BCH 351 Exam 1 Study Guide: Foundations of Biochemistry and Protein Structure

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Biochemical Functional Groups

Common Functional Groups in Biochemistry

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity. Recognizing these groups is essential for understanding biomolecular structure and function.

Hydroxyl (-OH): Found in alcohols and carbohydrates; can form hydrogen bonds.
Carbonyl (C=O): Present in aldehydes and ketones; polar and reactive.
Carboxyl (-COOH): Characteristic of amino acids and fatty acids; acts as an acid (proton donor).
Amino (-NH2): Found in amino acids; acts as a base (proton acceptor).
Sulfhydryl (-SH): Present in cysteine; forms disulfide bonds in proteins.
Phosphate (-PO42-): Found in nucleotides and phospholipids; involved in energy transfer.

Hydrogen Bonding and Non-Covalent Interactions: Atoms such as O, N, and F can participate in hydrogen bonding due to their high electronegativity and lone pairs.

Non-Covalent Interactions

Types and Roles in Protein Structure

Non-covalent interactions are essential for the structure and function of biomolecules, especially proteins.

Hydrogen Bonds: Attraction between a hydrogen atom bonded to an electronegative atom (donor) and another electronegative atom (acceptor).
Ionic (Electrostatic) Interactions: Attraction between oppositely charged groups (e.g., salt bridges).
Van der Waals Forces: Weak, non-specific interactions due to transient dipoles.
Hydrophobic Interactions: Nonpolar groups aggregate to minimize contact with water, driven by entropy increase in the solvent.

Hydrophobic Effect: Water promotes the aggregation of nonpolar molecules, increasing the entropy of the system.

Dipole Moments: Molecules with polar bonds have dipole moments, which can be represented by arrows pointing from positive to negative charge.

Hydrogen Bond Donors and Acceptors: Donors have H attached to O/N; acceptors are O/N with lone pairs.

Chemical Properties of Acids and Bases

Acid-Base Chemistry in Biological Molecules

Understanding acid-base properties is crucial for predicting biomolecular behavior in different environments.

Acidic Groups: Carboxyl, phosphate, and some side chains (e.g., Asp, Glu, C-terminus).
Basic Groups: Amino, imidazole, and some side chains (e.g., Lys, Arg, His, N-terminus).
Acid Dissociation Constant (Ka): Expressed as an equilibrium:

Henderson-Hasselbalch Equation: Used to calculate pH or pKa:

Titration Curves: Graphs showing pH changes as acid/base is added; inflection points correspond to pKa values.
Ampholyte: A molecule with both acidic and basic groups (e.g., amino acids).
Isoelectric Point (pI): The pH at which a molecule carries no net charge.
Zwitterion: A molecule with both positive and negative charges but overall neutral.
Buffers: Weak acids/bases that resist pH changes; effective within ±1 pH unit of their pKa.

Reaction Thermodynamics, Equilibrium, and Kinetics

Energetics of Biochemical Reactions

Thermodynamics and kinetics determine whether and how fast biochemical reactions occur.

Free Energy (ΔG): Determines spontaneity of a reaction.
Relationship to Enthalpy (ΔH) and Entropy (ΔS):

Spontaneous Reactions: ΔG < 0 (exergonic); Non-spontaneous: ΔG > 0 (endergonic).
Hydrophobic Interaction Thermodynamics: Driven by entropy increase as water molecules are released from nonpolar surfaces.
Chemical Equilibrium: Forward and reverse reaction rates are equal; described by equilibrium constant (K).
Chemical Kinetics: Describes the rate at which equilibrium is reached.
Standard vs. Non-Standard Conditions: ΔG°' is standard free energy change; actual ΔG depends on concentrations.

Equilibrium Constant (K): Ratio of product to reactant concentrations at equilibrium.
Reaction Quotient (Q): Same as K but for non-equilibrium conditions.

Biochemical Reaction Coupling

Making Unfavorable Reactions Favorable

Cells couple unfavorable reactions (ΔG > 0) to favorable ones (ΔG < 0) to drive necessary processes.

Reaction Coupling: The overall ΔG is the sum of individual ΔG values.

Example: ATP hydrolysis is often coupled to biosynthetic reactions to make them favorable.

Biochemical Redox Reactions

Oxidation-Reduction in Biochemistry

Redox reactions involve the transfer of electrons between molecules, crucial for energy metabolism.

Oxidation: Loss of electrons; Reduction: Gain of electrons.
Oxidant: Electron acceptor; Reductant: Electron donor.
Standard Reduction Potential (E°'): Tendency of a molecule to accept electrons.
Free Energy of Redox Reactions:

n = number of electrons transferred; F = Faraday's constant.

Amino Acid Structures and Properties

Structure, Codes, and Chemical Properties

Amino acids are the building blocks of proteins, each with unique side chains affecting their properties.

General Structure: Central α-carbon, amino group, carboxyl group, hydrogen, and R group (side chain).
Drawing at Different pH: At low pH, amino acids are fully protonated; at high pH, fully deprotonated.
Codes: Each amino acid has a three-letter and single-letter code (e.g., Glycine: Gly, G).
D and L Forms: Stereoisomers; L-form is predominant in proteins.
Chemical Features: Side chains determine acid/base properties, hydrophobicity, hydrophilicity, and H-bonding potential.
Titration Curves: Show ionization states as pH changes; inflection points correspond to pKa values.
Isoelectric Point (pI): Calculated as the average of pKa values that bracket the zwitterion.

Example: For glycine,

Structure and Properties of Peptides

Peptide Bond and Polypeptide Properties

Peptides are formed by condensation reactions between amino acids, creating amide (peptide) bonds.

Peptide Bond: Formed between carboxyl group of one amino acid and amino group of another; planar and rigid due to partial double-bond character.
α-Carbon Position: The α-carbons of adjacent residues are separated by the peptide bond.
Drawing Polypeptides: Use single- or three-letter codes to represent sequences.
pI of Polypeptides: Determined by the ionizable groups in the sequence and the solution pH.
Titration Curves: More complex due to multiple ionizable groups.
Charge State: At low pH, polypeptides are positive; at high pH, negative; at pI, zwitterionic.

Secondary, Tertiary, and Quaternary Structural Elements of Proteins

Levels of Protein Structure

Proteins have hierarchical structures that determine their function.

Primary Structure: Linear sequence of amino acids.
Secondary Structure: Local folding patterns (α-helix, β-sheet) stabilized by hydrogen bonds.
Torsion/Dihedral Angles (φ, ψ, ω): Define backbone conformation; φ (N–Cα), ψ (Cα–C), ω (peptide bond, usually 180°).
α-Helix: Right-handed coil; 3.6 residues per turn; stabilized by H-bonds between n and n+4 residues.
Helix Dipole: Macrodipole created by aligned peptide dipoles; N-terminus partial positive, C-terminus partial negative.
β-Sheet: Extended strands connected by H-bonds; can be parallel or antiparallel.
Ramachandran Plot: Graphical representation of allowed φ and ψ angles; used to assess protein structure quality.
Protein Interior/Exterior: Hydrophobic residues typically buried; hydrophilic residues exposed.
Amphipathic Helix: Helix with both hydrophobic and hydrophilic faces; predicted using a helical wheel diagram.
Monomer vs. Oligomer: Monomer is a single polypeptide; oligomer is a complex (homo-oligomer: identical subunits; hetero-oligomer: different subunits).
Quaternary Structure: Assembly of multiple polypeptide chains; confers unique functional properties (e.g., cooperativity).

Myoglobin and Hemoglobin

Oxygen Transport Proteins

Myoglobin and hemoglobin are globular proteins that bind oxygen, but differ in structure and function.

Myoglobin: Monomeric; stores oxygen in muscle.
Hemoglobin: Tetrameric; transports oxygen in blood.
Apoprotein: Protein without its prosthetic group; Holoprotein: Protein with its prosthetic group (e.g., heme).
Oxygen Binding: Involves heme group; Fe2+ binds O2.
Dissociation Constant (Kd): Reflects affinity for ligand; lower Kd means higher affinity.
Fractional Saturation (Y):

Allostery: Regulation of protein activity by binding at a site other than the active site.
Cooperativity: Binding of one ligand affects binding of others (positive: increases affinity; negative: decreases affinity).
Hemoglobin Effectors: O2, CO2, H+, and 2,3-BPG modulate oxygen affinity, facilitating oxygen delivery and CO2 transport.

Fibrous Proteins

Structure and Function of Fibrous Proteins

Fibrous proteins provide structural support and strength to cells and tissues.

α-Keratin: Found in hair, nails, and skin; coiled-coil structure.
β-Keratin: Found in silk and feathers; β-sheet structure.
Collagen: Major component of connective tissue; triple helix structure; rich in glycine and proline.
Fibroin: Main protein in silk; antiparallel β-sheet structure.

These proteins are characterized by repetitive sequences and extensive secondary structure, providing mechanical strength and elasticity.