Amino Acids and Other Important Biomolecules Flashcards
To learn the different representations of AA's and their chemical properties. To help learn the difference between relative and absolute configuration. To be able to recognize different representations of important biomolecules come test day.
What are the different ways to represent L-amino acids?
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.
Which relative configuration of amino acids (L or D) can be incorporated directly into proteins by living systems?
The L form (Levo)
What is the structure for glycine?
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.
What is the bond-line structure for alanine?
Alanine is a nonpolar amino acid, with a methyl (CH3) R group.
Although different nomenclature, absolute configuration (R, and S designation) are interchangeable with dextro and levo (relative configuration). What is the difference?
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.
For the Fischer projection of a monosaccharide, how do you determine if it’s relative configuration is L or D?
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.
What relative configuration of carbohydrates (L or D) can be utilized by living systems?
Predominantly the D form of carbohydrates.
What is the bond-line structure for valine?
Valine is a nonpolar amino acid with an isopropyl R group connecting to the ɑ carbon.
What is the bond-line structure for leucine?
Leucine is another nonpolar amino acid with a tertbutyl alkyl R substituent connecting to the α carbon.
What is the bond-line structure for cysteine?
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.
What is the bond-line structure for histidine?
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 pka of ~6.0.
What is the bond-line structure for isoleucine?
Isoleucine is a nonpolar amino acid with a secbutyl R substituent connected to the α carbon.
What is the bond-line structure for tryptophan?
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.
What is the bond-line structure for aspartic acid?
What is the bond-line structure for glutamic acid?
What is the bond-line structure for glutamine?
Note that this is the same structure for glutamic acid but is an amide instead of a carboxylic acid.
What is the bond-line structure for asparagine?
Note that this is the same structure for aspartic acid but is an amide instead of a carboxylic acid.
What is the bond-line structure for phenylalanine?
What is the bond-line structure for methionine?
What is the bond-line structure for lysine?
What is the bond-line structure for proline?
What is the bond-line structure for arginine?
What is the bond-line structure for serine?
What is the bond-line structure for tyrosine?
What is the bond-line structure for threonine?
List the name, three letter-code, one letter-code, and classification of this amino acid:
Alainine
Ala
A
Nonpolar
List the name, three letter-code, one letter-code, and classification of this amino acid:
Valine
Val
V
Nonpolar
List the name, three letter-code, one letter-code, and classification of this amino acid:
Arginine
Arg
R
Basic/Polar
Exists as cation at physiological pH
List the name, three letter-code, one letter-code, and classification of this amino acid:
Tyrosine
Tyr
Y
Polar
List the name, three letter-code, one letter-code, and classification of this amino acid:
Asparagine
Asn
N
Polar/Amide
List the name, three letter-code, one letter-code, and classification of this amino acid:
Tryptophan
Trp
W
Nonpolar, aromatic
List the name, three letter-code, one letter-code, and classification of this amino acid:
Cysteine
Cys
C
Acidic/Polar
(Can act as a Bronsted acid, donating the proton on -SH)
Although Cys can act as a Bronsted acid, we typically think of cysteine residues being oxidized to form disulfide bridges.
List the name, three letter-code, one letter-code, and classification of this amino acid:
Threonine
Thr
T
PolarHydroxylic
List the name, three letter-code, one letter-code, and classification of this amino acid:
Glutamine
Gln
Q
Polar/Amide
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.
List the name, three letter-code, one letter-code, and classification of this amino acid:
Serine
Ser
S
Polar/Hydroxylic
List the name, three letter-code, one letter-code, and classification of this amino acid:
Glutamic Acid
Glu
E
Acidic/Polar
Exists as anion at physiological pH
List the name, three letter-code, one letter-code, and classification of this amino acid:
Proline
Pro
P
Nonpolar/Aliphatic
When incorporated into a protein, proline constrains the rotational freedom around the -Nalpha-Calpha bond thus diminishing the structural flexibility of polypeptide regions containing proline. Proline is known as the “helix-breaker”
List the name, three letter-code, one letter-code, and classification of this amino acid:
Glycine
Gly
G
Nonpolar/Aliphatic
The smallest of the amino acids
List the name, three letter-code, one letter-code, and classification of this amino acid:
Phenylalanine
Phe
F
Nonpolar/Aromatic
List the name, three letter-code, one letter-code, and classification of this amino acid:
Histidine
His
H
Can act as an Bronsted acid/base
(typically exists as an aromatic cation)
List the name, three letter-code, one letter-code, and classification of this amino acid:
Methionine
Met
M
Nonpolar
List the name, three letter-code, one letter-code, and classification of this amino acid:
Isoleucine
Ile
I
Nonpolar/Alilphatic
List the name, three letter-code, one letter-code, and classification of this amino acid:
Lysine
Lys
K
Basic/Polar
Exists as cation at physiological pH
List the name, three letter-code, one letter-code, and classification of this amino acid:
Leucine
Leu
L
Nonpolar/Aliphatic
List the name, three letter-code, one letter-code, and classification of this amino acid:
Aspartic Acid
Asp
D
Acidic/Polar
Will exisit as an anion at physiological pH
List the name, three letter-code, one letter-code, and classification of this amino acid:
Tryptophan
Trp
W
Nonpolar, aromatic
