Unit 1 test scheduled for 24 September.
This unit naturally follows from the chemistry you studied last year. The assumption is that you are familiar with the important basic principles of your chemistry. This includes the structure of the atom and its subatomic components, isotopes, how to use the periodic table, chemical bonding including ionic, covalent, and polar bonds, the basic properties of the common groups of elements, the various types of chemical reactions, bond energy, endothermic/exothermic reactions, the properties of acids and bases and their relationship to pH.
If this material is unfamiliar to you, then review last year's notes and become familiar with this material Module 5 and the first half of Module 6 in your text have a good review of this material. We will not spend time in class reviewing.
Learning Objectives: The successful student will be able to ...
- name the four common types of macromolecules of biological systems, carbohydrates, lipids, proteins, and nucleotides.
- explain how many macromolecules are polymers constructed many monomers linked together.
- describe the role of dehydration reactions in the synthesis of polymers such as polysaccharides and lipids.
- describe what a peptide bond is and its role in protein synthesis.
- recognize diagrams of these macromolecules and describe their structural and functional properties.
- describe in detail specific examples of each type of macromolecule and their functions.
Lesson One: Introduction and the basic types of macromolecules. Read pages 29-32.
View this Brightstorm video, "Organic Compounds."
Although most of the molecules in the cells of living organisms are small (e.g. salts, water, and dissolved gases), some of the most important compounds in cells are the very large carbon based macromolecules that make up the physical structure of the cell, regulate its metabolic activities, supply the cell with energy, and form the genetic material of the organism. As this course progresses throughout the year, there will be few units that do not rely on the information your will learn in these lessons. Consider this unit as the foundation for work you will be doing all year long.
Now for some basics. Go to Module 6 and view the diagrams of the simple organic molecules in Figure 8, page 31. Notice a few important things. All these molecules contain the element carbon. As such they are often called "organic" compounds. A simple definition of organic compounds are substances that contain carbon. At one time the prevision that these compounds are produced by biological systems was part of the definition, but modern chemistry has made that obsolete. However, many of these molecules are important constituents of cells; hence the field of science called biochemistry. Learn the names and be able to recognize the most common functional groups we will encounter in this course; alcohols, carbolic acids, ethers, esters, and amines. The diagrams on this page are of some very simple examples of compounds containing these functional groups. There are links to much larger and more complicated compounds with these groups that we will study later.
Homework U01-1, due 9 September. List and define the five functional groups discussed above and give one specific example of each. Use examples that are not used in Figure 8. Email your answer using your Fontbonne account.
Also, answer the online questions for Module 6.
Lesson Two: Carbohydrates. Read pages 45-48.
View this Brightstorm video, "Carbohydrates."
Go to Module 9, Carbohydrates. A defining characteristic of these compounds are the three elements they contain and their relative proportions to one another (1 carbon: 2 hydrogen: 1 oxygen). Some of the simplest carbohydrates are the sugars. You will be introduced to three examples; glucose, maltose, and sucrose. Be sure you understand why these compounds are carbohydrates and which compounds are monosaccharides and which are disaccharides. Glucose will be by far the most important sugar for us. Be able to recognize a diagram of glucose. These simple sugars (i.e. monomers) are often linked together to form larger carbohydrates (i.e. polymers). Carbohydrates composed of two simple sugars are called disaccharides (e.g. sucrose and lactose) and larger compounds of many linked sugars are polysaccharides (e.g. starch, cellulose, glycogen).
Homework U01-2, Due 11 September. Email the answers to the following questions using your Fontbonne account.
- Explain why glucose and fructose can have the same molecular formula but different chemical and physical properties.
- Explain why you know that a compound with the formula C12H24O5 is probably not a carbohydrate.
- List three different polysaccharides and describe their function in biological systems in your own words.
Lesson Three: Dehydration and hydrolysis reactions.
In this lesson you will explore how monosaccharide monomers (e.g. glucose) are linked together to produce polymers (e.g. sucrose and starches). Go to the animation of dehydration/hydrolysis reactions at the Biology Department of Lone Star College in North Harris, Texas. Try the first generalized animation and then the second one for carbohydrate metabolism. This second animations demonstrates the synthesis of the disaccharide sucrose from the monosaccharides glucose and fructose. Notice that water is a product of dehydration reactions and a reactant of the reverse hydration reaction. You will learn that these reaction are not restricted to carbohydrates; they are also involved in the synthesis of lipids and proteins. In cells, all these reactions require a protein catalyst (an enzyme) to facilitate the reaction.
Homework U01-3, Due 13 September. Watch the animation of sucrose synthesis carefully. You may also want to go back to your text and look at the diagrams of sucrose, glucose, and fructose again. In your own words, what are the functional groups of glucose and fructose that interact to form the link between the two molecules in a dehydration reaction? What is the functional group that is formed in sucrose by this reaction? Email your answers using your Fontbonne account. Below is another animation from YouTube that you might find helpful.
Also, answer the online questions for Module 9.
Lesson Four: Lipids. Read pages 50-52.
View this Brightstorm video, "Lipids."
Lipids are a very diverse group of compounds both in terms of their structure and their biological functions. Some are important sources of cellular energy, others are major structural components of cell membranes, and other function as chemical messengers (hormones). Fats and oils (along with waxes) are among the most common lipids in our cells. Look at the diagram of a fatty acid, Figure 6. This is a very simple molecule that consists of a long chain of carbons with a carboxyl group at one end. Fatty acids are the building blocks of more complicated lipids that play a major role in cell membrane structure and energy metabolism. Cell metabolism attaches three fatty acids to a 3-carbon glycerol using a dehydration reaction. Molecules with this general glycerol + 3 fatty acids structure are called triglycerides.
Be sure you understand the important differences in the structure of saturated and unsaturated lipids. These structural differences also have consequences for the physical properties and cellular functions of these compounds. Finally, understand what the terms cis/trans and omega fatty acids mean. They have important health implications for your diet.
Steroids are also considered by some authors to be lipids. They have a very different structure than triglycerides involving multiple ringed molecules. Steroids include many of the hormones (e.g. estrogen and testosterone) as well as cholesterol. Cholesterol has a terrible reputation as a health risk, but it also plays a vital role in the structure of cell membranes. Go to the cholesterol page to see the typical structure of a steroid lipid.
Homework U01-4, Due 16 September. Email the answers to the following questions using your Fontbonne account.
- Look at the triglyceride molecule on Figure 7. Write the molecular formula for this compound. What would be the formula for a carbohydrate with the same number of carbons?
- Raid your refrigerator or pantry at home and find at least four different food products with the nutritional labels intact. For each, list the total amount of cholesterol, saturated fat, unsaturated fat, and trans fat in a standard serving.
Also, answer the online questions for Module 10.
Lesson Five: Amino acids. Read pages 54-55.
View this Brightstrom video, "Proteins."
Among the very largest molecules in cells are the proteins. These molecules play a huge variety of functions in cells and come in many different shapes. Indeed, it is the 3D shape of a protein that often determines its function; more on that later. Just as large carbohydrates and lipids, proteins are polymers. The monomer building block of proteins are small molecules called amino acids. In addition to carbon, hydrogen, and oxygen atoms, amino acids also contain nitrogen and in some cases sulfur atoms. There are 20 different amino acids used in biological systems to build proteins. A crucial point is to understand that what makes one kind of protein different from another is the number, type, and sequence of amino acids in each protein molecule. Think of amino acids as letters of an alphabet and proteins as words. Just as with English, very different words can be spelled using the same set of letters arranged in different order. We use a dictionary to determine how to spell words correctly; cells use their genes (made of DNA) to determine how to synthesize proteins specifying the unique sequence of amino acids in the molecule
Go to the animated web site created by John Kyrk. On the opening page you will see the formula and molecular models of the simplest amino acid, glycine. As you move your cursor over the atoms in the model, the identity of each atom is revealed. Find the central alpha carbon. Bonded to opposite sides of this carbon are the two functional groups that give "amino acids" their name. Be sure you can identify these two groups. Now click on the small red "carrot" near the left hand margin to go to the next page. Here you will find a chart of the 20 amino acids. As you move the cursor over the name of each amino acid, you see its molecular structure and important information about the compound such as basic vs acid, polar vs non polar, presence of sulfur, if it is an essential element in our diet, etc. For each amino acid find the central alpha carbon, identify the two common functional groups. In addition, notice that there is a third group, called the variable or "R" group that is unique to each different amino acid.
Homework U01-5, Due 18 September. Email the answers to the following questions using your Fontbonne account.
Go to the Amino Acids and Proteins Lesson and answer questions 1 to 11.
Lesson Six: Proteins. Read pages 55-57.
You learned in the previous lesson that amino acids are the monomers that build the larger protein polymers. In this lesson you will study the details of this process. Keep in mind that the specific order in which amino acids are added to the growing protein is ultimately determined by the information contained in the cell's genes (DNA). We will spend a great deal of time on this later in the year.
Return to John Kyrk's web site. If necessary review the material on amino acids. Now click on the middle "carrot" on the left margin to view the synthesis of a "polyalanine" molecule. This is simply a short protein (or polypeptide) made of several alanine amino acid linked together. The important point to observe here are which functional groups involved in this reaction. The bond produced between two amino acids is called a "peptide" bond. This is an ordinary covalent bond similar to what you studied last year. The special name simply refers to the fact that we're talking about protein molecules. Also notice that water is formed as a by-product of this reaction. As in virtually all chemical reactions that take place in the cell, these reactions require the assistance of protein catalysts (i.e. enzymes).
Now go to Kimball's polypeptide page. Here you will find another example of peptide bonding and an explanation of the role of the amine and carboxyl group in their formation. The majority of proteins do not exist as simple chains of amino acids. Rather they are folded in very specific shapes (secondary structure) which then are folded again (tertiary structure). Often two or more proteins are then combined into one large functional molecule (quaternary structure). These 3D folding patters of proteins are essential to their proper functions. Many proteins (e.g. enzymes) work by changing their shape in very specific ways under different conditions. Follow these links and in particular note the following.
- Secondary structure: Distinguish between alpha and beta chains. Understand the general role of the amino acid functional groups and hydrogen bonds. Don't worry about the other details.
- Tertiary structure: Appreciate the importance of this level of organization to the proper functioning of proteins and how mutations can alter their efficiency. Be able to describe examples.
- Quaternary structure: Be able to describe examples.
Homework U01-6, Due 20 September. Email answers to the following questions using your Fontbonne account.
- What is the by-product formed when two amino acids are linked together in a peptide bond? What does this suggest to you regarding the type of chemical reaction involved? Explain.
- What is a hydrogen bond? In your own words, write a brief paragraph explaining the role of hydrogen bonds in the formation of the the secondary and tertiary structure of proteins.
- In your own words, briefly describe two examples of mutations that disrupt the 3D structure of proteins and as a consequence cause serious medical problems.
Also, answer the online questions for Module 11.
Lesson Seven: Nucleotides. This lesson will be covered at a latter date
We will not spend a great deal of time in this unit on nucleotides and the polymers they form because they are so unique and important they deserve a separate unit of study. Therefore, in this lesson we will limit our study to the basic structure of a typical nucleotide and a brief discussion of their general functions in cells.
Nucleotides are relatively small molecules that contain ringed structures containing nitrogen. In addition, they contain one or more phosphate groups (PO4-3) which are crucial to their function. Go to Kimball's nucleotide page. In the upper right hand corner is a diagram of a typical nucleotide. Be sure you can list and describe the three basic components of any nucleotide: the five carbon sugar (ribose or deoxyribose), the nitrogen base (several types), and the phosphate groups (1 to 3 of them).
Nucleotides have several important functions is the cell.
- The covalent bonds between the phosphate groups are "high energy" bonds and nucleotides can act as chemical energy carriers supplying the cell with its energy needs. ATP is the best example of this.
- Nucleotides can also function as chemical messengers in the cell helping to regulate the activity of protein enzymes and DNA.
- Polymers of nucleotides function as the genetic material of the cell, DNA, and RNA, a related molecule.
We will study these functions of nucleotides in great detail in future units.
Homework, Due 26 September. Email your answers using your Fontbonne account.
- What do the sugars ribose and deoxyribose have in common? What is the difference between the two?
- Name the two basic categories of nitrogenous bases. How are they different from one another? Give two examples of each.
- What do the initials "DNA" and "RNA" stand for? Do their names suggest a difference you might find in the structure of these two molecules? Explain.
Helpful Web Sites.