or detergent bars) can prevent the scalp/skin from maintaining a normal pH, resulting in “dry” (= less healthy) skin and an increased risk of infection. Thus, some shampoo manufacturers add chemicals to their shampoos to lower the pH closer to the skin’s normal of pH 5, and these shampoos are often marketed as “pH-balanced” shampoos. I have heard knowledgeable people, including dermatologists, say that it is better for one’s skin to not take daily showers, or at least to not use soap (just rinse with water) if someone feels that a daily shower is a “must.” (Interestingly, while I have not seen actual scientific studies on this, I have heard/read that our scalp secretes chemicals which help to repel head lice, and the suggestion that the increased incidence of head lice among school children in our country may, in part, be related to the fact that parents are actually keeping their children’s hair “too clean,” thereby preventing the accumulation of an adequate supply of natural repellant on their hair.)

Buffers

A buffer is a substance which minimizes the change in pH or [H⁺]. Different buffers work best at different pH ranges. Notice that what’s happening here is that a buffer protects from too great of a change in pH. By no means is this anything like the equivalent of lowering/minimizing the pH, which would have the effect of creating a strong acid. The concept of pH and the utilization of buffers to maintain “normal” pH ranges are important in our bodies and in other branches of in biology. For example, an enzyme called pepsin digests protein in our stomachs, but must have an acid environment to function (most of the enzymes in our bodies only function within certain pH ranges). Not all of the food we eat is acidic, and might destroy (or neutralize) the normal stomach pH, thus making the pepsin ineffective, unable to digest dietary protein. To prevent this from happening, the buffers in our stomach keep the pH fairly constant, within a range of about pH 1 to 3. However, antacids such as Tums^® or Rolaids^® are so “strong” that they overwhelm the person’s stomach’s buffers’ ability to function properly, drastically changing the pH of the stomach contents, and therefore, pepsin’s ability to digest the protein in one’s diet. Calcium, by the way, is absorbed better into one’s body if the stomach contents are acidic, thus antacids also interfere with our bodies’ ability to properly absorb calcium. To properly absorb dietary calcium, it should be consumed along with acidic or slightly acidic substances (such as milk or orange juice), and not mixed in with antacids. While there may be legitimate uses for antacids (such as when a doctor prescribes them to assist in treating ulcers), frequent, “casual” use of antacids may actually stimulate the production of more stomach acid as the user’s system struggles to overcome them and return the body to normal. As another example, our blood must remain very close to around pH 7.4, and if it deviates too much, a person could get very sick or die. Yet, when we transport carbon dioxide from our cells to our lungs, it turns into carbonic acid in the deoxygenated blood. Thus, if it weren’t for buffers, our blood would be a drastically different pH depending on how much carbon dioxide was dissolved in it.

References:

SAS Chem – Elements

http://www.starsandseas.com/SAS%20OrgChem/SASElements.htm

Library of PDB files for molecules alphabetically

http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html

Organic Building Blocks Lab

Background - Organic Molecules

There are four basic groups of organic molecules: Proteins, Carbohydrates, Lipids, and Nucleic Acids. These molecules are made by bonding different organic groups to each other in differing orders.

All organic molecules contains methyl groups, and most contain hydroxyl groups. For example, you can describe the basic amino acid, the molecule that makes proteins, as a molecule that contains a methyl group, an amine group, and a carboxyl group, plus one R-group that varies from amino acid to amino acid. Carbohydrates have 3-6 methyl groups, with about the same number of hydroxyl groups, and maybe containing a carboxyl group. Lipids are strings of methyl groups, with one carboxyl group at one end. Nucleic Acids have alternating methyl and amine groups.

Organic building blocks
Organic Group	Formula	Compounds
1. Methyl	—CH3 and —CH2	proteins, carbohydrates, lipids, nucleic acids, etc.
2. Hydroxyl	—OH	alcohol
3. Carboxyl	—COOH and —COO^–	proteins, lipids
4. Amino	—NH2	proteins, amino acids, nucleic acids
5.:Sulfydrl	—SH	some amino acids, Thiols
6. Phosphate	—PO4	organic phosphates like ATP, DNA, RNA

For this lab you are going to use the molecular modeling kits to investigate how many ways a group of Carbon atoms may be bonded together, what the 6 organic building blocks are, what the essential components of organic compounds are, and what distinguishes the 4 main groups of organic compounds from each other.

STEP 1: Explore Carbon Bonding

Bond 5 Carbon atoms to each other as many ways as you can. You may use single, double, and triple bonds.

DRAW each configuration in your LAB NOTES.

STEP 2: BUILDING BLOCK CREATION

Create _____ Methyl, ____ Hydroxyl, ____ Carboxyl, ____ Amino, ____ Sulfydrl, and ____ Phosphate structures.

DRAW a picture of one molecule for each of these in your LAB NOTES.

STEP 3: BUILD AN ORGANIC MOLECULE

Using the structures created in STEP 2 build a _________________ molecule.

DRAW a picture of it in your LAB NOTES.

STEP 4: BUILD ANOTHER TYPE OF ORGANIC MOLECULE

Using the remaining building blocks build a __________________molecule.

DRAW a picture of it in your LAB NOTES.

STEP 5: TRADE or SWAP TO BUILD YOUR LAST ORGANIC MOLECULE

Now look at the remaining structures you have determine what you need to build a ___________________ molecule. On the bid cards write what structure you need and which one you would trade (you don’t need it) and pass the card to the next group to see if you can arrange a trade to complete your molecule.

DRAW the resulting molecule in your LAB NOTES. Raise your hand to show rest of class your final molecules.

LAB QUESTIONS:

1. How many configurations of the Carbon atoms did you make?

2. What are the 3 most common elements used in the models you built for this exercise?

3. Based on what you already know about acids and bases, are alcohols typically acids or bases?

4. Could you create any of these organic molecules without Carbon? YES/NO

5. If yes to #4, list two.

6. Could you create any of these organic molecules without Oxygen?

7. If yes to #6, list two.

8. Could you create any of these organic molecules without Hydrogen?

9. If yes to #8, list two.

10. Do you understand organic compounds better now?

5. CARBOHYDRATES

Glucose	Galactose	Fructose