Understanding Amino Acids

• Amino acids are the building blocks of proteins
• Proteins are made of amino acids
• Amino acids contain an amino group, carboxylic acid group and a variable side chain

Amino Acid Symbol

• A typical amino acid contains an amino group, alpha carbon, side chain (R group), and carboxylic acid group
• Alpha-amino acids, also known as standard amino acids, have both the amino and carboxylic group attached to the same carbon

Standard vs Non-Standard Amino Acids

• There are 20 alpha-amino acids, otherwise known as standard amino acids, that are found in proteins
• Standard amino acids have the amino and carboxylic groups present on the alpha-carbon
• There are approximately 700 non-standard amino acids which have different functions
• Proteins contain L-alpha-amino acids, while microorganisms contain both D- and L-alpha-amino acids
• Alpha-amino acids frequently occur in proteins
• Alpha-amino acids are known as standard, while beta and gamma-amino acids are considered non-standard
• Non-standard amino acids are present with specific functions

Amino Acid Classifications

• Amino acids are classified based on their R group, including nonpolar, polar uncharged, acidic, and basic

Nonpolar, Aliphatic R Group Amino Acids

• Includes Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), and Methionine (Met, M)

Aromatic R Groups Amino Acids

• Includes Phenylalanine (Phe, F), Tyrosine (Tyr, Y), and Tryptophan (Trp, W)

Polar, Uncharged R Groups Amino Acids

• Includes Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Proline (Pro, P), Asparagine (Asn, N), and Glutamine (Gln, Q)

Positively Charged R Groups Amino Acids

• Includes Lysine (Lys, K), Histidine (His, H), and Arginine (Arg, R)

Negatively Charged R Groups Amino Acids

• Includes Aspartate (Asp, D), and Glutamate (Glu, E)

Functions of Amino Acids

• Used for the formation of other amino acids
• Act as building blocks for peptides and proteins
• Function as neurotransmitter substances, such as GABA
• Work as hormones, for example, thyroxine which is derived from tyrosine
• Serve as pigments, e.g., melanin from tyrosine
• Act as vitamins, e.g, beta-alanine
• Some amino acids like ornithine and citrulline, are important reactants in the formation of urea in the liver

Synthesis of Amino Acids

• Nine of the 20 standard amino acids are "essential" because the human body cannot create them; they must be consumed in food
• Some amino acids may be conditionally essential for some ages and medical conditions differently, and may also differ between species
• Amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology, due to their biological significance

Essential Amino Acids

• Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine

Non-Essential Amino Acids

• Alanine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Proline, Serine, Tyrosine, Arginine, Histidine, and Glycine

Forms of Amino Acids

• Amino acids exist in neutral forms with -NH2 and -COOH groups or as zwitterions with -NH3+ and -COO- groups
• A zwitterion has both positive and negative charges in one molecule
• Around 20 amino acids are commonly found in most proteins

Peptide Bonds

• Peptide bonds are chemical bonds which join the carboxyl group of one amino acid to the amino group of another
• A peptide bond is an amide-type covalent chemical bond
• Alpha-amino acids are connected through this bond from C1 of one to N2 of another
• A peptide or protein chain consists of this linkage

Proteins

• Proteins are large biomolecules and macromolecules with one or more long chains of amino acid residues
• Proteins perform various functions from catalyzing metabolic reactions and DNA replication, responding to stimuli, providing structure, and transporting molecules
• Proteins differ in their sequence of amino acids which is dictated by the nucleotide sequence of their genes, and it usually results in a specific 3D structure to determine its activity

Primary Structure

• The protein primary structure is defined by the sequence of amino acids liked together in a polypeptide chain

Secondary Structure

• The protein secondary structure is the local spatial conformation of the polypeptide backbone, not including the side chains

Tertiary Structure

• The three-dimensional arrangement of the polypeptide chain in space of a protein
• Generally stabilized by outside polar hydrophilic hydrogen and ionic bond interactions
• Stabilized by internal hydrophobic interactions between nonpolar amino acids

Quaternary Structure

• Refers to the arrangement of multiple protein chains or subunits
• Held together by hydrogen bonds and van der Waals forces
• Forms a functional protein