BIOL 219 (Fall)

Physical Biology of the Cell


 
Instructors:
J. Vogel (Coordinator)
Bellini 269
(514) 398-5880
jackie.ord Physicsvogel@mcgill.ca
S. Weber TBA (514) 398-2042 steph.weber@mcgill.ca
P. François Rutherford Physics (514) 398-1635 paul.francois2@mcgill.ca
A.Mittermaier Otto Maass (514) 398-3085 anthony.mittermaier@mcgill.ca
G. Bub McIntyre 1128 (514) 398-8148 gil.bub@mcgill.ca
Workload:
4 credits (3-1-5)
Prerequisites:
1 year of college calculus, chemistry and physics or equivalents, BIOL 112 or equivalent
       
Corequisites:      
MATH 222 and CHEM 212 or equivalents    
       
Restrictions:      
Not open to students who have taken ANAT 212, BIOC 212, BIOL 200 and BIOL 201
Content:

BIOL 219 is an introduction to molecular and cell biology using physical biology perspectives, and equally prepares interdisciplinary students for more advanced courses in the biological and physical sciences. Technologies and methodologies, both experimental and computational, are included in the presentation of each thematic module.

Module 1: Overview of a living cell; prokaryotic and eukaryotic, biophysical perspectives
1.1. Design features of cells
1.2. Major classes of biological molecules; examples
1.3. Length and time scales

Module 2: Proteins, enzymes and reactions
2.1. Protein structure (1, 2, 3 and quaternary)
2.2. Sculpting protein structure (modifications)
2.3. Protein folding and quality control (chaperone example)
2.4. Enzyme characteristics, reaction and energy potential
2.5. Orders of kinetic reactions
2.6. Allostery
2.7. Cooperativity

Module 3: Energy
3.1. Overview of metabolism
3.4. Physical basis of energy in biological systems
3.5. Making ATP with oxygen, part I
3.6. Making ATP with oxygen, part II
3.7. Origins of life, how to make ATP without oxygen
3.8. Photosynthesis (physical perspective)

Module 4: Information storage and flow
4.1. DNA and RNA structure; RNA structure-function
4.2. The physical basis of the genetic code
4.3. 1D (sequence) and 2D linear structure of coding and non-coding sequences
4.4. 3d organization of the genome, human and yeast chromosome examples
4.5. Origins of variation: splice variants, mutations, TNs, paralogs
4.6. Transcription; monocistronic and polycistronic
4.7. Regulation of transcription: Thermodynamics
4.8. Regulation of transcription: Kinetics
4.9. Overview of translation (includes nuclear export)
4.10 Regulation of translation (examples)

Module 5: Biological machines and ensembles
5.1. Physical properties of the cytoplasm
5.2. Molecular self-assembly I: Phase separation (thermodynamic models)
5.3. Molecular self-assembly II: Polymerization (kinetic models) and polymer mechanics
5.4. The cytoskeleton- actin and microtubules (structure of monomer and polymer, etc)
5.5. DNA and RNA replication machineries
5.6. Intracellular transport I: passive mechanisms, diffusion
5.7. Intracellular transport II: active mechanisms, molecular motors

Module 6: Control in cell division
6.1. Oscillators, feedback, noise
6.2. Biological control; oscillators, feedback, thresholds in detail
6.3. Control of cell cycle transitions
6.4. Dynamics in mitosis I; DNA replication, DNA repair
6.5. Dynamics in mitosis II; chromosome segregation machinery
6.6. Checkpoint examples, biophysical perspectives

Module 7: Cell signaling and polarity
7.1. Overview of symmetry breaking, emergent polarity
7.2. Cell morphology/polarization through intracellular signaling; receptor G-protein signaling (mating pathway example); small GTPases Cdc42, Rho etc.
7.3. Asymmetric cell divisions, stem cells
7.4. Secretory machineries; endo and exocytosis
7.5. Cellular interactions (ECM) through intercellular signaling (delta/notch)
7.6. Enforcing properties among cells in tissues (planar polarity)

Module 8: Neuroscience
8.1. Neurons and electrical potential, transduction
8.2. Neurotransmitters, control
8.3. Example of a simple circuit

Readings:
Lodish Molecular Cell Biology 8th edition and selected material from Nelson, “Biological Physics”
Method:
3 Lectures plus 1 compulsory tutorial per week
Evaluation:

Problem sets, mid-term exams and final exam


McGill University values academic integrity. Therefore all students must understand the meaning and consequences of cheating, plagiarism and other academic offences under the Code of Student Conduct and Disciplinary Procedures (see http://www.mcgill.ca/integrity/ for more information).

Last update: March 21, 2017