Protein Folding Name________________________________

Modeling 3-D Structure Date___________________Block_____

Proteins are macromolecules made up of long chains of amino acids joined by peptide
bonds that form complex folded structures. Proteins are responsible for numerous
functions including structure, storage, hormones, enzymes, the immune system, transport
of molecules (such as hemoglobin) and receptors & markers. A protein’s 3 -D structure is
determined by the interactions of its side chains on the amino acids that make it up. This
structure determines how a protein functions and interacts with other molecules in the
body. The human genome contains over 30,000 different proteins!

Directions

1. Grab a pipe cleaner and evenly space out 1 2 beads along the length of it.
Randomly draw out of your beads so there is no particular order to the colors
you choose.
2. If each bead represents one amino acid.
Q: What do you think the space in between the beads represents?
A:

3. Your pipe cleaner at this point represents the ____________________ structure of

a protein. (primary, secondary, tertiary or quaternary)

4. The first thing you should do is fold your pipe cleaner into either a zig zag
formation or a spiral formation. These represent the formation of alpha helices or
beta pleated sheets. These shapes form because of the hydrogen bonding of the
carboxyl and amino groups of the amino acids.

5. At this stage your pipe cleaner represents the ____________________ stage of

protein structure.

6. Each color bead is a different type of amino acid. There are 20 in real life but we
are simplifying it. Each amino acid’s R-group gives it different chemical
properties. The chart below explains the properties of each amino acid and how
it affects the folding of the protein.

Bead Color Chemical Properties of R How it affects protein folding

group
Blue Basic/hydrophillic Basic amino acids will form salt
bridges with acidic amino acids. Since
they are hydrophilic they will be near
the outside of the protein.
Red Acidic/hydrophillic Acidic amino acids will form salt
bridges with basic amino acids. Since
they are hydrophilic they will be near
the outside of the protein.
Yellow Hydrophobic Hydrophobic amino acids remain in
the interior of the protein and attract
to other hydrophobic amino acids.
 White Polar/hydrophillic Polar amino acids are the outermost
amino acids.
Green R group contains sulfer Green beads represent the amino acid
cysteine. Cysteine contains a sulfer in
the R group. Two cysteine beads will
covalent bond to form a disulfide
bridge. Paper clip the beads together.

7. Fold your pipe cleaner so that each green bead is paper clipped to another
green bead. If you have an uneven number then just leave the last one alone.

8. Next fold your pipe cleaner so that the acidic (red) amino acids are near your
(blue) basic amino acids forming salt bridges.

9. Next fold your hydrophobic (yellow) beads to the interior of your protein and be
sure that the hydrophilic ones are on the outside.

10. Your pipe cleaner protein now represents the _____________________

structure of a protein. (primary, secondary, tertiary, quaternary)

11. Draw your best sketch of your protein (you don’t have to draw the beads).
How does it compare to your neighbor’s?

Your Protein Your Neighbor’s Protein

12. Describe how the primary sequence of amino acids ultimately determines
what 3-D shape the protein will take on.
13. Try to link your protein to your neighbor’s by hooking together any
unpaired cysteines. If there are none of those, try to wrap your acidic amino
acids to their basic ones and vice versa. By making this connection you are
representing the

_______________________________ structure of a protein.

14. What would happen to the shape of your prot ein if accidentally a green
bead was switched with a yellow bead? How do you think this would affect the
overall function of the protein?

15. Denaturing is the process by which the protein permanently unfolds and
loses its 3-D tertiary structure. This can be caused by extreme heat, acidity,
basicity or salinity in some cases. Knowing this, answer the following in terms of
protein structure, folding and function.

a. Why is it bad to run a fever for too long or run a temperature that’s too high?

b. What would happen to the proteins in your eyes if you were to splash acid up
while not wearing goggles?

c. Why does cooked meat look different than raw meat?

 d. Carbon dioxide, when in contact with water (ie. Blood) turns into carbonic
acid. If you were to be trapped in a room with no oxygen, how would this
affect the proteins in your blood?

HOMEWORK PROBLEMS:
1. Label the peptide bond(s) in the following polypeptide:

2. Describe the 4 levels of protein structure and what causes each.

3. Use your text to describe the different ways proteins are used in cells .