Amino Acids Flashcards
(157 cards)
1
Q
What are the 2 functional groups of amino acids?
A
Amino group (NH2) and carboxyl group (COOH)
2
Q
What is a alpha-carbon
A
carbon that bonds the amino and the carboxyl is the same carbon
3
Q
What are the 4 components of amino acids?
A
Amino group, carboxyl group, hydrogen and a side chain (R-group)
4
Q
What does the side chain do?
A
Determines the proprieties and the functions of the amino acid
5
Q
What are called the 20 alpha-amino acids encoded by the human genetic code?
A
Proteinogenic amino acids
6
Q
What do you call the carbon when the alpha-carbon is in the center?
A
Chiral (stereogenic)
7
Q
How is the amino acid when the alpha-carbon is chiral?
A
Optically active
8
Q
What is the only amino acid non optically active?
A
Glycine
9
Q
How come Glycine isn’t optically active?
A
It has an hydrogen as the side chain, so it’s achiral
10
Q
What type of amino acids are all chiral amino acids used in eukaryotes?
A
L-Amino acids
11
Q
How do you draw an L-amino acid in the Fisher projection?
A
The amino group is drawn on the left
12
Q
What type of configuration has almost all of amino acids in Cahn-ingold-Prelog System
A
(S) absolute configuration
13
Q
Which amino acid is the exception of the Cahn-Ingold-Prelog System?
A
Cysteine has an (R) absolute configuration
14
Q
Why cysteine has a (R) absolute configuration?
A
The CH2SH group has priority over the COOH group
15
Q
What are the amino acids with non-polar, nonaromatic side chains?
A
Glycine, Alamine, Valine, Leucine, Isoleucine, Methionine, Proline
16
Q
What are the 3 letter and the 1 letter name for Glycine?
A
Gly and G
17
Q
What are the 3 letter and the 1 letter name for Alamine?
A
Ala, A
18
Q
What are the 3 letter and the 1 letter name for Valine?
A
Val, V
19
Q
What are the 3 letter and the 1 letter name for Leucine?
A
Leu, L
20
Q
What are the 3 letter and the 1 letter name for isoleucine?
A
Ile, I
21
Q
What are the 3 letter and the 1 letter name for Methionine?
A
Met, M
22
Q
What are the 3 letter and the 1 letter name for Proline?
A
Pro, P
23
Q
What are the 3 letter and the 1 letter name for Tryptophan
A
Trp, W
24
Q
What are the 3 letter and the 1 letter name for Phenylalanine?
A
Phe, F
25
What are the 3 letter and the 1 letter name for Tyrosine
Tyr, Y
26
What are the 3 letter and the 1 letter name for Serine
Ser, S
27
What are the 3 letter and the 1 letter name for Threonine
Thr, T
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What are the 3 letter and the 1 letter name for Arginine
Arg, R
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What are the 3 letter and the 1 letter name for Asparagine
Asn, N
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What are the 3 letter and the 1 letter name for Aspartic acid
Asp, D
31
What are the 3 letter and the 1 letter name for Glutamic acid
Glu, E
32
What are the 3 letter and the 1 letter name for Cysteine
Cys, C
33
What are the 3 letter and the 1 letter name for Glutamine
Gln, Q
34
What are the 3 letter and the 1 letter name for Histidine
His, H
35
What are the 3 letter and the 1 letter name for Lysine
Lys, K
36
Which amino acid is the smallest?
Glycine
37
Which amino acid is achiral?
Glycine
38
What is the side chain of Glycine?
A single H
39
What are the 2 amino acids with a sulfur atom in their side chain?
Methionine and cysteine
40
Why is methionine relatively non polar?
The sulfur atom is attached to a methyl group
41
What causes the 5 membered chain in Proline?
Limit its flexibility and has an effect on its role in secondary structure
42
What makes Proline unique?
The amino nitrogen's becomes part of the side chain
43
What are the amino acid with aromatic side chains?
Tryptophan, Phenylalanine and Tyrosine
44
What is the only double ring amino acid?
Tryptophan
45
What is the side chain of Phenylalanine?
Benzyl (benzene ring + CH2 group)
46
How can we compare the Phenylalanine and the Tyrosine polarity?
Phenylalanine is less polar (relatively non-polar) and Tyrosine is more polar (relatively polar)
47
What the difference between Phenylalanine and Tyrosine?
Phenylalanine with an OH added
48
What are the amino acids with polar side chains?
Serine, Threonine, Cysteine, Asparagine and Glutamine
49
What are the two amino acids with polar side chains that has an OH group in their side chain?
Serine and Threonine
50
What the effect of having a OH group making Serine and Threonine highly polar amino acids?
They are able to participate in hydrogen bonding
51
What Asparagine and Glutamine have in common?
Both have amide side chains
52
What is Cysteine side chain?
Thiol side chain
53
What is a thiol side chain?
-SH group
54
Why is the thiol group prone to oxydation?
It's thiol side chain (S-H bond if longer and weaker than O-H bond + the sulfur is more electronegative than the O)
55
What is the main difference between Asparagine/Glutamine and Aspartate/Glutamate?
Aspartate and Glutamate have a carboxylate group (-COO-)
56
What are the amino acids with a side chain negatively charged (acidic)?
Aspartic acid (aspartate) and Glutamic acid (glutamate)
57
What is aspartate compared to aspartic acid and glutamate compared to glutamic acid?
They are the anion (deprotonated aspartic acid or glutamic acid)
58
What are the amino acids with positively charged (basic) side chains?
Arginine, Lysine and Histidine
59
How many nitrogens are there in Arginine side chain?
3
60
What is Imidazole?
The aromatic ring with 2 nitrogens in Histidine
61
Where are amino acids with long alkyl side chains?
In the interior of the protein because it is HYDROPHOBIC
62
How are amino acids with charged side chains?
Hydrophilic
63
What are the amino acids with long alkyl side chains?
Alanine, Isoleucine, Valine, Phenylalanine
64
What are the amino acids with charged side chains?
Positively charged Histidine ,Arginine, Lysine, Negatively charged glutamate and aspartate and amides asparagine and glutamine
65
What are the amino acids more in the middle of the protein?
Cysteine, Glycine, Leucine, Methionine, Proline, Serine, Threonine, Tryptophan, Tyrosine
66
What is the acid group in the amino acid?
Carboxylic group (COOH)
67
What is the basic group in the amino acid?
Amino group (NH2)
68
What are amphoteric species?
Can either accept or donate a proton depending on the environment pH
69
What does ionizable group do in acidic conditions?
Tends to gain protons (protonated)
70
What does ionizable group do in basic conditions?
Tends to lose protons (deprotonated)
71
What means the pKa
pH where on average half of the molecules are protonated and half are deprotonated
72
Why does amino acids have 2 or more pKa
Because at least 2 groups can be protonated/deprotonated
73
What is the average pKa for carboxyl group?
2
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What is the average pKa for amide group?
9-10
75
At pH 1, what would be the charge an amino acid?
Positively charged (amino group and carboxylic acid group are both protonated. Amino = positively charged. Carboxylic acid = neutral charge)
76
At pH 7.4, what would be the charge of an amino acid?
Electrically neutral. Amino protonated (positively charged) and carboxylic deprotonated (negatively charged).
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How do you call an electrically neutral amino acid?
Zwitterions or dipolarions
78
At pH 10.5, what would be the charge of an amino acid?
Negatively charged. Amino acid deprotonated (negatively charged) and carboxyl deprotonated (negatively charged).
79
Why would the titration of an amino acid would look like 2 or 3 monoprotic titration curves?
If the side chain is charged it will be 3 curves
80
What happens to the titration curve when the pH is close to the pKa
The curve flattens
81
What is the pI
Isoelectric point (when every molecule is now electrically neutral
82
How do you calculate the pI of an neutral amino acid?
(pKa amino group + pKa carboxyl group)/2
83
How do you calculate the pI of an acid amino acid?
(pKa R group + pKa carboxyl group)/2
84
How do you calculate the pI of an acid amino acid?
(pKa amino group + pKa R group)/2
85
What are peptide made from?
Residue (amino acid subunits)
86
How many residue are in a dipeptide?
2
87
How many residue are in a oligopeptide?
20 or less
88
How many residue are in a polypeptide?
More than 20
89
What are peptide bonds?
Bonds between an COO- group of aa1 and NH3+ group of aa2
90
Peptide bond formation is made with what reaction?
Condensation or déshydratation (results in the removal of a water molecule (H2O)
91
How else can a peptide bond formation be viewed as?
Acyl substitution reaction
92
How is a peptide bond formed?
The electrophilic carbonyl carbon of aa1 is attacked by the nucleophilic amino group of aa2. The hydroxyl group of the carboxylic group is kicked off
93
What does resonance causes?
Rotation of the protein backbone around C-N amide bonds is restricted (not around other bonds that are single bonds) = protein more rigid
94
What is resonance?
C-N bond in the amide gets a partial double bond character
95
How do you read a peptide bond?
From N-Terminus (amino-terminus) to C-Terminus (carboxy-terminus)
96
What is hydrolysis?
Breaking down peptides into amino acids by adding an hydrogen atom to the amide group and a OH group to the carboxyl group
97
What are hydrolytic enzymes?
Enzymes that does hydrolysis
98
Hame 2 hydrolytic enzymes
Trypsin and Chymotrypsin
99
Where does trypsin acts?
At the carboxyl end of arginine and lysine
100
Where does Chymotrypsin acts&
At the carboxyl end of phenylalanine, tryptophan and tyrosine
101
What are examples of what a protein can be?
Enzymes, hormones, membrane pores and receptors, elements of cell structure
102
What is the primary structure of a protein?
Linear arrangement of aa coded in DNA, from N-terminus to C-terminus
103
How are primary structure stabilized?
By covalent peptides bonds between adjacent aa
104
How can you find the primary structure of a protein?
In a lab while doing sequencing (from the DNA or the protein itself)
105
True or False, the primary structure encodes all the information needed for higher structural levels?
True
106
What is the secondary structure?
Neighbouring aa (either in alpha-helix or beta-pleated sheet)
107
Secondary structure is created by what?
Hydrogen bonding between nearby aa
108
How are secondary structure stabilized?
Intramolecular hydrogen bonds between residues
109
What direction goes the alpha-helix formation?
Clock-wise around a central axis
110
How are intramolecular hydrogen bonds are matched in alpha-helix?
From carbonyl oxygen atom to the amide hydrogen 4 residue down
111
How are the side chains placed in alpha-helices&
Pointing away of the helix core
112
What is an example of alpha-helix protein?
Keratin
113
What are beta-pleated sheets like?
Parallel or antiparallel, chains along side another. Pleated or rippled shape
114
How are the intramolecular hydrogen bonds are matched in beta-pleated sheets?
From atoms from adjacent chains
115
How are the side chains orientated in beta-pleated sheets?
Above and below the plane of the sheet
116
What is an protein example of beta-pleated sheet?
Fibroin
117
What happens if a proline is in a alpha-helix formation?
It's rigid cyclic structure would cause a kink in the peptide chain in the middle of the alpha-helix
118
When could you see a proline in an alpha-helix formation?
If it's in protein that crosses the cell membrane
119
Where would a proline be placed in an alpha-helix formation?
At the start
120
Where would you rarely see a proline in a beta-pleated sheet?
In the middle
121
Where would you find a proline in a beta-pleated sheet?
In the turns between the chains
122
What are the 2 types of proteins?
Fibrous and globular
123
What is the shape of a fibrous protein?
Sheets or long strands
124
Name an example of fibrous protein
Collagen
125
Name an example of globular protein
Myoglobin
126
How are tertiary and quaternary structure made?
Protein folding
127
What determines the tertiary structure?
Hydrophilic and hydrophobic interactions between R-groups of aa.
Hydrogen bonding
Acid-base interactions
Disulfide bonds
128
What is the mechanism of hydrophilic and hydrophobic interactions that causes the protein to fold?
The hydrophobic residue wants to be inside of the protein. The hydrophobic residues inside the protein pull hydrophilic bonds such as N-H and C=O inside so they can form electrostatic interactions and hydrogen bonds that'll stabilize the protein from the inside.
129
Phenylalanine is a highly hydrophobic group, where will it will almost always be in the protein?
It will mostly be inside, not on the surface of the protein
130
What are residues at the surface of the protein usually like?
Hydrophilic and polar or charged
131
What are salt bridges?
Acid-base interactions between aa with charged groups
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What are disulfide bonds?
When 2 cysteine oxidized into 1 cystine
133
What does disulfide bonds do to the protein?
Create loops
134
What determines how wavy or curly our hair is?
Disulfide bonds
135
What is required to do a disulfide bond?
The loss of 2 protons and 2 electrons
136
What is called the intermediate state while the protein in folding?
Molten globules
137
What is denaturation?
When a protein loses its 3D structure
138
What is a salvation layer?
The layer formed around a solute with the solvant
139
What are quaternary structure made from?
Protein that contains more than 1 polypeptides chain.
140
What is a quaternary structure?
Aggregate of smaller globular particules or subunits
141
What does the quaternary structure represents?
The functional form of a protein
142
Does every protein has a quaternary structure?
No
143
What are examples of quaternary structure?
Hémoglobine and immunoglobulin G
144
What are the similarity between hémoglobine and immunoglobuline G
They both have 4 subunits
145
Why would one be in quaternary structure?
More stable,
Limits the amount of DNA needed to encode protein complex
Bring catalytic sites closer together
Induce cooperatively or allosteric effets
146
What is the point of bringing catalytic sites closer together?
Intermediates from one reaction are directly shuttled to a second reaction
147
What are conjugated proteins?
Proteins that gives part of their function ro a covalently attached molecule
148
What are called the group giving the conjugated protein their function
Prosthetic group
149
Lipoprotein, glycoprotein, nucleoproteins, what are they?
Prosthetic groups made from either lipid, carbohydrate or nucleic acid respectfully
150
Other than giving functionality to a protein, what can a prosthetic group do?
Direct protein to be delivered to a certain location
151
Is denaturation reversible?
It can be. It is usually irreversible tho
152
What can't an unfolded protein do?
Catalyse reactions
153
What are the 2 main causes of denaturation?
Heat and solute
154
How does heat can desaturate a protein?
While the Temp is rising, the kinetic energy level is too. Once it's high enough, it can overcome the hydrophobic-hydrophilic reaction holding the protein together
155
How can solute denaturate a protein?
Break disulfide bridges
Overcome hydrogen bonds and other side chains interactions holding alpha-helix and beta-pleated sheets
Solubilize protein
156
What does solubilizing a protein does?
Disrupt the non covalent bonds and promote denaturation
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