Amino acids
Essential Amino Acids
• 10 amino acids not synthesized by the body
• arg, his, ile, leu, lys, met, phe, thr, trp, val
• Must obtain from the diet
• All in diary products
• 1 or more missing in grains
and vegetables
• All proteins are composed of the 20 standard amino acids. They are referred to as α-amino acids with the exception of proline
-Amino Acids
NH2 always attached to the -carbon
(the carbon attached to COOH)
C = -carbon
H2N C
H
COOH
R
• In the physiological pH range, both the carboxylic acid group and the amino groups of the α-amino acids ionize. An Amino acid can therefore act as both an acid and a base.
• This property is called amphoteric, and they are referred to as ampholytes.
Physiological Amino Acids
• Molecules that bear charged groups of opposite polarity are called zwitterions or dipolar molecules.
H C
COO-
R
NH3+
Amino Acids as Acids and Bases
• Ionization of the –NH2 and the –COOH group
• Zwitterion has both a + and – charge• Zwitterion is neutral overall
+
NH2–CH2–COOH H3N–CH2–COO–
glycine Zwitterion of glycine
• Because they are dipoles, they have physical properties characteristic of ionic substances.
• This makes amino acids more soluble in polar solvents than in nonpolar ones.
• Most α-amino acids are very soluble in water but largely insoluble in most organic solvents
pH and ionization
H+ OH–
+ +
H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–
COO–
Positive ion zwitterion Negative ion
Low pH neutral pH High pH
• α-amino acids polymerize through the elimination of a water molecule the resulting CO-NH linkage is known as a peptide bond.
• Polymers composed of 2,3,a few(3-10), and many amino acids residues are known respectively as dipeptides, tripeptides, oligopeptides, and polypeptides.
Peptides
• Amino acids linked by amide (peptide) bonds
Gly Lys Phe Arg Ser
H2N- -COOH
end Peptide bonds end
Glycyllysylphenylalanylarginylserine
Learning Check AA4
Write the three-letter abbreviations for the following tetrapeptide:
H3N CH
CH3
C
O
N
H
CH C
O
N
H
CH C
O
N
H
CH C O-
OCH
CH CH3
CH3
CH2
SH
CH2
CH2
S
CH3
Solution AA4
Ala-Leu-Cys-Met
H3N CH
CH3
C
O
N
H
CH C
O
N
H
CH C
O
N
H
CH C O-
OCH
CH CH3
CH3
CH2
SH
CH2
CH2
S
CH3
The Peptide Bond
Amide bond formed by the –COOH of an amino acid and the –NH2 of the next amino acid
O CH3
+ | | + |
NH3–CH2–COH + H3N–CH–COO–
O CH3
+ | | |
NH3–CH2–C – N–CH–COO–
| peptide bond H
• A protein is an organic polymer composed of amino acids bonded together in one or more chains.
Proteins
• An amino acid has a central carbon atom, to which are bonded a carboxyl group, an amino group, a hydrogen atom, and a variable side chain designated as R, as shown in the following structural formula.
Structure of an Amino Acid
• Amino acids bond to each other by forming a peptide bond, an amide group formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another.
Structure of an Amino Acid
Structure of an Amino Acid
• Two amino acids linked by a peptide bond form a dipeptide.
Bonding in -Amino Acids
A peptide linkage
There are 20 amino acids commonly found in proteins.
CNH
H
H
R
C
O
N
H
C
H
R'
CO
OH
• A chain of two or more amino acids linked by peptide bonds is called a peptide.
Structure of an Amino Acid
• The term polypeptide is applied to a chain of ten or more amino acids.
• Proteins may have one or several polypeptide chains, and each chain must have an exact sequence of amino acids.
Classification of Amino Acids
• Classified according to their side chains polarity. (R groups)
• This is because in their native conformations, largely in response to the tendency to remove their hydrophobic side chains from contact with water and to solvate their hydrophilic side chains.
• According to this classification scheme, there are three major groups.
• 1. those w/nonpolar R groups
• 2. Uncharged polar R groups
• 3. charged polar R groups
Types of Amino Acids
Nonpolar R = H, CH3, alkyl groups, aromatic
OPolar ll
R = –CH2OH, –CH2SH, –CH2C–NH2,
(polar groups with –O-, -SH, -N-)
Polar/Acidic
R = –CH2COOH, or -COOH
Polar/ Basic
R = –CH2CH2NH2
Learning Check AA1
Identify each as (1) polar or (2) nonpolar
A. NH2–CH2–COOH (Glycine)
CH3
| CH–OH
|
B. NH2–CH–COOH (Serine)
Solution AA1
Identify each as (1) polar or (2) nonpolar
A.(2) NH2–CH2–COOH (Glycine)
CH3
| CH–OH |
B. (1) NH2–CH–COOH (Serine)
Non polar amino acids ( hydrophobic )
• (9)
• Glycine, Alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, and tryptophan
Uncharged polar side chains( hydrophilic)
• (6) these have Hydroxyl, Amide, or Thiol groups
• Serine, threonine, asparagine, glutamine, tyrosine, cysteine.
Charged polar side chains( ionic)
• Can be positively or negatively charged.
• The basic amino acids are (+) charged at Physiological pH values.
• Lysine, arginine, and histidine.
• The acidic amino acids are (-) charged above pH 3
• Aspartic acid, glutamic acid
Learning Check AA2
CH3 CH3
+
H3N–CH–COOH H2N–CH2–COO–
(1) (2)
Select from the above structures
A. Alanine in base.
B. Alanine in acid.
Solution AA2
CH3 CH3
+
H3N–CH–COOH H2N–CH2–COO–
(1) (2)
Select from the above structures
A. (2) Alanine in base.
B. (1) Alanine in acid.
• The 20 amino acids vary considerably in their physical and chemical properties such as polarity, acidity, basicity, aromaticity, flexibility, ability to cross link, ability to hydrogen bond, and chemical reactivity. These characteristics, several that are interrelated contribute to proteins great range of properties.
Non standard amino acids
• The 20 common amino acids are by no means the only amino acids that occur in biological systems. Non standard amino acid residues are often important constituents in proteins. The changes comes from a conformation rearrangement in their 3-D structures. These are called D-amino acids and are quite prevalent in many antibiotics.
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