Amino Acids: Structure and Properties

Basic Structure of Amino Acids

Amino acids are the building blocks of proteins, each containing a central carbon atom (the alpha carbon) bonded to four groups: an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

• Non-ionized form: The amino group (-NH2) and carboxyl group (-COOH) are uncharged.

• Ionized form: At physiological pH, the amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).

• Alpha carbon: The central carbon to which all groups are attached.

• Carbon 1: The carboxyl carbon is often referred to as carbon 1 in amino acid numbering.

Side Chains (R Groups)

The chemical nature of the R group determines the properties and classification of amino acids:

• Acidic: R group contains a carboxyl group; negatively charged at physiological pH (e.g., aspartic acid).

• Basic: R group contains an amino group; positively charged at physiological pH (e.g., lysine).

• Polar: R group contains polar bonds (Unequal sharing of electrons) but is uncharged (e.g., serine). Hydrophilic

• Non-polar: R group is hydrophobic, often containing hydrocarbons (e.g., leucine).

Functional Groups in Amino Acids

• Amino group (-NH2): Basic group, can accept a proton.

• Carboxyl group (-COOH): Acidic group, can donate a proton.

• Carbonyl group (C=O): Found in peptide bonds and some side chains.

• Hydroxyl group (-OH): Present in some side chains (e.g., serine, threonine).

• Phosphate group (-PO42-): Found in phosphorylated amino acids.

• Sulfhydryl group (-SH): Present in cysteine, important for disulfide bonds.

Residue

A residue refers to an amino acid unit within a polypeptide chain after condensation reactions have removed water.

Peptide Bond Formation

• Peptide bond: Covalent bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.

• Condensation reaction: Reaction that joins two molecules with the removal of water.

• Hydrolysis reaction: Reaction that breaks a bond by adding water.

Monomers and Polymers

• Monomer: A single amino acid unit.

• Polymer: A chain of amino acids (polypeptide or protein).

Protein Structure and Function

Levels of Protein Structure

• Primary structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding patterns stabilized by hydrogen bonds, including:

  • Alpha helix: Right-handed coil stabilized by hydrogen bonds between the carbonyl group of one residue and the amino group of the fifth residue ahead.

  • Beta-pleated sheet: Sheet-like arrangement formed by hydrogen bonds between backbone atoms in different segments of the chain.

  • Proline effect: Proline disrupts alpha helices due to its rigid ring structure.

• Tertiary structure: The overall 3D shape of a single polypeptide, stabilized by:

  • Hydrogen bonds (between R groups or between R group and backbone)

  • Hydrophobic interactions (non-polar side chains cluster away from water)

  • Van der Waals forces (weak attractions between atoms)

  • Disulfide bonds (covalent bonds between cysteine residues)

  • Ionic bonds (between charged side chains)

• Quaternary structure: Association of multiple polypeptide subunits (e.g., hemoglobin, ribosomes).

Protein Structure Implies Function

• Human blood cell example: Hemoglobin's quaternary structure allows efficient oxygen transport.

• Collagen: Triple helix structure provides tensile strength to connective tissues.

• TATA box-binding protein: Binds to DNA to initiate transcription.

• Porin: Forms pores in membranes for molecule transport.

• Chymotrypsin: Digestive enzyme with a specific active site formed by key residues.

Molecular Chaperones

Proteins that assist in the proper folding of other proteins, preventing misfolding and aggregation.

Phosphorylation

• Phosphorylation: Addition of a phosphate group to a protein, often regulating activity.

• Kinase: Enzyme that adds phosphate groups.

• Phosphatase: Enzyme that removes phosphate groups.

Spongiform Encephalopathy and Prions

• Spongiform Encephalopathy: Neurodegenerative disease caused by misfolded prion proteins.

• Prions: Infectious proteins that induce misfolding in normal proteins.

Thermodynamics and Enzyme Function

First Law of Thermodynamics

Energy cannot be created or destroyed, only transformed from one form to another.

Potential and Kinetic Energy

• Potential energy: Stored energy due to position or structure (e.g., in chemical bonds).

• Kinetic energy: Energy of motion.

• Polar bonds: Have lower potential energy than non-polar bonds due to unequal sharing of electrons.

• Non-polar bonds: Have higher potential energy.

Enthalpy and Entropy

• Enthalpy (H): Total energy of a system, including heat content.

• Exothermic: Reaction releases heat ().

• Endothermic: Reaction absorbs heat ().

• Entropy (S): Measure of disorder or randomness.

Second Law of Thermodynamics

In any energy transfer, the entropy of the universe increases.

Gibbs Free Energy

• Gibbs free energy (G): Determines whether a reaction is spontaneous.

Equation:

• Exergonic reaction: Releases free energy (), spontaneous.

• Endergonic reaction: Requires input of energy (), non-spontaneous.

• Spontaneous reactions: Occur without input of energy.

• Non-spontaneous reactions: Require energy input.

Reaction Progress

• Reactants: Starting materials in a chemical reaction.

• Transition states: High-energy, unstable states during a reaction.

• Products: Substances formed by the reaction.

Activation Energy

• Activation energy (Ea): Energy required to initiate a reaction.

• Temperature effects: Higher temperature increases reaction rate by providing more energy to reach the transition state.

• Concentration effects: Higher reactant concentration increases the likelihood of collisions and reaction rate.

• Enzymatic effects: Enzymes lower activation energy, increasing reaction rates.

Enzyme Cofactors and Regulation

• Cofactors: Inorganic ions (e.g., Mg2+, Zn2+) required for enzyme activity.

• Coenzymes: Organic molecules (e.g., NAD+, FAD) that assist enzymes.

• Prosthetic groups: Non-polypeptide units tightly bound to enzymes, essential for function.

Evolution of Enzymatic Optimization

• pH: Each enzyme has an optimal pH for activity.

• Temperature: Each enzyme has an optimal temperature for activity.

Enzyme Inhibition and Regulation

• Competitive inhibition: Inhibitor competes with substrate for the active site.

• Allosteric regulation: Regulator binds to a site other than the active site, causing conformational change.

  • Activation: Allosteric activator increases enzyme activity.

  • Inhibition: Allosteric inhibitor decreases enzyme activity.

• Covalent bond modification: Enzyme activity regulated by covalent addition or removal of groups (e.g., phosphorylation).

• Enzyme-specific protease: Enzyme that activates or deactivates other enzymes by cleaving peptide bonds.

• Phosphorylation: Addition of phosphate group, often regulating enzyme activity (e.g., mitogen-activated protein kinase).

• Allosteric feedback inhibition: regulatory mechanism in which the end product of a metabolic pathway binds to an allosteric site on an enzyme earlier in that pathway

Table: Types of Amino Acid Side Chains

Example: Hemoglobin Structure and Function

• Hemoglobin is a protein with quaternary structure, composed of four polypeptide subunits.

• Each subunit contains a heme group that binds oxygen, allowing efficient oxygen transport in blood.

Additional info: This guide expands on the provided outline with definitions, examples, and explanations to ensure a comprehensive understanding of protein structure and enzyme function for General Biology students.