Amino Acids Overview and Classification

Amino Acids

• Amino acids are organic compounds that combine to form proteins.
• They are the building blocks of proteins.
• Key elements are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).
• There are approximately 300 amino acids found in nature.
• The general formula of an amino acid is R-CH(NH2)-COOH.
• An amino acid has a basic amino group (-NH2), an acidic carboxyl group (-COOH), and a unique R group (or side chain).
• "Amino acid" is short for α-amino carboxylic acid (α-amino).

Structure of Amino Acids

• Specific structures and chemical formulas are provided for various amino acids (e.g., Glycine, Alanine, Serine, etc). Refer to the provided images for details.

Classification of Amino Acids

• Amino acids are categorized into three groups:
  • Essential: Cannot be produced by the body, must be obtained from food.
  • Non-essential: Can be produced by the body.
  • Conditionally essential: Typically not essential, except during illness or stress.
• Specific examples of amino acids in each category are listed. Refer to the provided image for details.

Acid-Base Properties

• Each amino acid has an isoelectric point (pI) where the overall charge on the amino acid molecule is zero.
• Examples of isoelectric points are provided for various amino acids (e.g., aspartic acid, glycine, histidine, arginine).
• A zwitterion is a molecule with at least one positive and one negative charge.
• In acidic conditions, the carboxyl group gains a proton and the amino acid acts as a base.
• In alkaline conditions, the amino group loses a proton and the amino acid acts like an acid.

Physical Properties

• Amino acids are colorless, crystalline solids.
• They have a high melting point.
• Soluble in water, slightly soluble in alcohol, and with difficulty in methanol, ethanol, and propanol.
• They decompose upon heating to high temperatures.
• All amino acids (except glycine) are optically active.
• A peptide bond links amino acids.

Sources of Amino Acids

• Amino acids perform various biological and chemical functions in the body, including building/repairing tissues, enzyme function, digestion etc.
• The body synthesizes some amino acids.
• Other amino acids (essential amino acids) need to be consumed through protein-rich foods.

Deficiency of Amino Acids

• Amino acid deficiencies can cause various health problems, including edema, anemia, insomnia, diarrhea, depression, hypoglycemia, loss of appetite, fat deposits in the liver, and skin/hair problems.

Proteins

• Proteins are large biomolecules composed of one or more chains of amino acid residues.
• One of the most abundant organic molecules in living organisms.
• Perform diverse functions (e.g., structural components, catalysts [enzymes], hormones, and regulators of cellular processes).
• Proteins are involved in DNA replication, molecule transportation, and catalyzing various metabolic reactions, as well as structural support to cells.
• Proteins are broken down into amino acids.

Peptides and Proteins

• Peptides: Chains of fewer than 50 amino acids.
  • Oligpeptides: 2 to 20 amino acids.
  • Dipeptides and Tripeptides: 2 and 3 amino acids.
• Proteins: Chains of more than 50 amino acids. Typically 100-10,000 amino acids linked together.
• Amino acids are joined by peptide bonds.
• Edman Degradation is a method to sequence amino acids in peptides.

Amino Acids that Make Up Proteins

• Lists amino acid names and structures.

General Structure of Proteins

• The general formula for proteins is RCH(NH2)COOH.
• Proteins have primary, secondary, tertiary, and quaternary structures.
• Primary structure: The linear sequence of amino acids.
• Secondary structure: Folding patterns (e.g., α-helix, β-pleated sheet) stabilized by hydrogen bonds.
• Tertiary structure: The 3D shape of the protein.
• Quaternary structure: The arrangement of multiple polypeptide chains into a functional enzyme complex (e.g., hemoglobin).

Protein Folding and Misfolding

• Protein folding is the process by which a linear chain of amino acids folds into a 3D structure.
• Chaperones assist in protein folding.
• Denaturation is the loss of a protein's 3D structure, usually caused by heat, pH changes, or chemicals.
• Renaturation is possible if the denaturation process isn´t too severe.
• Misfolding can lead to diseases like Alzheimer's, Parkinson's, Huntington's and Creutzfeldt-Jakob.

Protein-Protein Interactions

• Protein-Protein Interactions (PPI) are the physical contact between two or more protein molecules.
• Interactions can be non-covalent and covalent.

Protein Applications

• Many proteins, like insulin and antibodies, are used in medicine.
• Proteins (e.g., casein, whey, soy protein) are used in food products (e.g., dairy alternatives, protein bars).
• Proteins (e.g., keratin) are utilized in personal care products.

Enzymes

• Enzymes are biological catalysts that speed up biochemical reactions without being consumed.
• All biochemical reactions in cells require enzymes.
• Enzymes are typically proteins.
• Some RNA molecules (ribozymes and DNAzymes) can also act as catalysts.

Structure of Enzymes

• Enzymes have primary, secondary, tertiary, and quaternary structures.
• The primary structure defines the enzyme's function.
• Secondary structures (like α-helices and β-sheets) provide stability.
• Tertiary structures provide the 3D shape necessary for substrate binding and catalysis.
• Quaternary structure involves multiple polypeptide chains.

Active Site

• The active site is the region of an enzyme where the substrate binds and catalytic activity occurs.
• Enzyme specificity relates to the active site fitting with the specific substrate.
• The amino acid residues in the active site determine the precise function of the enzyme.

Enzyme Mechanism of Action

• Lock-and-key model describes enzymes and substrates as having complementary shapes, while the induced fit model proposes enzymes adjust their shape to fit substrates precisely.
• Enzyme-substrate complex is when enzyme and substrate interact.
• Both models explain how enzymes interact with their substrates to facilitate chemical reactions.

Enzyme Catalysis

• Enzymes increase the rate of chemical reactions by lowering the activation energy.
• Enzymes stabilize the transition state of the reaction (to make it proceed easily).

Industrial and Biotechnological Applications

• Enzymes are used in various industries:
• Biocatalysis: Enzyme use in pharmaceuticals, fine chemicals, and biofuels.
• ELISA: Enzyme-based diagnostic methods.
• Food industry: Proteases and amylases in various food processes.
• Waste management: Enzyme use in waste remediation.

Enzyme Inhibitors and Drugs

• Enzyme inhibitors are molecules that bind to enzymes and decrease their activity.
• Competitive, non-competitive, and uncompetitive are types of reversible inhibitors.
• Inhibitors can be used as therapeutic agents to treat diseases.
• Allosteric inhibitors can turn off enzymes by binding to different sites to change the enzyme´s shape.

Three Types of Reversible Inhibition

• Competitive inhibitors: Bind to the enzyme's active site, preventing substrate binding.
• Non-competitive inhibitors: Bind to a site other than the active site, changing the enzyme's shape.
• Uncompetitive inhibitors: Bind only to the enzyme-substrate complex, preventing the reaction.
• Allosteric inhibitors: Bind to a specific site, altering the enzyme's shape.

This quiz covers the fundamentals of amino acids, including their structure, functions, and classification. Learn about essential, non-essential, and conditionally essential amino acids, as well as their roles as building blocks of proteins. Test your knowledge on this crucial topic in biochemistry.