Cellular biology and biochemistry for engineers
BIO-105
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Cellular Biology and Biochemistry for Engineers
Organization of the course :
please watch the video explaining the course organization.
Teaching Assistant:
Ayberk OZKIRLI email : ayberk.ozkirli@epfl.ch
Reference textbooks :
1. Essential Biology (Campbell Reece Simon)
Read on line : use the link provided below.
- Link to the Moodle site for the 2022 class: (Text and media area)
- link to the Moodle site for 2022 (URL)
- * * * * * * * * * * * (Text and media area)
- Link to Essential Biology (3rd) online (URL)
- Essential Biology (7th) Campbell (File)
- 2. Essential Cell Biology (Alberts) (Text and media area)
- Essential Cell Biology (5th) Alberts (File)
- 3. Hilllis Sadava Hill Price Principles of Life (2... (Text and media area)
- chapter 4 (1) (URL)
- ch 4 (2) (URL)
- Ch 4 (3) (URL)
- Ch 4 (4) (URL)
- ch 4 (5) (URL)
- Ch 4 (6) (URL)
- Ch4 (7) (URL)
- link to the Switch channel (URL)
September 21, 2021 (week 1)
Hierarchical organization: atoms, molecules, cells, organisms.
- 2021 welcoming video (URL)
- atomic level: (Text and media area)
- Atomic structure : shell, subshell, orbital (File)
- molecular level: (Text and media area)
- Lecture 1 (Text and media area)
- slides lecture 1-1 (File)
- slides lecture 1-2 (File)
- Exercises : (Text and media area)
September 28, 2021 (week 2)
Plasma membrane, osmosis
- Tuesday 14:15 - 16 :00 : &... (Text and media area)
- Lecture 2 2021 : (Text and media area)
- slides week 2 (2021) (File)
- animated 3D model of bilayer (URL)
- FRAP (URL)
- Hemolysis (File)
- animation : hemolysis (URL)
- 2021 recording 1 in INF-119 (URL)
- 2021 recording 2 in INF-119 (URL)
- Lecture 2 2020 : (recorded) (copy) (Text and media area)
- link to lecture 2 part 1 (URL)
- link to lecture 2 part 2 (URL)
- link to lecture 2 part 3 (URL)
- Exercises : (Text and media area)
- Exercises 1 2021 (File)
October 5th, 2021 (week 3)
Protein in the plasma membrane.
looking for the conformation with the lowest energy level- Lecture 3 (2021) (Text and media area)
- 2021 dias sem 3 (File)
- hydropathy plot (File)
- Lecture 3 (2020) (copy) (Text and media area)
- link to the recorded lecture part 1 (URL)
- link to the recorded lecture part 2 (URL)
- link to lecture 3 part 3 (URL)
- slides week 3 (2020) (File)
- Exercises : (Text and media area)
- Exercises 2 2021 (File)
- link to Seq. Manipulating Suite (URL)
- Link to get random prot. seq. (URL)
- link to generate hydropathy plots (URL)
October 12th, 2021 (week 4)
Resting membrane potential
Energy / Metabolism
mitochondrial ATP synthase
- Lecture 4 (2021) : energy (Text and media area)
- 2021 slides for lecture 4 (Energy) (File)
- recording 1 week 4 2021 (URL)
- recordiing 2 week 4 2021 (URL)
- resting membrane potential animation (File)
- Resting membrane potential (2020) (Text and media area)
- link to the lecture on resting membrane potential (URL)
- simulation ion channels (URL)
- Slides resting membrane potential (File)
- Na+ K+ pump (File)
- resting membrane potential (1) (URL)
- resting membrane potential (from Hillis) (URL)
- Resting Membrane Potential (yvcc) (URL)
- additional, non mandatory tutorials : (Text and media area)
- origin of resting membrane potential (URL)
- link to Introduction to Bioelectricity (MOOC) (URL)
- Lecture 4 (2020) : energy (copy) (Text and media area)
- link to lecture 4 part 1 Energy (URL)
- slides week 4 Energy part 1 (File)
- video on phothosynthesis (detailed) (File)
- Alberts ch 14 Energy (File)
- Animation photosynthesis (File)
- Exercises : (Text and media area)
- exercises 3 BIO-105 2021 (File)
October 19th, 2021 (week 5)
Energy (part 2)
DNA : basics
- Lecture 5 (2021)slides on energy : the last ... (Text and media area)
- 2021 recording 1 week 5 (URL)
- ATP synthase (File)
- 2021 recording 2 week 5 (URL)
- 2021 dias week 5 second hour (File)
- Lecture 5 (2020) (copy) (Text and media area)
- link to video week 5 part 1 (URL)
- slides week 5 ATP synthesis (File)
- link to video week 5 part 2 ATPsynthase (URL)
- exercises : (Text and media area)
- Exercises 4 (week 5) 2021 (File)
October 26th, 2021 (week 6)
DNA Replication
Molecular technics : PCR, microsatellites analysis
- Lecture 6 (2021) (Text and media area)
- 2021 recording 1 week 6 (URL)
- 2021 slides week 6 part 1 (File)
- 2021 recording 2 week 6 (URL)
- 2021 slides week 6 part 2 (File)
- Exercises : (Text and media area)
- 2021 exercises 5 (week 6) (File)
- Probable schedule for the exam (not yet confirmed)... (Text and media area)
- Lecture 6 (2020) (Text and media area)
- link to video 6 part 1 Basics on DNA (URL)
- dias week 6 part 1 (copy) (File)
- link to tutorial 9.1 (URL)
- link to video week 6 part 2 (URL)
- video week 6 part 3 Replication in E. coli (URL)
- Animation replication in E. coli (File)
- video week 6 part 4 (URL)
- animation DNA helicase (File)
- video week 6 part 5 P C R (URL)
- animation : PCR (File)
- slides week 6 P C R (File)
- Hillis : concept 9.2 (replication) (URL)
- Albert's chapter 6 (File)
November 2, 2021 (week 7)
Gene expression : 1 transcription
- Lecture 7 (2021) : (Text and media area)
- 2021 slides for week 7 (File)
- 2021 week 7 recording 1 (URL)
- 2021 week 7 recording 2 (URL)
- Lecture 7 (2020) : (copy) (Text and media area)
- HeLa cells mitosis (File)
- Animation on mitosis (File)
- animation on meiosis (File)
- video lecture 7 part 1 (URL)
- slides lecture 7 part 1 (File)
- video week 7 part 2 (URL)
- slides week 7 part 2 (File)
- Telomere (File)
- Exercises : (Text and media area)
- 2021 Exercises 6 (week 7) (File)
November 9th (week 8)
Gene expression : 2 translation
- Lecture 8 (2021)slides : 2nd part of last week (Text and media area)
- 2021 week 8 recording 1 (URL)
- 2021 week 8 recording 2 (URL)
- Exercises : (Text and media area)
- 2021 Exercises 7 (week 8) (File)
- Lecture 8 (2020) (copy) (Text and media area)
- slides week 8 (2020) (File)
- video week 8 part 1 (transcription) (URL)
- link to tutorial 14.1 (RNApolymerase) (URL)
- video week 8 part 2 (translation) (URL)
- tutorial 14.3 (transcription & translation) (URL)
- translation (eEF-1 correct) (File)
- animation : translation (elongation cycle) (File)
- gene expression (animation) (File)
November 16th (week 9)
Genetics 1 : chromosomes and genes transmission
- Lecture 9 (2021) (Text and media area)
- 2021 slides week 9 (File)
- 2021 week 9 recording 1 (URL)
- 2021 week 9 recording 2 (URL)
- Exercises : (Text and media area)
- 2021 series 8 (week9) (File)
- Lecture 9 (2020) (copy) (Text and media area)
- slides week 9 part 1 (File)
- video week 9 part 1 (URL)
- video week 9 part 2 (URL)
- slides week 9 part 2 (File)
- Exercises : (copy) (Text and media area)
November 23 (week 10)
Genetics 2 :
- Lecture 10 (2021) (Text and media area)
- 2021 recording 2 (week 10) (URL)
- 2021 recording 1 (week 10) (URL)
- 2021 slides week 10 (File)
- animation on meiosis (copy) (File)
- Exercises : (Text and media area)
- 2021 series 9 (week 10) (File)
- Lecture 10 (2020) (Text and media area)
- video lect 10 part 1 autosomal dominant (URL)
- slides week 10 part 1 (File)
- video lecture 10 part 2 (URL)
- slides lect 10 part 2 (File)
- Tutorial on X-linked inheritance (URL)
November 30th (week 11)
1. X inactivation : mutation of XIC
2. genetic distance
- Lecture 11 (2021) (Text and media area)
- 2021 slides week 11 (File)
- 2021 recording 1week 11 (URL)
- Recording for the 2nd hour is not available : plea... (Text and media area)
- video week 11 part 1 (copy) (URL)
- Exercises : (Text and media area)
- 2021 series 10 (week11) (File)
- Lecture 11 (2020) (copy) (Text and media area)
- slides week 11 part 1 (File)
- video week 11 part 1 (URL)
- slides week 11 p2 Genetic distance (File)
- video week 11 p 2 Genetic distance (URL)
December 7th
1. Genetic distance (last slides from last week)
2. Cell to cell communication : paracrine communication
- Lecture 12 (2021) (Text and media area)
- Erratum : corrected version (File)
- 2021 recording 1 week 12 (URL)
- 2021 slides week 12 (File)
- 2021 week 12 recording 2 (URL)
- Exercises : (Text and media area)
- 2021 series 11 (week 12) (File)
- chapter 16 cell signaling (File)
- Lecture 12 (2020) (copy) (Text and media area)
- slides week 12 (2020) (File)
- video week 12 part 1 (URL)
- video week 12 part 2 (URL)
December 14th, 2021
- Lecture 13 2021 : communication part 2 (Text and media area)
- 2021 week 13 recoding 1 (URL)
- 2021 week 13 recoding 2 (URL)
- 2021 time permiting (File)
- explanations on obese yellow mice (URL)
- Exercises : last series = Last Year Exam !!!!!! (Text and media area)
- 2021 exercises 12 (week 13) (File)
- Answers for last year exam (File)
- Lecture 13 2020 : Cancer not covered in 2021 (Text and media area)
- video week 13 p1 (URL)
- slides week 13 p 1 (2020) (File)
- slides wee 13 p2 (2020) (File)
- video week 13 part 2 (URL)
- video week 13 part 3 (URL)
December 21, 2021
Last lecture :
Correction / discussion of last year exam. No new material that may come in the exam, no exercise this week.
- Course 2021 : (Text and media area)
- 2021 week 14 recording 1 (URL)
- 2021 week 14 recording 2 (URL)
- Course 2020 : (copy) (Text and media area)
- 2020 video : informations about the 2020 final exam (URL)
- Compartments & endosymbiosis (File)
Christmas break
January 29 2022, 08:15 - 11:15
EXAM :
room CE 3
Material allowed : 3 A4 paper sheets (= 6 pages). Any content is allowed on these 6 pages : hand written or printed text, formulas, figures, ... .
No other material is allowed : electronic calculators are not allowed.
Remember to have a photo ID available with you and to comply with the COVID regulations.