chm 12901 general chemistry with a biological focus unit 9 study guides

Key Concepts and Definitions

• Atoms consist of protons, neutrons, and electrons with protons and neutrons in the nucleus and electrons orbiting in shells
• Molecules form when two or more atoms bond together through covalent, ionic, or hydrogen bonds
• Thermodynamics studies the relationships between heat, energy, and work in chemical reactions and physical processes
• Kinetics investigates the rates of chemical reactions and the factors influencing them such as temperature, concentration, and catalysts
• Biochemistry applies chemical principles to biological systems (enzymes, metabolism, DNA)
• Analytical techniques include spectroscopy, chromatography, and electrophoresis to identify and quantify chemical compounds
• Problem-solving strategies involve dimensional analysis, stoichiometry, and applying chemical equations to real-world scenarios
• Biological systems rely on chemical processes (cellular respiration, photosynthesis) and interactions (protein folding, enzyme-substrate complexes) at the molecular level

Atomic and Molecular Structure

• Atomic number represents the number of protons in an atom determines the element's identity
• Mass number is the sum of protons and neutrons in an atom's nucleus
• Isotopes are atoms of the same element with different numbers of neutrons (carbon-12, carbon-13, carbon-14)
• Electron configuration describes the arrangement of electrons in an atom's orbitals follows the Aufbau principle, Hund's rule, and the Pauli exclusion principle
  • Aufbau principle states that electrons fill orbitals in order of increasing energy (1s, 2s, 2p, 3s, etc.)
  • Hund's rule requires that electrons occupy separate orbitals within a subshell before pairing up
  • Pauli exclusion principle allows a maximum of two electrons with opposite spins in each orbital
• Molecular geometry is determined by the arrangement of atoms in a molecule (linear, trigonal planar, tetrahedral) affects polarity and reactivity
• Lewis structures represent the bonding and lone pair electrons in a molecule using dots

Chemical Bonding and Interactions

• Chemical bonds form when atoms share or transfer electrons to achieve a stable electronic configuration
• Covalent bonds involve the sharing of electrons between atoms (single, double, triple bonds) and can be polar or nonpolar
• Ionic bonds result from the electrostatic attraction between oppositely charged ions (sodium chloride, potassium phosphate)
• Metallic bonds occur in metals where valence electrons are delocalized and shared among many atoms
• Hydrogen bonds are attractive forces between a hydrogen atom bonded to an electronegative atom (nitrogen, oxygen, fluorine) and another electronegative atom
• Van der Waals forces are weak intermolecular attractions (dipole-dipole, London dispersion) that affect properties like boiling point and solubility
• Bond energy is the amount of energy required to break a chemical bond influences the stability and reactivity of molecules
• Resonance structures represent the delocalization of electrons across multiple atoms in a molecule (benzene, carbonate ion)

Thermodynamics and Kinetics

• Thermodynamics deals with the relationships between heat, energy, and work in chemical reactions and physical processes
• First law of thermodynamics states that energy cannot be created or destroyed, only converted from one form to another
• Enthalpy ($\Delta H$) is the heat content of a system at constant pressure
  • Exothermic reactions release heat to the surroundings and have a negative $\Delta H$
  • Endothermic reactions absorb heat from the surroundings and have a positive $\Delta H$
• Entropy ($\Delta S$) measures the disorder or randomness of a system
• Gibbs free energy ($\Delta G$) predicts the spontaneity of a reaction based on changes in enthalpy and entropy ($\Delta G = \Delta H - T\Delta S$)
• Kinetics studies the rates of chemical reactions and the factors influencing them
• Reaction rate is the change in concentration of reactants or products per unit time
• Rate law expresses the relationship between the reaction rate and the concentrations of reactants (rate = $k[A]^m[B]^n$)
• Activation energy is the minimum energy required for reactants to overcome and proceed to products
• Catalysts lower the activation energy of a reaction without being consumed increase the reaction rate

Biochemical Applications

• Biochemistry applies chemical principles to biological systems and processes
• Enzymes are biological catalysts that speed up chemical reactions in living organisms by lowering the activation energy
  • Enzymes have specific active sites that bind to substrates through complementary shape and interactions
  • Michaelis-Menten kinetics describes the relationship between enzyme concentration, substrate concentration, and reaction rate
• Metabolism encompasses the chemical reactions involved in the breakdown (catabolism) and synthesis (anabolism) of molecules in cells
• Cellular respiration is the process by which cells break down glucose to produce ATP (adenosine triphosphate), the primary energy currency of the cell
• Photosynthesis is the process by which plants and other organisms convert light energy into chemical energy stored in glucose
• DNA (deoxyribonucleic acid) is the genetic material that stores and transmits hereditary information
  • DNA consists of four nucleotide bases (adenine, thymine, guanine, cytosine) paired through hydrogen bonding (A-T, G-C)
  • The double helix structure of DNA arises from the complementary base pairing and the sugar-phosphate backbone
• Proteins are macromolecules composed of amino acids linked by peptide bonds
  • Protein structure includes primary (amino acid sequence), secondary (alpha helices, beta sheets), tertiary (3D folding), and quaternary (multiple subunits) levels
  • Protein function depends on its structure and can include catalysis, transport, signaling, and structural roles

Analytical Techniques

• Analytical techniques are used to identify, quantify, and characterize chemical compounds and mixtures
• Spectroscopy techniques measure the interaction of electromagnetic radiation with matter
  • UV-Vis spectroscopy measures the absorption of ultraviolet and visible light by molecules (conjugated systems, transition metal complexes)
  • Infrared (IR) spectroscopy detects the vibrations of chemical bonds (functional groups)
  • Nuclear magnetic resonance (NMR) spectroscopy probes the magnetic properties of atomic nuclei (protons, carbon-13) to determine molecular structure
• Chromatography techniques separate mixtures based on the differential partitioning of components between a stationary phase and a mobile phase
  • Gas chromatography (GC) uses a gas as the mobile phase and is suitable for volatile compounds
  • High-performance liquid chromatography (HPLC) employs a liquid mobile phase under high pressure for separating non-volatile compounds
• Electrophoresis separates charged molecules (proteins, DNA fragments) based on their migration in an electric field
• Mass spectrometry (MS) measures the mass-to-charge ratio of ionized molecules to determine molecular mass and structural information
  • MS can be coupled with separation techniques (GC-MS, LC-MS) for enhanced analytical capabilities

Problem-Solving Strategies

• Dimensional analysis is a problem-solving method that uses the units of measurement to guide calculations and convert between quantities
• Stoichiometry involves calculating the quantitative relationships between reactants and products in a chemical reaction based on the balanced equation
  • Mole ratios are used to determine the amounts of reactants consumed or products formed
  • Limiting reagent is the reactant that is completely consumed in a reaction and determines the maximum yield of products
• Applying chemical equations to real-world scenarios requires identifying the relevant species, writing a balanced equation, and using stoichiometric relationships
• Estimating and approximating values can simplify calculations and provide a reasonable range for the answer
• Breaking down complex problems into smaller, manageable steps helps to organize the information and approach the solution systematically
• Checking units and significant figures throughout the problem-solving process ensures consistency and validity of the final answer
• Interpreting results in the context of the problem and evaluating their reasonableness is crucial for drawing meaningful conclusions

Connections to Biological Systems

• Biological systems rely on chemical processes and interactions at the molecular level
• pH plays a crucial role in biological processes as it affects the structure and function of biomolecules (enzymes, proteins)
  • Buffers are solutions that resist changes in pH when small amounts of acid or base are added maintain a stable pH in biological fluids (blood, cytoplasm)
• Osmosis is the movement of water across a semipermeable membrane from a region of high water potential (low solute concentration) to a region of low water potential (high solute concentration)
  • Osmotic pressure is the pressure required to stop the flow of water across a semipermeable membrane
  • Cells maintain osmotic balance through the transport of ions and small molecules (sodium-potassium pump, aquaporins)
• Redox reactions involve the transfer of electrons between species and play important roles in biological energy production (cellular respiration, photosynthesis)
• Enzyme kinetics and inhibition are important considerations in drug design and pharmacology
  • Competitive inhibitors bind to the active site of an enzyme and compete with the substrate
  • Non-competitive inhibitors bind to an allosteric site on the enzyme and change its conformation, reducing its activity
• Protein-ligand interactions are the basis for many biological processes (hormone-receptor binding, antigen-antibody recognition) and can be studied using techniques like X-ray crystallography and NMR spectroscopy
• Lipids are hydrophobic molecules that serve as structural components of cell membranes (phospholipids), energy storage (triglycerides), and signaling molecules (steroids)
  • The fluid mosaic model describes the structure of cell membranes as a fluid phospholipid bilayer with embedded proteins
• Carbohydrates are important for energy storage (glycogen, starch), structural support (cellulose, chitin), and cell-cell recognition (glycoproteins, glycolipids)