Amino Acids and Other Important Biomolecules

Question 1

What are the different ways to represent L-amino acids?

Answer 1

The MCAT will test your knowledge of both bond-line skeletal structures and Fisher projections, when it comes to amino acids. You will also have to know the charges and chemical properites belonging to each amino acid. Sometimes, bond-line structures and Fisher projections can be confusing/misleading when it comes to determining absolute configuration. For Fisher projections, placing the amine group on the left represents the levo form.

(Image obtained from pearson.com)

Question 2

Which relative configuration of amino acids (L or D) can be incorporated directly into proteins by living systems?

Answer 2

The L form (Levo)

Question 3

What is the structure for glycine?

Answer 3

Glycine is the smallest amino acid, with only two hydrogen atoms connected to the alpha carbon forming its R group. Becuase of glycine’s size and freedom of rotation at the alpha carbon, its incorporation into a helix destablizes the structure.

Note the methylene (CH₂) group at the ɑ position.

Question 4

What is the bond-line structure for alanine?

Answer 4

Alanine is a nonpolar amino acid, with a methyl (CH₃) R group.

Question 5

Although different nomenclature, absolute configuration (R, and S designation) are interchangeable with dextro and levo (relative configuration). What is the difference?

Answer 5

Absolute configuration designates the spatial arrangement around one chiral center of a molecule, while relative configuration labels the molecule as a whole. Relative configuration (D or L) designation does not reveal anything about the optical rotation for a given molecule.

Question 6

For the Fischer projection of a monosaccharide, how do you determine if it’s relative configuration is L or D?

Answer 6

Examine the last chiral carbon farthest away from the most oxidized group, if the OH is pointing to the left it is typically L (there are a few exceptions to this rule) and if the OH is pointing right it is R.

Question 7

What relative configuration of carbohydrates (L or D) can be utilized by living systems?

Answer 7

Predominantly the D form of carbohydrates.

Question 8

What is the bond-line structure for valine?

Answer 8

Valine is a nonpolar amino acid with an isopropyl R group connecting to the ɑ carbon.

Question 9

What is the bond-line structure for leucine?

Answer 9

Leucine is another nonpolar amino acid with a tertbutyl alkyl R substituent connecting to the α carbon.

Question 10

What is the bond-line structure for cysteine?

Answer 10

Cystein is a hydrophilic amino acid with a thiol (-SH) group connecting to the β carbon.

Cysteine is an exception to the relative configuration of amino acids that are readily incorporated into human proteins, with a R designation due to the thiol sulfulr taking priority.

Question 11

What is the bond-line structure for histidine?

Answer 11

Histidine is a polar amino acid with an imidazole group attached to the β carbon. Histidine’s pyrrole-like nitrogen is able to be protonated and has a pk_a of ~6.0.

Question 12

What is the bond-line structure for isoleucine?

Answer 12

Isoleucine is a nonpolar amino acid with a secbutyl R substituent connected to the α carbon.

Question 13

What is the bond-line structure for tryptophan?

Answer 13

Tryptophan is a nonpolar amino acid with a large, aromatic R substituent at the β carbon. Becuase the lone pair on the R group’s nitrogen is involved in aromatic conjugation, it is not ionizable.

Question 14

What is the bond-line structure for aspartic acid?

Answer 14

Question 15

What is the bond-line structure for glutamic acid?

Answer 15

Question 16

What is the bond-line structure for glutamine?

Answer 16

Note that this is the same structure for glutamic acid but is an amide instead of a carboxylic acid.

Question 17

What is the bond-line structure for asparagine?

Answer 17

Note that this is the same structure for aspartic acid but is an amide instead of a carboxylic acid.

Question 18

What is the bond-line structure for phenylalanine?

Answer 18

Question 19

What is the bond-line structure for methionine?

Answer 19

Question 20

What is the bond-line structure for lysine?

Answer 20

Question 21

What is the bond-line structure for proline?

Answer 21

Question 22

What is the bond-line structure for arginine?

Answer 22

Question 23

What is the bond-line structure for serine?

Answer 23

Question 24

What is the bond-line structure for tyrosine?

Answer 24

Question 25

What is the bond-line structure for threonine?

Answer 25

Question 26

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 26

Alainine Ala A Nonpolar

Question 27

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 27

Valine Val V Nonpolar

Question 28

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 28

Arginine Arg R Basic/Polar | Exists as cation at physiological pH

Question 29

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 29

Tyrosine Tyr Y Polar

Question 30

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 30

Asparagine Asn N Polar/Amide

Question 31

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 31

Tryptophan Trp W Nonpolar, aromatic

Question 32

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 32

Cysteine Cys C Acidic/Polar | (Can act as a Bronsted acid, donating the proton on -SH) ## Footnote Although Cys can act as a Bronsted acid, we typically think of cysteine residues being oxidized to form disulfide bridges.

Question 33

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 33

Threonine Thr T PolarHydroxylic

Question 34

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 34

Glutamine Gln Q Polar/Amide ## Footnote To help remember the one-letter code, the person who created the one-letter classification system for amino acid (Dr. Margaret Dayhoff) had a lisp when she spoke. When she said "glutamine" it sounded like she was saying "Q-tamine" so they decided to label it as Q.

Question 35

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 35

Serine Ser S Polar/Hydroxylic

Question 36

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 36

Glutamic Acid Glu E Acidic/Polar | Exists as anion at physiological pH

Question 37

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 37

Proline Pro P Nonpolar/Aliphatic ## Footnote When incorporated into a protein, proline constrains the rotational freedom around the -N_alpha-C_alpha bond thus diminishing the structural flexibility of polypeptide regions containing proline. Proline is known as the "helix-breaker"

Question 38

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 38

Glycine Gly G Nonpolar/Aliphatic ## Footnote The smallest of the amino acids

Question 39

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 39

Phenylalanine Phe F Nonpolar/Aromatic

Question 40

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 40

Histidine His H Can act as an Bronsted acid/base | (typically exists as an aromatic cation)

Question 41

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 41

Methionine Met M Nonpolar

Question 42

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 42

Isoleucine Ile I Nonpolar/Alilphatic

Question 43

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 43

Lysine Lys K Basic/Polar | Exists as cation at physiological pH

Question 44

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 44

Leucine Leu L Nonpolar/Aliphatic

Question 45

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 45

Aspartic Acid Asp D Acidic/Polar | Will exisit as an anion at physiological pH

Question 46

List the name, three letter-code, one letter-code, and classification of this amino acid:

Answer 46

Tryptophan Trp W Nonpolar, aromatic