Chapter 1: Amino Acids, Peptides, and Proteins (Kaplan) Flashcards
Remarkably, the difference between the normal form of hemoglobin (HbA) and the one that causes sickle cell disease (HbS), is a seemingly minor one. All it takes is a change in a single amino acid on the surface of hemoglobin: the ___ amino acid in 2 of its 4 chains is changed from ________ acid to ______. That minor difference allows the deoxygenated form of HbS to aggregate and precipitate, which leads to the sickled shape – and all the symptoms – of sickle cell disease.
6th glutamic acid to valine p. 3
Amino acids are molecules that contain two functional groups: an amino group (____) and a carboxyl group (_____).
- NH2
- COOH
The alpha-amino acids are the group in which the amino group and the carboxyl group are bonded to the same carbon, the _____-______ of the carboxylic acid. This means the carbon that is ________ to the carboxyl carbon.
alpha-carbon
adjacent
p. 4
Amino acids DO/ DO NOT need to have both the amino and carboxyl groups bonded to the same carbon.
do NOT
Name an example of an amino acid in the body which is not specified by a codon in the genetic code or incorporated into proteins.
ornithine, one of the intermediates in the urea cycle, which is the metabolic process by which the body excretes excess nitrogen
p. 4
The AAMC has specifically stated they’ll focus on the 20 alpha-amino acids encoded by the human genetic code, also called ____________ amino acids.
proteinogenic
What does chiral/ achiral mean?
Chiral means it’s asymmetric in such a way that the structure and its mirror image are not superimposable.
Achiral means that the object IS superimposable on its mirror image.
The term chiral comes from the Greek word for hand.
All chiral amino acids used in eukaryotes are _-amino acids.
L-amino acids
Name the 7 amino acids that fall into the category of nonpolar, nonaromatic side chains.
GAVLIMP
glycine
alanine
valine
leucine
isoleucine
methionine
proline
p. 6
Name the 3 amino acids that have uncharged aromatic side chains.
tryptophan, phenylalanine, tyrosine
(TPT)
p. 6
Which amino acid is achiral and also the smallest amino acid?
glycine
p. 5
Proline is unique in that it forms a ______ amino acid. In all the other amino acids, the amino group is attached ____ to the alpha-carbon. In proline, however, the amino nitrogen becomes a part of the side chain, forming a 5-membered ring. That ring places notable constraints on the flexibility of proline, which limits where it can appear in a protein and can have significant effects on the proline’s role in secondary structure.
cyclic
only
p. 6
Except for _______, all amino acids are chiral – and except for ________, all of them have an (S) absolute configuration.
glycine
cysteine
An imine is specifically a molecule with a…
Some textbooks problematically describe proline as an imino acid bc the amino nitrogen forms 2 bonds to carbon.
…carbon-nitrogen double bond.
p. 6
Phenylalanine has a benzyl side chain. What does that mean?
Benzyl means a benzene ring plus a -CH2 group.
p. 6
5 amino acids have side chains that are polar but not aromatic. Name them.
Which is the 1 polar amino acid that is aromatic and has a neutral charge?
(Mnemonic: SAG-C-2T)
Serine, Asparagine, Glutamine, Cysteine, Threonine
Tyrosine is aromatic and neutral.
(Remember also that tyrosine is aromatic, but asparagus is not, which is how you can remember that asparagine is the A in the mnemonic, since there are 3 other amino acids that start with A.)
p. 7
Asparagine and glutamine have amide side chains. What is unique amount these amino acids?
Unlike the amino group common to all amino acids, the amide nitrogens do not gain or lose protons with changes in pH; they do not become charged.
p. 7
Cysteine contains a thiol (-SH) group in its side chain. Why is the S-H bond weaker than the O-H bond?
What is the significance of this?
because sulfur is larger and less electronegative than oxygen
It leaves the thiol group in cysteine prone to oxidation.
p. 7
Only 2 of the 20 amino acids have negative charges on their side chains at physiological pH (7.4). What are they?
aspartic acid and glutamic acid
p. 8
Note that ________ is simply the deprotonated form of aspartic acid, and _________ is the deprotonated form of glutamic acid.
aspartate
glutamate
*on the MCAT you are likely to see these anion names instead of acid names because most acids in cells exist in the deprotonated form.
p. 8
Strongly hydrophobic amino acids tend to be found in the ________ of proteins.
interior
p. 9
The amino acids with long _____ side chains – alanine, isoleucine, leucine, valine, and phenylalanine – are all strongly hydrophobic, and thus more likely to be found in the interior of proteins.
alkyl
p. 9
All the amino acids with charged side chains – __________ charged histidine, arginine, and lysine, plus __________ charged glutamate and aspartate – are hydrophilic, as are the amides asparagine and glutamine. The remaining amino acids lie somewhere in the middle and are neither particularly hydrophilic nor particularly hydrophobic.
POSITIVELY
NEGATIVELY
p. 9
The histidine residue in chymotrypsin’s ______ ____ removes a proton from the -COOH group in an aspartic acid residue, which can then deprotonate a serine residue.
active site
p. 8
What is the aromatic ring in histidine with 2 nitrogen atoms called?
an imidazole
p. 8