02 Basic AminoAcids

Amino Acids
With Dr. Kevin Ahern
Paulina seok, paulinam757@gmail.com

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Part 1 - Amino Acids
Structure and Chemistry
• Building blocks of proteins
• Essential amino acids
• Basic structure
• Stereochemistry
• Side chain chemistry
• Properties
• Ionization
• Bonding

Amino Acids & Proteins
Workhorses of Cell
• Catalysis
• Signaling
• Structure
• Energy/gradient generation
• Proteins comprised of 20-21 Amino Acids

Amino Acids
Essential Amino Acids
Essential Nonessential
Histidine Alanine
Isoleucine Arginine
Leucine Aspartic acid
Lysine Cysteine
Methionine Glutamic acid
Phenylalanine Glutamine
Threonine Glycine
Tryptophan Proline
Valine Serine
Tyrosine
Asparagine
Selenocysteine

Basic of Structure
Elements
Alpha amino acids
O
Alpha carbon H
R C C
N O
H H
H

Basic of Structure
Elements
Alpha amino acids
O
Alpha carbon H Alpha carboxyl
R C C
N O
H H
H

Basic of Structure
Elements
Alpha amino acids
O
R C C
Alpha amine N O
H H
H

Basic of Structure
Elements
Alpha amino acids
Differences in R groups
O
R C C
Alpha amine N O
H H
H

Basic of Structure
Elements
Alpha amino acids
O
H
Alpha carboxyl R C C
Examples
Alpha carbon O N O
H H
H
R
HS OH
Alpha amine
NH2
Cysteine

Basic of Structure
Elements
Alpha amino acids
O
H
Alpha Carboxyl R C C
Examples
Alpha Carbon O N O
H H
H
OH
R
NH2 Alpha Amine
Phenylalanine

Amino Acids
Stereochemistry
D and L Isomers
Asymmetric carbon
D-Glyceraldehyde L-Glyceraldehyde
Allmost all biological amino acids are in the L configuraton

Amino Acids
R-Group Categories
Hydrophobic Hydrophilic Ionic
Aromatic Hydroxyl Carboxylates

Trp, Phe, Tyr Ser, Thr, Tyr Asp, Glu
Aliphatic Sulfhydryl Amines

Met, Ile, Leu, Val, Gly, Cys Lys, His, Arg
Ala, Pro
Carboxyamides
Asn, Gln
Some amino acids (Tyr & Gly) appear in more than one category.
Authors differ in how they categorize amino acids.

Amino Acids
Aromatic R-Groups
OH
Alpha carboxyl HN NH2

Tryptophan
Alpha carbon O O
OH OH
NH2 Alpha amine NH2

HO
Tyrosine Phenylalanine

Amino Acids
Aromatic R-Groups
Charges at physiological pH
O
Ionizes at high pH
O -
R HN NH3 +
Tryptophan
O O
O - O -
R
HO
NH3 + NH3 +
Tyrosine Phenylalanine

Amino Acids
Aliphatic R-Groups
O O O CH3 O
H3C
O - H O - O - H3C
O -
NH3 + NH3 + NH2 +
NH3 +
Alanine Glycine Proline Isoleucine
O O
CH3 O
- S
H3C H3C O -
O - H3C O
H3C NH3 + NH3 +
NH3 +
Leucine Valine Methionine
Amino Acids
Carboxylate R-Groups
Charges at Physiological pH
O O O
O
O - O - O -
O - NH3 + NH3 +
Aspartic acid Glutamic acid

Amino Acids
Hydroxyl R-Groups
Charges at Physiological pH
OH O
H3C O -
NH3 +
Threonine
O
O
HO O - O -
Ionizes at high pH
NH3 + NH3 +
HO
Serine Tyrosine

Amino Acids
Sulfhydryl R-Group
HS - O -
NH3 +
Ionizes at high pH = 8
Cysteine

Amino Acids
Carboxamide R-Groups
O O O
O
O - H2N O -
NH2 NH3 + NH3 +
Asparagine Glutamine

Amino Acids
Ionizable Amine R-Groups
H3N +
O -
NH3 +
Lysine
NH2 O O
+ H
N
+
H2N N O - O -
H
NH3 + HN NH3 +
Arginine Histidine

Amino Acids
Ionization
COOH COO- COO- COO-
H3N+ CH pK1 H3N+ CH pK2 H3N+ CH pK3 H2N CH
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
Charge = +1
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
Charge = 0
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
Charge = -1
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Ionization
COOH COO- COO- COO-
CH2 CH2 CH2 CH2
COOH COOH COO- COO-
14
12 pK3
10
Charge = -2
pH 8
pK2
6 pl
pK1
4
2
0 Equivalents
0 0,5 1 1,5 2 2,5 3 of OH

Amino Acids
Additional Information
Amino Acid 3-Letter 1-Letter Slide-chain Slide-chain charge Hydropathy Absorbance 𝛆𝛆 at 𝛌𝛌max MW
polarity (pH 7.4) Index 𝛌𝛌max(nm) (mM-1 cm-1) (Weight)
Alanine Ala A Nonpolar Neutral 1.8 89
Arginine Arg R Basic polar Positive -4.5 174
Asparagine Asn N Polar Neutral -3.5 132
Aspartic acid Asp D Acidic polar Negative -3.5 133
Cysteine Cys C Nonpolar Neutral 2.5 250 0.3 121
Glutamic acid Glu E Acidic polar Negative -3.5 147
Glutamine Gln Q Polar Neutral -3.5 146
Glycine Gly G Nonpolar Neutral -0.4 75
Histidine His H Basic polar Positive (10%) Negative (90%) -3.2 211 5.9 155
Isoleucine Ile I Nonpolar Neutral 4.5 131
Leucine Leu L Nonpolar Neutral 3.8 131
Lysine Lys K Basic polar Positive -3.9 146
Methionine Met M Nonpolar Neutral 1.9 149
Phenylalanine Phe F Nonpolar Neutral 2.8 257, 206, 188 0.2, 9.3, 60.0 165
Proline Pro P Nonpolar Neutral -1.6 115
Serine Ser S Polar Neutral -0.8 105
Threonine Thr T Polar Neutral -0.7 119
Tryptophan Trp W Nonpolar Neutral -0.9 280, 219 5.6, 47.0 204
Tyrosine Tyr Y Polar Neutral -1.3 274, 222, 193 1.4, 8.0, 48.0 181
Valine Val V Nonpolar Neutral 4.2 117

This document is a property of: Paulina seok
Note: This document is copyright protected. It may not be copied, reproduced, used, or
distributed in any way without the written authorization of Lecturio GmbH.


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Amino Acids

With Dr. Kevin Ahern

Paulina seok, paulinam757@gmail.com

• Building blocks of proteins

• Essential amino acids

• Side chain chemistry

Paulina seok, paulinam757@gmail.com

• Proteins comprised of 20-21 Amino Acids

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

NH2 Alpha Amine

Paulina seok, paulinam757@gmail.com

Allmost all biological amino acids are in the L configuraton

Paulina seok, paulinam757@gmail.com

Hydrophobic Hydrophilic Ionic

Aromatic Hydroxyl Carboxylates

Aliphatic Sulfhydryl Amines

Authors differ in how they categorize amino acids.

Paulina seok, paulinam757@gmail.com

Alpha carboxyl HN NH2

NH2 Alpha amine NH2

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Aspartic acid Glutamic acid

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

Paulina seok, paulinam757@gmail.com

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