Chapter 1: Amino Acids, Peptides & Proteins Flashcards
(104 cards)
1
Q
What components do all amino acids share?
A
A amino group, a carboxyl group, and an R group
2
Q
Define proteinogenic amino acids
A
The 20 alpha-amino acids that are encoded by the human genetic code
3
Q
Which amino acids are chiral?
A
All except for glycine
4
Q
Which of the chiral amino acids have an (S) absolute configuration
A
All chiral AAs (all but glycine) except for cysteine
5
Q
Three-letter abbreviation for Alanine
A
Ala
6
Q
Three-letter abbreviation for Arginine
A
Arg
7
Q
Three-letter abbreviation for Asparagine
A
Asn
8
Q
Three-letter abbreviation for aspartic acid / aspartate
A
Asp
9
Q
Three-letter abbreviation for cysteine
A
Cys
10
Q
Three-letter abbreviation for glutamic acid / glutamate
A
Glu
11
Q
Three-letter abbreviation for glutamine
A
Gln
12
Q
Three-letter abbreviation for glycine
A
Gly
13
Q
Three-letter abbreviation for Histadine
A
His
14
Q
Three-letter abbreviation for Isoleucine
A
Ile
15
Q
Three-letter abbreviation for Leucine
A
Leu
16
Q
Three-letter abbreviation for lysine
A
Lys
17
Q
Three-letter abbreviation for Methionine
A
Met
18
Q
Three-letter abbreviation for phenylalanine
A
Phe
19
Q
Three-letter abbreviation for proline
A
Pro
20
Q
Three-letter abbreviation for serine
A
Ser
21
Q
Three-letter abbreviation for threonine
A
Thr
22
Q
Three-letter abbreviation for tryptophan
A
Trp
23
Q
Three-letter abbreviation for tyrosine
A
Tyr
24
Q
Three-letter abbreviation for valine
A
Val
25
One-letter abbreviation for alanine
A
26
One-letter abbreviation for arginine
R
27
One-letter abbreviation for asparagine
N
28
One-letter abbreviation for aspartic acid / aspartate
D
29
One-letter abbreviation for cysteine
C
30
One-letter abbreviation for glutamic acid / glutamate
E
31
One-letter abbreviation for glutamine
Q
32
One-letter abbreviation for glycine
G
33
One-letter abbreviation for histadine
H
34
One-letter abbreviation for isoleucine
I
35
One-letter abbreviation for leucine
L
36
One-letter abbreviation for lysine
K
37
One-letter abbreviation for methionine
M
38
One-letter abbreviation for phenylalanine
F
39
One-letter abbreviation for proline
P
40
One-letter abbreviation for serine
S
41
One-letter abbreviation for threonine
T
42
One-letter abbreviation for tryptophan
W
43
One-letter abbreviation for tyrosine
Y
44
One-letter abbreviation for valine
V
45
Amino acid category for glycine
Non-polar, non-aromatic
46
Amino acid category for alanine
Non-polar, non-aromatic
47
Amino acid category for valine
Non-polar, non-aromatic
48
Amino acid category for leucine
Non-polar, non-aromatic
49
Amino acid category for isoleucine
Non-polar, non-aromatic
50
Amino acid category for methionine
Non-polar, non-aromatic
51
Amino acid category for proline
Non-polar, non-aromatic
52
Amino acid category for tryptophan
Aromatic
53
Amino acid category for phenylalanine
Aromatic
54
Amino acid category for tyrosine
Aromatic
55
Amino acid category for serine
Polar
56
Amino acid category for threonine
Polar
57
Amino acid category for asparagine
Polar
58
Amino acid category for glutamine
Polar
59
Amino acid category for cysteine
Polar
60
Amino acid category for aspartate
Acidic/negatively charged
61
Amino acid category for glutamate
Acidic / negatively charged
62
Amino acid category for arginine
Basic / positively charged
63
Amino acid category for lysine
Basic / positively charged
64
Amino acid category for histidine
Basic / positively charged
65
Define amphoteric species
Something that can either accept a proton or donate a proton, depending on the pH of their environment.
66
What makes amino acids amphoteric species?
They have both an acidic carboxylic acid group and a basic amino group
67
What is the pKa of a group?
The pH at which, on average, half of the molecules of a species are deprotonated
68
If pH < pKa then....
The majority of species are protonated
69
If pH > pKa then....
The majority of species are deprotonated
70
What is a zwitterion?
A molecule with both a positive and negative ion; dipolar ions
71
Which amino acids have ionizable side-chains? (7)
histidine, arginine, lysine, aspartate (aspartic acid), glutamate (glutamic acid), cysteine, tyrosine
72
For which amino acids with ionizable side chains do you calculate PI using the larger two pKa values?
histidine, arginine, lysine
73
For which amino acids with ionizable side chains do you calculate PI using the smaller two pKa values?
aspartate/aspartic acid, glutamate/glutamic acid, cysteine, and tyrosine
74
Amino acids with acidic side chains have pI values well _______ 6
below
75
Amino acids with basic side chains have pI values well __________ 6
above
76
At very acidic pH values, amino acids tend to be _________ly charged
Positively charged
77
At very basic pH values, amino acids tend to be _________ly charged
negatively charged
78
The surface of a protein tends to be rich in amino aicds with ________ ________ __________
Charged side chains
79
Strongly hydrophobic amino aicds tend to be found where?
In the interior of proteins
80
Residues are another name for:
Amino acid subunits
81
What are dipeptides made of?
Two amino acid residues
82
What are tripeptides made of?
Three amino acid residues
83
What does the term oligopeptides refer to?
Relatively small peptides, up to about 20 residues
84
What does the term polypeptides refer to?
Relatively larger peptides, with chains longer than about 20 residues
85
Define an electrophile
Any molecule, ion or atom that is in some manner deficient in electrons; it accepts a pair of electrons to form a new bond
86
Define a nucleophile
Any molecule, ion or atom, that has lone electrons to donate; tends to be negatively charged or neutral with an extra pair of electrons
87
Primary structure of proteins is stabilized by what?
The covalent peptide bonds between two adjacent amino acids
88
alpha-helices coil in what direction?
Counter clockwise
89
What bond structures stabilize alpha-helices?
intramolecular hydrogen bonds between a carbonyl oxygen and an amide hydrogen four residues down the peptide chain
90
What direction do the side chains point in an alpha-helix structure?
Away from the helix core
91
Two main shapes of proteins
Fibrous: long sheets or strands
Globular: spherical
92
Define molten globules
The intermediate states as a protein is forming its proper 3D structure
93
Define denaturation
When a protein loses its tertiary structure
94
Define conjugated proteins
Quaternary proteins that derive part of their function from covalently attached molecules called prostetic groups
95
Lipoproteins, glycoproteins, and nucleoproteins are all examples of what?
Conjugated proteins
96
In and L amino acid fischer projection, which group is positioned on the left?
The amino group
97
The stereochemistry of the alpha-carbon for all chiral aa's in eukaryotes is (L or D?) and all have a (R or S?) configuration, except for ______?
L; S; cysteine
98
What are the non-polar, non-aromatic amino acids? (7)
glycine, alanine, valine, leucine, isoleucine, methionine, proline
99
What are the aromatic amino acids? (3)
tryptophan, phenylalanine, tyrosine
100
What are the polar amino acids? (5)
serine, threonine, asparagine, glutamine, cysteine
101
What are the acidic (negatively charged) amino acids? (2)
aspartate, glutamate
102
What are the basic (positively charged) amino acids? (3)
lysine, arginine, histidine
103
pKa of amino group
around 9
104
pKa of carboxyl group
around 2
