🧬Biochemistry Unit 1 – Introduction to Biochemistry and Water

Key Concepts and Definitions

• Biochemistry studies the chemical processes within and related to living organisms
• Involves the study of biomolecules (carbohydrates, lipids, proteins, and nucleic acids) and their interactions
• Encompasses the structure, function, and metabolism of these biomolecules
• Investigates the chemical reactions and pathways that sustain life
• Explores the relationship between the structure and function of biomolecules
• Includes the study of enzymes, which are biological catalysts that speed up chemical reactions
• Examines the role of energy in biological systems, including the production and utilization of ATP (adenosine triphosphate)

Biochemistry Basics

• Biochemistry is an interdisciplinary field that combines principles from chemistry and biology
• Focuses on understanding the molecular basis of life and how chemical processes contribute to living systems
• Involves the study of the four major classes of biomolecules: carbohydrates, lipids, proteins, and nucleic acids
  • Carbohydrates serve as energy sources and structural components (cellulose in plant cell walls)
  • Lipids provide energy storage, insulation, and are key components of cell membranes (phospholipids)
  • Proteins perform a wide range of functions, including catalysis (enzymes), transport (hemoglobin), and structural roles (collagen)
  • Nucleic acids (DNA and RNA) store and transmit genetic information
• Investigates metabolic pathways, which are series of chemical reactions that convert nutrients into energy and biomolecules
• Explores the regulation of biochemical processes, such as gene expression and enzyme activity
• Applies knowledge to various fields, including medicine (drug development), agriculture (crop improvement), and biotechnology (genetic engineering)

Structure and Properties of Water

• Water is a simple molecule composed of two hydrogen atoms covalently bonded to one oxygen atom (H2O)
• Exhibits a bent geometry with an angle of approximately 104.5° between the hydrogen atoms
• Has a high boiling point (100°C) and heat capacity due to hydrogen bonding between water molecules
• Is an excellent solvent for polar and ionic compounds due to its polarity and ability to form hydrogen bonds
  • Dissolves a wide range of substances, including salts, sugars, and amino acids
• Has a high surface tension, allowing water to form droplets and enabling insects to walk on water
• Expands when frozen, making ice less dense than liquid water (ice floats on water)
• Plays a crucial role in maintaining the temperature stability of living organisms due to its high specific heat capacity

Water's Role in Biochemical Processes

• Water serves as a medium for biochemical reactions, providing a suitable environment for molecules to interact
• Participates in hydrolysis reactions, where water is used to break down larger molecules into smaller components (digestion of polymers)
• Is involved in condensation reactions, where water is released as smaller molecules combine to form larger ones (synthesis of polymers)
• Acts as a reactant in photosynthesis, where water is split into hydrogen and oxygen by light energy
• Maintains the structure and function of biomolecules through hydrophobic interactions and hydrogen bonding
  • Helps proteins fold into their native conformations
  • Stabilizes the double helix structure of DNA
• Facilitates the transport of substances within living organisms, such as nutrients and waste products
• Regulates body temperature through evaporation (sweating) and heat absorption

Hydrogen Bonding and Its Significance

• Hydrogen bonding is a type of intermolecular force that occurs between a hydrogen atom bonded to an electronegative atom (such as oxygen or nitrogen) and another electronegative atom
• Arises from the unequal sharing of electrons in polar covalent bonds, creating partial positive and negative charges
• Is stronger than other intermolecular forces (van der Waals forces) but weaker than covalent or ionic bonds
• Plays a crucial role in determining the properties of water, such as its high boiling point, surface tension, and ability to dissolve polar substances
• Contributes to the secondary structure of proteins, stabilizing α-helices and β-sheets
• Maintains the complementary base pairing in the double helix structure of DNA (adenine with thymine, guanine with cytosine)
• Influences the folding and stability of RNA molecules
• Affects the interactions between biomolecules and their aqueous environment

pH and Buffer Systems

• pH is a measure of the acidity or basicity of a solution, defined as the negative logarithm of the hydrogen ion concentration: $pH = -log[H+]$
• The pH scale ranges from 0 to 14, with 7 being neutral, values below 7 indicating acidity, and values above 7 indicating basicity
• In biochemical systems, pH plays a critical role in determining the structure and function of biomolecules
  • Enzymes have optimal pH ranges for their activity, outside of which their function may be impaired
  • Changes in pH can affect the ionization of amino acids, influencing protein folding and stability
• Buffer systems are mixtures of weak acids and their conjugate bases that resist changes in pH when small amounts of acid or base are added
• Buffers work by absorbing excess hydrogen ions (H+) or hydroxide ions (OH-) to maintain a relatively constant pH
• Common biological buffers include bicarbonate (HCO3-) and phosphate (HPO4-) systems
• Buffer systems are essential for maintaining the pH of bodily fluids within a narrow range, ensuring proper functioning of biochemical processes

Biomolecules and Water Interactions

• Water interacts with biomolecules through various types of non-covalent interactions, including hydrogen bonding, electrostatic interactions, and hydrophobic interactions
• Polar and charged groups of biomolecules (such as the hydrophilic heads of phospholipids) interact favorably with water through hydrogen bonding and electrostatic interactions
• Non-polar groups of biomolecules (such as the hydrophobic tails of phospholipids) tend to aggregate and minimize their contact with water, driven by hydrophobic interactions
• The hydrophobic effect is the tendency of non-polar substances to aggregate in aqueous solutions to minimize their contact with water molecules
  • Plays a crucial role in the formation of lipid bilayers and the folding of proteins
• Water forms hydration shells around dissolved ions and polar molecules, stabilizing their structures and influencing their interactions
• The interaction of water with biomolecules affects their solubility, folding, and function
  • Proteins fold into their native conformations to minimize the exposure of hydrophobic amino acids to water
  • Lipid bilayers self-assemble to shield their hydrophobic tails from water while exposing their hydrophilic heads

Practical Applications and Examples

• Understanding the role of water in biochemical processes is crucial for developing effective medications
  • Drugs often need to be water-soluble to be transported throughout the body and interact with their targets
• The study of enzyme kinetics and the effect of pH on enzyme activity is essential for optimizing industrial processes (food processing, detergent production)
• Knowledge of the hydrophobic effect is applied in the design of detergents and soaps, which contain both hydrophilic and hydrophobic components to dissolve grease and oils
• The principles of hydrogen bonding and pH are used in the development of pH-sensitive drug delivery systems (controlled release of insulin in response to changes in blood sugar levels)
• Buffer systems are employed in various industrial and laboratory settings to maintain stable pH conditions (fermentation processes, cell culture media)
• The understanding of water's role in the structure and function of biomolecules is fundamental to the field of structural biology (X-ray crystallography, NMR spectroscopy)
• The study of water's interactions with biomolecules is crucial for understanding the behavior of food systems (emulsions, gels) and designing functional food products