Molecules of Life and Water
Colleen Conway, Ph.D. Margaret Franzen, Ph.D.

This Jmol Exploration was created using the Jmol Exploration Webpage Creator from the MSOE Center for BioMolecular Modeling.

version 2.0
Exploration Content


Learning Objectives

  • Students differentiate between monomers and polymers (macromolecules)

  • Students describe chemical features and functions of different types of macromolecules

  • Students use models to differentiate between polar and nonpolar bonds

Monomers and Polymers

Macromolecules are very large molecules that are made up of small molecules that are joined together.

Macromolecules are often called polymers, meaning 'many parts.' Those small molecules that are the building blocks or subunits of macromolecules are called monomers, which means 'one part.'

Polymerization is the process of linking monomers together to form a polymer:

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When you click on any of the Jmol buttons in this tutorial, an interactive structure will appear in the Jmol window at the right. You may click and drag with your mouse button to rotate the image. If you hover over an atom with your cursor, a small pop-up will identify the atom using standard chemical symbols. Check it out with the button below, showing the subunits of a polymer.

segment of polymer, with alternating monomers in blue and orange

Answer questions 1-3 on your worksheet.

Condensation Reaction

Monomers polymerize through reactions called condensation reactions. Condensation reactions are also called dehydration reactions, because the new covalent bond formed on the polymer results in the loss of a water molecule.

In a condensation reaction, a monomer is added to the growing chain (monomer in) and water is released (water out).

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Answer question 4 on your worksheet.


The reverse reaction can also occur. Polymers can break down into monomers. This type of reaction is called a hydrolysis reaction. In this reaction, water reacts with the bond linking the monomers, and one monomer is separated from the polymer chain.

In a hydrolysis reaction, a water molecule is added (water in) and a monomer is released from the polymer(monomer out).

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Answer question 5 on your worksheet.

Classes of Macromolecules

In the next few weeks of BIO 100, we will begin talking about macromolecules. There are four classes of macromolecules that are essential for life.

  • carbohydrates

  • lipids

  • proteins

  • nucleic acids

Water, while not a macromolecule, is also essential for life. As you can see in the reactions above, water is essential for the polymerization and for the hydrolysis of these macromolecules.

Molecules of Life


In this section, you will explore the structure of macromolecules - the large structures of life. Each section includes information about the macromolecule and the monomers used to build it, as well as a short video showing models of both a representative monomer, and a polymer composed of numerous monomers. Each macromolecule has one monomer colored in green. 'Macro' means 'big' - and you'll see that each macromolecule consists of many monomers!

Although you do not need to memorize these structures, you need to 'read' the structures to complete the table. Some of the structures use chemical shorthand - if there is a bend in the 'stick' structure that is not labeled, it is a carbon atom.

All the monomers contain hydrogen, but these atoms are not always drawn in the chemical structure.

As you work through the sections, you'll be directed to answer questions on your worksheet. (You might wish to preview the questions before you start .) You may also wish to refer to your textbook as you complete the table.

Models in the Molecules of Life set follow a standard color scheme used in biology and chemistry. This is known as the CPK color scheme (after the last initial of three scientists who developed the scheme). The colors are as follows:

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All of the models in this set are magnified 20 million times (20 x 106 times).

Answer question 6 on your worksheet.


The monomers of carbohydrates are called monosaccharides. Monosaccharides are energy-rich molecules that provide fuel for your body. Glucose is a monosaccharide that plants build from carbon dioxide and water and energy from the sun in a process called photosynthesis. The energy in glucose is released when organisms break down food during cellular respiration. This energy is captured as ATP and used to power life processes.


Complex carbohydrates (polysaccharides) consist of many monosaccharide (simple sugar) molecules joined together. Plants use glucose monomers to build two different linear polymers: either starch or cellulose. You, as a human being, have an enzyme (protein) that cuts off the individual glucose monomers of starch - but not cellulose - so that glucose can be oxidized to release its energy. When you eat a meal, some of the glucose is stored in a branched polysaccharide called glycogen. Glycogen rapidly releases glucose to provide energy.


Answer all parts of question 7 on your worksheet.

Cell Membranes

The building blocks of cell membranes are phospholipids. They are not technically monomers because they are not connected covalently. Phospholipids are unusual molecules with two distinct properties. One portion of the molecule is a long water-avoiding (hydrophobic) carbon tail. The other portion is a water-seeking (hydrophilic) head group containing phosphate. In your cells, phospholipid molecules spontaneously assemble into a lipid bilayer with the hydrophobic carbon tails buried and hidden from the polar water molecules in the cell. The polar phosphate portion of phospholipids is on the surface, exposed to water.

phospholipid and cell membrane

Phospholipid bilayers form cell membranes to separate the inside of your cells from the outside. The hydrophobic nature of a phospholipid bilayer prevents the free movement of most small molecules into and out of your cells. Proteins embedded in cell membranes allow ions and small molecules to pass through the membrane. Each protein has a specific shape that allows it to transport a specific molecule - such as water - into or out of the cell.

section of plasma membrane

Answer all parts of question 8 on your worksheet.


Amino acids are the monomers of proteins. Twenty amino acids are used to construct proteins. Each amino acid shares a common backbone with an amino group and a carboxylic acid group (hence the name 'amino acid'). But each amino acid has a unique sidechain, with a unique shape and unique chemical properties. The amino acids are joined together through their common backbone atoms in a unique sequence - specified by your DNA - that spontaneously folds into a compact shape following basic principles of chemistry and physics.

In the Jmol animation of asparagine below, several features shared by all amino acids are highlighted. The flashing purple region is the backbone amino group, and flashing yellow region is the backbone carboxylic acid. Finally, all backbone atoms, including the amino group, the carboxylic acid group and the central a-carbon to which they are attached, is highlighted in green.

amino acid and protein (aquaporin)

These linear chains of amino acids are called proteins. Your body produces approximately 100,000 different proteins, each with a specific sequence and a specific shape that allows it to perform a specific function. Aquaporins are channel proteins that facilitate the selective diffusion of water in single file across a cell membrane. Thirteen variants of aquaporin have been identified in humans. Each is composed of 250-300 amino acids. Two polar asparagine amino acids located near the center of the channel guide the water molecules rapidly through the membrane.


Answer all parts of question 9 on your worksheet.

Nucleic Acids

Nucleotides are the building blocks for your DNA and RNA> There are four nucleotides in DNA, each composed of a base - adenine (A), thymine (T), guanine (G) or cytosine (C) - a deoxyribose sugar and a phosphate group. In RNA, the deoxyribose is replaced by ribose, and the thymine base is replaced by uracil. In both DNA and RNA, enzymes called polymerases join the monomer nucleotides together through their common sugar-phosphate backbone to make long polymers. Cells use the unique sequence of nucleotides in DNA as a code to build the correct sequence of amino acids in a protein.

In the Jmol animation of adenine, the sugar-phosphate backbone common to all nucleotides is highlighted as follows: the phosphate group flashes purple, then the sugar group flashes orange, and finally, the sugar-phosphate backbone flashes in green."

nucleotide and DNA

Nucleic acids such as deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are polymers composed of nucleotides joined by their shared sugar-phosphate backbones. DNA is a long, linear polymer of the nucleotides A, G, C, and T. The sequence of these four nucleotides in your DNA specifies the sequence of amino acids in your proteins. The two complementary strands of DNA wrap around each other to form a right-handed double helix. This double helix contains complementary A-T and G-C base pairs. In 2001, researchers determined the exact nucleotide sequence of the 3.2 billion base pairs of the human genome.


Answer all parts of question 10 on your worksheet.


Life happens in water. The human body is about 70% water. This unique polar solvent provides the medium in which the macromolecules of your cells float. Biomolecules interact with each other in your cells following basic principles of chemistry and physics.

water and ice

Water can exist in any one of three states - gas (vapor), liquid or solid. At 0° Celcius (32° Farenheit) the thermal motion of the water molecules slows to the point that stable hydrogen bonds form between the molecules and an ice lattice forms. Ice floats since ice lattices are less dense than liquid water. This causes lakes to freeze from the top down, insulating the life beneath. Water molecules can form more than a dozen crystalline structures depending on temperature and pressure; however, nearly all ice on the Earth's surface and in its atmosphere is a hexagonal phase noted as ice Ih.

hexagonal ice

Answer all parts of question 11 on your worksheet.


Much like Lego blocks can be connected through a common 'linking mechanism' to build a wide variety of structures, living things contain hundreds of thousands of macromolecules - sometimes called biomolecules because they are associated with life - that are constructed of a limited number of building blocks that are connected through common features between the subunits.

This activity explored four classes of macromolecules: carbohydrates, lipids (the cell membrane is one example), proteins and nucleic acids. In addition to these major classes of macromolecules, cells can combine these four classes into even more complex molecules, including glycoproteins (sugar and protein), lipoproteins (lipid and protein), nucleoproteins (nucleic acid and protein) and lipopolysaccharides (lipid and sugar).

To process what you have learned and review your understanding of this material, answer questions 12-18 on your worksheet.

Water Kit


This portion of the exercise explores water in greater detail. The models in this activity are at a much larger scale than in the Molecules of Life you just explored. At this larger scale, you will explore the interactions between individual atoms of different molecules (intermolecular interactions).

The models in this activity use magnets to simulate interactions between polar atoms. Two atoms that have a similar partial charge (either d+ or d-) will repel each other, and atoms with opposite charge will attract each other. If an atom is non-polar, it has no magnet. Note that when two polar atoms interact, you'll also hear the 'click' of the magnets.

The models in this activity use the standard CPK color scheme, with gray carbon atoms, red oxygen atoms and white hydrogen atoms.

Exploring the Structure of Water

Click the button below to see a water molecule in the Jmol window at the right. You may click and drag your mouse over the image to rotate it, and you can hover the cursor over an individual atom to identify it.


Answer question 19 on your worksheet.

Interactions Between Water Molecules

If you have access to the water molecule models, explore the interactions between two water molecules. If you don't have the models available, observe the interactions in the videos below.

oxygen-oxygen interactions
hydrogen-hydrogen interactions
oxygen-hydrogen interactions

Answer questions 20-23 on your worksheet.

Interactions with Sodium Chloride

The cpk color for sodium (Na) is blue, and chlorine (Cl) is green. Observe the interactions between sodium chloride (NaCl) and water.

interaction with sodium chloride

Answer question 24 on your worksheet.

Interactions Between Water and Ethane

Ethane (C2H6) is a short hydrocarbon. Hydrocarbons are combinations of carbon and hydrogen atoms. Ethane is an odorless, colorless gas that can be used as a fuel, a freezing agent, and in making other chemicals. Explore how ethane interacts with water.

water interactions with ethane

Answer questions 25-26 on your worksheet.

Interactions Between Water and Ethanol

Ethanol (C2H5OH) is a volatile flammable colorless liquid. Also known as ethyl alcohol or as grain alcohol, it is best known as the alcohol in alcoholic beverages, but it is also used in thermometers, as a solvent, and as fuel. Explore how water interacts with ethanol.

water interactions with ethanol

Answer questions 27-30 on your worksheet.


Models, like the models we used in Parts 1 and 2 of today's lab are useful, but they are not perfect. A model cannot perfectly replicate a biological molecule or a biological process.

Answer questions 31-32 on your worksheet.