11. Biochemistry Flashcards
oligopeptide
small chain of amino acids
polypeptide
long chain of amino acids
alpha carbon stereocenter
all human amino acids, due to the 4 substituents (r group, hydrogen, carboxylic acid, and an amine
absolute configuration
all native configurations are L- amino acids,
L and D configurations
CHO on top with a dash, CH2OH on bottom with a dash, OH to the left on a wedge for L- conformation, and OH on the right with a wedge for D- conformation, the remaining right or left side has a H on a wedge
L&D vs. R&S
R&S goes by electro negativity, L&D go by CHO on top and CH2OH on bottom, and placement of OH determines postion
order of deprotonation
alpha- COOh group, then acidic R group, then His R group, then alpha NH3+ group then basic R groups
COOH groups
pKa 2
-R group (acidic)
pKa 4 (Asp 3.7, Glu 4.5)
-R group (His)
pKa 6
NH3+ group
pKa 9
-R group (basic)
pKa 11-12 (Lys 10.7, Arg 12)
essential amino acids
body cannot synthesize these
non-essential amino acids
body can make its own
zwitterion
dipolar amino acid with a positively and negatively charged AA
amino acids are weak acids
weak acids, each amino acid has 2 acidic protons (COOH and NH3+), when pH is near pKa of one of the acidic protons the amino acid acts as a buffer.
isoelectric point (pI)
pH at which a molecule carries no net charge, (pI for a molecule with two pKa’s the pI is the average of the two pKa’s, pH lower than pI, molecule will have a net positive charge, pH higher than pI the molecule will have a net negative charge. pI is similar to equivalence point but instead of neutral pH it is neutral charge
pIneutral
average of pKa-amine group and pKa-carboxyl group.
pIacidic
average of pKa-acidic R group and pKa-carboxyl group.
pIbasic
average of pKa-amine group and pKa-basic R group.
titration curves
aspartic acid into base, buffer, equivalence, end, buffer, equivalence, end. phenylalanine into base, buffer, half eq, equivalence, end
peptide bond formation
dehydration synthesis and acyl substitution. The amine group nitrogen (nucleophile) from the NEW amino acid attacks the carbonyl carbon (electrophile) on the C-TERMINUS of the growing peptide chain (aided by the enzymatic function of the ribosome).
peptide chain conversions
written, read and synthesized from N-terminus –> C-terminus
