C4 Amino acids and drug-target interactions Flashcards
1
Q
3 letter code and 1 letter code for alanine
A
Ala
A
2
Q
3 letter code and 1 letter code for arginine
A
Arg
R
3
Q
3 letter code and 1 letter code for asparagine
A
Asn
N
4
Q
3 letter code and 1 letter code for aspartic acid
A
Asp
D
5
Q
3 letter code and 1 letter code for cysteine
A
Cys
C
6
Q
3 letter code and 1 letter code for glutamic acid
A
Glu
E
7
Q
3 letter code and 1 letter code for glutamine
A
Gln
Q
8
Q
3 letter code and 1 letter code for glycine
A
Gly
G
9
Q
3 letter code and 1 letter code for histidine
A
His
H
10
Q
3 letter code and 1 letter code for isoleucine
A
Ile
I
11
Q
3 letter code and 1 letter code for leucine
A
Leu
L
12
Q
3 letter code and 1 letter code for lysine
A
Lys
K
13
Q
3 letter code and 1 letter code for methionine
A
Met
M
14
Q
3 letter code and 1 letter code for phenylalanine
A
Phe
F
15
Q
3 letter code and 1 letter code for proline
A
Pro
P
16
Q
3 letter code and 1 letter code for serine
A
Ser
S
17
Q
3 letter code and 1 letter code for threonine
A
Thr
T
18
Q
3 letter code and 1 letter code for tryptophan
A
Trp
W
19
Q
3 letter code and 1 letter code for tyrosine
A
Tyr
Y
20
Q
3 letter code and 1 letter code for valine
A
Val
V
21
Q
how are amino acids and peptides conventionally represented?
A
- N-terminus on the left
- C-terminus on the right
22
Q
describe the stereochemistry and chirality of the alpha-carbon in amino acids
A
- nearly always S
- nearly always chiral (not in glycine)
23
Q
describe the side chains and backbone of proteins / amino acids
A
- side chains are the R groups of the amino acids in the protein
- the rest of the amino acid forms the backbone (repeating structure that doesn’t change in proteins regardless of the R groups)
24
Q
what are the 6 different classifications of amino acids acids?
A
alkyl
(neutral) polar
sulfur-containing
aromatic
anionic
cationic
25
which 6 amino acids are in the alkyl classification?
glycine
alanine
valine
leucine
isoleucine
proline
26
which 4 amino acids are in the (neutral) polar classification?
serine
threonine
asparagine
glutamine
27
which 2 amino acids are in the sulfur-containing classification?
cysteine
methionine
28
which 3 amino acids are in the aromatic classification?
phenylalanine
tyrosine
tryptophan
29
which 2 amino acids are in the anion classification?
aspartic acid
glutamic acid
30
which 3 amino acids are in the cationic classification?
histidine
lysine
arginine
31
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
glycine
Gly
G
alkyl
32
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
alanine
Ala
A
alkyl
33
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
valine
Val
V
alkyl
34
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
leucine
Leu
L
alkyl
35
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
isoleucine
Ile
I
alkyl
36
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group. what is special about this amino acid in protein chains?
proline
Pro
P
alkyl
proline has a tertiary amide group in protein chains
37
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
serine
Ser
S
polar
38
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
threonine
Thr
T
polar
39
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
asparagine
Asn
N
polar
40
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
glutamine
Gln
Q
polar
41
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
cysteine
Cys
C
sulfur-containing
42
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
methionine
Met
M
sulfur-containing
43
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
phenylalanine
Phe
F
aromatic
44
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
tyrosine
Tyr
Y
aromatic
45
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
tryptophan
Trp
W
aromatic
46
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
aspartic acid
Asp
D
anionic
47
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
glutamic acid
Glu
E
anionic
48
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
histidine
His
H
cationic
49
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
lysine
Lys
K
cationic
50
what amino acid is this? state its full name, 3 letter code, 1 letter code and classification group.
arginine
Arg
R
cationic
51
what does Phe77 mean in a diagram representing a peptide?
the phenylalanine amino acid is the 77th amino acid in that polypeptide
52
state some non-covalent interactions
electrostatic interactions
hydrogen bonds
pi-pi interactions
hydrophobic interactions
53
simply describe pi-pi interactions
pi bonds interacting (a form of aromatic interaction)
54
explain electrostatic interactions in terms of peptide-drug interactions
cationic and anionic amino acids can become ionised and have charge and can then be attracted to ionised drugs
55
describe hydrogen bonds and their ideal conditions for them to occur in
- common example of strong dipole-dipole interaction
- occur between HBD and HBA
- distance and angle are important (have to be close enough to interact, shorter distance increases strength of attraction)
- ideally linear and located close together
- in image, top bond will be stronger due to linear angle between the orbitals
56
which of the atoms in an amide is an HBA, N or O? and why?
- nitrogen is not an HBA
- its lone pair is delocalised and therefore not available to donate
- oxygen is an HBA
- lone pairs are localised so they are available to donate
57
why are carboxylic acids only rarely HBDs?
- they are acids!
- proton has often dissociated so it is not there or available to be donated
58
despite having a localised lone pair, what functional group is not often an HBA?
amines
59
what does this image show you about OH groups?
can act as an HBA and HBD at the same time
60
explain how aromatic interactions work
- aromatic rings are planar and have pi rings of electrons above and below so there is a region of negative charge above and below the ring and positive regions at the sides
- aromatic rings interact in a T shape because the positive sides interact with the negatively top/bottom (shown in images)
61
describe a simplified image of a parallel displaced aromatic interaction
62
what is a cation-pi interaction?
- a positive functional group can also interact with the negative top/bottom of an aromatic ring
63
describe the background of Sildenafil
- brand name is Viagra
- discovered by accident
- used to treat erectile dysfunction and pulmonary hypertension
- inhibitor of PDE5 and leads to smooth muscle relaxation
64
what does phosphodiesterase do?
breaks phosphodiester bond
65
what is cGMP?
- cyclic guanosine monophosphate
- cyclic nucleotide
- 'second messenger' (triggers intracellular signal transduction cascades)
66
what does sildenafil inhibit?
phosphodiesterase type 5 (PDE5)
67
describe the interactions that Sildenafil makes
- sildenafil shown in red
Glutamine-281:
- R group is an amide
- dotted lines are hydrogen bonds
Phenylalanine-284
- dotted line is an edge to base aromatic interaction (T shape)
