BIOL 1260: Water and Organic Molecules

• Fundamental chemistry concepts covered are the properties of water and organic molecules
• The class for Spring 2025 is taught by Dr. Maximilian Lyon
• The class is scheduled for MWF from 12:00-12:50 pm in ISE 211

Housekeeping

• Office hours are Thursday, 11 am - 12 pm with Betsy in Ritter 314
• Office Hours are Friday, 10 am - 11 am with Lyon in Macelwane 100
• Office Hours are Sunday, 5 pm - 6 pm with Katie in Ritter 323
• Attendance/participation will start being tracked next week
• There is assistance available for those with Achieve access issues

iClicker Setup

• The course name is BIOL 1260-05 Maximilian Lyon
• The iClicker can be joined at https://join.iclicker.com/ASPD
• Only use your SLU email for iClicker
• Start iClicker at the beginning of each class
• A laptop/phone/tablet can be used for iClicker
• If there are connection issues, use a different device or follow the trouble shooting tips https://mhe.my.site.com/iclicker/s/article/Attendance-Geolocation-Tips

Learning Objectives

• Describe and differentiate covalent, ionic, and hydrogen bonds
• Based on relative electronegativity of atoms, determine if a covalent bond is polar or nonpolar
• For polar covalent bonds, identify which atom carries partial positive, and which carries partial negative charge
• Explain why chemical functional groups or molecules are either hydrophilic (water-soluble) or hydrophobic (insoluble in water)
• Predict whether molecules or chemical groups, in water, release or gain protons, and impact on pH

Elements and Atoms

• Elements are pure substances that cannot be further broken down and have the same properties
• The smallest unit of an element is an atom, composed of different amounts of 3 particles
• Protons have a +1 charge and neutrons are in the nucleus, combined they define mass
• Electrons orbit in clouds, and have a -1 charge

Defining Elements

• Atomic number is the number of protons
• Atomic symbol is a shorthand for the element (C for carbon)
• Mass number is the number of protons plus neutrons
• Isotopes have a different number of neutrons and a different mass
• Elements can have different numbers of neutrons, but must have the same number of protons

Electron Arrangement

• Electrons are arranged in shells
• The first shell holds up to 2 electrons; later shells hold up to 8
• Lowest energy shells must be full before another one can be added

Valence Electrons

• The outermost shell contains the valence electrons
• Valence electrons can interact with other atoms

Electronegativity

• Atoms are more stable when their valence is 0
• To achieve a valence of 0, electrons must be transferred or shared
• Electronegativity is how strongly a nucleus pulls in electrons
• More electronegative atoms are more likely to take electrons
• Oxygen (O) has an electronegativity of 3.4
• Chlorine (Cl) has an electronegativity of 3.2
• Nitrogen (N) has an electronegativity of 3.0
• Carbon (C) has an electronegativity of 2.6
• Phosphorus (P) has an electronegativity of 2.2
• Hydrogen (H) has an electronegativity of 2.2
• Sodium (Na) has an electronegativity of 0.9
• Potassium (K) has an electronegativity of 0.8

Equal Sharing: Covalent Bonds

• When electronegativity is similar, electrons are shared
• Sharing forms a covalent bond that holds atoms together
• A molecule is any number of covalently bound atoms
• Same or very similar electronegativity results in 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 atoms become δ-, less electronegative atoms become δ+
• These partial charges can attract. If H is involved, form hydrogen bonds between molecules

Ionization and Ionic Bonds

• Extreme electronegativity differences result in electron transfer, then both atoms become ions
• The atom that gains electrons becomes a negatively charged anion
• The atom that loses electrons becomes a positively charged cation
• Positive and negative charges attract and forming an ionic bond

Ranking of Bond Strength

• Covalent bonds involve electrons shared in orbitals, and require between 200-500 kJ/mole to break single bonds, and 500-700 kJ/mole to break double bonds
• Ionic bonds involve electrons transferred with electrostatic reaction between oppositely charged ions, and require between 1,100-20,000 kJ/mole to break within ionic crystal
• Hydrogen bonds involve electrostatic attraction between slightly positively charged H and slightly negatively charged O and N atoms, and require between 4-50 kJ/mole to break
• van der Waals interactions involve transient electrostatic attraction between two atoms, each in a nonpolar covalent bond, and require less than 4 kJ/mole to break

Representations of Biomolecules

• Molecular formulas list the types and number of atoms present (e.g. NH2CH2COOH)
• Structural formulas show what is bound to what
• Ball-and-stick models show 3D relationship between atoms
• Space-filling models show relative sizes, most accurate

Water: Polarity and Hydrogen Bonding

• Water molecules are polar, the oxygen atom is partially negative (-), and hydrogen atoms are partially positive (+)
• Hydrogen bonds are weak attractions between partially positive hydrogens and partially negative atoms (usually O or N) in other molecules
• Solid lines represent covalent bonds and dotted lines represent hydrogen bonds

Water as a Solvent

• Life is based on water
• Most molecules in cells are water
• Water is an excellent solvent
• Water dissolves most polar and ionic molecules

Hydrophilic and Hydrophobic Molecules

• Many important biomolecules are soluble in water
• Hydrophilic/water-loving molecules dissolve in water
• Water usually breaks ionic bonds but not covalent bonds
• Nonpolar compounds are hydrophobic/water fearing and do not dissolve in water
• Hydrophobic molecules have few if any full or partial charges
• Large non-polar molecules can be held together by extremely weak van der Walls interactions

pH

• Covalent bonds of water molecules can spontaneously break
• pH = concentration of free H+ ions
• pH = -log[H+]
• High pH means less H+

The pH 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 and a reference for other solutions
• Lower pH is acidic and releases H⁺ (H⁺ donor)
• High pH is basic and accepts H⁺ (H⁺ acceptor)
• Strong acids/bases always give/take H⁺

Carbon and Functional Groups

• Carbon is the basis for organic molecules
• A cell is mostly water; functional groups dictate how molecules interact with water (and each other)
• Functional groups: Methyl, Carbonyl, Hydroxyl, Sulfhydryl, Amino, Phosphate, Carboxyl
• R represents the rest of the molecule
• Aq means dissolved in water

Ionizing Groups

• Amino groups, in water, attract a H⁺ ion (proton) and become positively charged (base)
• Carboxyl groups, in water, release a proton and becomes negatively charged (acid)
• Phosphate groups, in water, releases 2 protons and winds up with 2 negatively charged O (acid)

Reminders

• Complete the reading quiz by Wednesday at 12:00 pm
• Read Chapters 3.1, 4.1, and 4.4
• Find course highlights at https://macmillan.vitalsource.com/home/subscribe/maximilian.lyon%40slu.edu

Notes for Dr. Lyon's BIOL 1260 class focusing on water and organic molecules. The class will cover the properties of water and organic molecules. Important logistical information includes iClicker setup and office hours.