Lecture 1_ Bio 2

Page 1: Course Introduction

• Title: Welcome to General Biology II

Page 2: Instructor Information

• Instructor: Katie Pagnucco, BSc. Western University (2003-2007)MSc. University of Alberta (2007-2010)PhD McGill University (2010-2015)Post-doc UQAM (2015-2017)

• Pronouns: She/her

• E-mail: katie.pagnucco@johnabbott.qc.ca

• Office: AME-309

• Office Hours:

  • Tuesday: 1:00 PM - 3:00 PM

  • Thursday: 1:00 PM - 4:00 PM

• Research Interests:

  • Community ecology

  • Food web dynamics

  • Aquatic ecology

Page 3: Course Units Overview

• Unit I: Biomolecules

  • Review and expansion

• Unit II: DNA

  • History and structure

  • Replication

  • Gene expression and regulation

  • Biotechnology

• Unit III: (Details about this unit are not included)

Page 4: Texts

• Required:

  • Lab manual: General Biology II lab manual (available at bookstore)

• Optional:

  • Textbook: Campbell, N.A., et al. 2021. Biology (Third Canadian ed.). Pearson/Benjamin Cummings. 1552 p.

  • OpenStax Biology 2e

Page 5: Marking System

• Lecture Marking:

  • Class tests (3)

    • 3 x 12% = 36%

  • Class work/homework: 5%

  • Final Exam: 30%

• Laboratory Marking:

  • Lab work: 10%

  • Lab assignments (2)

    • 2 x 3% = 6%

  • Research Project: 13%

  • Tentative dates for Class Tests are in the Course Outline

Page 6: Class Work/Homework

• 6 in-class quizzes will be conducted throughout the semester.

• Format: Multiple choice; answers submitted individually after discussion with classmates.

• Covers material from the previous two weeks.

• Platform: Plickers

• Practice assignments available for preparation; these will not be graded.

• Platform: Google Forms

Page 7: Student Expectations

• Arrive on time to class.

• No distractions (talking or otherwise) to classmates.

• Turn assignments in on time:

  • Late submissions incur a 10% per day deduction for lab projects.

  • Other assignments must be completed on time for credit, else they will receive a grade of 0 but feedback will still be given.

Page 8: Tips for Success in BIO

1. Attend Lectures:

   • Come prepared (rested, with materials).

   • Lecture slides posted on Sundays.

2. Take Notes:

   • Slides are text-heavy; additional material will be covered during class.

3. Review Notes:

   • Review your notes within 24 hours of class for retention.

Page 9: Academic Integrity

• Zero tolerance for cheating and plagiarism.

  • E.g., submission of copied work from Internet or peers is considered plagiarism.

• Assignments, tests, and lab reports will receive a ZERO for violations.

Page 10: Course Outline

• Encouraged to read the Course Outline for further details.

Page 11: Anonymous Feedback Form

• Students can submit anonymous feedback on the course and instructor anytime during the semester.

• Questions include teaching style, lecture pacing, and interactivity suggestions.

Page 12: Introduction to Organic Molecules

• Topic: Organic Molecules, Acids, and Bases, Isomers.

Page 13: Review Activity

• Activity: Kahoot to review Basic Chemistry.

Page 14: Acids and Bases

• Water is in a state of dynamic equilibrium.

• Water molecules dissociate at the same rate they are being reformed.

Page 15: Impact of Acids and Bases

• Changes in concentrations of H+ and OH- affect cell chemistry.

• Pure water has equal concentrations of H+ and OH-.

• Addition of acids/bases modifies these concentrations.

• The pH scale describes whether a solution is acidic or basic.

Page 16: The pH Scale

• Acidic solutions: pH < 7

• Basic solutions: pH > 7

• Most biological fluids have pH values between 6 and 8.

Page 17: Definitions of Acids and Bases

• Acid: Increases H+ concentration in a solution by donating H+.

• Base: Reduces H+ concentration in a solution by picking up H+.

• The pH is defined as: pH = −log [H+]; [H+] = 10^-pH.

Page 18: Properties of Acids

• Weak acids (HA) do not dissociate significantly in water.

• When an acid donates a proton, the resulting species is called a conjugate base (A-).

• Acid strength determined by dissociation constant, Ka.

• Dissociation Reaction: HA ⇌ H+ + A-.

Page 19: Ka and pKa

• Dissociation Constant:

  • Ka = [H+][A-]/[HA]

  • When Ka < 1, [HA] > [H+][A-], indicating weak dissociation.

  • Lower Ka value = weaker acid.

  • pKa = -log Ka; lower pKa = stronger acid.

Page 20: pKa Importance

• pKa is specific to a molecule under specific conditions.

• Key equation:

  • pH = pKa + log ([A-]/[HA])

• When pH = pKa, concentrations of acid and conjugate base are equal.

Page 21: Practice Question

• Acetic acid (pKa = 4.75) has a pH of 6.75.

• Ratio of acid to conjugate base: 1:100 (calculation shown).

Page 22: Role of Buffers

• Internal pH of cells must remain close to 7.

• Buffers minimize changes in H+ and OH- concentrations.

• Buffers contain weak acid/base pairs that act reversibly with H+ ions.

Page 23: Organic Molecules Definition

• Chemical compounds that contain carbon, excluding:

  • Simple oxides of C (CO, CO2)

  • Carbonates (H2CO3...)

  • Cyanides

  • Allotropes of Carbon (e.g., graphite, diamond).

Page 24: Importance of Carbon

• Carbon forms diverse molecules by bonding with up to four other atoms.

• Tetravalence allows for the creation of large, complex molecules.

• Carbon most frequently bonds with H, O, and N.

Page 25: Distinctive Properties

• Properties of organic molecules depend on:

  • The carbon skeleton

  • The molecular components attached to it.

Page 26: Variability in Organic Molecules

• Skeletons can vary in:

  • Length

  • Double bonds

  • Branching

  • Rings

Page 27: Isomers

• Isomers: same molecular formula, different structures/properties.

  • Types of Isomers:

    • Structural isomers: different covalent arrangements.

    • Stereoisomers: same bonded atom sequence, different 3D orientations.

    • Cis-trans (geometric): same bonds, different spatial arrangements.

    • Enantiomers: mirror images.

Page 28: Isomers Visual Representation

• Various representations of structural and stereoisomers with examples shown.

Page 29: Case Study of Isomers

• Thalidomide Example:

  • 'R' isomer reduces morning sickness.

  • 'S' isomer causes birth defects.

  • Drug prescribed in the 1960s and 1970s led to thousands of birth defects due to this.

Page 30: Continuation on Organic Molecules

• Properties depend on carbon skeleton and attached molecular components.

Page 31: Functional Groups

• Functional groups are key components for chemical reactions in organic molecules.

• Their arrangement imparts unique properties; e.g., estradiol and testosterone differ in just two functional groups, leading to different biological functions.

Page 32: Major Functional Groups

• Seven key functional groups:

  1. Hydroxyl group

  2. Carbonyl group

  3. Carboxyl group

  4. Amino group

  5. Sulfhydryl group

  6. Phosphate group

  7. Methyl group.

Page 33: Hydroxyl Group

• Structure: -OH

• Example: Ethanol (alcohol in beverages)

  • Polar due to electronegative oxygen, forms hydrogen bonds with water to help dissolve sugars.

Page 34: Carbonyl Group

• Structure: C=O

• Examples:

  • Acetone (ketone)

  • Propanal (aldehyde)

  • Sugars with ketones are called ketoses; those with aldehydes are called aldoses.

Page 35: Carboxyl Group

• Structure: -COOH

• Example: Acetic acid (vinegar)

  • Acts as acid by donating H+ due to polar bond between oxygen and hydrogen.

Page 36: Amino Group

• Structure: -NH2

• Example: Glycine (amino acid)

  • Acts as a base; can pick up H+ from the surrounding solution.

Page 37: Sulfhydryl Group

• Structure: -SH

• Example: Cysteine (sulfur-containing amino acid)

  • Forms cross-links to help stabilize protein structure.

Page 38: Phosphate Group

• Structure: -OPO3^2-

• Involved in many important chemical reactions in cells

  • Contributes negative charge and ability to react with water, releasing energy.

Page 39: Methyl Group

• Structure: -CH3

• Example: 5-Methyl cytosine (DNA component)

  • Affects gene expression and can influence the structure and function of hormones.

Page 40: Identifying Functional Groups

• Example molecule contains:

  • Carboxyl group

  • Amino group

Page 41: Additional Functional Groups

• Another example molecule illustrates:

  • Hydroxyl group

  • Methyl group

  • Amino group

  • Carbonyl group (ketone) and amide groups.