Biochemistry: Molecular Genetics and Macromolecules

Genetic Biochemistry

• Genetic biochemistry is the chemistry of processes and substances that store and transmit biological information
• It's also the province of molecular genetics, which seeks to understand heredity and the expression of genetic information in molecular terms

Macromolecules

• Many macromolecules are polymers, formed by condensation reactions of monomers
• Examples of macromolecules:
  • Proteins
  • Polysaccharides
  • Nucleic acids
  • Lipids

Biological Functions of Macromolecules

• Polysaccharides: structure, energy storage
• Nucleic acids: storage and transcription of genetic information
• Proteins: structure, enzymes, hormones, receptors
• Lipids: energy storage, membranes

Biochemistry as a Biological Science

• The cell is the basic unit of biological organization
• Cell types:
  • Prokaryotes (always unicellular, including true bacteria and archaea)
  • Eukaryotes (may be unicellular or multicellular)

Cell Structure

• Prokaryotic cell structure:
  • Plasma membrane and cell wall
  • Cytoplasm with cytosol, DNA, and ribosomes
  • Cell surface may have pili and flagellae

The Role of Water in Biological Processes

• Water serves as the universal intracellular and extracellular medium due to its:
  • Ability to form hydrogen bonds
  • Polar character
• Hydrophilic substances can readily dissolve in water
• Water is an excellent solvent for ionic compounds due to:
  • Hydration shells
  • High dielectric constant

Energy, Heat, and Work

• Bioenergetics: the study of how organisms capture, transform, store, and utilize energy
• Systems:
  • Isolated: exchanges neither energy nor matter
  • Closed: exchanges energy but not matter
  • Open: exchanges both energy and matter
• Human and organisms are considered open systems
• Internal energy (U) includes all forms of energy that can be exchanged via physical or chemical processes

Free Energy: The Second Law in Open Systems

• Free energy (ΔG) determines the favorability of a process
• ΔG = ΔH - TΔS
• Processes with -ΔG are exergonic (favorable), while those with +ΔG are endergonic (unfavorable)
• Enzymes increase reaction rates but do not change the favored direction
• The entropy of an open system can decrease

High Energy Phosphate Compounds

• These compounds have very large negative free energies of hydrolysis
• Examples:
  • ATP
  • Phosphocreatine
  • Phosphoenolpyruvate
• Hydrolysis reactions release orthophosphate (Pi), which increases entropy and is therefore favored
• Resonance stabilization applies to all phosphate hydrolysis reactions

Biochemistry: Course Overview

• Attendance in laboratories and seminars is mandatory, with only one allowed absence without excuse and one allowed lateness per semester
• Late arrivals are considered absences, with a 5-point deduction for every subsequent lateness
• Students must submit a doctor's excuse for absences within 7 days to the course coordinator

Assessment Structure

• Total of 200 points
• Exam (final): 100 points
• Midterms (winter and summer): 25 points each
• Seminars and labs: 10 points each (winter and summer)
• Lectures: 5 points each (winter and summer)

Literature

• Required textbooks: Harpers Illustrated Biochemistry (at least 29th Edition), Lubert Stryer's Biochemistry (at least 4th Edition), and Biochemistry: Concepts and Connections
• Recommended texts: None listed

What is Biochemistry?

• Biochemistry is the study of the structure, organization, and functions of living matter in molecular terms
• Three principal areas of biochemistry:
  • Structural chemistry of living matter's components and their relationships to biological function
  • Metabolism: the totality of chemical reactions that occur in living matter
  • Genetic biochemistry: the chemistry of biological information storage and transmission

Biochemistry as a Chemical Science

• Macromolecules: proteins, polysaccharides, nucleic acids, and lipids
• Many macromolecules are polymers formed by condensation reactions of monomers
• Biological functions of macromolecules:
  • Polysaccharides: structure, energy storage
  • Nucleic acids: storage and transcription of genetic information
  • Proteins: structure, enzymes, hormones, receptors
  • Lipids: energy storage, membranes

Biochemistry as a Biological Science

• The cell is the basic unit of biological organization
• Prokaryotes (e.g. bacteria, archaea) are unicellular, with a plasma membrane, cell wall, cytoplasm, and freely floating DNA and ribosomes
• The cell surface may have pili, flagellae, and other features

The Matrix of Life: Weak Interactions in an Aqueous Environment

• Noncovalent interactions:
  • Hydrogen bonds
  • Dipole-dipole interactions
  • Van der Waals forces
• Importance of weak interactions in biomolecular structures

The Role of Water in Biological Processes

• Hydrogen bonding in biological structures
• Water serves as a universal intracellular and extracellular medium due to its ability to form hydrogen bonds and its polar character
• Water is an excellent solvent for ionic compounds
• Hydration of ions in solution
• Nonpolar substances (hydrophobic, lipophilic) have limited solubility in water

Ionic Equilibria

• Brønsted-Lowry definition of acids and bases
• Strong acids and bases, and their conjugate forms
• Buffered solutions:
  • Minimize pH changes upon addition of acid or base
  • Functioning near the pKa, where the conjugate acid and base are present in nearly equimolar concentrations

Energetics of Life

• Bioenergetics: the study of energy capture, transformation, storage, and utilization in living organisms
• Energy, heat, and work
• Internal energy (U): the total energy of a system
• Thermodynamic systems:
  • Isolated: no exchange of energy or matter
  • Closed: exchange of energy, but not matter
  • Open: exchange of both energy and matter

Free Energy and Chemical Reactions

• Gibbs free energy (G): a function of state that includes both energy and entropy
• Free energy change (ΔG) = ΔH - TΔS
• Favorable processes: negative ΔG
• Unfavorable processes: positive ΔG
• High-energy phosphate compounds:
  • ATP and its hydrolysis reactions
  • Free energy sources in biological systems