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

3. amino acids Flashcards

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
Q

why are the polar amino acids polar?

A

they contain functional groups that form hydrogen bonds with water (consist of mostly O’s or N’s)

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26
Q

which polar amino acid is the least polar + why

A

cysteine, it has a sulfhydryl group and is a weak acid

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27
Q

describe the role of cysteine in protein shape

A

2 cysteine residues can oxidize to form a disulfide bridge to form a dimeric amino acid called cystine

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28
Q

which amino acids are basic (+ charged)

A

lysine, arginine, and histidine

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29
Q

describe the R groups of the basic amino acids

A

positively charged residues all have some sort of N, but the protonated forms have different number of hydrogens

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30
Q

which amino acids are acidic (- charged)

A

aspartate and glutamate

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31
Q

which amino acids are aromatic rings and relatively non-polar

A

phenylalanine, tyrosine, tryptophan

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32
Q

T or F; the aromatic amino acids absorb ultraviolet light

A

true

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33
Q

what is the purpose of the aromatic amino acids being able to absorb uv light

A

used to help identify samples with protein

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34
Q

which aromatic amino acid is the best at uv absorption

A

tryptophan

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35
Q

alanine

A

Ala, A

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36
Q

arginine

A

Arg, R

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37
Q

asparagine

A

Asn, N

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38
Q

aspartate

A

Asp, D

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39
Q

cysteine

A

Cys, C

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40
Q

glutamate

A

Glu, E

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41
Q

glutamine

A

Gln, Q

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42
Q

glycine

A

Gly, G

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43
Q

histidine

A

His, H

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44
Q

isoleucine

A

Iso, I

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45
Q

leucine

A

Leu, L

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46
Q

lysine

A

Lys, K

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47
Q

methionine

A

Met, M

48
Q

phenylalanine

A

Phe, F

49
Q

proline

A

Pro, P

50
Q

serine

A

Ser, S

51
Q

threonine

A

Thr, T

52
Q

tryptophan

A

Trp, W

53
Q

tyrosine

A

Try, Y

54
Q

valine

A

Val, V

55
Q

Ala

A

alanine

56
Q

Arg

A

arginine

57
Q

Asn

A

asparagine

58
Q

Asp

A

aspartate

59
Q

Cys

A

cysteine

60
Q

Glu

A

glutamate

61
Q

Gln

A

glutamine

62
Q

Gly

A

glycine

63
Q

His

A

histidine

64
Q

Iso

A

isoleucine

65
Q

Leu

A

leucine

66
Q

Lys

A

lysine

67
Q

Met

A

methionine

68
Q

Phe

A

phenylalanine

69
Q

Pro

A

proline

70
Q

Ser

A

serine

71
Q

Thr

A

threonine

72
Q

Trp

A

tryptophan

73
Q

Try

A

tyrosine

74
Q

Val

A

valine

75
Q

A

A

alanine

76
Q

R

A

arginine

77
Q

N

A

asparagine

78
Q

D

A

aspartate

79
Q

C

A

cystine

80
Q

E

A

glutamate

81
Q

Q

A

glutamine

82
Q

G

A

glycine

83
Q

H

A

histidine

84
Q

I

A

isoleucine

85
Q

L

A

leucine

86
Q

K

A

lysine

87
Q

M

A

methionine

88
Q

F

A

phenylalanine

89
Q

P

A

proline

90
Q

S

A

serine

91
Q

T

A

threonine

92
Q

W

A

tryptophan

93
Q

Y

A

tyrosine

94
Q

V

A

valine

95
Q

how is hydropathy quantified

A

by measuring the free-energy difference (delta G) of the amino acid side chain as it moves from a hydrophobic solvent to water

96
Q

what does a positive hydropathy value indicate

A

more positive=more hydrophobic side chain

97
Q

what does a negative hydropathy value indicate

A

more negative=more hydrophilic

98
Q

how many amino acids have been found

A

over 500

99
Q

what is a post-translational modification

A

it’s when a common amino acid is permanently modified after being incorporated into the polypeptide chain

100
Q

are the 500+ amino acids found in proteins? what is their purpose

A

no; they still have important metabolic roles though (ie urea cycle in the liver)

101
Q

what are amino acid derivatives

A

common amino acids modified by enzymes to produce biologically important amines

102
Q

list some of the amino acid derivatives

A

GABA, histamine, capsaicin, adrenaline, vanillin, auxin

103
Q

T or F: amino acids can act as weak acids and bases

A

true; because they’re charged at pH=7

104
Q

which group of the amino acid will donate protons

A

NH3+

105
Q

which group of the amino acid will accept protons

A

COO-

106
Q

why does each amino acid have two pKa values

A

two protons can be donated from a fully deprotonated backbone

107
Q

how many inflection points should there be on an amino acid titration curve

A

at least 2

108
Q

what is pI and what is the charge at this point

A

isoelectric point. The net charge is zero

109
Q

what is the pI formula

A

(pK1+pK2)/2

110
Q

how many of the amino acids have an ionizable side chain

A

7 of 20

111
Q

what is the result of having an ionizable side chain

A

they have another value, pKR

112
Q

define residue

A

residue describes one amino acid in a polypeptide chain

113
Q

what type of reaction forms a peptide bond

A

condensation reaction (aka dehydration)

114
Q

how do you name peptides

A

replace the -ine or -ate with -yl

for asparagine, glutamine, and cysteine: replace the -e with -yl

115
Q

how do you name a full peptide

A

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
Q

what components of the amino acids contribute to the charge of the peptide

A

only the amino and carboxyl groups are ionized at cellular pH. The remainder doesn’t contribute to the charge

117
Q

how do you determine the overall charge of a peptide

A

sum any individual charges on: amino terminus, carboxyl terminus, and any ionizable R groups

BIOL 2421 - Cellular Biochem (21 decks)

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