Biochemistry_slides_S3-4 (1)

Chapter 2: Water: The Solvent for Biochemical Reactions

Chapter Outline

• (2-1) Water and Polarity

• (2-2) Hydrogen Bonds

• (2-3) Acids, Bases, and pH

• (2-4) Titration Curves

• (2-5) Buffers

(2-1) Water and Polarity

• Water is a polar molecule due to its bent molecular geometry and electronegativity difference between hydrogen and oxygen.

• The polarity of water allows it to dissolve many substances, making it an excellent solvent in biochemical reactions.

(2-2) Hydrogen Bonds

• Hydrogen bonds are weak attractions between the hydrogen atom of one molecule and a highly electronegative atom of another molecule (e.g., N, O).

• Hydrogen bonds are crucial in stabilizing structures of proteins and nucleic acids.

(2-3) Acids, Bases, and pH

• Acid: A substance that donates protons (H+ ions) in a solution.

• Base: A substance that accepts protons, increasing hydroxide ions (OH-) in a solution.

• pH: A measure of the acidity or basicity of a solution, defined as negative logarithm of hydrogen ion concentration.

  • Neutral pH = 7, Acidic < 7, Basic > 7.

(2-4) Titration Curves

• Titration measures the change in pH as a strong base is added to an acid.

• The equivalence point marks the complete neutralization of the acid, characterized by a sharp change in pH.

(2-5) Buffers

• Buffers: Mixtures that resist changes in pH when small amounts of acids or bases are added.

  • Composed of a weak acid and its conjugate base.

• Examples: CH3COOH/CH3COONa and H2CO3/NaHCO3.

Water and Synthesis

• Condensation/Hydrolysis Reactions:

  • Condensation: Formation of larger biomolecules by removing water (e.g., synthesis of polypeptides, polysaccharides).

  • Hydrolysis: Breakdown of biomolecules by adding water (e.g., breaking peptide bonds).

Peptides

• Peptide bonds form between amino acids via condensation (removal of water) and can be hydrolyzed to break them.

• The reaction involves:

  • Structure: H3N-CH-C(OH) + H-N-CH-COO⁻ ➔ H3N-CH-C-N-CH-COO⁻ + H2O

Carbohydrates

• Carbohydrate formation involves reactions such as:

  • Hemiacetal Formation: A carbonyl compound reacts with an alcohol, resulting in carbohydrate structures.

  • Examples: Formation of α-D-Glucose or β-D-Glucose through hydrolysis and condensation reactions.

Polynucleotides

• Polynucleotide formation involves phosphodiester bonds during condensation, linking nucleotides together to form nucleic acid chains:

  • Each bond involves the removal of a water molecule.

Fatty Acids

• Fatty acid molecules are important in forming lipids, and their structure includes:

  • Head group: typically contains a phosphate group, which may interact with water.

  • Tail: hydrophobic portion composed of carbon chains.

Solvent Properties of Water

• Water's solvent properties arise from its ability to form hydrogen bonds and interact with various solutes:

  • Hydrophilic: Substances that dissolve in water (ionic/polar).

  • Hydrophobic: Substances that do not dissolve in water (nonpolar).

  • Amphipathic: Molecules such as detergents that have both hydrophilic and hydrophobic regions.

pH and Acidity

• The strength of an acid can be expressed using the dissociation constant (Ka); higher Ka indicates a stronger acid.

• The Henderson-Hasselbalch equation relates pH, pKa, and concentrations of acid and conjugate base:

  • pH = pKa + log([A-]/[HA]).

Buffer Systems

• Buffers play a critical role in maintaining stable pH in biological systems.

• Buffers contain weak acids and their conjugate bases, providing a means for organisms to manage pH levels effectively.

Chapter 2: Water: The Solvent for Biochemical Reactions

Chapter Outline

• (2-1) Water and Polarity

• (2-2) Hydrogen Bonds

• (2-3) Acids, Bases, and pH

• (2-4) Titration Curves

• (2-5) Buffers

(2-1) Water and Polarity

Water (H2O) is a highly polar molecule characterized by its bent molecular shape, which arises from the tetrahedral arrangement of its electron pairs. The electronegativity difference between hydrogen (H) and oxygen (O) atoms results in a partial positive charge (δ+) on the hydrogen atoms and a partial negative charge (δ-) on the oxygen atom. This polarity allows water to engage in dipole-dipole interactions, making it an exceptional solvent for a wide range of inorganic and organic substances, thus playing a critical role in biochemical reactions, such as cellular metabolism and energy transfer.

(2-2) Hydrogen Bonds

Hydrogen bonds are relatively weak intermolecular forces that occur between a hydrogen atom covalently bonded to an electronegative atom (such as oxygen or nitrogen) in one molecule and another electronegative atom in a different molecule. They are vital in stabilizing the three-dimensional structures of proteins, such as α-helices and β-pleated sheets, and are fundamental to the double helix structure of DNA. The dynamic nature of hydrogen bonds also allows for the flexibility necessary for biochemical processes, including enzyme-substrate interactions and molecular recognition.

(2-3) Acids, Bases, and pH

• Acid: A substance that can donate protons (H+ ions) to a solution, increasing the concentration of hydrogen ions. Common examples include hydrochloric acid (HCl) and acetic acid (CH3COOH).

• Base: A substance that can accept protons, thus raising the concentration of hydroxide ions (OH-) in a solution. Sodium hydroxide (NaOH) is a strong base commonly used in laboratory settings.

• pH: It is defined as the negative logarithm of the hydrogen ion concentration in a solution, calculated as pH = -log[H+]. The pH scale ranges from 0 to 14, where a neutral pH of 7 indicates equal concentrations of H+ and OH-. A pH below 7 is considered acidic, while a pH above 7 denotes basicity.

(2-4) Titration Curves

Titration is a quantitative analytical method used to determine the concentration of an unknown acid or base by neutralizing it with a titrant of known concentration. The titration curve plots pH versus the volume of titrant added. The equivalence point, where the amount of titrant added neutralizes the acid, is marked by a steep increase in pH. Understanding the shape of the titration curve helps in determining the strength of the acid and base involved and is crucial in biochemical assays and pharmaceutical applications.

(2-5) Buffers

Buffers are solutions that maintain a relatively stable pH when small amounts of acids or bases are introduced. A buffer system typically consists of a weak acid and its conjugate base or a weak base and its conjugate acid. This resilience to pH changes is critical in biological systems where enzymes and biochemical processes function optimally within specific pH ranges. Examples of buffer systems include the acetic acid/sodium acetate (CH3COOH/CH3COONa) buffer and the carbonic acid/bicarbonate (H2CO3/NaHCO3) buffer, which are instrumental in physiological pH regulation.

Water and Synthesis

Condensation/Hydrolysis Reactions:

• Condensation: This process involves the formation of larger biomolecules through the removal of water molecules, such as in the synthesis of proteins (polypeptides) and carbohydrates (polysaccharides). For instance, during peptide bond formation, an -OH group from the carboxyl group of one amino acid and an -H atom from the amine group of another amino acid are eliminated, leading to water release.

• Hydrolysis: In contrast, hydrolysis is the breakdown of these biomolecules by the addition of water, which disrupts bonds, such as peptide bonds, thereby facilitating metabolism and energy release.

Peptides

Peptide bonds form through a condensation reaction between amino acids, characterized by the linkage of the amino group of one amino acid to the carboxyl group of another, releasing water in the process. This bond can be hydrolyzed again, demonstrating the dynamic nature of peptide synthesis and degradation:

Structure: [ H_3N-CH-C(OH) + H-N-CH-COO⁻ \rightarrow H_3N-CH-C-N-CH-COO⁻ + H_2O ]

Carbohydrates

Carbohydrate formation includes reactions such as hemiacetal formation, where a carbonyl (aldehyde or ketone) reacts with an alcohol, resulting in carbohydrate structures. For example, the formation of glucose derivatives like α-D-Glucose and β-D-Glucose involves hydrolysis and condensation reactions that modify the properties of sugars and their roles in metabolism.

Polynucleotides

Polynucleotides comprise nucleotide monomers linked by phosphodiester bonds, resulting from condensation reactions that remove water. Each phosphodiester bond imparts directionality and stability to nucleic acid chains, a fundamental feature for DNA and RNA functions in heredity and protein synthesis.

Fatty Acids

Fatty acids play a crucial role in lipid formation and are characterized by a hydrophilic head, often containing a phosphate group that interacts favorably with water, and a long hydrophobic tail made up of carbon chains, making them essential for the structure of cell membranes (phospholipids) and energy storage (triglycerides).

Solvent Properties of Water

Water's solvent properties stem from its robust ability to form hydrogen bonds with various solutes.

• Hydrophilic: Molecules that readily dissolve in water include ionic and polar substances, which can interact with the polar nature of water.

• Hydrophobic: Substances that do not dissolve in water, such as nonpolar molecules, do not interact favorably with water molecules.

• Amphipathic: These molecules possess both hydrophilic and hydrophobic regions (e.g., detergents), allowing them to interact with both water and fats, which is crucial in biological membranes.

pH and Acidity

The strength of an acid can be quantified using the dissociation constant (Ka), where a higher Ka value signifies a stronger acid due to its greater ability to donate protons. The Henderson-Hasselbalch equation relates pH, pKa, and the concentrations of acid and conjugate base, and it is expressed as:[ pH = pKa + log([A^-]/[HA]) ] This equation is particularly useful in biochemistry for understanding buffer systems and metabolic pathways.

Buffer Systems

Buffers are pivotal in maintaining stable pH levels in biological systems, which is critical for enzyme functionality and metabolic processes. Buffer systems consist of weak acids and their conjugate bases, effectively neutralizing small amounts of added acids or bases, thus ensuring the pH remains within narrow limits essential for life processes.