Biochemistry: Amino Acids

• Biochemistry is the study of the chemical processes and substances that occur within living organisms.
• It combines biology and chemistry to investigate the structure, function, and interactions of biological molecules such as proteins, nucleic acids, carbohydrates, and lipids.
• It encompasses a range of scientific disciplines, including genetics, microbiology, forensics, and medicine.

Amino Acids

• Amino acids are organic compounds that contain both amino and carboxyl functional groups.
• They are the building blocks of proteins.
• They serve as precursors to many biomolecules, including neurotransmitters, hormones, and pigments.
• Common structure includes a central carbon atom (the α-carbon) bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (-H), and a variable side chain (R group).

Classification of Amino Acids

• Classified based on the properties of their side chains (R groups).
• These can be nonpolar, polar uncharged, positively charged (basic), or negatively charged (acidic).
  • Nonpolar amino acids have hydrophobic side chains, meaning they tend to cluster together in the interior of proteins, away from water. Examples include alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine.
  • Polar uncharged amino acids have side chains that are hydrophilic (water-loving) but do not carry a charge at physiological pH. They can form hydrogen bonds with water and other molecules. Examples include serine, threonine, cysteine, asparagine, and glutamine.
  • Positively charged (basic) amino acids have side chains that are positively charged at physiological pH. Examples include lysine, arginine, and histidine.
  • Negatively charged (acidic) amino acids have side chains that are negatively charged at physiological pH. Examples include aspartic acid and glutamic acid.
• Some amino acids are also classified as essential, non-essential, or conditionally essential.
  • Essential amino acids cannot be synthesized by the human body and must be obtained through diet.
  • Non-essential amino acids can be synthesized by the human body.
  • Conditionally essential amino acids are essential only under certain conditions, such as during illness or stress.

Properties of Amino Acids

• They are amphoteric, meaning they can act as both acids and bases.
• In acidic solutions (low pH), the amino group (-NH2) can accept a proton (H+) and become positively charged (-NH3+).
• In basic solutions (high pH), the carboxyl group (-COOH) can donate a proton and become negatively charged (-COO-).
• At a specific pH, called the isoelectric point (pI), an amino acid exists as a zwitterion, where it carries both a positive and negative charge but has a net charge of zero.
• The pI is characteristic for each amino acid and depends on the pKa values of its amino and carboxyl groups, as well as the pKa of its side chain if it contains an ionizable group.

Essential Amino Acids

• Histidine
• Isoleucine
• Leucine
• Lysine
• Methionine
• Phenylalanine
• Threonine
• Tryptophan
• Valine

Nonessential Amino Acids

• Alanine
• Arginine
• Asparagine
• Aspartic acid
• Cysteine
• Glutamic acid
• Glutamine
• Glycine
• Proline
• Serine

Uncommon Amino Acids

• Selenocysteine: An amino acid that is incorporated into proteins during translation. It contains selenium instead of sulfur.
• Pyrrolysine: An amino acid that is found in some archaea and bacteria. It is genetically encoded.
• Hydroxyproline: A modified version of proline. It is found in collagen.
• γ-Carboxyglutamate: A modified version of glutamate. It is found in clotting factors.

Functions of Amino Acids

• Building Blocks of Proteins: Amino acids are the monomers that polymerize to form proteins. The sequence of amino acids in a protein determines its three-dimensional structure and function.
• Protein Synthesis: During protein synthesis, amino acids are linked together by peptide bonds to form polypeptide chains.
• Neurotransmitters: Some amino acids act as neurotransmitters, carrying signals between nerve cells in the brain. Examples include glutamate and gamma-aminobutyric acid (GABA).
• Precursors to Other Molecules: Amino acids serve as precursors for the synthesis of other important biomolecules, such as porphyrins (components of hemoglobin), nucleotides (components of DNA and RNA), and hormones (e.g., thyroid hormones derived from tyrosine).
• Metabolic Intermediates: Amino acids participate in various metabolic pathways, serving as intermediates in the synthesis and breakdown of carbohydrates, lipids, and other molecules.
• Energy Source: While not their primary role, amino acids can be catabolized to produce energy when carbohydrate and lipid stores are depleted.
• Regulation of Gene Expression: Some amino acids or their derivatives can regulate gene expression by binding to transcription factors or other regulatory proteins.
• Antioxidant Activity: Some amino acids, such as cysteine and methionine, contain sulfur atoms that can act as antioxidants, protecting cells from damage caused by reactive oxygen species (free radicals).
• Immune Function: Certain amino acids, such as arginine and glutamine, play important roles in immune function, supporting the growth and activity of immune cells.
• Nitrogen Balance: Amino acids are involved in maintaining nitrogen balance in the body, as they are the primary source of nitrogen.
• Structural Support: Some amino acids, such as proline and glycine, contribute to the structural integrity of proteins, allowing them to form specific shapes and conformations.

Peptide Bond Formation

• Amino acids are linked together by peptide bonds to form polypeptide chains.
• A peptide bond is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another, with the removal of a water molecule (dehydration).
• The resulting chain of amino acids is called a peptide, and longer chains are called polypeptides or proteins.

Protein Structure

• The sequence of amino acids in a protein determines its three-dimensional structure and function.
• There are four levels of protein structure:
  • Primary structure: The linear sequence of amino acids.
  • Secondary structure: Localized, repeating structures such as alpha helices and beta sheets, stabilized by hydrogen bonds between amino acid residues.
  • Tertiary structure: The overall three-dimensional structure of a single polypeptide chain, determined by interactions between amino acid side chains, including hydrophobic interactions, hydrogen bonds, disulfide bonds, and ionic bonds.
  • Quaternary structure: The arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein.

Importance of Amino Acids in Nutrition

• Important for human health.
• Essential in the diet to support growth, repair, and maintenance of tissues, as well as the synthesis of enzymes, hormones, and other biomolecules.
• Deficiencies in one or more essential amino acids can lead to various health problems, including impaired growth, muscle wasting, immune dysfunction, and neurological disorders.
• Dietary sources of amino acids include meat, poultry, fish, eggs, dairy products, legumes, nuts, and seeds.
• A balanced diet that provides adequate amounts of all essential amino acids is crucial for maintaining optimal health.