🔮Chemical Basis of Bioengineering I Unit 3 – Molecular Structure & Interactions

Key Concepts

• Atoms consist of protons, neutrons, and electrons which determine an element's properties
• Chemical bonds form between atoms to create molecules and compounds
  • Covalent bonds involve sharing of electrons between atoms
  • Ionic bonds involve transfer of electrons resulting in positively and negatively charged ions
• Molecular geometry refers to the three-dimensional arrangement of atoms in a molecule
  • Shapes include linear, trigonal planar, tetrahedral, and octahedral
• Intermolecular forces are attractive or repulsive forces between molecules
  • Types include van der Waals forces, hydrogen bonding, and dipole-dipole interactions
• Biological macromolecules are large molecules essential for life processes (proteins, carbohydrates, lipids, nucleic acids)
• Molecular interactions in biological systems involve specific binding between molecules
  • Examples include enzyme-substrate interactions and antibody-antigen binding
• Lab techniques for studying molecular structure include spectroscopy, chromatography, and X-ray crystallography

Atomic Structure and Chemical Bonding

• Atoms are the basic building blocks of matter composed of protons, neutrons, and electrons
• Protons have a positive charge, neutrons have no charge, and electrons have a negative charge
• The number of protons in an atom determines its atomic number and element identity
• Electrons occupy specific energy levels or orbitals around the nucleus
  • Valence electrons in the outermost shell participate in chemical bonding
• Chemical bonds form when atoms share or transfer electrons to achieve a stable electronic configuration
• Covalent bonds involve sharing of electrons between atoms to form molecules (H2, O2, CH4)
  • Can be single, double, or triple bonds depending on the number of electron pairs shared
• Ionic bonds involve transfer of electrons from one atom to another resulting in ions (NaCl, CaCl2)
  • Positively charged cations and negatively charged anions are held together by electrostatic attraction

Molecular Geometry and Shapes

• Molecular geometry refers to the three-dimensional arrangement of atoms in a molecule
• Shapes are determined by the number of electron groups (atoms and lone pairs) around the central atom
• VSEPR theory predicts molecular shapes based on minimizing electron pair repulsion
  • Electron groups arrange themselves to be as far apart as possible
• Linear shape occurs when there are two electron groups around the central atom (CO2, HCN)
• Trigonal planar shape occurs with three electron groups arranged in a plane (BF3, SO3)
• Tetrahedral shape occurs with four electron groups arranged in a tetrahedron (CH4, NH4+)
• Octahedral shape occurs with six electron groups arranged in an octahedron (SF6, [Co(NH3)6]3+)
• Molecular shape affects physical and chemical properties such as polarity, solubility, and reactivity

Intermolecular Forces

• Intermolecular forces are attractive or repulsive forces between molecules
• Van der Waals forces are weak attractions between molecules caused by temporary dipoles
  • Includes London dispersion forces and dipole-induced dipole interactions
• Hydrogen bonding is a strong attraction between a hydrogen atom bonded to N, O, or F and another electronegative atom
  • Responsible for unique properties of water and stabilization of DNA base pairs
• Dipole-dipole interactions occur between polar molecules with permanent dipoles
  • Alignment of positive and negative ends of dipoles results in attraction
• Ion-dipole interactions occur between ions and polar molecules (Na+ and H2O)
• Hydrophobic interactions are the tendency of nonpolar substances to aggregate in aqueous solution
  • Driven by the exclusion of nonpolar molecules by water
• Intermolecular forces influence properties such as boiling point, solubility, and surface tension

Biological Macromolecules

• Biological macromolecules are large molecules essential for life processes
• Proteins are polymers of amino acids that perform various functions (enzymes, structural proteins, antibodies)
  • Amino acids are linked by peptide bonds to form polypeptide chains
  • Protein structure includes primary, secondary, tertiary, and quaternary levels
• Carbohydrates are molecules composed of carbon, hydrogen, and oxygen (sugars, starches, cellulose)
  • Monosaccharides are simple sugars that serve as building blocks (glucose, fructose)
  • Disaccharides are formed by linking two monosaccharides (sucrose, lactose)
  • Polysaccharides are long chains of monosaccharides (starch, glycogen, cellulose)
• Lipids are hydrophobic molecules that include fats, oils, and steroids
  • Triglycerides are composed of glycerol and three fatty acids
  • Phospholipids have a hydrophilic head and hydrophobic tails, forming cell membranes
• Nucleic acids are polymers of nucleotides that store and transmit genetic information (DNA, RNA)
  • DNA is a double-stranded helix composed of four nucleotide bases (A, T, C, G)
  • RNA is single-stranded and involved in protein synthesis (mRNA, tRNA, rRNA)

Molecular Interactions in Biological Systems

• Molecular interactions in biological systems involve specific binding between molecules
• Enzyme-substrate interactions involve the binding of a substrate to an enzyme's active site
  • Enzymes catalyze biochemical reactions by lowering the activation energy
  • Specificity is achieved through complementary shape and chemical interactions
• Antibody-antigen binding is a specific interaction between an antibody and an antigen
  • Antibodies are proteins produced by the immune system to recognize and bind foreign substances
  • Antigens are molecules that elicit an immune response, such as bacteria, viruses, or toxins
• Receptor-ligand interactions involve the binding of a ligand (hormone, neurotransmitter) to a receptor protein
  • Binding triggers a cellular response, such as signal transduction or ion channel opening
• DNA-protein interactions are essential for processes like replication, transcription, and regulation
  • Transcription factors bind specific DNA sequences to control gene expression
  • DNA polymerase binds to DNA template to synthesize new strands during replication
• Carbohydrate-lectin interactions are specific bindings between sugars and lectin proteins
  • Involved in cell-cell recognition, adhesion, and signaling (selectins, galectins)
• Molecular interactions are driven by a combination of hydrogen bonding, electrostatic interactions, and van der Waals forces

Lab Techniques and Applications

• Various lab techniques are used to study molecular structure and interactions in bioengineering
• Spectroscopy techniques measure the interaction of molecules with electromagnetic radiation
  • UV-visible spectroscopy measures absorption of light in the visible and ultraviolet regions
  • Infrared spectroscopy detects molecular vibrations and functional groups
  • Nuclear magnetic resonance (NMR) spectroscopy provides information about molecular structure and dynamics
• Chromatography techniques separate mixtures based on differences in molecular properties
  • High-performance liquid chromatography (HPLC) separates compounds based on their interaction with a stationary phase
  • Gas chromatography (GC) separates volatile compounds based on their partitioning between a gas and liquid phase
  • Affinity chromatography separates proteins based on their specific binding to ligands
• X-ray crystallography determines the three-dimensional structure of molecules by analyzing X-ray diffraction patterns
  • Requires the formation of a crystalline sample of the molecule of interest
  • Provides detailed information about the positions of atoms and chemical bonds
• Microscopy techniques allow visualization of biological structures at high resolution
  • Electron microscopy (EM) uses a beam of electrons to image samples, providing higher resolution than light microscopy
  • Atomic force microscopy (AFM) measures surface topography and interactions using a probe tip
• Calorimetry measures heat changes during molecular interactions and reactions
  • Isothermal titration calorimetry (ITC) measures binding affinity and thermodynamics of molecular interactions
• These techniques are essential for characterizing molecular structure, interactions, and function in bioengineering applications

Real-World Bioengineering Examples

• Molecular structure and interactions play a crucial role in various bioengineering applications
• Drug design and development rely on understanding molecular interactions between drugs and their targets
  • Structure-based drug design uses knowledge of the target protein's structure to design complementary molecules
  • High-throughput screening identifies compounds that bind to a target of interest
• Biomaterials engineering involves designing materials that interact favorably with biological systems
  • Hydrogels are cross-linked polymer networks that mimic the extracellular matrix and support cell growth
  • Surface modification techniques control the interaction of materials with proteins and cells (PEGylation, peptide conjugation)
• Tissue engineering aims to create functional tissue substitutes by combining cells, scaffolds, and bioactive molecules
  • Scaffolds provide a three-dimensional structure for cell attachment and growth
  • Growth factors and cytokines are incorporated to guide cell differentiation and tissue formation
• Biosensors are devices that detect specific molecules or biological events using molecular recognition elements
  • Enzyme-based biosensors use the specific binding of enzymes to their substrates to generate a measurable signal
  • Antibody-based biosensors (immunosensors) detect the presence of specific antigens
  • DNA biosensors (genosensors) detect specific DNA sequences through hybridization with complementary probes
• Protein engineering involves modifying the structure and function of proteins for specific applications
  • Directed evolution techniques introduce random mutations and select for improved variants
  • Rational design uses knowledge of protein structure to make targeted modifications
• Gene therapy relies on the delivery of genetic material into cells to treat or prevent diseases
  • Viral vectors are engineered to deliver therapeutic genes into target cells
  • Non-viral vectors, such as lipid nanoparticles, are used to deliver DNA or RNA
• These examples highlight the importance of understanding molecular structure and interactions in developing bioengineering solutions to real-world problems