Proteins and Amino Acids Practice Problems

Write the appropriate structure of a DNA segment that contains 4 nucleotides with the sequence shown below.

(3' end) T-A-C-G (5' end)

True or False. The bonds between the carbonyl carbon and nitrogen in the backbone of a peptide can freely rotate.

When a decapeptide is partially hydrolyzed, the following peptides are produced:

(i) Ser, Trp            (ii) His, Val, Gln        (iii) Ile, Tyr          (iv) Glu, Asn, Pro

(v) Val, Ile, His     (vi) Trp, Glu, Ser      (vii) Pro, Gln

What is the sequence of the decapeptide if it reacts with Edman's reagent to produce PTH-Ser?

Specify the peptides generated by the cleavage of Ser-Gln-Arg-Val-Ile-Trp-Phe-Lys-Pro-Cys-Lys-Tyr-Met-Glu with trypsin.

How would a protein found in the nonpolar interior of a membrane fold?

After being treated with maleic anhydride, trypsin only cleaved the given polypeptide on the C-side of arginine and not on the C-side of lysine. Why? 

A polypeptide composed of 13 unique amino acids undergoes partial hydrolysis to yield the following peptides:

(i) Arg, Gln, Thr   (ii) Leu, Arg            (iii) Phe, Cys, Gln       (iv) Thr, Arg

(v) Glu, Lys, Pro  (vi) Met, Ala, Pro     (vii) Leu, Tyr, Arg        (viii) Gln, Lys, Cys

(ix) Pro, Met        (x) Lys, Glu, Gln       (xi) Gln, Phe                (xii) Val, Ala

If the reaction of the intact polypeptide with carboxypeptidase A releases Leu, what is the sequence of the polypeptide? 

Which tripeptide has a more readily cleaved C-terminal peptide bond by Carboxypeptidase A and why? Gly-Val-Glu or Gly-Val-Leu

Determine the alkyl halide needed to prepare isoleucine via acetamidomalonic ester synthesis.

Which of the following alkyl halides can be used to produce tyrosine via acetamidomalonic ester synthesis? 

The herbicide shown below is an ester derivative of glyphosate. Although only a small amount of the herbicide is required to kill a plant, it shows little toxicity against humans. Assuming that it kills plants by inhibiting an enzyme needed for the synthesis of phenylalanine, suggest why this powerful herbicide has little effect on humans.

Show how you would prepare alanine via bromination followed by amination.

Show how to prepare any of the standard amino acids from the compound shown below. You can use any reagents you need to accomplish the synthesis.

Show how you would utilize reductive amination to form valine from an appropriate α-ketoacid.

Show how to prepare any of the standard amino acids from the compound shown below. You can use any reagents you need to accomplish the synthesis.

Dimethylallyl diphosphate isomerase binds to DMADP as a result of electrostatic interactions between the diphosphate of DMADP and the active site amino acid residues. Describe the properties of the active site that allow it to hold DMADP in place so that the enzymatic reactions can proceed.

Consider the compound N-benzyloxycarbonyl isoleucine shown below: 

Provide the equations for the formation (via acylation) and catalytic hydrogenolysis of N-benzyloxycarbonyl isoleucine.

Show how Strecker synthesis can be used to yield glutamic acid.

Illustrate how Strecker synthesis can be used to yield asparagine. Determine the stereochemistry of the expected synthetic product.

Chargaff’s rule states that there are equimolar amounts of cytosine and guanine and also equimolar amounts of thymine and adenine in DNA. Determine if each statement is true or false.

i. Chargaff’s rule implies that equal amounts of thymine and cytosine are present in DNA.

ii. Chargaff’s rule implies that the sum of the pyrimidine residues does not equal the sum of the purine residues.

iii. Chargaff’s rule applies to an individual strand of DNA.

Draw the product when 3-cyclopentylpropanoic acid is treated with Br₂/PBr₃. (Ignore stereochemistry)

Give the product when 2-bromo-3-methylbutanoyl bromide is treated with excess NH₃.

Provide the reactants for the Strecker synthesis of leucine. (Ignore stereochemistry)

The Strecker synthesis is a method for preparing α-amino acids by reacting an aldehyde with NH₄Cl in the presence of KCN. Acid-catalyzed hydrolysis of the nitrile yields the amino acid. Draw the nitrile that forms in the following synthesis.

The Strecker synthesis is a method for preparing α-amino acids by reacting an aldehyde with NH₄Cl in the presence of KCN. Acid-catalyzed hydrolysis of the nitrile yields the amino acid. Identify the aldehyde required to prepare alanine.

What amino acid is obtained when the Strecker synthesis is performed using 3-methylbutanal?

Show how you would prepare the compound shown below via a Strecker synthesis.

Determine the products of the reaction shown below.

Determine the product of the reaction shown below.

Show how to prepare any of the standard amino acids from the compound shown below. You can use any reagents you need to accomplish the synthesis.

Name the functional group present in the following compounds and show the products of their complete hydrolysis.

A student tried to synthesize the octapeptide Thr-Pro-Glu-His-Tyr-Asn-Ile-Gln in the lab and got a yield of 85% for the addition of each amino acid to the chain. What is the overall yield for the synthesis of Thr-Pro-Glu-His-Tyr-Asn-Ile-Gln?

Draw the dipeptides formed in the reaction of N-protected alanine and glycine.

An aldolase and its substrate form an imine, which could be predicted by labeling the d-galactose-1,6-bisphosphate at the C-2 position with 14C as the substrate. As a result of the reduction of NaBH₄, a radioactive product was obtained and isolated to hydrolyze in the acidic solution. Draw the final product after hydrolysis.

What product is obtained in the reaction of the lysine side chain with succinic anhydride?

Give the structure of the tetrapeptide Ser-Cys-Met-Asp and highlight the peptide bonds in red to indicate them.

Provide the arrow-pushing mechanism for the first step of the Strecker synthesis shown below.

Draw the arrow-pushing mechanism for the second part of the Strecker synthesis shown below.

A polypeptide was digested with trypsin, resulting in three different fragments. Identify the possible sequences of the original polypeptide from the given data and suggest an additional experiment that could help identify the primary structure of this polypeptide.

Polypeptide A:

1. Gly-Thr-Arg-Gly-Lys

2. Ser-Ile-Lys-Leu-Arg

3. Glu-Ala-Val

Predict what would be left after these sequences are treated with the indicated enzyme:

a. Ala-Lys-Val-Glu-Lys-Ala-Thr by carboxypeptidase A

b. Glu-Tyr-Arg-Leu-Met-Ser-Glu-Asn by cyanogen bromide

c. Lys-Thr-Pro-Arg-Arg-Thr-Glu-Ala by trypsin

Outline the steps to synthesize isoleucine using N-phthalimidomalonic ester synthesis method.

Provide a reaction scheme for the synthesis of valine using the Strecker synthesis.

Show the synthesis of valine using a combination of the Hell-Volhard-Zelinsky and amination reactions. (Ignore stereochemistry)