Download Folding a Toober Model of the Zinc Finger Questions

Folding a Toober Model of the Zinc Finger Questions
 Note: When folding tertiary structure using the sidechains you
will need the following information:
Acidic: Negative
Basic: Positive
Cystine: Sulfer

1. Proteins have 3-4 levels of protein structure. The zinc finger has how many of
these levels? Explain what forms each level (what is it & the type of bonds)
a. Primary Structure:
b. Secondary structure:
i.
ii.
c. Tertiary Structure:
d. Quaternary Structure:
2. Both alpha helices and beta sheets are stabilized by hydrogen bonds. Are the
atoms involved in these hydrogen bonds part of the backbone or the sidechains?
3. Describe the difference in how the backbone atoms and the sidechain atoms of the
amino acids are involved in protein structure and folding.
4. How does a zinc atom help stabilize the zinc finger?
5. Zinc fingers often bind to DNA. How might the arginine sidchain (positivelycharge) shown on your model be involved in DNA binding?
Folding a protein part 2
1. With your partner choose 15 sidechains that have the following properties:
a. 2 positively charged (blue)
b. 2 negatively charged (red)
c. 1 methionine & 2 other polar (white)
d. 6 non-polar (yellow)
e. 2 cysteine (green)
Methionine
2. Place your sidechains with methionine next to the blue cap (rest in any order)
equally spaced along your toober (about 3” apart). Write down your primary
structure:
3. Fold it into secondary structure: Draw or take a picture- label the types of
secondary structure & the hydrogen bonds
a. Hint: fold no more than 1/3 of the chain into a single secondary structure.
This will give you more room to work with the molecule in tertiary.
4. Fold it into tertiary structure: Remember this is the sidechain interactions
a. Hydrophobic fold to the inside away from water and hydrophilic
sidechains
b. Charged fold to the outside and are attracted to opposite charges (neg-pos
attraction stabilizes the protein)
c. Polar sidechains are attracted to each other and the water on the outside
d. Cysteine sidechains can form covalent disulfide bonds/bridges between
them
e. Take a picture or draw. Label the interactions between sidechains
5. Bonus: With a second group, fold both proteins together into a quaternary
structure. Take a picture or draw. Label the interactions between sidechains.