Biochemistry Exam 1 Study Guide: Foundations of Molecular Structure, Water, Thermodynamics, and Acid-Base Chemistry

Introduction to Biochemistry

Bonding Versatility of Carbon and Stereochemistry

Carbon is a unique element in biochemistry due to its ability to form diverse and stable covalent bonds, enabling the complexity of biomolecules. Stereochemistry refers to the spatial arrangement of atoms in molecules, which is crucial for biological function.

• Carbon Bonding: Forms single, double, and triple bonds; can bond with hydrogen, oxygen, nitrogen, and other carbons.

• Constitutional Isomers: Compounds with the same molecular formula but different connectivity of atoms.

• Stereoisomers: Same sequence of bonded atoms, but different spatial arrangement.

• Geometric Isomers (cis/trans): Differ in arrangement around a double bond or ring structure.

• Chiral Center: A carbon atom attached to four different groups, leading to non-superimposable mirror images (enantiomers).

• Enantiomers: Stereoisomers that are mirror images and non-superimposable.

• Diastereomers: Stereoisomers that are not mirror images.

• Conformation: Different spatial arrangements of atoms that can be interconverted by rotation about single bonds.

• Configuration: Fixed arrangement of atoms that cannot be changed without breaking covalent bonds.

Example: Glucose and galactose are constitutional isomers; D- and L-glucose are enantiomers.

Types of Isomers

• Structural (Constitutional) Isomers: Same formula, different connectivity.

• Cis-Trans Isomers: Atoms oriented on the same (cis) or opposite (trans) sides of a bond.

• Enantiomers: Mirror images, non-superimposable.

• Diastereomers: Not mirror images, differ at one or more chiral centers.

Bond Strengths in Biochemistry

Bonds vary in strength and play different roles in molecular stability and interactions.

• Covalent Bonds: Strongest, 100-500 kJ/mol.

• Ionic Bonds: 40 kJ/mol.

• Hydrogen Bonds: 12-30 kJ/mol.

• Van der Waals Interactions: 1-2 kJ/mol.

Order of Strength (Strongest to Weakest): Covalent > Ionic > Hydrogen > Van der Waals

Conformation vs. Configuration

• Conformation: Atoms can rotate freely about single bonds, allowing different shapes (e.g., staggered vs. eclipsed ethane).

• Configuration: Atoms are connected in a fixed arrangement; cannot be changed without breaking bonds (e.g., cis/trans isomers, enantiomers).

Physiological Significance of Enantiomers

• Enantiomers can have different biological activities due to their interaction with chiral biological molecules (e.g., enzymes, receptors).

• One enantiomer may be therapeutically active, while the other is inactive or harmful.

Water and Aqueous Chemistry

Properties of Water

Water's unique structure and properties are essential for life and biochemical reactions.

• Polarity: Water is a polar molecule due to its bent shape and unequal sharing of electrons.

• Hydrogen Bonding: Each water molecule can form up to four hydrogen bonds, leading to high cohesion and surface tension.

• Dipole Moment: Oxygen is more electronegative, giving water a partial negative charge at oxygen and partial positive at hydrogens.

• Van der Waals Forces: Weak, non-covalent interactions between molecules in close proximity.

• Noncovalent Interactions: Individually weak, but collectively strong in large numbers (e.g., protein folding, DNA base pairing).

• Solvent Properties: Water dissolves polar and ionic substances due to its polarity.

• Hydrophobic Effect: Nonpolar molecules aggregate in water, minimizing their exposure to water and increasing entropy.

• Amphipathic Molecules: Contain both polar and nonpolar regions (e.g., phospholipids).

Types of Substances Dissolved in Water

• Polar Substances: Dissolve easily (e.g., salts, sugars).

• Nonpolar Substances: Do not dissolve; aggregate due to the hydrophobic effect (e.g., oils).

Hydrophobic Effect and Thermodynamics

• Hydrophobic Effect: Aggregation of nonpolar molecules in water, driven by increased entropy of water molecules.

• Thermodynamics: Exclusion of nonpolar molecules increases entropy; hydrogen bonding among water molecules is maximized.

Water Structure Around Solutes

• Polar/Charged Solutes: Surrounded by hydration shells; soluble.

• Nonpolar Solutes: Water forms ordered cages; insoluble.

Thermodynamics in Biochemistry

First and Second Laws of Thermodynamics

• First Law (Conservation of Energy): Energy cannot be created or destroyed, only transformed.

• Second Law (Entropy): Entropy (disorder) of the universe increases in spontaneous processes.

Gibbs Free Energy ($\Delta G$)

• Represents the usable energy in a system.

• Exergonic Reactions: $\Delta G < 0$; spontaneous; release energy.

• Endergonic Reactions: $\Delta G > 0$; nonspontaneous; require energy input.

• Enthalpy ($\Delta H$): Heat content of the system.

• Entropy ($\Delta S$): Measure of disorder.

Gibbs Free Energy Equation:

$\Delta G = \Delta H - T\Delta S$

Thermodynamics and Macromolecule Synthesis

• Spontaneous reactions increase entropy or release heat.

• Coupled reactions can drive nonspontaneous processes (e.g., ATP hydrolysis).

Acid-Base Chemistry in Biochemistry

Acids, Bases, and Buffers

• Weak Acids/Bases: Do not completely dissociate in water.

• Conjugate Base (A-): Formed when an acid loses a proton.

• pKa: $pK_a = -\log K_a$; lower pKa means stronger acid.

• Buffer: Solution that resists changes in pH when small amounts of acid or base are added.

• Buffering Region: pH range within 1 unit above and below the pKa.

Relationship Between pH, pKa, and Ka

• pH: $pH = -\log [H^+]$

• pKa: $pK_a = -\log K_a$

• Henderson-Hasselbalch Equation:

$pH = pK_a + \log \left( \frac{[A^-]}{[HA]} \right)$

Acid Dissociation and Buffering

• When pH > pKa, the acid will deprotonate (lose H+).

• When pH < pKa, the acid will remain protonated.

• Buffers act as both proton donors and acceptors when pH ≈ pKa.

Sample Calculations

• Given Ka, calculate pKa: $pK_a = -\log K_a$

• Given [H+], calculate pH: $pH = -\log [H^+]$

• Use Henderson-Hasselbalch to relate pH, pKa, and ratio of acid/base.

Summary Table: Biological Polymers

Macromolecule	Monomer
Nucleic acids	Nucleotides
Proteins	Amino acids
Polysaccharides	Monosaccharides

Key Terms and Definitions

• Isomer: Compounds with the same molecular formula but different structures.

• Chirality: Property of a molecule that is not superimposable on its mirror image.

• Hydrophobic: Water-fearing; nonpolar substances that do not dissolve in water.

• Hydrophilic: Water-loving; polar substances that dissolve in water.

• Amphipathic: Molecules with both hydrophobic and hydrophilic regions.

• Buffer: Solution that resists changes in pH.

• Enthalpy ($\Delta H$): Heat content of a system.

• Entropy ($\Delta S$): Measure of disorder.

• Gibbs Free Energy ($\Delta G$): Usable energy for work in a system.

Additional info: Some explanations and examples have been expanded for clarity and completeness, based on standard biochemistry curriculum.