Fundamental Chemistry Concepts - Properties of Water, Organic Molecules PDF

Fundamental chemistry concepts: The properties of water and organic molecules Spring 2025 Dr. Maximilian Lyon MWF, 12:00-12:50 pm ISE 211 Housekeeping Office hour and SI schedule: Thursday: Betsy 11-12 pm in Ritter 314 Friday: Lyon 10-11 am i...

Fundamental chemistry concepts: The properties of water and organic molecules Spring 2025 Dr. Maximilian Lyon MWF, 12:00-12:50 pm ISE 211 Housekeeping Office hour and SI schedule: Thursday: Betsy 11-12 pm in Ritter 314 Friday: Lyon 10-11 am in Macelwane 100 Sunday: Katie 5-6 pm in Ritter 323 Attendance/participation will start tracking next week Let me know if you have Achieve access issues Let’s make sure iClicker is set up! Course name - BIOL 1260-05 Maximilian Lyon https://join.iclicker.com/ASPD ONLY USE YOUR SLU EMAIL Start iClicker at the beginning of each class You can use a laptop/phone/tablet If you have connection issues, try a different device or follow steps here: https://mhe.my.site.com/iclicker/s/article/Attendance-Geolocation-Tips Is the glass half full or half empty? As the hamster eats the pizza it is taking in energy that is: A. High entropy B. Low entropy Entropy Low High Is the glass half full or half empty? After the hamster finishes eating it runs on its wheel. The energy it consumed is transformed with the waste energy being lost as ____ energy: A. Light B. Chemical C. Kinetic D. Heat E. Potential Learning Objectives 1. Describe and differentiate covalent, ionic, and hydrogen bonds. Based on the relative electronegativity of the atoms forming a covalent bond, determine whether the bond is polar or nonpolar. 2. In a polar covalent bond, identify which atom carries a partial positive and which carries a partial negative charge. 3. Explain why a chemical functional group or a molecule is hydrophilic (water-soluble) or hydrophobic (insoluble in water). 4. Predict whether a molecule or chemical group, in water, releases or gains protons, and how that affects the pH of a solution. My dear Watson Elements are pure substances that can not be broken down further and have the same properties Smallest unit of an element is an atom, composed of different amounts of 3 particles Protons (+1 charge) and neutrons are in the nucleus, total number defines mass Electrons orbit in clouds (-1 charge) Defining elements Atomic number = number of protons Atomic symbol is a shorthand for the element (C for carbon) Mass number is the protons + neutrons Atomic number 6 C 14 Carbon Atomic symbol 6 Atomic element C Carbon Isotopes have a different number of neutrons and a different mass Mass number 12 Same protons, same element If you want the full details, take chemistry Electrons are arranged in shells First shell holds up to 2 electrons, later ones hold up to 8* Electron Highest energy electrons are in the farthest shell Lowest energy electrons are in the nearest shell Lowest energy shells must be full before another one can be added Surface Pressure The outermost shell contains the valence electrons Valence electrons can interact with other atoms Sodium Atom (Na) Chlorine Atom (Cl) 11 protons 17 protons 11 electrons 17 electrons Net charge: 0 Net charge: 0 Sodium Ion (Na+) Chlorine Ion (Cl-) 11 protons 17 protons 10 electrons 18 electrons Net charge: +1 Net charge: -1 Just know the relative trends Atoms are more stable when their valence is 0 To get valence to 0, electrons must be transferred or shared Electronegativity – how strongly a nucleus pulls in electrons More electronegative = more likely to take electrons O>>N>C≈H Equal sharing If electronegativity is similar, electrons will be shared This sharing forms a covalent bond that holds them together A molecule is any number of covalently bound atoms Same or very similar electronegativity gives a nonpolar bond Unequal sharing If the difference is large, electrons are pulled more towards one nucleus This leaves a partial (δ) + or – charge on both atoms More electronegative becomes δ-, less becomes δ+ These partial charges can attract, and (if H is involved) form hydrogen bonds between molecules Ionization Extreme electronegativity differences result in electron transfer, both become ions The atom that gains the electron becomes a negatively charged anion The atom that loses the electron becomes a positively charged cation Positive and negative charges attract forming an ionic bond Ranking bond strength Biomolecules get real big Lists the atoms present Shows what is bound to what Shows 3D relationship between atoms Shows relative sizes, most accurate Water: it’s what plants crave Water is polar, oxygen is partially negative (δ-), hydrogen is partially positive (δ+) Hydrogen bonds are weak attractions between partially positive hydrogens and partially negative atoms (usually O or N) in other molecules Solid lines = covalent bond, dotted lines = hydrogen bond The universal solvent Life is based on water Most molecules in cells are water Water is an excellent solvent (dissolves things) Water dissolves (most) polar and ionic molecules Nature.com/scitable Your insides are dissolving! Many important biomolecules are soluble in water Sugars Proteins and DNA Hydrophilic – “water-loving,” dissolves in water Water usually breaks ionic bonds but NOT covalent bonds Levy, Yaakov, and José N. Onuchic. "Water and proteins: A love–hate relationship." Proceedings of the National Academy of Sciences 101.10 (2004): 3325-3326. The bag part of fleshbags Nonpolar compounds are hydrophobic – “water fearing” and do not dissolve in water Have few if any full or partial charges Large non-polar molecules can be held together by extremely weak van der Walls interactions Defining pH Covalent bonds of water molecules can spontaneously break H2O ⇌ OH - + H + Water Hydroxide ion Hydrogen ion (proton) pH = concentration of free H+ ions pH = -log[H+] (just means high pH means less H+) Acid/base scale Water is constantly breaking and reforming Pure water at room temperature has 10-7 moles/L of H+ and OH- pH 7 is considered neutral, reference for other solutions Lower pH = acidic, releases H+ (H+ donor) High pH = basic, accepts H+ (H+ acceptor) Strong acids/bases always give/take H+ The other elements Carbon is the basis for organic molecules, what about O, P, N, S? Cell is mostly water, functional groups say how molecules interact with water (and each other) Methyl Carbonyl Hydroxyl Sulfhydryl Amino Phosphate Carboxyl Non-polar Polar Polar Polar Charged (aq) Charged (aq) Charged (aq) R – rest of the molecule (aq) – dissolved in water Ionizing groups (KNOW THESE!) AKA the most electronegative Which element is MOST LIKELY to form polar bonds? A. Carbon B. Hydrogen C. Nitrogen D. Oxygen E. They are all equally likely What makes something hydrophobic What kind of substance would be least likely to dissolve in water? A. One with only polar covalent bonds B. One with only non-polar covalent bonds C. One with only ionic bonds D. All would dissolve easily E. None would dissolve easily Target time! What part of this molecule is most likely to be attracted to water? For next class: Complete the reading quiz – due Wednesday at 12:00 pm Read Chapters 3.1, 4.1, and 4.4 (selected only) 4.4: Cell walls provide support and protection Follow my highlights: https://macmillan.vitalsource.com/home/subscribe/maximilian.lyon%40slu.edu