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Unit 1 – Chemistry of Life (Vocabulary Flashcards)

Unit 1 – Course Introduction

  • Instructional Team & Supports
    • Professor: Dr. Kat Ray King (they/she)
    • Seizure Service Dog: Cooper (also provides moral support in class)
    • PAL: ReeseVarel
    • UTA: Angie Barszcz
    • REACH Tutoring: https://reach.louisville.edu/tutoring/
    • We’re here to help you — please ASK!
  • Common Questions about BIOL 240 vs BIOL 241
    • Difference between BIOL 240 and BIOL 241
    • BIOL 240: Lectures primarily; introduces unifying concepts.
    • BIOL 241: Labs; more focused on designing and implementing experiments to test concepts from lecture.
    • Is this harder than BIOL 102?
    • It’s different — a different course with different goals.
    • What are we learning this semester?
    • Unifying concepts of biology such as cellular and molecular components of life, evolution, and genetics.
  • What do you want to get out of your college classes? (Video reference)
    • Zeinab Yasser, Sulaiman Al Rajhi Colleges; Father Guido Sarducci's Five Minute University concept references.
  • How learning happens in this course
    • Zone of Proximal Development (Vygotsky):
    • Learner can do unaided vs learner can do with guidance vs learner cannot do yet.
    • We provide guidance to push outside comfort zones; move from what you can do to what you cannot do yet.
    • Active Learning in class: problem-solving & application practice during class with instructor support.
  • Active Learning vs Traditional Lectures: course data overview
    • Freeman et al. (2014) – 225 studies comparing classroom types show differences in failure rates between traditional lectures and active learning.
    • Key data (average failure rates):
    • In active learning: 21.8\%
    • In traditional lecture: 33.8\%
    • Clicker questions prompt: interpret data and select correct statement about failure rates (A/B/C options on slides).
  • Conceptual shift in how knowledge is built
    • Transmission of Knowledge (Traditional Lecture): “I’ll transmit my knowledge to you by telling you about it.”
    • Construction of Knowledge (Active Learning): “I’ll create situations so that you construct your own knowledge and understanding with ongoing feedback.”
    • Social Construction of Knowledge: collaborative learning and knowledge building in social contexts.
  • How to study for deeper questions
    • Use Learning Objectives (LOs) as a framework, not just a checklist of facts.
    • LO-driven study strategy: pre-class preparation, in-class application, and post-class review.
  • Note-taking findings (from Glass & Kang, 2018)
    • Pen/paper vs laptop/tablet: no difference in lecture comprehension.
    • Long-term retention is reduced when taking notes on a laptop/tablet.
    • Recommendation: take notes from recorded lectures and class sessions; transcripts/ PDFs will be provided.
  • Course Components & Grading (as per the syllabus)
    • Letter Grades (grading schema)
    • A: 90\% or higher
    • B: 80-89\%
    • C: 70-79\%
    • D: 55-69\%
    • F: <55\%
    • No +/- scaling offered; details in Start Here module on Blackboard.
    • Grading Summary (approximate distribution):
    • Orientation Assignments: 2\%
      • 3 assignments worth 5\text{ or }10\text{ points} each (total 20\text{ points})
    • Class participation using iClicker: 10\%
      • 5 pts per lecture, capped at 100 pts (out of 110 pts offered)
      • Total: 100\text{ points}
    • Pre-Class and Homework Assignments: 25\%
      • Worth 10\text{ pts each}, lowest 2 scores dropped
      • Total: 250\text{ points}
    • Perusall Questions/Comments: 6\%
      • 5 pts per week, capped at 60 pts (out of 65 pts offered)
    • Quizzes: 7\%
      • 8 group quizzes, 10 pts each, drop lowest score
      • Total: 70\text{ points}
    • Exams: 50\%
      • 5 exams, 100\text{ pts} for each; 40–50 questions per exam
      • Total: 500\text{ points}
    • Total: 1000\text{ points}
    • One of the first assignments is the syllabus assignment due Thursday.
    • True/False/Multiple-Choice style clarifications (example from slides)
    • Pre-class assignments are due BEFORE class; we review some via Clickers; we’ll expand topics in class.
    • Recorded lectures & Live Class will include a mix of new information and practice via clickers, drawing, application questions, etc.
    • Group quizzes are available; you can chat with group mates if you choose.
    • iClicker setup and Blackboard navigation
    • Ensure iClicker is working; visit Blackboard Start Here → Accessing iClicker for setup.
  • Important dates & reminders
    • Upcoming due dates are located on Blackboard within unit folders.
    • Reading assignments appear after the content they cover.
    • DUE BY 1 HOUR BEFORE CLASS:
    • THURSDAY: Watch D1 video lectures (D2 folder); complete pre-class atoms assignment (D2 folder); watch D2 video lectures (D2 folder)
    • TUESDAY: Watch D3 video lectures (macromolecules and cells); complete D3 pre-class assignments
    • Special upcoming due dates:
    • DUE BY THURSDAY BEFORE CLASS: Syllabus & Blackboard Assignment; Respondus Lockdown Browser Assignment (test system before Concept Assessments & Exams)
    • In-class Tuesday: Quiz 1 (group quiz, in-person, requires Respondus)
    • Weekly schedule continues similarly for most days; find all due dates on Blackboard.
  • Perusall & Week 1 Reading
    • Week 1 Reading Assignment due Sunday 11:59 PM; post at least four responses per week (questions or detailed comments)
    • Completing all pages of the reading earns 1 point; time spent reading is required for full credit.
    • Perusall Tutorial resources are provided to guide usage.
  • Blackboard/Syllabus Orientation
    • Orientation steps: Click Orientation → Read Pages/Click Links → Complete Activities
    • When finished, you’re done for the day.
  • Chemistry of Life: Recorded Lectures (Parts 1 & 2)
    • Part 1 Topics: Bonds (types and formation), Water (structure and properties), Acids/Bases (pH)
    • Part 2 Topics: Review of LOs for acids/bases, bonds, water; continuation of LO-focused content
  • Key Learning Objectives (LOs) for Unit 1 – Chemistry of Life
    • Acids/Bases
    • Describe how acids and bases affect the pH of an aqueous solution (the change they make to pH and what they do to change the pH)
    • Define buffer and its application for pH in biological systems
    • Calculate ext{pH} and ext{pOH} given hydrogen or hydroxide ion concentration and calculate hydrogen or hydroxide ion concentration given pH or pOH
    • Bonds
    • Determine the number of atomic bonds an atom can form based on its valence electrons
    • Describe the different types of atomic bonds (polar covalent, nonpolar covalent, and ionic) and how each form in terms of unequal/equal sharing of electrons or stealing electrons
    • Identify the type of atomic bond that will form between C, H, N, O, F based on their valences and relative electronegativities
    • Predict the properties of molecules (no charge, partial charges, or full charges) based on the chemical bonds within them
    • Water
    • Define hydrogen bonding and how/why it forms through partial charges
    • Explain what makes molecules hydrophilic and hydrophobic
    • Describe each of water’s unique properties below and how they impact life: as a solvent; adhesion and cohesion; moderation of temperature; expansion upon freezing
    • Describe how hydrogen bonding allows for water’s unique properties
    • LOs: Daily partial LO lists are provided in class; complete LO lists posted on Blackboard
  • Core concepts – Atoms, Bonds, and Electrons (Chemistry of Life)
    • Atoms are the smallest unit of matter that life builds from; understanding atomic properties helps explain life processes.
    • Periodic table and electrons: shell model; each shell besides the first holds up to 8 electrons.
    • Electrons and chemical bonds: chemical bonds form via sharing or transfer of electrons to fill outer shells; octet rule emphasis.
    • Electronegativity trends: H ≈ C < N < O < F; H < O; important relationships:
    • H ~ C; H < N; C << O; H << O (relative electron affinity and bonding behavior)
  • Covalent Bonds & Polarity
    • Covalent bond = sharing of electrons.
    • Electronegativity trend: ext{H} \approx \text{C} < \text{N} < \text{O} < \text{F}
    • Nonpolar vs Polar Covalent:
    • Nonpolar: bonded atoms have similar electronegativities
    • Polar: bonded atoms have different electronegativities
    • Example: ext{H–H} is nonpolar; ext{H–F} is polar
  • Polarization & Partial Charges (Video Questions)
    • Shared electrons spend more time around the more electronegative atom, creating partial charges (δ+ and δ−)
    • Sample question: polar covalent bond yields partial charges; identify which side is δ+ and which is δ−
    • Fluorine is highly electronegative; oxygen and nitrogen also high; hydrogen is less electronegative than these.
  • Hydrogen Bonds
    • Definition: hydrogen bonds are attractions between a partially positive hydrogen atom and a partially negative atom (such as F, O, or N)
    • Importance for water structure and function; network of hydrogen bonds gives water its unique properties
  • Ions, Ionic Bonds, and Hydration
    • Ionic bonds: electrons are not shared; ions form when elements lose or gain electrons
    • Cation: positively charged ion; Anion: negatively charged ion
    • OIL RIG (or LEO says GER): oxidation-reduction shorthand for electron transfer
    • In aqueous solutions, salts dissolve due to hydration shells around ions
  • Hydrophilic vs Hydrophobic
    • Hydrophilic: polar molecules with partial or full charges that interact with water
    • Hydrophobic: nonpolar molecules with no charge; do not easily interact with water
    • Example: oil (hydrophobic) vs water (polar interaction)
  • Water’s Properties and Life
    • Key properties to life: solvent capability; adhesion and cohesion; temperature moderation; expansion upon freezing
    • Ice is less dense than liquid water due to hydrogen bonding network; this allows aquatic life to survive in cold climates
    • Water as solvent, and hydrogen bonding underpin life-supporting chemical reactions
  • Acids, Bases, and the pH Scale
    • Water self-ionization and definitions: acids donate H⁺; bases accept H⁺; pH scale measures acidity
    • Acidity/basicity rules:
    • Neutral: [H^+] = [OH^-]
    • Acidic: [H^+] > [OH^-]
    • Basic: [H^+] < [OH^-]
    • pH and pOH relationship: ext{pH} + ext{pOH} = 14
    • Calculation examples:
    • If ext{pH} = 9, then [OH^-] = 10^{-\text{pOH}} = 10^{-(14-9)} = 10^{-5}
    • If given [H^+] = 10^{-8}, then ext{pH} = -\log_{10}([H^+]) = 8
    • Common reference values: internal pH of most cells is around ext{pH} \approx 7; human blood around ext{pH} \approx 7.4; critical survival range is very narrow (death if > 7.8 or < 7 for a few minutes)
  • Buffers & Blood Buffering System
    • Buffers minimize changes in H⁺ or OH⁻ by buffering: they can accept H⁺ if there are too many in solution or donate H⁺ if needed
    • Blood buffering via carbonic acid system: \mathrm{CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+}
    • Carbonic acid acts as a buffer in blood: if pH rises (H⁺ concentration falls), the equilibrium shifts to the right to add more H⁺ back, stabilizing blood pH
    • Rise in pH corresponds to a drop in H⁺ and drives the reaction to the right to restore H⁺ balance
  • Special Notation and LO Tracking
    • In-class LOs are provided daily; a complete LO list is posted on Blackboard
    • The course emphasizes LO-based study and ongoing assessment to prepare for exams
  • Quick Reference: Key Formulas and Concepts (summary)
    • Acid-base concepts
    • ext{pH} = -\log_{10}([H^+])
    • ext{pOH} = -\log_{10}([OH^-])
    • ext{pH} + \text{pOH} = 14
    • Hydration and ionic dissolution
    • Salt dissolution in water involves hydration shells around ions
    • Bonding basics
    • Covalent bond: \text{shared electrons}
    • Ionic bond: \text{electrostatic attraction between oppositely charged ions}
    • Water structure and hydrogen bonding
    • Hydrogen bonds contribute to water’s high cohesion, surface tension, and solvent properties
    • LO-driven study approach
    • Use LOs to organize study, diagnose prior knowledge, and create a personal study guide

Unit 1 – Chemistry of Life

  • Today’s Topics
    • Bonds: types of bonds and how bonds form based on electronegativity
    • Water: water’s structure and the unique properties that support life
    • Acids/Bases: concepts of pH, how acids and bases affect pH, buffer definitions and applications
  • Learning Objectives (LOs) for Unit 1
    • Acids/Bases LO details (as listed above)
    • Bonds LO details (as listed above)
    • Water LO details (as listed above)
    • LO-based study guidance: use LO as framework; diagnostic before pre-assignments; answer LO questions during study; revisit LO after assignments; focus on least-confident LO first; responsibility for every LO element
  • Atoms, Electrons, and Periodic Table (Chemistry of Life, starting points)
    • Atoms: smallest unit of matter; foundational for biological processes
    • Electron shells: first shell holds a fixed number; every shell besides the first can hold up to 8 electrons
    • Valence and octet: bonds form to fill outer shells and reach stable configurations
    • Periodic table relationships among elements influence bonding behavior (e.g., electronegativity differences)
  • Electronegativity and Bond Types
    • H ≈ C < N < O < F (relative electronegativities)
    • Covalent bonds: sharing of electrons
    • Nonpolar covalent: similar electronegativities
    • Polar covalent: different electronegativities
    • Example relationships to understand polarity: H–H nonpolar; H–F polar
  • Quick Conceptual Review: Video Questions (sample concepts from slides)
    • Polar covalent bonds create partial charges (δ+ on less electronegative, δ− on more electronegative partner)
    • The most electronegative element in a pair typically bears the partial negative charge
    • Example prompts often require identifying δ+ and δ− in given molecules
  • Water and Hydrogen Bonding
    • Hydrogen bonds are charge-based attractions between a partially positive hydrogen and a partially negative atom (O, N, F)
    • Hydrogen bonding underpins water’s unique properties and many biological processes
  • Ionic Bonds and Hydration (Ions and Water)
    • Ionic bonds result from electron transfer (no sharing) and electrostatic attraction between cations and anions
    • In water, ions are stabilized by hydration shells
    • OIL RIG mnemonic: Oxidation Is Loss, Reduction Is Gain (contextual for electron transfer)
  • Hydrophilic vs Hydrophobic in Biological Context
    • Hydrophilic: interactions with water due to charges or polar groups
    • Hydrophobic: nonpolar regions that minimize contact with water; drives membrane formation and protein folding in cells
  • Properties of Water Relevant to Life
    • Water as solvent: dissolves many solutes critical for biochemistry
    • Adhesion and Cohesion: water’s attraction to itself and to other surfaces
    • Temperature Moderation: high specific heat and heat of vaporization stabilize organisms and environments
    • Expansion Upon Freezing: ice is less dense than liquid water, allowing aquatic life to survive in cold temperatures
  • pH, Buffers, and Human Physiology
    • Blood pH homeostasis relies on buffering systems (e.g., carbonic acid/bicarbonate buffer)
    • Buffers help maintain stable internal environments across organisms
  • Important Reminders for Practice
    • LO-driven study requires you to understand both definitions and applications; practice with calculations and concept application
    • Expect LO-based questions on quizzes and exams; ensure you can explain both concept and calculation
  • Quick Reference – Key Equations & Concepts (condensed)
    • Acid-base: ext{pH} = -\log{10}([H^+]);\quad [H^+] = 10^{- ext{pH}};\quad ext{pOH} = -\log{10}([OH^-]);\quad [OH^-] = 10^{- ext{pOH}};\quad ext{pH} + \text{pOH} = 14
    • Carbonic acid buffering in blood: \mathrm{CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+}
    • Hydrogen bonds: ext{H–bond: } ext{H}^+ \dots \text{A}^-; A = \text{F, O, N}
    • Ionic dissolution in water: hydration shells around ions; aqueous solution notation: \text{NaCl (aq)} etc.