Biochemistry Study Guide: Biomolecules, Protein Structure, and Enzyme Mechanisms

Biomolecules and Biological Macromolecules

Introduction to Biomolecules

Biomolecules are organic molecules essential for life, including carbohydrates, lipids, proteins, and nucleic acids. Biological macromolecules are large, complex molecules formed by polymerization of smaller subunits.

• Cells: The basic unit of life, composed of various biomolecules.

• Non-covalent interactions: Weak interactions (hydrogen bonds, ionic bonds, van der Waals forces, hydrophobic interactions) crucial for biomolecular structure and function.

• Water: The medium of life: Water's polarity and ability to form hydrogen bonds make it essential for biological processes.

• Hydrophilic, hydrophobic, and amphipathic: Molecules can be water-loving (hydrophilic), water-fearing (hydrophobic), or both (amphipathic), affecting their behavior in aqueous environments.

Acids, Bases, and pH

Fundamentals of Acidity and Alkalinity

Acids and bases are substances that donate or accept protons, respectively. The pH scale measures the hydrogen ion concentration in a solution.

• pH: Defined as $pH = -\log[H^+]$.

• The Henderson-Hasselbalch equation: Relates pH, pKa, and the ratio of conjugate base to acid: $pH = pK_a + \log\left(\frac{[A^-]}{[HA]}\right)$.

• Titration curves: Graphs showing pH changes as acid or base is added to a solution, useful for determining buffering capacity.

Amino Acids and Protein Structure

Amino Acids: Building Blocks of Proteins

Amino acids are organic compounds containing amino and carboxyl groups. They polymerize to form proteins, which perform diverse biological functions.

• Proteins are linear polymers of amino acids: Linked by peptide bonds.

• The peptide bond has partially double bond character: Restricts rotation, contributing to protein structure.

• Primary structure of proteins: The linear sequence of amino acids.

• Role of the amino acid sequence in protein structure: Determines higher-level structures and function.

• Architecture: The hierarchy of structural organization: Includes primary, secondary, tertiary, and quaternary structures.

Secondary Structure in Proteins

Secondary structure refers to local folding patterns stabilized by hydrogen bonds.

• Secondary valence forces: Non-covalent interactions stabilizing secondary structure.

• Fibrous proteins: Structural proteins with elongated shapes (e.g., collagen, keratins).

• Structure of α- and β-keratins: α-keratin forms coiled coils; β-keratin forms sheets.

• Collagen: Triple helix structure, major component of connective tissue.

Tertiary and Quaternary Structure of Proteins

Tertiary structure is the overall 3D shape of a single polypeptide; quaternary structure describes the assembly of multiple polypeptides.

• Chaperones: Proteins that assist in folding other proteins.

• Prions: Infectious proteins that can cause disease by inducing misfolding.

Enzyme Kinetics

Basic Principles of Enzyme Activity

Enzyme kinetics studies the rates of enzyme-catalyzed reactions and factors affecting them.

• Energy of activation, transition state: Enzymes lower the activation energy required for reactions by stabilizing the transition state.

• Action of a catalyst: Catalysts increase reaction rates without being consumed.

• Michaelis-Menten equation: Describes the rate of enzymatic reactions: $v = \frac{V_{max}[S]}{K_m + [S]}$.

• Steady-state: Assumes the concentration of the enzyme-substrate complex remains constant during the reaction.

• Turnover number: Number of substrate molecules converted per enzyme per unit time.

• Enzyme inhibition: Inhibitors decrease enzyme activity; can be reversible or irreversible.

Enzyme Mechanisms

How Enzymes Work

Enzymes accelerate reactions by various mechanisms, including proximity effects and acid-base catalysis.

• Proximity effect: Enzymes bring substrates close together to facilitate reaction.

• General-base and general-acid catalysis: Enzyme side chains act as proton donors or acceptors.

• Nucleophilic and electrophilic catalysts: Enzymes may use nucleophilic or electrophilic groups to stabilize reaction intermediates.

• Flexibility: Enzyme conformational changes can enhance catalysis.

• Mechanism of chymotrypsin: A classic example of serine protease catalysis involving acyl-enzyme intermediates.

• Specificity is the result of molecular recognition: Enzymes are highly specific for their substrates due to precise active site architecture.

• Regulation of enzyme activities: Enzyme activity can be modulated by various mechanisms, including allosteric regulation and covalent modification.

• Partial proteolysis: Zymogens: Inactive enzyme precursors activated by proteolytic cleavage.

• Phosphorylation, and phosphorylases: Addition of phosphate groups regulates enzyme activity.

• Adenylylation: Addition of adenylyl groups as a regulatory mechanism.

• Disulfide reduction: Reduction of disulfide bonds can affect protein structure and function.

• Allosteric effectors (qualitative): Molecules that bind to sites other than the active site to modulate enzyme activity.

Example Table: Protein Structure Hierarchy

The following table summarizes the levels of protein structure and their characteristics.

Level	Description	Stabilizing Forces
Primary	Linear sequence of amino acids	Peptide bonds
Secondary	Local folding (α-helix, β-sheet)	Hydrogen bonds
Tertiary	3D structure of a single polypeptide	Hydrophobic interactions, disulfide bonds, ionic bonds
Quaternary	Assembly of multiple polypeptides	Non-covalent interactions, sometimes covalent bonds

Additional info: Some points have been expanded for clarity and completeness, and standard biochemistry definitions and equations have been added to ensure the notes are self-contained and suitable for exam preparation.