Proteins 1 - amino acids 09/04 Traish Flashcards
1
Q
G
A
glycine
gly
hydrogen R group
2
Q
A
A
alanine
ala
beta carbon
3
Q
V
A
valine
val
dimethyl branch at the beta carbon
4
Q
L
A
leucine
leu
dimethyl branch at the gamma carbon
5
Q
first five letters of the greek alphabet
A
alpha beta gamma delta epsilon
6
Q
I
A
isoleucine
ile
methyl ethyl branch at beta carbon
7
Q
P
A
proline
pro
five member ring including primary amino group
8
Q
F
A
phenylalanine
phe
benzene ring at beta carbon
9
Q
Y
A
tyrosine
tyr
phenol group at beta carbon
pKa 10.1
10
Q
W
A
tryptophan trp beta indole group (5 member ring off beta C w/ delta N and benzene)
11
Q
amino acid with indole group
A
W
12
Q
what is an indole group
A
five member ring with secondary amino group and benzene
13
Q
S
A
serine
ser
beta hydroxl group
14
Q
T
A
Threonine
thre
ethyl + beta hydroxyl group
15
Q
C
A
Cysteine
cys
beta thiol group
pKa 8.3
16
Q
pKa of the functional group of cysteine
A
8.3
17
Q
pKa of the functional group of tyrosine
A
10.1
18
Q
M
A
methionine
met
gamma methyl thiol group
19
Q
D
A
aspartic acid
asp
beta carboxyl group
pKa 3.9
20
Q
pKa of the functional group of aspartic acid
A
3.9
21
Q
E
A
glutamic acid
glu
gamma carboxyl group
pKa 4.2
22
Q
N
A
asparagine
asn
beta amide group
23
Q
pKa of the functional group of asparagine
A
functional group does not ionize. trick question!
24
Q
pKa of the functional group of glutamine
A
functional group does not ionize. trick question!
25
Q
glutamine
gln
gama amide group
26
R
arginine
arg
delta guanidinium group
pKa 12.5
27
what is a guanidinium group?
three amino groups bonded to a central carbon. one is double bonded
28
H
histidine
his
beta 5 membered ring with 2 Nitrogen (imidozole group)
pKa 6.0
29
pKa of the functional group of histidine
6.0
30
K
lysine
lys
epsilon amino group
pKa 10.0
31
pKa of the functional group of arginine
12.5
32
pKa of the functional group of lysine
10.0
33
7 amino acids with functional group pKa's are:
D,E,R,H,K,Y,C
34
pKa of the functional group of glutamic acid
4.2
35
do human amino acids exist in the D or L configuration?
L
36
do serine and threonine ionize?
no, just H-bond
37
what aa residue can form strong, heat stable covalent bonds with another of itself?
cysteine, di-sulfide bonds
38
which aa's absorb UV light?
F, Y, W, the aromatics
39
~what wavelength of light do F, W, and Y abosorb?
~280 nm
40
which aa essentially lacks a side chain?
glycine
41
which aa residue is the smallest and least sterically hindering?
glycine G gly
42
which aa is useful in terminating secondary structures?
P pro proline
43
is glycine hydrophobic?
no, it can fit into hydrophobic or hydrophilic environments due to minimal side chain
44
are Y and W predominantly polar or non-polar?
non-polar
45
can Y and W hydrogen bond?
yes
46
these two aa's are negatively charged at pH 7.37
D and E
47
these aa's are positively charged at pH 7.37
R and K
48
what is net charge of H at pH 7.37
0 (pKa side chain is 6)
49
this aa functions as an efficient acid-base catalyst at physiological pH
H (pKa 6)
50
this aa is found in sharp turns of the pp backbone
G (small R group confers high flexibility)
51
this aa confers a high degree of local flexibility on the polypeptide
G
52
this aa occurs abundantly in certain fibrous proteins (such as collagen) due to its flexibility and small size
G
53
this aa is the most rigid of the 20
P
54
can all aa's act as buffers?
yes, all have weakly acidic C terminus and weekly basic N terminus
55
henderson hasselbalch equation
pH = pKa + log(conj base/acid)
56
an ampholyte is
a molecule that possesses both acidic and basic groups
57
a zwitterion is
an ampholyte with equal numbers of + and - charges
58
what is an isoelectric point?
the pH at which the net charge for all forms of an ampholyte is 0
59
in isoelectric focusing, which end is + and which is - ?
cathode is - (attracts +)
| anode is + (attracts -)
60
galvanic cell which ends are + and - ?
cathode is +
| anode is -
61
electrolytic cell which ends are + and - ?
cathode is -
| anode is +
62
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
63
how do you calculate pI for an aa with acidic side chain?
(pKa1 + pKa2) / 2
64
how do you calculate pI for an aa with neutral side chain?
(pKa1 + pKa2) / 2
65
how do you calculate pI for an aa with basic side chain?
(pKa2 + pKa3) / 2
66
which aa's have pI's found between pKa's 1 and 2 and not 3?
D, E, Y, C
67
which aa's have pI's found between pKa's 2 and 3?
R, H, K
68
on a titration graph with pH y-axis & moles OH- x-axis, what do ~horizontal and ~vertical regions signify?
```
horizontal = pKa
vertical = pI
```
69
a polyampholyte is..
a molecule with multiple acidic and basic groups
70
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
71
what is the ~pKa of a guanidinium group?
~12
72
what is the ~pKa of an imidozole group?
~6.5
73
what is the ~pKa of a thiol group?
~8.5
74
what is the ~pKa of a phenol group?
~10
75
what is the is the ~pKa of an inisitol group?
trick question -- inisitol group does not ionize
76
what is the is the ~pKa of an amide group?
trick question -- amide group does not ionize
77
what is the is the ~pKa of an aa N terminus?
~2
78
what is the is the ~pKa of an aa C terminus?
~9.5
79
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
80
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.
