Biochemistry : Amino Acids and Proteins

Study concepts, example questions & explanations for Biochemistry

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Example Questions

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Example Question #1 : Amino Acids And Proteins

Which of the following chemical elements are involved in a peptide bond?

I. Carbon and nitrogen

II. Nitrogen and hydrogen

III. Carbon and oxygen

Possible Answers:

I only

II and III

I and II

II only

Correct answer:

I only

Explanation:

A peptide bond is a covalent bond that connects adjacent amino acid molecules. The bond occurs between a carboxylic acid group on one amino acid and an amino group on the other. Specifically, the carbon atom from the carboxylic acid and the nitrogen atom from the amino group form a peptide bond; therefore, only carbon and nitrogen participate in a peptide bond.

Nitrogen and hydrogen make up the amino group (), whereas carbon and oxygen make up the carboxylic acid group (). Remember that an amino acid has a central carbon. The central carbon always has an amino group, a carboxylic acid, and a hydrogen atom. The fourth group is different for each amino acid, which gives them unique properties. 

Example Question #2 : Amino Acids And Proteins

Disrupting disulfide bonds of a polypeptide molecule alters its __________ structure, and disrupting hydrogen bonds alters its __________ structure. 

Possible Answers:

secondary . . . secondary

tertiary . . . secondary

secondary . . . tertiary

tertiary . . . tertiary

Correct answer:

tertiary . . . secondary

Explanation:

A protein molecule can have four different structural levels. Primary structure consists of the sequence of amino acids making up the polypeptide. Secondary structure consists of the sequence of amino acids and the intermolecular forces and covalent bonds that form between amino acid backbone components. Examples of intermolecular forces in secondary structures include hydrogen bonding, van der Waals forces, and dipole-dipole interactions.

Tertiary structure involves covalent bonds, dipole-dipole interactions, and hydrophobic interactions between amino acid R-groups. Tertiary structure is responsible for the 3-dimensional shape of the polypeptide. An example of a covalent bond found in tertiary structure is the disulfide bond. This bond occurs between sulfur molecules in cysteine amino acids; therefore, disrupting the bonds stated in the question will alter the tertiary structure.

Quaternary structure occurs when two or more polypeptide chains interact with each other and form bonds. 

Example Question #3 : Amino Acids And Proteins

A researcher denatures a polypeptide. What can you conclude about this denatured polypeptide? 

Possible Answers:

The hydrophobic side chains will be replaced with hydrophilic side chains

It will have beta-pleated sheets, but will not have alpha helices

It will have a reduced number of amino acid residues

It will have lost its intermolecular forces between nitrogen and hydrogen atoms

Correct answer:

It will have lost its intermolecular forces between nitrogen and hydrogen atoms

Explanation:

Denaturing a polypeptide is the process of disrupting the secondary, tertiary, and quaternary structures. This means that denaturing a protein will lead to disruption in intermolecular forces such as hydrogen bonds. Recall that hydrogen bonds occur between a hydrogen atom and either a nitrogen, oxygen, or fluorine atom; therefore, denaturing a polypeptide will cause a disruption in the intermolecular forces between nitrogen and hydrogen (hydrogen bonds).

Secondary structures can form unique structures called beta-pleated sheets or alpha helices. The beta-pleated sheets are formed when a polypeptide chain folds in such a way that it loops back to lie adjacent to an earlier segment. Alpha helices are formed when a polypeptide chain twists and forms a helical structure. Note that both of these structures involve intermolecular forces (hydrogen bonds, van der Waals, etc.) between amino acids. Denaturing a polypeptide will disrupt both of these structures.

Recall that a denatured polypeptide will not lose its peptide bonds; therefore, the polypeptide will have its original number and sequence of amino acids (primary structure). The side chains of amino acids will not change during denaturation. The intermolecular forces and disulfide bonds between adjacent amino acids will change, but the composition of each amino acid won’t change.

Example Question #4 : Amino Acids And Proteins

Which of the following polypeptide chains will have an overall negative charge at blood pH?

I. D-K-A-R-H-F

II. R-A-A-D-P-P

III. E-P-H-D-V-W

Possible Answers:

I and II

III only

II only

II and III

Correct answer:

III only

Explanation:

To answer this question you need to know the single letter codes for the given amino acids.

D-K-A-R-H-F is aspartic acid - lysine - alanine - arginine - histidine - phenylalanine.

R-A-A-D-P-P is arginine - alanine - alanine - aspartic acid - phenylalanine - phenylalanine.

E-P-H-D-V-W is glutamic acid - phenylalanine - histidine - aspartic acid - valine - tryptophan.

To solve this question we need to figure out the overall charges of the three polypeptide chains. Recall that five amino acids are charged under physiological conditions (pH of 7.4). These five amino acids are glutamic acid (E), aspartic acid (D), arginine (R), lysine (K), and histidine (H). Glutamic acid and aspartic acid have an overall  charge under physiologic pH. This occurs because their side chains are deprotonated. On the other hand, arginine, lysine, and histidine have a protonated side chain and have a  charge. Knowing this information we can solve for the overall net charge on the three polypeptide chains.

Polypeptide I: overall net charge of 

Polypeptide II: overall net charge of 

Polypeptide III: overall net charge of 

Example Question #5 : Amino Acids And Proteins

Out of the 20 amino acids, how many of them are essential (meaning they cannot be manufactured by the body)?

Possible Answers:

All amino acids are essential

Correct answer:

Explanation:

The amino acids histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine are considered essential amino acids as they cannot be made by the body. They need to obtained from outside sources/nutrients.

Example Question #1 : Amino Acids And Proteins

You want to separate glutamic acid (pI=3.22), leucine, (pI=5.98) and lysine (pI=9.74), by ion exchange chromatography, using resin that contains  groups. You deposit these amino acids on a balanced column at pH=2, and then elute the column, increasing the pH progressively up to pH=7. Indicate the elution order of these amino acids:

Possible Answers:

Leu, glu, lys

Glu, lys

Glu, leu, lys

Lys, leu, glu

Glu, leu

Correct answer:

Glu, leu

Explanation:

During ion-exchange chromatography, as you increase the pH of the mobile phase (the solution flowing through the column), you elute out proteins based on their isoelectric point (pI). So in this case, you first pass the pI of glutamic acid (Glu), and then that of leucine (Leu). You would never elute out the lysine, because the pI increase stops at 7 and never gets as high as lysine’s pI, 9.74. You have, however, successfully separated the three amino acids from each other, as the lysine remains in the column.

Example Question #7 : Amino Acids And Proteins

Sample A absorbs light at , and Sample B absorbs light at . Of the choices below, which macromolecules are likely to be present in each sample, respectively?

Possible Answers:

Nucleic acid and protein

Nucleic acid and carbohydrate

Protein and nucleic acid

Carbohydrate and nucleic acid

Protein and protein

Correct answer:

Nucleic acid and protein

Explanation:

Nucleic acids absorbs light at . The aromatic amino acids phenylalanine, tyrosine, and tryptophan absorb light at .

Example Question #8 : Amino Acids And Proteins

Which of the following properties of amino acids are incorrect?

Possible Answers:

Threonine and isoleucine are the only two amino acids with a 2nd chiral carbon

All of these are true

The natural amino acids generally occur as L-enantiomers

18 of the 19 amino acids are in the R configuration, while cysteine is the only amino acid in the S configuration.

Arginine is the amino acid with the highest  value

Correct answer:

18 of the 19 amino acids are in the R configuration, while cysteine is the only amino acid in the S configuration.

Explanation:

The opposite of the false statement is true: 18 of the 19 amino acids are in the S configuration, while cysteine is the only amino acid in the R configuration.

Example Question #9 : Amino Acids And Proteins

Protein I has a molecular weight of  and a pI of 6.5, protein II has a molecular weight of  and a pI of 8.0, and protein III has a molecular weight of  and a pI of 10.5.

If a sample containing proteins I, II, and III is run through a DEAE ion exchange column at pH 7.5, and the column is eluted with a  gradient, what is the order of elution?

Possible Answers:

III, II, I

I, III, II

I, then II and III simultaneously

I, II, III

III, then II and I simultaneously

Correct answer:

III, II, I

Explanation:

Diethylaminoethyl (DEAE) cellulose is a positive weak ion exchanger. Any molecules with a positive charge will elute through the column first, whereas molecules with a negative charge will adhere to the DEAE column and elute after the salt wash. Since protein III has a pI greater than the pH of the column, it has a positive charge and elutes first. Protein II elutes second because its pI is less than the pH but close in value. Therefore protein II contains less of a negative charge than protein I.

Example Question #10 : Amino Acids And Proteins

Which of the following contributes most to a protein's secondary and tertiary structure, respectively?

Possible Answers:

Disulfide bonding, hydrophobic interactions

Covalent bonding, hydrogen bonding

Peptide bonding, hydrogen bonding

Hydrogen bonding, hydrophobic interactions

Hydrogen bonding, disulfide bonding

Correct answer:

Hydrogen bonding, hydrophobic interactions

Explanation:

Hydrogen bonding stabilizes secondary structure to form alpha helices and beta sheets. Hydrophobic interactions between nonpolar side groups dictate a protein's tertiary structure. Disulfide bonds are involved in the determination of a protein's tertiary and quaternary structures, but they are not the primary contributors.

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