Amino Acid Structure and Classification

Amino Acid Structure

• Amino acids are organic molecules containing both carboxyl and amino groups.
• Amino acids are the building blocks of proteins.
• They contain a carboxylic acid group and an amino group on the alpha (α) carbon.
• Amino acids differ in their properties due to differing side chains.
• Side chains are called R groups.

α-Carbon

• The alpha carbon is an asymmetrical carbon atom giving the amino acids optical activity.

Amino Acid Structure

• Amino acids can be characterized as α, β, or δ depending on the location of the amino group in the carbon chain.
• α amino acids are found on the carbon adjacent to the carboxyl group.
• β amino acids are found on the 2nd carbon from the carboxyl group.
• δ amino acids are found on the 3rd carbon from the carboxyl group.

Amino Acids

• 20 standard amino acids are present in mammalian proteins.
• All amino acids have amphoteric properties, meaning they can act as both an acid and a base.
• All amino acids except glycine have optical activity.
• Amino acids are dipolar, having both charges.
• The positive end is NH3+.
• The negatve end is COO-.
• Non-standard amino acids come from modifications of standard amino acids.
• Amino acids have Stereoisomers.
• All amino acids except glycine have chiral carbon (asymmetrical carbon atom).
• L-amino acids are natural amino acids found in protein.
• D-amino acids are found in antibiotics and plant and bacterial cell walls.

Proline

• Proline is an imino acid, meaning it has a secondary amino group.

Amino Acid Abbreviations

• Each amino acid has a three letter abbreviation and a one letter symbol.
• The three letter abbreviation is commonly the first three letters of the amino acid name.
• The one-letter symbol is typically the first letter of the amino acid name.
• When these abbreviations are confusing, alternative abbreviations are used.

Amino Acid Functions

• Amino acids are the building blocks of proteins.
• Some amino acids and their derivatives function as neurotransmitters and other regulators.
• Neurotransmitters and regulators include L-dopamine, epinephrine, thyroxine, and histamine.

Classification of Amino Acids

• Essential or Non-Essential
• Glucogenic, ketogenic, or Glucogenic & ketogenic
• Neutral, acidic, and basic
• According to the side chain properties

Essential & Non-Essential Amino Acids

• Essential amino acids are not synthesized by the human body and must be obtained from the diet.
• Essential amino acids are present in dairy products.
• Sources of protein come from both animal and vegetable sources.
• Animal sources are complete proteins, meaning they contain all essential amino acids.
• Vegetable sources usually lack some essential amino acids.
• They are classified as semi-essential or conditionally essential amino acids, including arginine, cysteine, glutamine, glycine, and proline.

Essential Amino Acids

• Essential amino acids are: arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.
• Non-Essential amino acids are: alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine.

Complete Protein

• Complete protein contains all 10 essential amino acids.
• Incomplete protein lacks one or more essential amino acids.
• Most vegetable proteins are incomplete proteins with the exception of beans.
• Beans contain some complete protein.

Classification According to Side Chain Properties

• Non-polar (Hydrophobic)

• Side chain does not bind or give off protons.

• They promote hydrophobic interactions.

• They are clustered in the interior of a protein when in aqueous solution.

• They help give 3D shape to the protein structure.

• Non-polar (Hydrophobic), Aliphatic Amino Acids

• Glycine (Gly or G)

• Alanine (Ala or A)

• Valine (Val or V)

• Leucine (Leu or L)

• Isoleucine (Ile or I)

• Methionine (Met or M)

• Non-polar (Hydrophobic), Aromatic Amino Acids

• Phenylalanine (Phe or F)

• Tryptophan (Trp or W)

• Proline (Pro or P)

Polar (Hydrophilic) Uncharged Amino Acids

• Serine (Ser or S)

• Threonine (Thr or T)

• Cysteine (Cys or C)

• Tyrosine (Tyr or Y)

• Asparagine (Asn or N)

• Glutamine (Gln or Q)

• The six amino acids with polar, uncharged R groups are more hydrophilic due to the presence of hydroxyl groups, sulfur atoms, or amide groups.

• The SH group of two Cysteine residues in proteins can be oxidized to form a covalent disulfide bond.

• Cys often participates in hydrophobic interactions.

• Pro has a five-membered ring structure, being rigid in conformation and offering the least flexibility.

• Pro is often found in the bends of folded protein chains and on the surface of proteins.

Positively Charged (Basic) and Negatively Charged (Acidic) R Groups

• The most hydrophilic R groups are those either positively or negatively charged.
• Asp and Glu have a carboxyl group in their R groups.
• They have a net negative charge at pH 7.0.
• They are typically named aspartate and glutamate.
• Arg, Lys, and His have positively charged R groups at pH 7.0.
• Their R groups contain a guanidino, amino, or imidazole group respectively.
• The side chain of His can be positively or uncharged depending on the local environment near pH 7.0.

Polar (Hydrophilic) Charged Amino Acids

• Negatively charged

• Aspartic Acid (Asp or D)

• Glutamic Acid (Glu or E)

• Positively charged

• Lysine (Lys or K)

• Arginine (Arg or R)

• Histidine (His or H)

Cystine

• Cystine is a dimer of cysteine.

Sickle Cell Disease

• Sickle cell disease is a pathology that results from the substitution of polar glutamate by the non-polar valine in the B subunit of hemoglobin.

pK Value

• pK value measures the ability of an acid to donate a proton (dissociate).
• It is also known as pKa or the acid dissociation constant.
• pK value represents the pH at which 50% of the acid is dissociated.
• The pK values of α-carboxylic groups are typically in the range of 2.2.
• The pK values of α-amino groups are typically in the range of 9.4
• The smaller the pK value, the stronger the acid.
• The larger the pK values, the weaker the acid.

Zwitterion

• Zwitterion is a double ion.
• Zwitterion is formed when both NH3+ and COO- are ionized.
• At the isoelectric point (pI), the positive and negative charges in the zwitterion are equal.
• pI is the pH at which the molecule is electrically neutral.

Amino Acids as Acids or Bases

• Amino Acids as Acids

  • In solutions that are more basic than the pI, the —NH3+ in the amino acid donates a proton.

• Amino Acids as Bases

  • In solutions more acidic than the pI, the COO- in the amino acid accepts a proton.

pH and Ionization

• Acidic amino acids, such as aspartic acid, have a second carboxyl group that can donate and accept protons.
• The pI for aspartic acid occurs at a pH of 2.8.