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.
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
Attend Lectures:
Come prepared (rested, with materials).
Lecture slides posted on Sundays.
Take Notes:
Slides are text-heavy; additional material will be covered during class.
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:
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
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.