focus chapter 3 (amino acids) Flashcards
zwitterion
o Chemical compound that is electrically neutral but carry formal positive and negatice charge on different atoms
o amino acids that lack charged R groups are zwitterions at neutral pH
simple examples
o glycine
o alanine
aliphatic examples
o valine
o leucine
o isoleucine
o methionine
cyclic examples
proline
aromatic examples
o phenylalanine
o tyrosine
o tryptophan
hydroxyl examples
o serine
o threonine
amide examples
o asparagine
o glutamine
acidic examples
o aspartate
o glutamate
basic examples
o lysine
o arginine
o hisitidine
sulfhydryl examples
cysteine
simple amino acids
Ambivalent in terms of location in protein structures; they can be found in the inside and on the outside, and in relatively tight spaces due to their size
aliphatic amino acids
o Non-polar, hydrophobic side chains; with increasing hydrophobicity associated with C atoms
o Promote protein folding, thus often found in core regions of proteins.
cyclic amino acids
o contains a secondary amine group, which imposes rigid restraints on the N-Ca bond.
o disrupts secondary structures in proteins.
o often present at bends or turns in proteins.
aromatic amino acids
o All relatively non-polar.
o Partially buried on protein surface.
hydroxyl amino acids
o Polar but uncharged
o More hydrophilic than aliphatic due to the hydroxyl group
o Possibility of hydrogen-bonding
o Role in protein surface hydration.
amide amino acids
o Uncharged versions of aspartate and glutamate
o Hydrophilic; have hydrogen bonding characteristics that resemble the peptide backbone
o Non-ionizable
o Contain a terminal carboxamide group
o Chemically labile at extremes of pH.
acidic amino acids
o Simply replace the carboxamide group of asparagine or glutamine with a carboxyl group.
o Also called aspartic acid and glutamic acid (non-ionized forms)
o Lose protons and ionize above pH 5 (pKa ~4) to become negatively charged aspartate and glutamate at physiological pH
o Serve as nucleophiles in chemical reactions
o Involved in electrostatic interactions of proteins as well as H-bonding.
sulfhydryl amino acids
o High reactivity of sulfhydryl group, even compared to hydroxyl group (pKa of ~8.5)
o Most reactive AA susceptible to oxidation
o Can form stable complexes with metal ions such as mercurial
o Formation of disulfide bonds by pairs of sulfhydryl groups from cysteines that is often critical component of protein structure.
