Still, why is it important to study atoms, and molecules, and biochemistry in general? Permit me to give you several reasons why you should have a good understanding of biochemistry. First, we study these molecules because they are what make up all living things. So far in your study of biology, you have learned that cells are made of smaller structures including organelles. Yet cellular structures such as organelles are not the smallest bits of matter. These are made of smaller structures called molecules and molecules are made of smaller structures called atoms. So, we study atoms and molecules because that is the ‘stuff of which we are made.' Secondly, heart disease is the number one killer in the U.S. Prevention of this disease takes several paths. I am sure that you have heard of cholesterol, saturated fats, and unsaturated fats. They are as close to you as the nutrition label on the side of your food container. While we will study heart disease in greater detail at a later time, at this point we need to understand these molecules. Thirdly, cancer is the second killer of people in the U.S. One of the top three cancers is colon/rectal cancer. We can reduce our chance of getting this cancer type by eating fiber. Take a stroll down the cereal aisle of your local grocery store. Fiber is promoted everywhere. Lastly, I have always been amazed at how consumers are taken in for large sums of money for fad foods, diets, and medicines. It seems that someone is always discovering a new diet, or plant, or some such thing that will cure everyone. I recently received a tape that extolled the virtues of blue green algae. This tape claimed that it would cure many things, including behavior problems in children. Don't get me wrong! I am not saying that all new products are bogus. However, a basic understanding of biochemistry and the scientific method of research would go a long way in saving people lots of money.
Is it easy to study biochemistry? For many people, the answer is, "No." Is it beneficial to study biochemistry? Absolutely!
1. Atoms: What is an element? What elements are most abundant in living things? What is an atom? What are the parts of an atom and the charge on each?
Elements are the most simple form of matter. All matter is made of one or more elements linked together. Elements are the "kinds" of matter. Gold, silver, carbon, oxygen, and nitrogen are elements. The most common elements in living things are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. Elements are represented by either a single letter or two letters. You can remember these biologically important elements by saying their atomic symbols: CHNOPS.
The Greeks argued the question of the "cut ability" of matter. Some argued that it could be cut into infinitely smaller and smaller pieces. Others argued that there is a limit to which matter could be cut. The latter group was correct. An atom is the smallest "piece" of an element. Atoms are the "counting pieces" of the "stuff" called an element.
Atoms are made of positively charged particles called protons, neutral particles called neutrons, and negatively charged particles called electrons. The protons and neutrons are found in the core or nucleus of the atom and the electrons orbit the nucleus.
2. What is atomic number? Mass number? Sodium has an atomic number of 11 and a mass number of 23. How many protons, neutrons, and electrons are in an electrically neutral atom of sodium?
An element's atomic number is the number of protons in its nucleus. If you change the number of protons in an atom, it is a different element. (Kids, don't try this at home. It takes a nuclear reactor to do so.)
The mass number of an element is the number of protons and neutrons.
Number of neutrons = Mass number (Protons and Neutrons) - Atomic Number (Protons)
Since sodium has 11 protons, it has 23 - 11 = 12 neutrons, and 11 electrons. (The number of electrons is equal to the number of protons in a neutral atom.)
3. What is an isotope? How are they important?
Isotopes are atoms of an element that have different numbers of neutrons. For example, I am sure that you have heard of carbon-14 dating. (Although it has nothing to do with going to the movies with someone that you like.) Carbon has an atomic number of six. Each atom, therefore, has six protons. Most carbon atoms have a mass number of 12 and, therefore, six neutrons. Some carbon atoms have eight neutrons. This gives the atom a mass number of 14 rather than 12. Many isotopes are radioactive. In the case of carbon-14, it is used to age specimens that are up to 14,000 years old. Living organisms take in carbon, some of which is radioactive. As long as they are alive, the ratio of carbon-12 to carbon-14 is constant. However, once the organism dies, the carbon-14 decomposes (this is radioactivity) to carbon-12. The ratio of these elements is used to determine the specimen's age.
Isotopes are also important in medicine. X-ray machines use isotopes. Doctors also use radioactive substances ingested or injected into the body to image internal organs.
Radioactive isotopes are also used by ecologists to trace the movement of materials in the environment.
4. How many electrons can the first energy shell hold? The second? The third? How many electrons are in each shell of a sodium atom?
The protons and neutrons of an element are found in the nucleus. The
electrons are in motion around the nucleus. It's exciting to study the
history of our understanding of the atom. Our models of the atom have changed
as we have gained better insight into the atom. The current model states
that electrons are found in shells at varying distances from the nucleus
given by the table:
| Electron Shell | Number of Electrons |
| 1 | 2 |
| 2 | 8 |
| 3 | 8 (when it is the outermost shell.) |
Chemical bonds: Why in the world do we talk about electron shells? The answer is that atoms are rarely found by themselves in nature. Usually they are linked to other atoms by chemical bonds. So why do atoms bond together? The answer is that they "want" to have their outer electron shell filled. To complete this shell they may give off an electron or electrons, they may gain an electron or electrons, or they may share electrons. In doing so, chemical bonds are formed.
5. What is a compound? What is a molecule? What is the relationship between a compound and a molecule?
Pure elements are rare in nature. Often, atoms of different elements are joined together into molecules of a compound. Compounds are substances that are made of two or more elements joined together. The individual "pieces" of the compound are molecules. Molecules are to compounds as atoms are to elements.
6. What is an ion? An ionic bond?
Atoms are stable if: - all electrons are at their lowest possible shell, and - the outermost shell (the valence shell) is filled.
If an atom has only one or two electrons in its outermost shell, it may "donate" that electron to another atom or molecule. Its outer shell becomes filled this way. Remember sodium discussed above? It has one electron in the outermost shell. To complete this shell, it would either have to gain seven electrons or lose one. It loses one to become an atom with a charge of +1.
Ions are charged atoms.
Another way that an atom can become more stable is to "snitch" an electron or so from somewhere else. Chlorine has an atomic number of 17. It, therefore, has 2 electrons in the first shell, 8 in the second, and 7 in the third. Chlorine gains an electron to have a charge of -1.
You know that unlike charges attract. Sodium and chlorine ions will be attracted to one another to form sodium chloride (NaCl) -- table salt.
7. What is a covalent bond? On page 38, you also will also a representation of a glucose molecule. Copy this into your notes and draw all bonds among all molecules. Number the covalent bonds on this molecule. Do this by writing consecutive numbers on each bond. How many are there?
I have already mentioned that atoms can donate or snitch electrons to have their outer electron shell filled. In doing so, they become ions. The third way to fill the outer shell is to share elections. A covalent bond is one formed when atoms share electrons. As you look through this chapter, you will see a variety of molecules drawn. Covalent bonds are represented by "sticks" between the atomic symbols. O=O represents a double bond (four shared electrons) between two oxygen atoms. If you draw all the bonds in a glucose molecule, you will count 24 bonds among all the atoms of carbon, hydrogen, and oxygen.
8. Look at some of the molecules that are drawn in Chapter 3. What is the maximum number of covalent bonds formed by an atom of H? O? N? C?
As before, look at the "sticks" between the atoms. Hydrogen always (and only) forms one covalent bond. Oxygen always (and only) forms two. Nitrogen forms three. Carbon forms four.
.>MEMORY TIP< To remember the number of bonds, HONC. (Pronounce it.) You have one, two, three, and four covalent bonds on hydrogen, oxygen, nitrogen, and carbon.
Most of the time that two atoms form a covalent bond, the elections are not shared equally. This creates a partial positive and a partial negative region around the atoms. The partial positive region of one atom is attracted to a partial negative region of another atom. These attractions hold one molecule to another or others. A hydrogen bond is formed between a hydrogen atom and usually either an oxygen or nitrogen atom. These very weak bonds hold adjacent atoms together. For example, water molecules are held to one another by hydrogen bonds. Hydrogen bonds also hold the two "halves" of a DNA molecule together.
1. What is meant by the term, "carbon backbone?" What is a functional group? Copy these into your notebook.
To understand this analogy, consider your backbone. The vertebrae look alike (at first glance) and are linked together, one after another, to form your backbone. It serves the purpose of supporting the upper half of your body. In addition, other "things" attach to this backbone, The ribs attach to it just like the carbon atoms link together. This carbon backbone is what makes these molecules the same.
Just like your backbone, carbon atoms form long chains. Each carbon
atom can form four covalent bonds and they can bond to one another. This
is a carbon backbone. Other "things" attach to it. These are the functional
groups. Functional groups are small groups of molecules that are found
attached to a carbon backbone in living things. These functional groups is what make these molecules different from one another. Spend some time looking
at the molecules in this chapter. Can you recognize these functional groups
when they make up larger molecules? You should know these functional groups:
| Functional Group Name | Chemical Structure | Found in . . . |
| Hydroxyl | -OH | Sugars, alcohols |
| Aldehyde | carbon-oxygen double bond
at the end of a molecule |
Sugars |
| Ketone | carbon-oxygen double bond
in the middle of a molecule |
Sugars |
| Carboxyl | -COOH | Sugars, Fatty acids, Amino acids |
| Amino | -NH2 | Amino acids |
| Phosphate | -PO4 | DNA, RNA, ATP |
2. Carbohydrates: What is a carbohydrate? Be able to recognize drawings of different types of carbohydrates.
Sugars, starches, and "fiber" are examples of carbohydrates. What they all have in common is that they are either a single sugar, or made of sugars linked together like beads in a chain. The name tells you their chemical composition. "Carbo" is short for carbon (C) and "hydrate" is short for water (H2O.) (You have seen this suffix in the word dehydrated.) So, the general chemical formula for carbohydrates is CH2O.
3. What are monosaccharides? Name several. Draw a glucose molecule into your notes. For what functions do living things use monosaccharides?
"Monos" means single and "sakharon" means sugar. So, by the name you can see that monosaccharides are single, or simple, sugars. Examples are glucose, fructose, and ribose. (Note that they all end in "-ose.") They follow the general formula for carbohydrates given above: (CH2O)n where "n" is between 3 and 8. Glucose has the formula (which you should know) C6H12O6. This follows the 1:2:1 ratio. Fructose has the exact same formula! So how are they different? Well, they are alike in that both have a backbone made of six carbons and both have hydroxyl functional groups. (Look at the drawings in your text.) They differ in the position of the carbon-oxygen double bond. The straight chain of glucose is an aldehyde sugar and the straight chains of fructose is a ketone. By the way, look on the nutrition labels of the food that you eat. Notice how many of them contain "high fructose corn syrup." Sugars are sweet!
Living things use monosaccharides for quick energy and for building more complex carbohydrates. In fact, God has designed mitochondria to "run" on glucose.
4. What is a disaccharide? Name one. For what do living things use disaccharides?
"Di" means two. From the name, you can see that disaccharides are two monosaccharides linked together. Table sugar is sucrose which is made of a glucose molecule linked to a fructose molecule.
Plants transport sugars from the leaves (where they are made) to the roots (where some is needed for energy and building blocks) in the form of disaccharides.
5. What is condensation? What is hydrolysis? Draw two monosaccharides. Draw a circle around the proper groups to join these into a disaccharide by condensation.
If disaccharides are two sugars linked together, then how do they get linked together? By condensation reactions. Take two neighboring glucose molecules. (Look at your text.) The -OH (hydroxyl group) of one molecule is taken off by an enzyme. The -H is taken off the hydroxyl of a neighboring molecule. As this happens, the two sugars are now linked to one another. What is formed in the process? A water molecule! (HOH or H2O)
>MEMORY TIP< Have you ever had a cold drink and noticed water on the outside of the glass? The water was in the air and "came out of" the air to condense on the glass. If you wear glasses, you have had the experience of coming inside on a winter day and having water "come out of" the air and condense on your glasses. Remember that in chemical condensation, water is "coming out of" the sugar molecules as they link together.
Hydrolysis comes from the words "hydro" meaning water and "lysis" meaning loosing or splitting. So, in hydrolysis, a water molecule is split and the resulting -H and -OH are added back to a molecule to split it apart. One example of this reaction is splitting a disaccharide into two monosaccharides.
6. What is a polysaccharide? What are different ways that living things use polysaccharides? Name the specific molecules used.
"Poly" means many. Polysaccharides are long chains of monosaccharides linked together. Nutritionists call them "complex carbohydrates."
Living things use polysaccharides for:
7. Lipids: What is a lipid? What is a fatty acid? Draw a fatty acid in your notebook. Be able to recognize drawings of fatty acids and the different types of lipids.
Lipids are different from the other biomolecules in that they do not dissolve in water. Have you ever seen corn or soy oil floating on water as you cook?
Just as monosaccharides are the "building blocks" of polysaccharides, so fatty acids are the building blocks for many lipids. The "fatty" term means that they do not dissolve in water. They are made of long chains of carbons to which only hydrogen is attached. The "acid" term comes from the fact that they have a carboxyl functional group at one end of the molecule. (Carboxyl groups make biomolecules acids. Carboxyl groups are also found in amino acids.)
8. Of what are fats and oils made? What functions do they serve in living things? What are saturated fats? What are unsaturated fats?
The recipe for a fat or oil is:
What does it mean when we say that something, like a towel, is saturated? It means that it is holding as much as it can. What are saturated fats holding? Each carbon in the middle of the fatty acid backbone is holding as many hydrogens as it can -- two. What is an unsaturated fat? It is a fat with some of the carbons in the fatty acids holding only ONE hydrogen. This happens when there is a double bond in the carbon chain. This double bond has interesting consequences. It makes the molecule "kink." As a consequence, the molecules do not pack together as tightly. These are liquid oils. Saturated molecules are "straight" and pack together more tightly. These are solid fats.
Jobs of fats and oils include:
9. Of what is a phospholipid made? What functions do they serve in living things?
The recipe for a phospholipid is:
10. What are waxes? What functions do they serve in living things?
Have you noticed the shiny surface on plant leaves? This is a wax coating secreted by the epidermis of the leaf. What is its job? Remember that no lipid is water soluble. This wax layer keeps the water inside the plant leaf. However, many of our house plants are tropical plants. In the tropics the temperature is high and they also receive lots of precipitation. This combination is ideal for fungal growth. As a result, tropical plants often have a thick waxy cuticle to "get rid of" excess water and avoid fungal attack.
11. What is the structure of sterols? What functions do they serve in living things?
Sterols are like other lipids in not dissolving in water, but unlike them in that their structure is made of four linked carbon rings. They serve the following functions in living things:
12. Proteins: What is an amino acid? Draw one. Circle and label the amine and carboxyl groups. List the names of some amino acids.
Amino acids are made of a central carbon atom with the following attached to it:
13. What is a protein? Draw another amino acid next to the one that you drew in the last question. Show how they bond together. What are the primary, secondary, tertiary, and quaternary structures of proteins? What are fibrous and globular proteins? What functions do proteins serve in living things? List several. What is protein denaturation? Be able to recognize drawings of amino acids and polypeptides.
Just as monosaccharides are built into larger molecules called polysaccharides, so too amino acids are built into proteins. The amino acids are linked together by (surprise, surprise) condensation.
The order of amino acids in a protein is important. Sickle cell anemia is a genetic disease whereby the protein hemoglobin in our red blood cells has ONE "incorrect" amino acid. What makes one protein different from another is the sequence of amino acids and the length of the amino acid chain. The amino acid sequence is the primary structure of the protein. This chain of amino acids may either fold into a coil or form a sheet. These structures are the secondary structures of proteins. Proteins that have a helical structure are fibrous proteins (fibers.) These have important roles in holding animals together. The secondary structure of a protein may fold back onto itself to form a "ball" structure. This is the tertiary structure of proteins. These "balls" are called globular proteins. Enzymes are globular in shape. Sometimes, two or more amino acid chains (polypeptides) may link together. This is the quaternary structure of proteins. Each hemoglobin molecule in your red blood cells is made of four linked polypeptide bonds.
Proteins serve a number of important jobs. They serve as:
14. One function of proteins is to act as enzymes. Chapter 5 gives you an introduction to metabolism. Read the first part. Then, write a paragraph to describe what an enzyme is and why enzymes are important to living things.
15. Table 3.1 is an excellent summary of the material contained in this chapter. Learn it.
CEREAL BOX
Last revision: 1/22/09