All living organisms are composed primarily of carbohydrates, lipids, proteins, nucleic acids, and water. There are many similarities and differences among these different types of molecules. Your task is to identify some of the similarities and differences through use of molecular visualization. For this exercise you will use a web browser to visualize the structures using Jmol applets. Internet Explorer on PCs and Safari on Macintosh computers both work.

If you desire more information about Jmol, please visit the Jmol web site.

The following is a brief list of options for manipulating molecules:

• Display information about the molecular components:
• Display atom identity for carbohydrates, lipids, and inorganic molecules - Place cursor over atom. The single-letter code for the atom name (see below) will be displayed.
• Display atom and amino acid identity for proteins - Place cursor over atom. The three-letter code identifying the amino acid and the single-letter code for the atom name (see below) will be displayed.
• Display atom and nucleotide identity for DNA - The single-letter code identifying the individual nucleotide is displayed in brackets ([A] - adenine, [T] - thymine, [G] - guanine, [C] - cytosine) followed by additional numbers and letters and then the single-letter code for the atom (see below).
• Display a menu of commands - Place the cursor over Jmol and depress the mouse button.
• Rotate molecule in the X,Y plane - Place the cursor over the molecule, depress the mouse button, and move the mouse.
• Rotate molecule around a central axis - Place the cursor over the molecule, depress the mouse button while depressing the option key, and move the mouse from side to side.
• Zoom - Place the cursor over the molecule, depress the mouse button while depressing the shift key, and move the mouse towards or away from you.

Most molecules will display as Ball & Stick models with CPK coloring. The balls represent the atoms and the sticks represent the bonds. The following list includes the CPK colors for the more common atoms.

• Gray - carbon (C)
• White - hydrogen (H)
• Red - oxygen (O)
• Blue - nitrogen (N)
• Yellow - sulfur (S)
• Gold - phosphorus (P)
• Red-brown - zinc (Zn)

Some molecules have water molecules associated with them. These excess water molecules typically display only the red oxygen atoms unbonded to any atom. To hide water, go to the menu (depress mouse button over Jmol), choose Select, then Hetero, and then Water. Return to the Select menu and choose Invert Selection. Return to the Select menu and choose Display Selected Only.

Many large molecules (e.g., proteins and nucleic acids) don't display hydrogens. Please remember that all organic molecules have hydrogen bonded to free valence electrons of carbon, oxygen, and nitrogen even though they are not displayed.

Go to the Life's Molecules web site and begin your tour of the molecules that make us living organisms.

Dead or Alive?

The Life's Molecules list includes several examples of molecules that are not found in organisms (diamond and octane). View the following molecules and answer the questions. When you are asked to describe the basic structure of the molecule be certain to view it as a ball-and-stick model and identify the number of chains, chains with branches, rings, and rings with branches that are present.

Diamond

1. List the atoms that are present in diamond.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. Describe the basic structure of this molecule.

Octane

1. List the atoms that are present in octane.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. Describe the basic structure of this molecule.

Glucose

1. List the atoms that are present in glucose.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. Describe the basic structure of this molecule.

Cholesterol

1. List the atoms that are present in cholesterol.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. Describe the basic structure of this molecule.

Arachidonic Acid

1. List the atoms that are present in arachidonic acid.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. Describe the basic structure of this molecule.

CHE*Y Signal Transduction Protein

1. List the atoms that are present in this molecule.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. How many alpha helices are present in this molecule? (To view alpha helices and beta sheets change the display: Render Structures Cartoon, Color Cartoon by Scheme Secondary Structure.)




5. How many beta sheets are present in this molecule?




6. Describe the basic structure of this molecule.

ATP

1. List the atoms that are present in ATP.




2. List the different types of atom pairs that form bonds in this molecule.




3. How many bonds can each type of atom form?




4. Describe the basic structure of this molecule.

Questions

1. What generalizations can you make about the differences between the molecules found in living organisms and other types of molecules?







2. Which atoms are most common in biological molecules?







3. Which of these common atoms makes the most bonds?







4. What role does carbon play in biological molecules?







5. What properties of carbon allow it to play this role?







6. Which of these molecules is the largest? How do you know?

Structural Complexity

You have just completed a brief tour of the simple structures (e.g., chains, chains with branches, rings, and rings with branches) that comprise organic molecules. You have also determined that it is the versatility of the carbon atom that produces these different structures. Now let's look at higher levels of structural complexity. Two common secondary structures found in proteins are alpha helices and beta sheets, and of course the double helix is found in DNA.

Alpha Helix

Change the view of the Alpha Helix by choosing the following from the menu:

1. Render Structures Cartoon
2. Color Cartoon (choose a color)
3. Reload the molecule (refresh the browser window)
4. Render Scheme Sticks
5. Select Protein Backbone
6. Select Display Selected Only
7. Render Hydrogen Bonds On

Begin with the first amino acid (ALA 1) and move through the protein to answer the following questions.

1. Which atoms participate in hydrogen bonding in this protein?




2. List the different amino acid pairs that form hydrogen bonds in this molecule.










3. Is there a pattern to the position of the hydrogen bonds? If so, what is it?

Beta Sheet

Change the view of the Beta Sheet by choosing the following from the drop-down menu:

1. Render Structures Cartoon
2. Color Cartoon (choose a color)
3. Reload the molecule (refresh the browser window)
4. Render Scheme Sticks
5. Select Protein Backbone
6. Select Display Selected Only
7. Render Hydrogen Bonds On

Answer the following questions.

1. Which atoms participate in hydrogen bonding in this protein?




2. List the different amino acid pairs that form hydrogen bonds in this molecule.










3. Is there a pattern to the position of these hydrogen bonds? If so, what is it?

DNA (double helix)

Change the view of DNA by choosing the following from the drop-down menu:

1. Render Scheme Sticks
2. Select Nucleic Bases
3. Select Display Selected Only
4. Render Hydrogen Bonds On
5. Select Nucleic AT pairs
6. Reload the molecule (refresh the browser window)
7. Render Scheme Sticks
8. Select Nucleic Bases
9. Select Display Selected Only
10. Render Hydrogen Bonds On
11. Select Nucleic GC pairs

Answer the following questions.

1. Which atoms participate in hydrogen bonding in DNA?




2. List the different nucleotide pairs that form hydrogen bonds in this molecule, and record the number of hydrogen bonds that each nucleotide pair participates in.




3. Is there a pattern to the position and number of these hydrogen bonds? If so, what is it?

Questions

1. What role do hydrogen bonds play in proteins?







2. Why do proteins have such complex structures?







3. What role do hydrogen bonds play in DNA?

So Why Can't You Mix Oil and Water?

For this investigation you will need a little background information.

Atoms consist of a positively charged nucleus surrounded by a cloud of negatively charged electrons. Under many conditions there are equal numbers of positive and negative charges so the atom is electrically neutral. In molecules, atoms share their electrons to form chemical bonds. The shared electrons move around both nuclei to maintain the bond. Often the electrons are shared equally, maintaining electrical neutrality over the whole molecule. However, some nuclei attract electrons more strongly than others. (Chemists call this "electronegativity".) In these cases the electrons spend more of their time at the strongly attracting nucleus than at the weakly attracting nucleus. This leads to a charge imbalance on the molecule. The region that contains electrons more of the time becomes slightly negative and the region that is electron poor becomes slightly positive. This kind of molecule is said to be "polar".

In biological molecules, polarity is created by oxygen atoms. It has a strongly attractive nucleus that is able to pull electrons away from hydrogen and carbon.

Water

1. Write its chemical formula.




2. Would you predict that there is polarity in this molecule? Explain why or why not.

Octane

1. Write its chemical formula.




2. Would you predict that there is polarity in this molecule? Explain why or why not.

Stearic Acid

1. Write its chemical formula.




2. Would you predict that there is polarity in this molecule? Explain why or why not.

Cholesterol

1. Write its chemical formula.




2. Would you predict that there is polarity in this molecule? Explain why or why not.

Glucose

1. Write its chemical formula.




2. Would you predict that there is polarity in this molecule? Explain why or why not.

Polarity, or lack of polarity, determines how molecules interact with each other. One way to think about this is to consider how magnets behave. They have magnetic polarity indicated by a north and a south pole. You probably remember how these poles interact: North and south will attract but if you try to push two north poles or two south poles together, they will resist. Electrical polarity works in the same way: positively and negatively charged regions will attract while like charges repel.

Based on your answer to the water question above, predict how 3 or 4 water molecules would interact. (Draw your answer here.)

One final rule, significantly simplified for our purposes, is that interactions between charged regions of polar molecules are favored as are interactions between nonpolar molecules. In effect, polar molecules that can interact will do so and will "push aside" nonpolar molecules.

From the molecules list, choose a molecule that, based on your experience, you expect to mix with water:

1. What molecule did you choose?




2. From the model, can you identify regions that might be polar? (What are they? Why do you think that they are polar?)

From the molecules list, choose a molecule that, based on your experience, you would not expect to mix with water:

1. What molecule did you choose?




2. From the model, can you identify regions that might be polar? Nonpolar? (What are they? Why do you think that they are polar or nonpolar?)







3. At a molecular level, what happens when you mix oil and water?

Details, Details, Details

Open the file with glucose, fructose, and galactose.

1. Write the chemical formula for glucose.



2. Write the chemical formula for fructose.



3. Write the chemical formula for galactose.



4. What differences can you identify between the two molecules?

Open the file with sucrose and lactose.

1. Write the chemical formula for sucrose.



2. Write the chemical formula for lactose.



3. What differences can you identify between the two molecules?

Most humans are born with the ability to digest both sucrose and lactose. A few are unable to digest lactose from birth while many others lose the ability to digest it later in life. Their ability to digest sucrose remains unchanged. Explain these observations (e.g., Why can't sucrase breakdown lactose?).

Cellulose

1. Describe the structure of this molecule.





2. Identify the components (not atoms) of this molecule.

DNA and RNA

Compare DNA nucleotides (dAMP, dTMP, dGMP, dCMP) with RNA nucleotides (AMP, UMP, GMP, CMP).

How does the sugar in DNA nucleotides differ from the sugar in RNA nucleotides?