Lab #3 - Protein Structure
Amino Acids are small molecules used by cells to make proteins. There are 20 Amino
Acids and each one consists of two parts — a Backbone and a Side chain. The backbone is the
same in all 20 Amino Acids and the side chain is different in each one.
Each side chain consists of a unique combination of atoms, which determine its 3D shape
and its chemical properties. When different amino acids join together to make a protein,
the unique properties of each amino acid determine how the protein folds into its final 3D
shape. The shape of the protein makes it possible to perform a specific function in our
cells.
The activities described in this handout primarily focus on amino acid side chains. They will
help you understand how the unique properties of each side chain contribute to the
structure and function of a protein.
1. First, look at the components in your Amino Acid Starter Kit. Make sure you have:
Chemical Properties Circle
Amino Acid Chart
Mini-Toober with one Blue End Cap and one Red End Cap
21 Amino Acid Side Chain Models
2. Place each amino acid side chain on the Chemical Properties Circle according
to its chemical properties. The side chains are colored to reflect their
chemical properties according to the following coloring scheme:
Hydrophobic Side chains are Yellow
Hydrophilic Side chains are White
Acidic Side chains are Red
Basic Side chains are Blue
Cysteine Side chains are Green
1
3. Examine the side chains and their positions on the circle. Answer the following
questions.
a.
b.
c.
d.
e.
Do you see similarities or patterns in the side chains? _____ if so what
patterns or similarities are there?
_______________________________________________________
_______________________________________________________
_______________________________________________________
Hydrophobic side chains are primarily composed of ________ atoms.
Acidic side chains contain two ________ atoms. This is called a carboxyl
functional group.
Basic side chains contain _________________ atoms. This is called the
__________ functional group.
Hydrophilic side chains have various combinations of
_______________________________________________________
_______________________________________________________
_______________________________________________________
4. Once you have explored the chemical properties and atomic composition of each
side chain, you are ready to predict how proteins spontaneously fold up into
their 3D shapes.
a. From your experience with oil and water, which side chains might
position themselves on the interior of the protein, where they are
shielded from water? ________________________________
b. From your experience with magnets or electricity, which side chains
might be attracted to one another? _____________________
c. Would the final shape of the protein be a high energy state or a low
energy state for all of the atoms in the structure? ____________
5. Unwind the 4-foot mini-toober (foam covered wire) that is in your kit. Notice the
blue and red end caps on the ends of your mini-toober. The blue end cap
represents the N-terminus (the beginning) of the protein, and the red end cap
represents the C-terminus (the end) of the protein.
6. Now we are ready to construct the primary structure of your protein. Select
methionine from the chemical properties circle and place it closest to the blue
end cap.
Choose any other side chains from the chemical properties circle as long as you
have the right number of each color, as indicated below:
6 hydrophobic side chains
2 acidic side chains
2 basic side chains
2 cysteine side chains
1 methionine side shain
2 other polar side chains
Mix the side chains together and place them (in any order you
choose) on your mini-toober approximately 4 centimeters apart.
The sequence of Amino Acid Side chains that you determined when placing
them on the mini-toober is called the Primary Structure of your protein. As a
general rule the final shape of a protein is determined by its primary
structure (the sequence of its Amino Acids).
7. You will now learn about the Secondary Structure of proteins. Secondary
Structure consists of alpha helices and/or beta sheets. Proteins can be thought
of as a series of alpha helices and beta sheets, joined by loops of less regular
protein structure.
An alpha helix is a compact
right-handed helix, with 3.6
amino acids per turn of the
helix. The amino acid
side chains are bonded to the
alpha carbon of each amino acid
and radiate outward from the
helix. The alpha helix is stabilized by hydrogen bonds — weak
bonds between the amino nitrogen of one amino acid (x), and
the carbonyl oxygen of another
amino acid (x+4) located four
residues further along the chain.
A beta sheet is an extended,
zig-zag structure in which
individual strands are positioned parallel or anti-parallel
to each other to form flat
sheets in proteins. Since the
amino acid side chains are
bonded to the alpha carbons
of each amino acid, they are
alternately orientated above
and below the plane of the
sheet. The beta-sheet is stabilized by hydrogen bonds
between the amino nitrogen of
one amino acid and the carbonyl oxygen of another
amino acid in an adjacent beta
strand.
8. Fold the toober into its secondary structure. The first 22 inches from the Nterminus should be folded into a 2-stranded beta sheet. This can be made by
creating a zig-zag structure that is bent in the middle as shown in the photos
below. You can also add the plastic hydrogen bonds to your model to help hold it in
place.
9. Fold the remaining portion of your toober in to a right-handed alpha-helix.
This can be done by wrapping the mini-toober around the dowel rod to create
four 360 degree turns. Your mini-toober should now look similar to the one
shown below.
10. Now you can begin to fold your 15-amino acid protein according to the chemical
properties of its side chains. Remember all of these chemical properties affect
the protein at the same time!
-



Start by folding your protein so that all of the hydrophobic side
chains are buried on the inside of your protein, where they will be
hidden from polar water molecules.
Next, fold your protein so the acidic and basic (charged) side chains are on
the outside surface of the protein and pair one negative side chain with one
positive side chain so that they come within one inch of each other and
neutralize each other. This positive-negative pairing helps stabilize your
protein.
As you continue to fold your protein to apply each new property listed below,
you will probably find that some of the side chains you previously positioned
are no longer in place. For example, when you paired a negatively charged side
chain with a positively charged one, some of the hydrophobic side chains
probably move to the outer surface of your protein. Continue to fold until
the hydrophobic ones are buried on the inside again. Find a shape in which
all the properties apply.
Continue to fold you protein making sure that your polar side chains are also
on the outside surface of your protein where they can hydrogen bond with
water.

Last, fold your protein so that the two cysteine side chains are positioned
opposite each other on the inside of the protein where they can form a
covalent disulfide bond that helps stabilize your protein.

The final shape of your protein when it is folded is called the Tertiary
Structure.
11. Finally to demonstrate Quaternary structure, combine your polypeptide with
another lab table’s polypeptide.
Review Questions
Record the primary structure of your protein below. Use only the single letter
abbreviations of the amino acids.
Sketch your polypeptide. Color your side chains.
Questions
Part 1: Primary Protein Structure
1. Examine the structures of glycine and arginine, two of the 20 amino acids
biological organisms use to build their proteins.
Glycine
Valine
a. What do these two structures have in common? Draw a common
structure for an amino acid.
b. What makes these two structures different?
2. The first step in producing a protein in a cell is to link the amino acids
together to form a polypeptide. This linkage reaction is known as a
condensation reaction and is catalyzed, in biological systems, by the
ribosome. In the space below, draw out the condensation reaction that would
take place were you to join glycine and valine together in a dipeptide.
3. Examine your drawing. Are the two ends of the dipeptide molecule
identical? Biochemists often refer to the amino (N) terminus (or end) and
carboxyl terminus. Label the amino terminus and carboxyl (C) terminus on
your dipeptide from question 2.
4. Examine the quaternary structure of hemoglobin, at right. Hemoglobin is
the protein that transports oxygen in our red blood cells. How many
polypeptide chains make up a functional hemoglobin molecule? Can you
identify any secondary structures in this representation?
5. Sickle Cell Disease is a genetic condition that results from the substitution
of valine for glutamic acid in one of the hemoglobin polypeptides, as
indicated at right. Examine the structures of these two amino acids in the
chart on the next page. Based on just their structures, do you expect this
single amino acid substitution to have an effect on this protein’s structure?
Why or why not?
6. The substituted amino acid described in question 5 occurs at the outer
surface of the folded protein. How do you expect its location to affect
protein structure?
7. Extra Credit Opportunity: Go to the following website:
https:// fold.it/portal/
This is a protein folding website in which you can practice folding proteins
in digital puzzles and compete in folding games. I will give extra credit if
you complete all of the introduction puzzles and print them for me to see.
You may also bring them to me on a flash drive for me to see.
(http://foldit.wikia.com/wiki/FoldIt_Wiki)