Molecular Models: Amino Acids & Proteins

"Form ever follows function."

-Louis Sullivan (architect)
I. Examine protein primary structure using the CPK model kit
II. Examine protein secondary structure using pushfit models
III. Examine protein tertiary structure using physical and computer models
IV. Examine protein quaternary structure using a computer model
A. Protein primary structure

The CPK Model Kit

We will be using a model kit called the CPK model to build the structure of the amino acid, alanine. The atoms of the kit are color-coded:

black = carbon

red = oxygen

white = hydrogen

blue = nitrogen

Each set should contain: 1 C-carboxyl (trigonal) atom, 2 C-tetrahedral atoms, 8 hydrogen atoms, 1 N-amide (trigonal) atoms, 1 single-bond oxygen atoms (two-holed), 1 double-bond oxygen atoms (one-holed), 2 peptide linkers, and at least 6 ordinary linkers.

CPK space-filling models incorporate both the covalent and van der Waals radii of atoms into their design. They approximate the true shape of a molecule, and are particularly useful for studying molecular packing. Each element is represented in CPK models by a sphere of radius equal to the van der Waals radius. This is cut perpendicular to the direction of the chemical bonds so that when two atoms are joined by a linker, the correct value of the covalent bond length is obtained.

CPK models are constructed to a scale of 1.25 cm = 0.1 nm = 1 Å. 

The model pieces have different shapes.  Although it may be possible to link the appropriate atoms together using the wrong shaped pieces, the three-dimensional structure will not be correct and you may have difficulty seeing the features you are looking for.

The carbon atoms of the carboxyl groups are trigonal and can form bonds three other atoms. One is a double bond to oxygen. Tetrahedral carbons are used in molecules with four constituents bound to the carbon atom.

Nitrogen atoms are also trigonal and are used to form the amide (NH2) group of the amino acid.

Oxygen atoms are hemispherical (=O) or wedge shaped (-OH).

The atoms are connected together by "linkers" that press into the holes in the atoms. Except in special circumstances (more on this later) you will use only the normal (white) linkers.
Putting together and taking apart the atoms can be a real pain (and really painful too!). Fortunately there is a tool which can help. One end is used to pry the atoms apart, and the other is used to push linkers into holes.
tool1.gif tool2.gif

Steriochemistry of Alanine

The center carbon atom in an amino acid, called the a carbon, is asymmetric because it has four different substituents attached. This results in an asymmetric molecule in its three dimensional structure. Such molecules are also called "chiral". 

Chirality "game" (optional)

Two important classes of molecules containing asymmetric carbon atoms are amino acids and sugars.Amino acids in proteins all fall into one of the two stereoclasses: the L class. (Naturally occurring sugars fall into both L and D stereoclasses.

These two arrangements (L and D) cannot be converted into each other by rotating or translating the molecules; they are related by the symmetry operation of reflection, as in a mirror (like a left and a right hand).

1. Refer to the diagram and images below to build a CPK model of L-alanine, the naturally occurring form of the amino acid.
When building a three dimensional model of a molecule containing an asymmetric carbon atom, it is imperative to correctly orient the atoms attached to it. Notice that the COOH and CH3 groups are oriented vertically and go away from you. The NH2 and H groups are oriented horizontally and are coming toward you.

2. The D isomer of alanine can be made by switching any two groups attached to the chiral carbon. It can also be made accidentally if you have groups coming toward you when they are supposed to be going away or vice versa.  Collaborate with a neighboring group to compare L and D alanine (one of your groups should convert your molecule to the other form).

Attempt to superimpose the two molecules by rotating them.  Then attempt to superimpose one of the molecules with the image of the other in a hand mirror by rotating them.

3. Convert alanine to glycine by replacing the methyl (CH3) group with a hydrogen.  Now repeat the exercise in step 2.  Why are the results different?  (When you are finished, turn both glycines back into L alanine again.)

Formation of a Polypeptide

The peptide bond has several characteristics that are important in determining the secondary structure of proteins.

The peptide bond formed between the NH of one amino acid and the carboxyl group C=O of the second has a partial double bond character. There is no free rotation around the peptide bond and the C=O and N-H are in the same plane of the molecule.

Stryer Biochemistry

The other two bonds in the backbone of the polypeptide are able to rotate.

Stryer Biochemistry

 In order to prevent the free rotation of the peptide bond between two amino acids, the gray type of linkers which have a protruding "key" can be used. Some of the holes in the trigonal nitrogen and carbon atoms have slots into which the keys will fit. If you try hard you can force the bond to rotate, so make sure that the H and O atoms are actually opposite each other.


4. During the formation of the peptide bond, a molecule of water is removed, hence the process is a condensation reaction. Remove an H and OH as shown in the figures below to form a dipeptide made from your alanine and your neighbors'.
formula_amino1.gif formula_amino2.gif

The following animation shows the necessary steps.


5. Identify the carboxyl and amino termini of the dipeptide.

6. When you are finished, make sure that you have taken all of the atoms apart (it is not necessary to remove all of the linkers from their holes) and put a complete set in your bag.  Each set should contain: 1 C-carboxyl (trigonal) atom, 2 C-tetrahedral atoms, 8 hydrogen atoms, 1 N-amide (trigonal) atoms, 1 single-bond oxygen atoms, 2 double-bond oxygen atoms, 2 peptide linkers, and at least 6 ordinary linkers.

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B. Protein Secondary Structure

Build Alanine with a Pushfit Model Kit

Although space filling models illustrate molecular packing very well, skeletal ("ball and stick") models are easier to work with for most other applications.Their principal advantage is that the positions of the atoms and bonds can easily be seen. The atoms can therefore be positioned accurately to correspond to atomic coordinates calculated from geometric considerations or deduced from x-ray crystallographic analysis.When a model has been constructed, interatomic distance can easily be measured. The scale for the pushfit models is 1 cm = 1 Å.C, N and O atoms are represented by 0.5 cm diameter balls. H atomic positions are represented as the ends of short rods coming from the other atoms.

color code:  backbone = white 
  side-chain aliphatic carbon = gray 
Your kit contains model pieces to build 8 amino acid residues.


Special note: The most common problem in using these kits is confusion about the piece that contains the peptide bond (see above).  Although this is a single piece, it is actually part of two adjacent amino acids.  It is modeled as a single piece to prevent rotation around the peptide bond.  The practical implication of this is that when you build a polypeptide, you will always have parts of incomplete amino acids at both ends of the chain.

1. Construct L alanine with the pushfit model kit. It is important to assemble carefully so that you do not accidently make the D form.


Here is the piece that represents the rigid peptide bond and which contains part of two amino acids. Look at the first picture to see which of the atoms represents the amide nitrogen.  You will ignore the part of another amino acid shown on the lower part of the picture.
Pushfit_build1.gif Pushfit_build2.gif

Attach the chiral carbon as shown in the above picture on the right.

Here is the point at which you can make a big mistake. Notice that in the diagram, the CH3 group is supposed to go down and away from you. If you place the dark CH3 model unit either up and away from you or if you have the chiral carbon with the prongs coming toward you, you will inadvertently make the D form of alanine rather than the L form. Make sure that you do this correctly or later structures that you will build (such as the alpha helix) will not orient themselves correctly.
pushfit_build3yes.gif pushfit_build3no.gif

The model of L alanine is completed by attaching another of the peptide bond units to the remaining prong on the chiral carbon unit (Note that it also contains a part of the next amino acid as the first one did):


Build a Polypeptide in Extended Conformation

NOTE: The best strategy in this section is to build a polypeptide chain as described below and then twist it into the secondary structures (alpha helix, beta sheet), rather than trying to recreate them from scratch by looking at the diagrams.   

2. Build a polypeptide using all of the pieces in your Pushfit modeling kit.  To do so, just continue the previous steps.
Pushfit_build5.gif Pushfit_build6.gif

Bond Rotation


Varying the angle between adjacent rigid peptide units results in different protein secondary structures.  We will first form our polypeptide into an extended (linear) form, then modify its shape into two secondary structures commonly found in proteins. 

3. Adjust all alpha carbon angles to put the polypeptide into extended conformation.  This results in an alternation of the side atoms and R groups in adjacent amino acids as shown below. 

When viewed from the top, it can be seen that the backbone chain lies in a single plane.  The R groups are offset to alternate sides of this plane.

Build an Alpha Helix

4. Begin building the alpha helix by adjusting the bond angles on the backbone chain so that they look like the diagram below.  As this is done, the backbone will begin to coil into a helical shape, with the oxygens all pointing in one direction and the amino hydrogens pointing in the opposite direction.  This allows a hydrogen to hydrogen bond to an oxygen from the previous turn of the helix.   Be careful to notice the direction the helix is twisting.

5. Hint: starting with the N terminus at the bottom (as in diagrams), hydrogens should be pointed down, oxygens up and R groups out.  Please note: because the peptide units contain part of two amino acids fused together, the last atom on the C terminal end of the chain will be N, and vice versa.

6. By forming the helix into a tighter or looser spiral, it is possible to form hydrogen bonds between different oxygen and hydrogen atoms.  The correct "twist" on the helix is one that produces 3.6 residues per turn.  Refer to the left diagram below.  Find a red oxygen atom (white ball on your model) near the N terminus of the polypeptide.  Follow the backbone of the chain until you pass 3 more oxygen atoms.  The next nitrogen (white backbone atom with a white stub on your model) that follows is attached to the hydrogen that bonds to the oxygen that you started with.  Twist your chain around until each subsequent oxygen atom lines up with each subsequent hydrogen atom.

Stryer Biochemistry


Computer Models of the Alpha Helix and Beta Sheet

Click on the following link to open a new tab or window to examine the two secondary structures.

8. Alpha helix:
Click on each button at the bottom of the screen in order to see the features of the helix.  You can click and drag to rotate the molecule and look at it from different angles.  In particular, note the role played by the hydrogen bonds in giving strength to the structure.  Also notice how the R groups are oriented relative to the helix.  You can see this most clearly with an end-on view.  While looking end-on, click the spacefill button and see what happens to the center of the helix.

9. Antiparallel beta sheet:
Click on each button at the bottom of the screen in order to see the features of the sheet.   As with the alpha helix, note the role played by the hydrogen bonds in giving strength to the structure.  Why is this structure sometimes called a "pleated sheet".  Notice how the R groups are oriented relative to the sheet.  In the cartoon view, consider why this is called an "antiparallel" sheet. 

Alternative website:  If the site above is down, the questions can also be answered by visiting
However, the interface is a little less "user friendly".

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C. Protein Tertiary Structure

A polypeptide in its cellular environment will spontaneously fold itself into a characteristic three-dimensional structure that is related to the purpose that it serves in the cell.  In addition to the formation of secondary structures such as alpha helices and beta sheets, the secondary structures themselves move into particular positions within the folded polypeptide.  The overall shape of the molecule is called tertiary structure.  The positioning of parts of the polypeptide is influenced by interactions of hydrophilic R groups with water, attraction of hydrophobic R groups of one part of the polypeptide with another, and stabilization of the overall structure by disulfide bonds.

In the case of enzymes (catalytic proteins), the tertiary structure of the molecule produces an active site, a pocket which holds the substrate in a position favorable for facilitating the completion of the catalyzed reaction.

Physical Model of Trypsin

The notes for this section are included on the problem set page so that you can take it to the front of the classroom with you when you observe the TA demonstration. (Questions 1 and 2 are on the problem set page.)

Model of Trypsin

3. Go to the Index of Protein Structures at Molecules To Go, an NIH database.  When you click on the link below, the modeling applet will open in a frame with these instructions in the left frame.  In some versions of Internet Explorer, the left (text) frame is blank.  If that happens, right click on that frame and select "refresh".

Open database frame

Enter "trypsin" as a search term, then press Enter.  Click on the link labeled:


in the search results.  This structure may be fairly far down the list, and you can use the browser's ""Find" function in the Edit menu to speed up finding the name.  In the "Output requested" drop-down list, select JMOL PDB viewer.  Then click on the "submit request" button.

4. The initial model is in the ball and stick form.  Under "Display Style" you can drop down a list of other display styles.   "Wireframe" is a view similar to the physical model that you have already observed in the lab.  Change the display style to "Cartoons".  Then change the Color Style to "Secondary Structure" (this drop-down list may have wrapped down to the next line on your screen.

5. Click and drag to rotate the molecule.  Observe the alpha helices in the molecule. If you hold the shift key while clicking and dragging you can zoom in or out on the molecule.

6. Beta sheets are another secondary structure formed when adjacent strands are held together in a planar arrangement by repeating hydrogen bonds.  Observe the beta sheets in the molecule.  Are they flat or do they form barrels?  [Note: the individual arrows are not sheets.  They are polypeptide strands that form sheets.]  Look at the direction of the arrowheads to see the antiparallel nature of the sheets.

7. Observe how the ends of the strands in the beta sheets are connected.

8. You can make more sophisticated changes to the display by right-clicking in the modeling window and making selections from the resulting menus.  By changing the display characteristics appropriately, you can make it possible to visualize things that would be difficult to notice otherwise. 

We would expect hydrophobic side chains to project towards the center of the protein and away from the aqueous cellular environment around the protein. We would expect hydrophilic side chains to project outward.  So we will change the display to increase the apparency of side chains expected to be hydrophobic and hydrophillic. 

A. Change the display type to rods.  Change the Color Style to White.  Right click and choose: Select, Protein, Polar Residues.  Right click and choose: Color, Atoms, Blue.  (These are groups we expect to be hydrophillic.) 

B. Right click and choose: Select, Protein, Nonpolar Residues.  Right click and choose: Color, Atoms, Red.  (These are groups we expect to be hydrophobic.) 

C. Now we will highlight the side chains by getting rid of the backbone.  Right click and choose: Select, Protein, Backbone.  Right click and choose: Color, Atoms, Black.  Right click and choose: Color, Atoms, Make translucent. 

D. Click and drag the molecule so that you can examine it from various angles and decide if the orientations of the two types of side chains are generally as we predicted.  You can use a similar method to examine whether positively and negatively charged side chains (which are generally hydrophilic) tend to be oriented outwards on the surface of the molecule. 

Close the modeling frame

10. Active site of a trypsin-like enzyme (human tissue kallikrien 4). 

Click on the following link which should open in a new tab or window:

In the Contents section, click on III. Active Site. Skim the text of this section as you click on the gray squares that highlight the part of the molecule which is being described.  Do not get hung up on the details of how the binding site works.  What you should notice is how the position of particular amino acids create a pocket that facilitates specific interactions between the enzyme and its substrate.

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D. Protein Quaternary Structure

Several polypeptides (individual molecules) may combine to form a larger protein.  These polypeptides may be the same or different.  The combination of polypeptides in a given protein is called quaternary structure.  For example, normal adult hemoglobin is composed of a and b subunits acting in concert.  (which will open in a new tab or window)

1. Hemoglobin is a protein found in red blood cells whose quaternary structure is composed of four globin subunits.  Most hemoglobin in adults is composed of two alpha globins and two beta globins.  Click on the Select Alpha-Globins button then the Select Beta-Globins button to locate the four subunits. 

2. Click on the Single Out a Beta Globin button to observe the details of a single subunit.  Click on the Add Heme Group button.  The heme group is an iron-containing group that binds the oxygen carried by the red blood cell. 

3. Click on the Color Hydrophobic Amino Acids button.  Rotate the molecule and notice that most of the hydrophobic amino acids are in the interior of the subunit.

4. Go to the website .  Persons having the genetic disease sickle cell anemia have a mutation resulting in the change of a single hydrophilic amino acid, glutamate in position 6 to valine, a hydrophobic amino acid. 

A. Click on the HbS1-OFF/ON check-box to observe the position of this amino acid (colored green).  Under conditions of low oxygen concentration, a hydrophobic patch is exposed at another location on the protein.  Uncheck the HbS1-OFF/ON check-box and check the HbS2-OFF/ON check-box to observe the hydrophobic patch (shown in yellow).  It is more energetically favorable for the hydrophobic valine-6 on the betaglobin subunit of one hemoglobin molecule to aggregate with the hydrophobic patch on the betaglobin subunit of another hemoglobin molecule than to be exposed to the aqueous environment around the molecule.

B. Uncheck both boxes to see how the two proteins aggregate.  Check the beta2-Val6 - Spacefill/Wireframe check-box and rotate the molecule to see the details of how the two hydrophobic regions interact.  Repeated aggregation of many hemoglobin molecules causes the formation of long chains of hemoglobin molecules which create fibers that cause the red blood cells to have an abnormal sickle shape.

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