Proteins 1 - amino acids 09/04 Traish Flashcards
G
glycine
gly
hydrogen R group
A
alanine
ala
beta carbon
V
valine
val
dimethyl branch at the beta carbon
L
leucine
leu
dimethyl branch at the gamma carbon
first five letters of the greek alphabet
alpha beta gamma delta epsilon
I
isoleucine
ile
methyl ethyl branch at beta carbon
P
proline
pro
five member ring including primary amino group
F
phenylalanine
phe
benzene ring at beta carbon
Y
tyrosine
tyr
phenol group at beta carbon
pKa 10.1
W
tryptophan trp beta indole group (5 member ring off beta C w/ delta N and benzene)
amino acid with indole group
W
what is an indole group
five member ring with secondary amino group and benzene
S
serine
ser
beta hydroxl group
T
Threonine
thre
ethyl + beta hydroxyl group
C
Cysteine
cys
beta thiol group
pKa 8.3
pKa of the functional group of cysteine
8.3
pKa of the functional group of tyrosine
10.1
M
methionine
met
gamma methyl thiol group
D
aspartic acid
asp
beta carboxyl group
pKa 3.9
pKa of the functional group of aspartic acid
3.9
E
glutamic acid
glu
gamma carboxyl group
pKa 4.2
N
asparagine
asn
beta amide group
pKa of the functional group of asparagine
functional group does not ionize. trick question!
pKa of the functional group of glutamine
functional group does not ionize. trick question!
Q
glutamine
gln
gama amide group
R
arginine
arg
delta guanidinium group
pKa 12.5
what is a guanidinium group?
three amino groups bonded to a central carbon. one is double bonded
H
histidine
his
beta 5 membered ring with 2 Nitrogen (imidozole group)
pKa 6.0
pKa of the functional group of histidine
6.0
K
lysine
lys
epsilon amino group
pKa 10.0
pKa of the functional group of arginine
12.5
pKa of the functional group of lysine
10.0
7 amino acids with functional group pKa’s are:
D,E,R,H,K,Y,C
pKa of the functional group of glutamic acid
4.2
do human amino acids exist in the D or L configuration?
L
do serine and threonine ionize?
no, just H-bond
what aa residue can form strong, heat stable covalent bonds with another of itself?
cysteine, di-sulfide bonds
which aa’s absorb UV light?
F, Y, W, the aromatics
~what wavelength of light do F, W, and Y abosorb?
~280 nm
which aa essentially lacks a side chain?
glycine
which aa residue is the smallest and least sterically hindering?
glycine G gly
which aa is useful in terminating secondary structures?
P pro proline
is glycine hydrophobic?
no, it can fit into hydrophobic or hydrophilic environments due to minimal side chain
are Y and W predominantly polar or non-polar?
non-polar
can Y and W hydrogen bond?
yes
these two aa’s are negatively charged at pH 7.37
D and E
these aa’s are positively charged at pH 7.37
R and K
what is net charge of H at pH 7.37
0 (pKa side chain is 6)
this aa functions as an efficient acid-base catalyst at physiological pH
H (pKa 6)
this aa is found in sharp turns of the pp backbone
G (small R group confers high flexibility)
this aa confers a high degree of local flexibility on the polypeptide
G
this aa occurs abundantly in certain fibrous proteins (such as collagen) due to its flexibility and small size
G
this aa is the most rigid of the 20
P
can all aa’s act as buffers?
yes, all have weakly acidic C terminus and weekly basic N terminus
henderson hasselbalch equation
pH = pKa + log(conj base/acid)
an ampholyte is
a molecule that possesses both acidic and basic groups
a zwitterion is
an ampholyte with equal numbers of + and - charges
what is an isoelectric point?
the pH at which the net charge for all forms of an ampholyte is 0
in isoelectric focusing, which end is + and which is - ?
cathode is - (attracts +)
anode is + (attracts -)
galvanic cell which ends are + and - ?
cathode is +
anode is -
electrolytic cell which ends are + and - ?
cathode is -
anode is +
in isoelectric focusing on a gel with a supplied current, a net + charged aa will migrate to the ___; a net - aa will migrate to the ____
net + will migrate to the cathode
net - will migrate to the anode
how do you calculate pI for an aa with acidic side chain?
(pKa1 + pKa2) / 2
how do you calculate pI for an aa with neutral side chain?
(pKa1 + pKa2) / 2
how do you calculate pI for an aa with basic side chain?
(pKa2 + pKa3) / 2
which aa’s have pI’s found between pKa’s 1 and 2 and not 3?
D, E, Y, C
which aa’s have pI’s found between pKa’s 2 and 3?
R, H, K
on a titration graph with pH y-axis & moles OH- x-axis, what do ~horizontal and ~vertical regions signify?
horizontal = pKa vertical = pI
a polyampholyte is..
a molecule with multiple acidic and basic groups
which is an indicator of acidic vs basic aa, pKa or pI?
pI – examples where pKa does not indicate:
H is basic – acidic pKa but basic pI
C and Y are acidic – basic pKa but acidic pI
what is the ~pKa of a guanidinium group?
~12
what is the ~pKa of an imidozole group?
~6.5
what is the ~pKa of a thiol group?
~8.5
what is the ~pKa of a phenol group?
~10
what is the is the ~pKa of an inisitol group?
trick question – inisitol group does not ionize
what is the is the ~pKa of an amide group?
trick question – amide group does not ionize
what is the is the ~pKa of an aa N terminus?
~2
what is the is the ~pKa of an aa C terminus?
~9.5
this modified amino acid is an important component of mature collagen fibers, and the absence of this modification results in protein deformation and loss of fiber strength
hydroxyproline – permits sharp twisting of the collagen helix. absence of hydroxylation results in protein deformation and loss of collagen fiber strength
what is hydroxyproline
proline with a gamma hydroxyl group. modified post-translationally by prolyl hydroxylase in the ER lumen. permits sharp twisting of the collagen helix.
