Chemical biology is a burgeoning field that has rapidly risen to prominence. This surge of interest has been fuelled by chemical biology’s applicability to understanding critical processes in live cells or model organisms in real time. This success has arisen because chemical biology straddles a nexus between chemistry, biology, and physics. Thus, chemical biology can harness rapid chemistry to observe or perturb biological processes, that are in turn reported using physical assays, all in an otherwise unperturbed living entity.
Although its boundaries are endless, the multidisciplinary nature of chemical biology can make the field seem daunting; we beg to differ! Here, we deconstruct chemical biology into its core components, and repackage the material. In the process we build up for each student a practical and theoretical knowledge bank that will set these students on their way to understanding and designing their own chemical biology experiments.
We will discuss fluorescence as a general language used to read out biological phenomena as diverse as protein localization, membrane tension, surface phenomena, and enzyme activity. We will proceed to discuss protein labeling strategies and fusion protein design. Then we will discuss larger and larger scale chemical biology mechanism and screening efforts. Highlights include a large amount of new data, tailored in the lab videos, and a large number of skilled presenters.
A very warm welcome to you, our new recruits! We'll start you off by acquainting you with the answers to big questions like why study chemical biology and what makes it special. We'll then show some highlights of the course that you are about to take. Finally, we want you to understand some fundamentals, so we are going to start off with some core concepts framed from the perspective of chemical biology.
What's included
8 videos8 readings4 assignments
Show info about module content
8 videos•Total 58 minutes
Trailer•2 minutes
Welcome•1 minute
Why study chemical biology?•11 minutes
Course outline and highlights•9 minutes
The building blocks: monomeric units of proteins•9 minutes
The building blocks: monomeric units of DNA and membranes•9 minutes
Messengers and messages: posttranslational modifications, and pathways•8 minutes
Studying cellular processes with chemical biology in real time•8 minutes
8 readings•Total 84 minutes
Course Acknowledgements•5 minutes
📢 Important preliminary information: Evaluations and subtitles•10 minutes
The foundation: the cell•10 minutes
The workhorses: proteins, enzymes•12 minutes
Classical protein readouts•12 minutes
Flash mob: overview of protein analysis methods•10 minutes
Flash mob - Chemistry•15 minutes
📢 Important preliminary information: Evaluations and subtitles•10 minutes
4 assignments•Total 89 minutes
Components of a cell•22 minutes
Amino acids•24 minutes
Match technique to goal•15 minutes
Final Quiz Number 1•28 minutes
The Devil is in the Minutest Detail
Module 2•3 hours to complete
Module details
A picture used to paint a thousand words. But with the advent of multiple color imaging, microscopy can open a lens with which to view life that few other techniques are capable of. We are thus going to take you on a colorful tour that will show you specific fluorophores, explain why different fluorophores have different colors, and how to rationalize why a molecule is fluorescent. Then we will use these fluorophores in cells, to visualize important cellular processes.
What's included
5 videos5 readings3 assignments
Show info about module content
5 videos•Total 37 minutes
Welcome to Module 2•3 minutes
Light'em up! Fluorophores: structures, and fluorescent principles•9 minutes
Get out (almost) what you put in!•4 minutes
Traditional light microscopy – applications•10 minutes
Traditional light microscopy – precautions•11 minutes
5 readings•Total 70 minutes
Physics of fluorescence•15 minutes
Fluorescent proteins•10 minutes
RNA interference and genome editing•20 minutes
Plasmids and transfection•15 minutes
DNA double stranded breaks and γ-H2AX•10 minutes
3 assignments•Total 58 minutes
Jablonski diagram•16 minutes
Match color of fluorophore to structure•20 minutes
Final Quiz Number 2•22 minutes
A ruler over time and space! Fluorescent assays to measure complex parameters in real time
Module 3•4 hours to complete
Module details
Here we will discuss how different fluorescent techniques have found fantastically useful applications to understand specific biological regulation processes in vitro and in live cells. We will focus on chromatin regulation and regulation of membrane tension as these are two systems which, without such techniques, we would not have the level of understanding we have today.
What's included
12 videos5 readings6 assignments
Show info about module content
12 videos•Total 88 minutes
Welcome to Module 3•3 minutes
Creating modified chromatin •10 minutes
PRC2, a DNA binding complex linked to development and cancer•7 minutes
TIRF talk•7 minutes
On our TIRF•4 minutes
If your protein surfs on DNA, hit the TIRF to study it•9 minutes
PHF1 Prolongs the stable PRC2-DNA complex, promoting activity•8 minutes
Fluid mosaic model•5 minutes
Don’t get uptight! New methods to measure membrane tension•7 minutes
Getting a grip on membrane tension measurements•5 minutes
TORCing TORC: the many faces of the TOR proteins•8 minutes
TORCing it out: pathways that seek to sense and restore membrane tension•14 minutes
5 readings•Total 48 minutes
DNA organization in eukaryotes is linked to regulation•10 minutes
Kinetics of chemical reactions•6 minutes
Comparing chemical structures•6 minutes
Flash mob inteins•6 minutes
Model Organisms•20 minutes
6 assignments•Total 102 minutes
Making proteins via expressed protein ligation and alkylation•18 minutes
Hit the tirf: applications of TIRF microscopy•11 minutes
Analyzing data from TIRF experiments to gain mechanistic insights•17 minutes
Modern fluorescence methods, the spark of creativity•15 minutes
TORCing about Tor's role in membrane tension regulation•16 minutes
Final Quiz 3•25 minutes
Putting proteins to work for us
Module 4•4 hours to complete
Module details
The classical view of biological science is the laboratory worker working hard to understand a specific protein of interest. But through chemical biology, we have been able to employ proteins to do some of this important work for us. In this module you will learn how to deploy modified protein domains to perform custom-designed functions using light-based techniques as a readout.
What's included
11 videos3 readings4 assignments2 app items
Show info about module content
11 videos•Total 95 minutes
Welcome to Module 4•4 minutes
Tracking a specific protein in live cells & in real time•9 minutes
Molecular zipcodes•4 minutes
How to design your fusion protein•7 minutes
Design principle and optimization of SNIFITs•7 minutes
SNIFITs to ID neurotransmitters and drugs•11 minutes
Application to point of care diagnosis•8 minutes
Biological electrophiles, the cell’s way of saying “I’m stressed”?•8 minutes
Breaking the tether is not that bad•11 minutes
T-REX: a question of control(s)•16 minutes
T-REX rewiring of kinase activity through targeting AKT and PTEN: opposing forces meet •10 minutes
3 readings•Total 28 minutes
Many enzyme mechanisms proceed through a covalent enzyme intermediate that can be stabilized through mutagenesis•10 minutes
Small molecule signals•8 minutes
Weighing up our options•10 minutes
4 assignments•Total 82 minutes
Optimal considerations for making fusion proteins and employing them in chemical biology•24 minutes
Optimal considerations for making fusion proteins and employing them in chemical biology2•14 minutes
A bit on the nose? Choose the right SNIFITs•20 minutes
Final Quiz Number 4•24 minutes
2 app items•Total 55 minutes
Design your own SNIFIT•30 minutes
A perfect match?•25 minutes
Making light work of it on a larger and larger scale
Module 5•3 hours to complete
Module details
In recent years numerous chemical biology processes have harnessed light-induced chemistry to control biology in terms of turning on or off inhibition, and exerting remote control of localization or chemical reactivity, amongst numerous other examples not covered here. We shed some light on these processes and exemplify the full spectrum of procedures possible using such approaches.
What's included
9 videos2 readings4 assignments2 app items
Show info about module content
9 videos•Total 74 minutes
Welcome to Module 5•3 minutes
A fat lot of use? Proteins that bind and transport lipids•12 minutes
Greasing the wheels of discovery for new interactomes•9 minutes
Laser guided lipids•8 minutes
Deuterium labeling to assess how sphingosine originating in lysosomes is metabolized•7 minutes
Deuterium labeling and knockout combined•10 minutes
Mitochondria-released sphingosine does not elicit calcium signaling: global sphingosine release does•8 minutes
G-REX – a method to release specific electrophiles on demand•7 minutes
G-REX identifies important novel signaling proteins that function in fish•10 minutes
2 readings•Total 20 minutes
Sphingolipids•8 minutes
Endogenous electrophile signaling•12 minutes
4 assignments•Total 70 minutes
To cage or not to cage?•18 minutes
interpretation of pulse chase data from wild type and knockdown lines•13 minutes
Variables G-REX controls that traditional methods do not•15 minutes
Final Quiz Number 5•24 minutes
2 app items•Total 45 minutes
Identify conflicting pathways regulated by lipid signals•25 minutes
Match molecular tag with the correct subcellular locale•20 minutes
Casting wide your net
Module 6•3 hours to complete
Module details
We've learned how complex biology is, and how resourceful chemical biologist have started to peer into this complex landscape using custom-designed probes. But given the huge complexity of biology, we often have to start from ground zero, screening for a specific molecule or identifying a target of an interesting molecule. Here we will discuss methods that are ideal for these purposes in cells and in vitro.
What's included
8 videos1 reading4 assignments
Show info about module content
8 videos•Total 64 minutes
Welcome to Module 6•5 minutes
Peptide Nucleic Acid – Use in library synthesis and split and mix approach•13 minutes
In the lab - split and mix approach in a nutshell•5 minutes
PNA libraries show their MITE•9 minutes
It takes two: library diversification through DNA display•7 minutes
A STING operation: inhibiting a protein implicated in numerous inflammatory diseases•6 minutes
Performing the Screen•8 minutes
Mutagenesis: ensuring we stay on target•10 minutes
1 reading•Total 14 minutes
The more, the merrier: Phage display, necessity, strengths and weaknesses•14 minutes
4 assignments•Total 85 minutes
Workflow for split and mix•17 minutes
Different methods to achieve diversity•30 minutes
components and controls for Luciferase assay•14 minutes
Final Quiz Number 6•24 minutes
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Founded in 1559, the University of Geneva (UNIGE) is one of Europe's leading universities. Devoted to research, education and dialogue, the UNIGE shares the international calling of its host city, Geneva, a centre of international and multicultural activities with a venerable cosmopolitan tradition.
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5·
Reviewed on Dec 12, 2021
Amazing instuctors! Fabulous course, albeit challenging. I'd recommend it for those with a solid backgroud on related fields: Biophysics, Biochemistry, Chemistry, Biology, Genetics, etc.
R
RR
5·
Reviewed on Nov 15, 2020
Very challenging yet interesting topic. This is 21st century science towards revolutionizing Systems Biology and other science fields
L
LB
5·
Reviewed on Jul 22, 2021
Wonderful and fascinating course, an excellent introduction to the field of Chemical Biology. I feel really fortunate to learn from this great team of professors. Thank you very much!
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