MCAT Biology : Organic Chemistry, Biochemistry, and Metabolism

Study concepts, example questions & explanations for MCAT Biology

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Example Questions

Example Question #2 : Amino Acids

What is the reasoning behind the planar geometry of peptide bonds in proteins?

Possible Answers:

The carbon-nitrogen bond has partial double bond character

Steric hindrance

Proteins contain only L amino acids

The peptide bond is trans rather than cis

Hydrogen bonding

Correct answer:

The carbon-nitrogen bond has partial double bond character

Explanation:

The double bond character of the carbon-nitrogen bond results in a shorter bond compared to the normal length of a pure bond ( vs. ). The double bond resonance of peptide bonds aids to increase stability, while subsequently decreasing the rotation about that bond. The partial double bond results in the amide group being planar, thus allowing for either a cis or trans conformation of a peptide bond. Due to the preference for the trans orientation over the cis orientation, there is less steric hindrance between groups attached to the alpha-carbon atoms. Thus, the correct answer is that the carbon-nitrogen bond has partial double bond character.

Example Question #1 : Proteins

Which of the following amino acids is basic?

Possible Answers:

Lysine

Proline

Alanine

Phenylalanine

Correct answer:

Lysine

Explanation:

On the MCAT you must be able to recognize the following as basic amino acids: lysine, arginine, and histidine. Important acidic amino acids include aspartic acid (aspartate) and glutamic acid (glutamate). Important nonpolar amino acids include: methionine, alanine, isoleucine, proline, phenylalanine, tryptophan, valine, and leucine.

Example Question #3 : Amino Acids

Which two functional groups are included in every amino acid, and take part in amino acids binding together?

Possible Answers:

Amino group and sulfide group

Sulfide group and alcohol

Amino group and carboxyl group

Sulfide group and carboxyl group

Correct answer:

Amino group and carboxyl group

Explanation:

Every amino acid contains a carboxyl group and an amino group. These two functional groups are essential for amino acid binding and breaking.

While sulfide groups contribute to higher protein structure by forming disulfide bonds, they do not exist in every amino acid.

Example Question #6 : Amino Acids

What are the four categories of amino acids?

Possible Answers:

Polar, neutral, acidic, basic

Nonpolar, polar, acidic, neutral

Nonpolar, polar, acidic, basic

Nonpolar, polar, neutral, basic

Correct answer:

Nonpolar, polar, acidic, basic

Explanation:

Amino acids are categorized as nonpolar, polar, acidic, or basic. The category that an amino acid is placed into gives you an idea of where you might find the amino acid within a protein. For example, polar amino acids are commonly found on the outside of proteins, where other polar molecules (water) are likely to be found.

Example Question #7 : Amino Acids

A peptide bond is formed between __________.

Possible Answers:

two aromatic groups

two carboxyl groups

two amino groups

a carboxyl group and an amino group

an ester group and an amine group 

Correct answer:

a carboxyl group and an amino group

Explanation:

Each amino acid has an N and a C terminus. The N terminus contains an amino group and the C terminus contains a carboxylic acid group. In order to make a peptide linkage (and eventually create a polypeptide), a bond must form between the amino and carboxylic groups, with water as a byproduct.

Example Question #5 : Amino Acids

What would charge would you expect on alanine when placed in a solution with a pH of 1.00?

Possible Answers:

0 (neutral)

–1

More information is needed to answer the question.

+1

Correct answer:

+1

Explanation:

Since alanine is nonpolar, we know that the only parts of the amino acid that can be charged are the N-terminus and the C-terminus.

In an acidic solution, there is an excessive amount of protons available to protonate the amino acid. As a result, the carboxylic acid end and the amine end will both be fully protonated. This will result in an overall charge of +1, due to the nitrogen having three hydrogens attached.

Example Question #9 : Amino Acids

Which of the following components is not found in a nucleotide?

Possible Answers:

A sulfate group

A nitrogenous base

A five-carbon sugar

A phosphate group

Correct answer:

A sulfate group

Explanation:

Nucleotides are composed of a pentose sugar, phosphate group, and nitrogenous base. Nucleotides are the building blocks of nucleic acids, such as DNA and RNA. Phosphodiester bonds form between the phosphate group of one nucleotide and the 3' carbon of the pentose sugar on a second nucleotide to form a linkage. A nucleoside describes the molecule that is formed by a pentose sugar and nitrogenous base.

Sulfate groups are not found in nucleotides or nucleosides. 

Example Question #4 : Amino Acids

Which of the following amino acids is considered basic?

Possible Answers:

Glutamic Acid

Valine

Lysine

Tyrosine

Correct answer:

Lysine

Explanation:

Basic amino acids are those containing an amine group, while acidic contain a carboxylic acid group.

The basic amino acids are lysine (the correct answer), arginine, and histidine.

The acidic amino acids are glutamic acid (glutamate) and aspartic acid (aspartate).

Example Question #11 : Amino Acids

Proteins can have a maximum of four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt the folding strategies of proteins. Mercaptoethanol is an example of a protein denaturing agent; its mechanism for dismantling proteins is to disrupt the disulfide bonds found in the protein. When urea is introduced to a protein, the hydrogen bonds holding the protein together are disrupted. Heat can also be considered a denaturing agent, which has the potential to disrupt all intermolecular interactions in a protein.

Which of the following proteins would be least affected by the introduction of mercaptoethanol?

Possible Answers:

A protein with no proline amino acid residues

A protein that can not form alpha-helices

A protein that has no cysteine amino acid residues

A protein with no quaternary structure

Correct answer:

A protein that has no cysteine amino acid residues

Explanation:

Disulfide bonds are disrupted by the introduction of mercaptoethanol. Disulfide bonds are created by the interaction of two cysteine amino acids on different parts of the amino acid chain during the development of tertiary protein folding. As a result, a protein with few to no cysteine amino acids would be least affected by mercaptoethanol.

Alpha-helices are linked to secondary structure, and do not involve disulfide bonds. Similarly, quaternary structure is not determined by disulfide bonds; a protein without quaternary structure could still have disulfide bonds, which would be disrupted by mercaptoethanol. Proline is not involved in disulfide bonds, and its frequency would not affect the potency of mercaptoethanol to the protein.

Example Question #11 : Amino Acids

Which of the following forms of valine would be expected to exist under extremely acidic conditions?

Possible Answers:

Valine_cation

Valine

Valine_nothing

Valine_anionic

Correct answer:

Valine_cation

Explanation:

At low pH levels, we expect amino acids to exist in their cationic form. At a pH level equal to the isoelectric point (pI) we expect amino acids to exist as zwitterions, and at high pH levels we expect them to exist in their anionic forms.

Low pH causes protonation of the amino groups; high pH causes deprotonation of the carboxyl groups.

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