Mr Cole Chemistry

Proteins Questions

Proteins

Worksheet

1. Primary Structure

The following is a section of a protein. There is a trailing bond at both the N-terminus and C-terminus of the chain. Protein section structure
1a. State the name of the structure represented here.

Primary Structure

1b. The order of the amino acids here is -Tyr-Pro-Met-Ile-. Draw the skeletal structure of tyrosine.

Answer:

Tyrosine skeletal structure
1c. There is another methionine (Met) amino acid after the structure drawn here. Add the methionine to the diagram.

Answer:

The Methionine would be attached to the C-terminus of the Isoleucine (Ile) via a peptide bond (-CONH-). The side chain for Methionine is -CH2CH2SCH3.

Methionine added to protein chain
1d. State the conditions and reagent required to break down the section of protein shown above into its separate amino acids.

Answer:

Concentrated HCl and heat under reflux.

OR

Concentrated NaOH and heat, followed by neutralisation with HCl.

2. Secondary Structure

The diagram below shows sections of a polypeptide chain made of isoleucine and glutamic acid going from left to right. There are trailing bonds where the two amino acids drawn join on to the next amino acids in the polypeptide.
Polypeptide chain section
The protein structure involves a second polypeptide chain passing directly next to the chain depicted above, also made of isoleucine and glutamic acid. However, the second chain is running from right to left.
2a. Copy the first chain and add the second polypeptide chain adjacent to it. Draw in the hydrogen bonding that holds the two chains adjacent to each other.

Answer:

Antiparallel polypeptide chains with hydrogen bonding

The chains would be arranged in an antiparallel fashion (N-terminus to C-terminus aligned with C-terminus to N-terminus). Hydrogen bonds would form between the lone pair on the oxygen of the C=O group on one chain and the hydrogen of the N-H group on the adjacent chain.

2b. Explain how this hydrogen bonding arises.

Explanation:

Nitrogen and oxygen are both highly electronegative, making the C=O and N-H bonds polar. The lone pair of electrons on the oxygen atom is attracted to the partially positive (δ+) hydrogen atom attached to the nitrogen, forming a hydrogen bond.

2c. State which type of structure this process usually forms.

Secondary Structure

Specifically, this arrangement forms a β-pleated sheet.

Note: It is not an α-helix because the hydrogen bonds are forming between two separate polypeptide chains (interchain) rather than within a single spiral chain (intrachain).

3. Tertiary Structure & Bonding

3. The diagram below shows two amino acids that are physically next to each other in 3D space but from different sections of the protein primary structure. Describe the forces that hold these two chains together.
Amino acids in 3D space

Ionic Interactions (Salt Bridge)

Both R-groups will become ionised. The amine group acts as a base (accepting a proton) while the carboxylic acid acts as an acid (donating a proton). This results in an ammonium ion (-NH3+) on one chain and a carboxylate ion (-COO–) on the other. These oppositely charged groups are attracted to each other by strong electrostatic forces, forming a salt bridge.

4. Cysteine amino acids can be used to bond polypeptide chains together. Draw the skeletal formula for two cysteine amino acids on different polypeptide chains bonded together and describe the bonding. Compare the strength of this interaction between amino acids and the interactions described in questions 2 and 3.

Answer:

Disulfide bridge structure

A covalent bond (specifically a Disulfide Bridge) forms between the two sulfur atoms (S-S).

This interaction is significantly stronger than the hydrogen bonding in question 2 and the ionic attractions in question 3 because covalent bonds are much stronger than intermolecular forces.

5. The primary structure from question 1 is taken from the enzyme cytochrome P450 2D6. Cytochrome P450 2D6 catalyses the removal of methamphetamine from the body. It has no effect on the stereoisomer, levomethamphetamine.
Methamphetamine enantiomers
Explain why cytochrome P450 2D6 behaves in this way.

Active Site Stereospecificity

Enzymes have a specific 3D active site. The substrate must have the correct shape and stereochemistry to fit into this active site (Lock and Key or Induced Fit model). Methamphetamine has the correct 3D arrangement of atoms to bind to the active site, whereas its enantiomer, levomethamphetamine, does not fit and therefore cannot be catalysed.

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