Peptides and protein structure

GHK is a natural tripeptide found in human blood plasma.

The amino acid sequence of GHK is Lys-His-Gly

Each amino acid is represented by a three-letter abbreviation.

Lys = lysine His = histidine Gly = glycine

Glycine has the structure H₂NCH₂COOH

D₂O is used as the solvent when obtaining a¹H NMR spectrum for lysine.

Give one reason why D₂O is used rather than CCl₄ and one reason why D₂O is used rather than water.

D₂O rather than water

GHK is commonly used in cosmetics as part of anti-ageing treatments.

GHK binds to copper(II) ions in the body to form GHK–Cu

Figure 6 shows the structure of GHK–Cu

Use Figure 6 to determine the structure of the amino acid histidine, His

Lysine molecules can polymerise to give poly(lysine).

Increasing the temperature of an alkaline solution of poly(lysine) changes the type of secondary structure in poly(lysine), as shown.

Name the type of secondary structure before and after heating.

Type of secondary structure before heating

Type of secondary structure after heating

What is the structure of a dipeptide formed from the two amino acids shown?

The diagram shows part of the tertiary structure for a protein. Some of the amino acids in this structure are shown using the first three letters of their names.

The general formula of an amino acid is RCH(NH₂)COOH

Interactions between amino acid R groups are shown at positions T, U, V and W.

Which two R group interactions are a type of intermolecular force and a covalent bond?

Use the Data Booklet to help you answer this question.

Endomorphin - 2 is a peptide with the amino acid sequence shown.

Tyr–Pro–Phe–Phe–NH₂

Each amino acid is represented by a three-letter abbreviation.

Tyr = tyrosine Pro = proline Phe = phenylalanine

Figure 2 shows part of the structure of endomorphin - 2, showing the Tyr–Pro–Phe– part of the molecule.

The –NH₂ at the end of the amino acid sequence of endomorphin-2 shows that the terminal functional group is an amide, not an acid.

Complete the structure of endomorphin-2 in Figure 2.

Use the structure in Figure 2 to draw the skeletal formula of proline, Pro.

A student hydrolyses a sample of endomorphin - 2 to break it down into its constituent amino acids.

The student analyses the resulting mixture by thin-layer chromatography, TLC.

State a reagent and the conditions needed for the hydrolysis.

Figure 3 shows the apparatus used for the TLC.

There is a piece of the apparatus missing from Figure 3. This omission will result in an inaccurate chromatogram.

Identify the missing piece of the apparatus.

State and explain why this piece of the apparatus is needed.

State why the amino acids separate on the TLC plate.

When the solvent has risen up the TLC plate, the student removes the plate from the beaker and sprays it with a developing agent.

Figure 4 shows the result.

Name a suitable developing agent.

State why the developing agent is needed.

Determine the R_f value for Tyr.

Proteins are polymers made from amino acids. Part of the structure of a protein is shown.

–Cys–Ser–Asp–Phe–

Each amino acid in the protein is shown using the first three letters of its name.

Identify the type of protein structure shown.

Tick (✓) one box.

Draw a structure for the –Cys–Ser– section of the protein. Use the Data Booklet to help you answer this question.

Name the other substance formed when two amino acids react together to form part of a protein chain.

The general structure of an amino acid is shown.

R represents a group that varies between different amino acids. R groups can interact and contribute to protein structure.

Explain why the strength of the interaction between two cysteine R groups differs from the strength of the interaction between a serine R group and an aspartic acid R group.

Use the Data Booklet to help you answer this question.

Deduce the type of interaction that occurs between a lysine R group and an aspartic acid R group.

Which type of interaction between polypeptide chains is mainly responsible for maintaining the secondary structure of a protein in the form of an alpha helix?

The protein fibroin can be broken down into amino acids using an enzyme.

A student uses thin-layer chromatography (TLC) to identify these amino acids.

The student identifies two of the amino acids as alanine and serine.

Use Figure 3 to calculate the R_f value of the unknown amino acid. Show your working.

Use your R_f value and Table 1 to identify the unknown amino acid.

The amino acids cannot be seen as they move during the experiment.

State how the amino acids can be made visible at the end of the experiment.

State why each amino acid has a different R_f value.

This question is about thin-layer chromatography (TLC).

• A protein was hydrolysed to form a mixture of amino acids.

• A spot of this mixture was added to a TLC plate and the plate placed vertically in a small volume of solvent 1.

• When the solvent front reached nearly to the top of the plate, the plate was removed and allowed to dry.

• The plate was turned anticlockwise through 90° and placed vertically in a small volume of solvent 2.

• When the solvent front reached nearly to the top of the plate, the plate was again removed and allowed to dry.

• Figure 2 shows the final TLC plate.

Suggest a suitable reagent for the hydrolysis of a protein.

Suggest how the positions of the amino acids on the TLC plate were located.

Deduce the minimum number of amino acids present in the original mixture.

Suggest why it was necessary to use two different solvents.

Which structure shows part of a peptide link in a protein?

This question is about amino acids and peptide (amide) links.

Draw the structure of the zwitterion formed by phenylalanine.

Draw the structure of serine at high pH.

Draw the structures of both dipeptides formed when phenylalanine reacts with serine.

In each structure show all the atoms and bonds in the amide link.

An amide link is also formed when an acyl chloride reacts with a primary amine.

Name and outline a mechanism for the reaction between CH₃CH₂COCl and

Give the IUPAC name of the organic product.

Name of mechanism

Mechanism

IUPAC name of organic product