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BIOL 2421 - Cellular Biochem > 3. amino acids > Flashcards

3. amino acids Flashcards

(117 cards)

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1
Q

T or F: the backbone is consistent for all amino acids

A

true

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2
Q

T or F: all R groups are similar

A

false; R groups vary in structure, size, charge, and solubility in water

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3
Q

how are proteins formed

A

a folded linear chain of covalently-bound amino acids forms a protein

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4
Q

describe an amino acid’s charge at physiological pH

A

the amino group is protonated and the carboxyl group is ionized

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5
Q

what is the amino group at physiological pH

A

NH3+

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6
Q

what is the carboxyl group at physiological pH

A

COO-

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7
Q

define zwitterions

A

dipolar ions. These refer to the amino and carboxyl groups when they’re charged (pH=7)

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8
Q

what is the NET charge of the zwitterions

A

zero (one is + and one is -)

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9
Q

in an amino acid, what is the alpha carbon

A

alpha carbon is the one attacked to the amino group, carboxyl group, R group, and H

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10
Q

T or F; the alpha carbon is chiral

A

true, but only in 19 of 20 amino acids

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11
Q

in which amino acid is carbon NOT chiral

A

glycine, whose R group is a hydrogen

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12
Q

what are the two configurations of amino acids called

A

L and D

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13
Q

do amino acids have conformations or configurations. Why?

A

configurations; bonds need to be broken to switch between L and D

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14
Q

describe the process on figuring out if an amino acid is L or D

A

place the chiral carbon in the center with the carboxyl above it and the R group below. If the amino group is on the left=L, on the right =D

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15
Q

T or F: if no configuration is designated, we can assume the amino acid is D

A

false; always assume L unless specifically designated D

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16
Q

T or F; switching between L and D is favourable

A

false; it requires breakage of bonds

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17
Q

why do we use greek letters instead of numbers to name amino acids

A

because then the carboxyl carbon would have to be denoted number 1, and we don’t want this

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18
Q

which are the non polar amino acids

A

glycine, alanine, proline, valine, leucine, isoleucine, methionine

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19
Q

why are non-polar amino acids non-polar?

A

their R groups have lots of hydrocarbons, so they cluster together due to the hydrophobic effect

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20
Q

why is proline a unique non-polar amino acid

A

it’s cyclic, so it often introduces kinks or bends in a polypeptide chain

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21
Q

which of the non-polar amino acids has the smallest contribution to the hydrophobic effect + why

A

glycine, because it’s R group is only an H

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22
Q

which of the non-polar amino acids are the most significant in terms of the hydrophobic effect + why?

A

alanine, valine, leucine, and isoleucine. This is because they are solely C and H

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23
Q

describe methionine (non-polar amino acid)

A

it has a slightly polar thioether in the side chain, but is still grouped as non-polar

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24
Q

list the polar amino acids

A

serine, threonine, cysteine, asparagine, and glutamine

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25
why are the polar amino acids polar?
they contain functional groups that form hydrogen bonds with water (consist of mostly O's or N's)
26
which polar amino acid is the least polar + why
cysteine, it has a sulfhydryl group and is a weak acid
27
describe the role of cysteine in protein shape
2 cysteine residues can oxidize to form a disulfide bridge to form a dimeric amino acid called cystine
28
which amino acids are basic (+ charged)
lysine, arginine, and histidine
29
describe the R groups of the basic amino acids
positively charged residues all have some sort of N, but the protonated forms have different number of hydrogens
30
which amino acids are acidic (- charged)
aspartate and glutamate
31
which amino acids are aromatic rings and relatively non-polar
phenylalanine, tyrosine, tryptophan
32
T or F; the aromatic amino acids absorb ultraviolet light
true
33
what is the purpose of the aromatic amino acids being able to absorb uv light
used to help identify samples with protein
34
which aromatic amino acid is the best at uv absorption
tryptophan
35
alanine
Ala, A
36
arginine
Arg, R
37
asparagine
Asn, N
38
aspartate
Asp, D
39
cysteine
Cys, C
40
glutamate
Glu, E
41
glutamine
Gln, Q
42
glycine
Gly, G
43
histidine
His, H
44
isoleucine
Iso, I
45
leucine
Leu, L
46
lysine
Lys, K
47
methionine
Met, M
48
phenylalanine
Phe, F
49
proline
Pro, P
50
serine
Ser, S
51
threonine
Thr, T
52
tryptophan
Trp, W
53
tyrosine
Try, Y
54
valine
Val, V
55
Ala
alanine
56
Arg
arginine
57
Asn
asparagine
58
Asp
aspartate
59
Cys
cysteine
60
Glu
glutamate
61
Gln
glutamine
62
Gly
glycine
63
His
histidine
64
Iso
isoleucine
65
Leu
leucine
66
Lys
lysine
67
Met
methionine
68
Phe
phenylalanine
69
Pro
proline
70
Ser
serine
71
Thr
threonine
72
Trp
tryptophan
73
Try
tyrosine
74
Val
valine
75
A
alanine
76
R
arginine
77
N
asparagine
78
D
aspartate
79
C
cystine
80
E
glutamate
81
Q
glutamine
82
G
glycine
83
H
histidine
84
I
isoleucine
85
L
leucine
86
K
lysine
87
M
methionine
88
F
phenylalanine
89
P
proline
90
S
serine
91
T
threonine
92
W
tryptophan
93
Y
tyrosine
94
V
valine
95
how is hydropathy quantified
by measuring the free-energy difference (delta G) of the amino acid side chain as it moves from a hydrophobic solvent to water
96
what does a positive hydropathy value indicate
more positive=more hydrophobic side chain
97
what does a negative hydropathy value indicate
more negative=more hydrophilic
98
how many amino acids have been found
over 500
99
what is a post-translational modification
it's when a common amino acid is permanently modified after being incorporated into the polypeptide chain
100
are the 500+ amino acids found in proteins? what is their purpose
no; they still have important metabolic roles though (ie urea cycle in the liver)
101
what are amino acid derivatives
common amino acids modified by enzymes to produce biologically important amines
102
list some of the amino acid derivatives
GABA, histamine, capsaicin, adrenaline, vanillin, auxin
103
T or F: amino acids can act as weak acids and bases
true; because they're charged at pH=7
104
which group of the amino acid will donate protons
NH3+
105
which group of the amino acid will accept protons
COO-
106
why does each amino acid have two pKa values
two protons can be donated from a fully deprotonated backbone
107
how many inflection points should there be on an amino acid titration curve
at least 2
108
what is pI and what is the charge at this point
isoelectric point. The net charge is zero
109
what is the pI formula
(pK1+pK2)/2
110
how many of the amino acids have an ionizable side chain
7 of 20
111
what is the result of having an ionizable side chain
they have another value, pKR
112
define residue
residue describes one amino acid in a polypeptide chain
113
what type of reaction forms a peptide bond
condensation reaction (aka dehydration)
114
how do you name peptides
replace the -ine or -ate with -yl for asparagine, glutamine, and cysteine: replace the -e with -yl
115
how do you name a full peptide
list all the residue names together as one word. Each gets the -yl ending except for the last one where the name doesn't change
116
what components of the amino acids contribute to the charge of the peptide
only the amino and carboxyl groups are ionized at cellular pH. The remainder doesn't contribute to the charge
117
how do you determine the overall charge of a peptide
sum any individual charges on: amino terminus, carboxyl terminus, and any ionizable R groups

BIOL 2421 - Cellular Biochem (21 decks)

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