20 Amino Acids Flashcards
1
Q
3 letter code: Glycine
A
Gly
2
Q
1 letter code: Glycine
A
G
3
Q
3 letter code: Alanine
A
Ala
4
Q
1 letter code: Alanine
A
A
5
Q
3 letter code: Valine
A
Val
6
Q
1 letter code: Valine
A
V
7
Q
3 letter code: Leucine
A
Leu
8
Q
1 letter code: Leucine
A
L
9
Q
3 letter code: Isoleucine
A
Ile
10
Q
1 letter code: Isoleucine
A
I
11
Q
3 letter code: Proline
A
Pro
12
Q
1 letter code: Proline
A
P
13
Q
3 letter code: Phenylalanine
A
Phe
14
Q
1 letter code: Phenylalanine
A
F
15
Q
3 letter code: Tyrosine
A
Tyr
16
Q
1 letter code: Tyrosine
A
Y
17
Q
3 letter code: Tryptophan
A
Trp
18
Q
1 letter code: Tryptophan
A
W
19
Q
3 letter code: Cysteine
A
Cys
20
Q
1 letter code: Cysteine
A
C
21
Q
3 letter code: Methionine
A
Met
22
Q
1 letter code: Methionine
A
M
23
Q
3 letter code: Serine
A
Ser
24
Q
1 letter code: Serine
A
S
25
3 letter code: Threonine
Thr
26
1 letter code: Threonine
T
27
3 letter code: Asparagine
Asn
28
1 letter code: Asparagine
N
29
1 letter code: Glutamine
Q
29
3 letter code: Aspartic Acid
Asp
29
3 letter code: Glutamine
Gln
30
1 letter code: Aspartic Acid
D
31
3 letter code: Glutamic Acid
Glu
32
1 letter code: Lysine
K
32
1 letter code: Glutamic Acid
E
33
3 letter code: Lysine
Lys
34
3 letter code: Arginine
Arg
35
1 letter code: Arginine
R
36
3 letter code: Histidine
His
37
1 letter code: Histidine
H
38
Is glycine ionizable?
No
39
What amino acid has the smallest side chain?
Glycine
40
Is glycine polar or non-polar?
Technically neither, it's too small
41
Why is glycine not a stereoisomer
because glycine doesn't have 4 substituents
42
How is glycine related to the oral cavity
it is the most abundant amino acid in collagen which is everywhere in the oral cavity
43
Is alanine polar or non-polar?
non-polar, hydrophobic
44
Is valine polar or non-polar?
non-polar, hydrophobic
45
Is leucine polar or non-polar?
non-polar, hydrophobic
46
Is isoleucine polar or non-polar?
non-polar, hydrophobic
47
Is proline polar or non-polar?
non-polar, hydrophobic
48
What are the aromatic hydrocarbon side chains
Phenylalanine, Tyrosine, and Tryptophan
49
What is important to remember about aromatic hydrocarbon side chains
They don't have fixed double bonds, they have resonance
50
Is phenylalanine polar or non-polar
non-polar, hydrophobic
51
Is tyrosine polar or non-polar?
has both polar and non-polar characteristics, intermediate
52
is tryptophan polar or non-polar
has both polar and non-polar characteristics, intermediate
53
Which side chains contain sulfur
Cysteine and Methionine
54
What are the non-aromatic hydrocarbon side chains
Alanine, Valine, Leucine, Isoleucine, Proline
55
Is cysteine polar or non-polar
Doesn't fit either
56
Is methionine polar or non-polar
Non-polar and hydrophobic
57
What is important about Methionine
It is the amino acid that's used to initiate the synthesis of all proteins specified by the genetic code
58
What are the polar uncharged side chains
Serine, Threonine, Asparagine, Glutamine
59
Is serine polar or non-polar
Polar, hydrophilic
60
Is threonine polar or non-polar
polar, hydrophilic
61
Is asparagine polar or non-polar
polar, hydrophilic
62
What is special about asparagine
it has an amide
63
What are the polar charged side chains
Aspartic acid, glutamic acid, lysine, arginine, histidine
64
Is glutamine polar or non-polar
polar, hydrophilic
65
What is the pKa of Aspartic acid
~4
66
Is glutamic acid polar or non-polar
polar, hydrophilic
67
What amino group does lysine have
Epsilon amino group
68
Is lysine polar or non-polar
polar, hydrophilic
69
Is arginine polar or non-polar
polar, hydrophilic
70
Is histidine polar or non-polar
polar, hydrophilic
71
What is special about histidine
It has an imidazole
72
What is special about arginine
It has a guanidinium
73
Is glycine ionizable?
No
74
Is alanine ionizable?
No
75
Is valine ionizable?
No
76
Is leucine ionizable?
No
77
Is proline ionizable?
No
78
Is isoleucine ionizable?
No
79
Is phenylalanine ionizable?
No
80
Is Tyrosine ionizable?
Yes
81
Is tryptophan ionizable?
No
82
Is cysteine ionizable?
Yes
83
Is methionine ionizable?
No
84
Is serine ionizable?
No
85
Is threonine ionizable?
No
86
Is asparagine ionizable?
No
87
Is glutamine ionizable?
No
88
Is aspartic acid ionizable?
Yes
89
Is glutamic acid ionizable?
Yes
90
Is lycine ionizable?
Yes
91
Is arginine ionizable?
Yes
92
Is histidine ionizable?
Yes
93
x
x
94
x
x
95
What state is lysine at physiological pH
acidic
96
x
x
97
x
x
98
x
x
99
Phospholipids can have protein access channels, explain
You can put in protein access channels that will move things in and out in a regulated fashion --> you can modulate the fluidity of these membranes
100
Why can't phospholipids form a micelle
Because they are too bulky so we get a bilayer structure instead
101
Describe the aqueous phases of the phospholipid bilayers
The aqueous phases are on inside and outside of a membrane
The chemical barrier of the bilayer prevents these 2 fluids from mixing
102
Phospholipids are
amphipathic
103
Is phosphate polar or non-polar
polar
104
Will polar molecules pass through phospholipid bilayers?
No
105
What barriers are phospholipids great at being?
They are great chemical barriers but not rigid enough to be physical barriers
106
Explain phospholipid membrane movement
The membranes have an outer and inner leaflet, the phospholipids can move 3D within a leaflet laterally
Changing the properties can slow down (rigid) or speed up (increase the fluid) their movement
They cannot flip flop from 1 side to the other
107
Discuss the fluid mosaic model of biological membranes
Proteins will jiggle its way in the membrane and the bilayer will make space for the protein via its fluidity
Proteins can either be internal/transmembrane (with a polar interior channel that allows things to go through) or peripheral that has its tail sitting in the membrane (could be a defense membrane)
Often these proteins need to be able to move and aggregate with other proteins to perform these defense functions
108
Explain how fatty acids and soap work
Fatty acids in soap will find hydrophobic locations on the hand aka the virus lipid envelope and disrupt it.
The phospholipids now have somewhere else to go other than the aqueous environment = embed within micelles
So we are disrupting the virus' ability to infect us **like dissolves like**
109
What is the only amino acid that has a Nitrogen that makes 2 bonds with carbon?
Proline (it has an imino acid)
110
What is the terminology for the N group on the left side of amino acids
L- amino acid
111
What is the terminology for the N group on the right side of amino acids
D-amino acid
112
General properties of amino acids
making 4 bonds with carbons
4 different substituent groups attached to Carbon = chiral
Chiral - mirror images but not superimposable
L stereoisomer found only in proteins!!
113
What are the "wonders of Cysteine"
it has a sulfur, thiol group, and can form disulfide bonds
it is also ambiguous regarding polar or non-polarity
it participates in many biological oxidation/reduction reactions
only side chains of a protein that can form a covalent bond
114
pKa of Cysteine
~8
115
pH < pKa ?
acid
116
pH > pKa
base
117
pH = pKa
1/2
118
What is phosphorylation and why is it used
Phosphate is an acid and will react with the OH and forms phosphate ester
Used to regulate a protein's function
119
What does neutral side mean regarding amino acids?
the side chain is not ionizable
120
What is a Zwitterion
+ and - charges can balance each other
121
low pH means what regarding state and charge?
all groups in acid state
below pH 2
122
high pH means what regarding state and charge
everything base state and it becomes neutral
carboxyl group loses its proton and becomes negatively charged -1
above pH 10
123
how do you find the pI
you take the average of the like charges
ex: 2 + 6 / 2
124
What pKa should be used when asked the pKa of a carboxyl group found on the alpha carbon of a free amino acid
pKa of 2
125
what pKa should be used at any other time for a carboxyl group besides when carbon of a free amino acid is on one
pKa of 4
126
What pKa is influenced by the environment
imidazole, 6
amino groups, 10
phenol, 10
127
Properties of Tyrosine
aromatic ring with a hydroxyl group
can ionize if pH is high enough
can delocalize extra electron
neutral at physiological pH
128
Discuss electron delocalization and tyrosine
electron delocalization within the aromatic ring stabilizes the ionized species and reduces pK of Tyrosine relative to Serine
129
alpha-carboxyl approximate pK
2
130
side chain carboxyl pK
4
131
imidazole pK
6
132
alpha and side chain amino groups pK
10
133
phenol pK
10
134
Guanidinium pK
12
135
Explain guanidinium and its net charge delocalization
The pK of 12 basically means it will be in acid state and be +1
136
Peptide bond formation is thermodynamically ?
Unfavorable so it won't happen spontaneously
137
Structure gives rise to
Function
138
Proteins with similar charge to mass ratios will migrate at the ?
same rate in an electric field
139
limitations to simple electrophoresis
Size
Large proteins = more friction
