1-amino acids Flashcards
which C is C1
the C=O one
which C is C2
alpha carbon
do all amino acids have beta carbon
all but glycine
which aa have branced beta carbons
valine and isoleucine
which aa have branched gamma (4) carbons
leucine
what is the weight of free aa (average)
128Da
what is the weight of aa residue (average)
110Da
what makes the difference in average weight of free aa and residue
the mass of water from peptide bond formation
how many H bonds can histidine donate
2 when protonated
how many H bonds can histidine accept
none when protonated
1 if non protonated
how many H bonds can amides donate
2 (from NH2)
how many H bonds can amides accept
2 (2 lone pairs on C=)
how many H bonds can arginine donate (just the R group)
5
rate
Phe, Tyr, His, Trp
in order of decreasing polarity
His, tyr, Trp, Phe
where do tyrosine and tryptophan absorb strongly in ultraviolet
280nm
when does cysteine become cystine
oxidizing environments - extracellular/lumen
what is lost in the reaction to make cystine
2H+ and 2e-
is cysteine polar or non polar
polar
is cystine polar or non polar
non-polar
how are some uncommon amino acids made
modification of amino acids after incorporation into a polypeptide chain (PTM)
is L or D more common
L
what is the pKa of a functional group at the pH
when base and acid forms are equal
does the acid or base form predominate below the pKa
acid
does the acid or base form predominate above the pKa
base
what is a zwitterion
net charge at zero, has x amount of negative and x amount of positive
what does diprotic mean
there are two titratable groups (COOH and HN3+)
is it generally negative or positive above the pI
negative
is it generally negative or positive below the pI
positive
how do you find the net average charge on the moledule
add the net average charge on each potentially charged functional group
what is the isoelectric point of a moledule
pH at which the overall/net charge on a molecule is zero (equivalent negative and positive)
how do you calculate pI for diprotic amino acids
average of pK1 and pK2
how do you calculate pI for triprotic amino acids
average pK values bounding species with net 0 charge
how many buffering regions in triprotic amino acids
3
what can change the pKa for functional groups
presence of electron withdrawing groups or other charged groups
what does a +ve charge generally do to pKa
lower
(pulls e from groups that may be deprotonated, makes it easier)
what does a -ve charge generally do to pKa
raise
charges not as cancelled out so not as strong acid so higher pKa
if pKR of Sec is 5.43 and Cys has pKR of 8
what is pI of Sec compared to Cys
lower (pH7 cys=0 and Sec=-1, pI lower
also the average in the calculation will be lower)
