Amino Acids - MCAT Biological and Biochemical Foundations of Living Systems

All amino acids with the exception of glycine are optically active, as they have four unique groups attached to their alpha-carbons and are situated in the L configuration (amino terminus oriented to the left and carboxyl terminus to the right of the alpha-carbon). Not all amino acids are neutral at physiologic pH, as lysine and arginine are positively charged and apartate and glutamate are negatively charged due to their respective side chains. Finally, only ten of the twenty amino acids are essential, thus, the correct answer is that the amino acids found within human proteins are of the L configuration.

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.

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.

A depletion of amino acids would immediately impact protein and enzyme production in the cell. All proteins, including enzymes, are made from chains of amino acids. Lack of nutrients, such as amino acids, would eventually impact other processes listed.

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.

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.

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.

The middle of the phospholipid bilayer is composed of nonpolar fatty acid tails. As a result, we would expect to find a nonpolar amino acid in the middle of the bilayer as part of the integral protein. Leucine is a nonpolar amino acid, so it could be found in the middle.

All other amino acids listed are either polar or charged.

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.

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.

Serine and threonine are classified as hydrophilic amino acids and contain hydroxyl (-OH) groups in their side chains. Tyrosine, although it is considered hydrophobic, does contain a hydrophilic hydroxyl group in its side chain. The answer is I, IV, and V, as all of these contain hydrophilic functional groups.

Transmembrane proteins are embedded within the phospholipid bilayer of the cell membrane; therefore, the protein is exposed to the nonpolar fatty acid tails, the polar phospholipid heads, and the polar environments of the cytoplasm and extracellular space.

The questions asks which amino acids would be found facing the cytoplasm. Because the cytoplasm is polar, the amino acids interacting with the cytoplasm must also be polar. Glutamine, threonine, and tyrosine are all polar amino acids, making this the best answer. The other answers contain nonpolar amino acids (proline, leucine, cysteine, valine) causing these answers to be incorrect.

Phenylalanine:

Since the phenylalanine residue is at the C-terminus end of the molecule, only its carboxylic acid pKa is relevant, as its amine is involved in a peptide bond with arginine. At a pH of 7 (well above the carboxylic acid pKa of 2.58), the C-terminus carboxylic acid would be deprotonated and have a charge of .

Arginine:

For the middle amino acid, arginine, the only relevant pKa is that of its side chain since both its carboxylic acid and amino groups are involved in peptide bonds with neighboring amino acids. Since the side chain of arginine would be protonated at a pH of 7 (well below the sidechain pKa of 12.48), this amino acid would have a charge of .

Valine:

Finally, for valine, the relevant pKa to consider is the NH2 pKa of 9.72. At pH 7, this would also be protonated, resulting in a charge of .

The overall charge of the molecule at pH 7 would be .

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).

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.

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.

One mole is base is required to deprotonate each carboxylic acid or amine, until the amino acid exists in its most deprotonated and basic form. First, two moles of base would be needed to deprotonate the two acid groups on glutamic acid (one depicted on each end). Next, a third mole would be needed to deprotonate the amine to its neutral state. Three total moles is the correct answer.

Polypeptides are made from individual amino acids through formation of peptide bonds.

Monosaccharides are the fundamental units for carbohydrates, while fatty acids come together to form lipids. Nucleotides and phosphates are key components of the nucleic acids, RNA and DNA.

The isoelectric point is the pH where the amino acid solution is electrically neutral. In acidic conditions, the carboxylic acid and amino terminus will both be protonated. This results in a positive charge (due to the amine being protonated). In basic conditions, both ends are deprotonated, resulting in a negative charge.

If an amino acid is basic, that means that the pH must be above 7 in order to deprotonate the amine in the side chain. Only then will the amino acid be electrically neutral. All basic amino acids (three of them) have an isoelectric point above a pH of 7. All other amino acids have an isoelectric point at a pH below 7.