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A few fundamentals

A few fondamentals

History of crystallography

Do you have any idea how long crystallography has been around? How have researchers progressed over the decades in studying crystals and solving the three-dimensional structures of biological macromolecules?
Start by answering some questions in the quiz below to test your knowledge.

History of crystallography

1- The early days

2- The following

3- The contribution of CCP4

1 / 10

What are the objectives of CCP4?

2 / 10

What are the impacts of CCP4?

3 / 10

In what year did the history of X-ray crystallography begin?

4 / 10

Whose idea was it to carry out the first experiment in the diffraction of X-rays?

5 / 10

Why are X-rays called X-rays?

6 / 10

How were the first three-dimensional structures such as NaCl or zinc sulfide determined?

7 / 10

What simple law, written in 1912, describes a condition for which there is constructive interference?

8 / 10

What was the first macromolecule structure solved in 1959 by Max Perutz?

9 / 10

What means CCP4 ?

10 / 10

In 1915, Henry Bragg wrote a famous article. What did he describe in this article?

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Quitter

History of NMR

Do you know how long NMR has been around? How have researchers used it over the decades to study the three-dimensional structures of biological macromolecules in solution?
Start by answering some questions in the quiz below to test your knowledge.

History of RMN

1 / 3

What type of magnets were first used in NMR?

2 / 3

In what year was 2D NMR proposed for the first time?

3 / 3

What were the first substances to be measured by NMR (in bulk)?

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History of electron microscopy

How did the first microscopes, and then electron microscopes, emerge? How did the development of the individual components of the microscope lead to today’s atomic spatial resolution?

History of electron microscopy

Some key dates and milestones in the evolution of microscopy, then electron microscopy

1 / 4

The first electron microscope, built in 1931 by Ernst Ruska, provided a resolution of

2 / 4

The first microscope, developed by Antoni van Leeuwenhoek, produced images with a spatial resolution of

3 / 4

To generate an electron beam, modern electron microscopes use :

4 / 4

The resolution limit of an optical microscope, its resolution power, depends on :

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Quitter

History of computing

Computing also has its history, from the very first calculators to today’s powerful machines, what has been the path taken?
Before watching the video, check your knowledge by answering the questions below.

History of computing

1 / 4

The word Informatics is made up by combining the two words :

2 / 4

Match the technological progress with the year in which the first computers based on this progress appeared:

Printed circuit boards
Miniaturisation
Vacuum tubes
Transistors

3 / 4

In 1965, Gordon Moore stated the principle that the number of transistors should double every two years at a constant price.

4 / 4

The three binary operators used to build a computer are:

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History of 3D prediction

In the pipeline

LINUX

Do you know how to handle the LINUX language? To find out, start by answering the quiz questions below.

LINUX

Introduction to LINUX

1 / 4

What are the main components of a computer?

2 / 4

What makes it possible to coordinate operations between different computer parts?

3 / 4

In 1991, Linus Torwald wrote LINUX based on a :

4 / 4

Indicate the meaning of each of these commands

pwd
ls
cd
mv

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The correlation coefficient

In structural biology, we often need to compare two sets of data to assess their similarity, or to compare data with a model.
What is a correlation coefficient? What can it do in structural biology?
To see if you know what a correlation coefficient is and what it can do for you, start by answering some questions in the quiz below.

Correlation coefficient

1 / 6

In crystallography, the cc1/2 is used to decide :

2 / 6

True or false: A high correlation coefficient between two phenomena means that they are causally related.

3 / 6

The value of a correlation coefficient varies:

4 / 6

In crystallography, the R-factor is used to calculate the difference between ...

5 / 6

True or false: Correlation coefficient can be used to compare data not on the same scale.

6 / 6

A cc1/2 is calculated in electron microscopy to determine the resolution limit of a Coulomb potential map:

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The Fourier transform

In the early 19th century, Joseph Fourier developed the revolutionary idea that the sine and cosine trigonometric functions could be used to decompose any function. The transform that was named after him is a mathematical tool that can be used to understand and implement many digital signal and image processing techniques. Among its many applications, it can be found in all structural biology methods.
To find out if you are familiar with this function, and its relative the Patterson function, start by answering the questions in the quiz below.

Fourier transform

Introduction,

The phase problem,

The Patterson function

1 / 11

When solving a structure by crystallography, the Patterson function is used as:

2 / 11

From one or more diffraction datasets, the Patterson function provides :

3 / 11

In the calculation of the electron density by means of the inverse Fourier transform, the unknown is :

4 / 11

The mathematical function used to move from reciprocal space to real space is :

5 / 11

What are the two essential pieces of information we need to reconstruct the frequency of a periodic signal?

6 / 11

The simple sinusoidal curve that describes a periodic signal is :

7 / 11

An important property of the Patterson function is that peak height is proportional to:

8 / 11

En 1915, Henry Bragg understands that ...

9 / 11

The number of electrons at each point x, y, z of a crystal unit cell corresponds to:

10 / 11

Each structure factor calculated from the intensity of a diffraction spot is made up of :

11 / 11

The amplitude of each structure factor F(hkl) is calculated from the intensity I(hkl) of each index hkl. It contains information about :

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What is a 3D structure?

What is a three-dimensional structure?
How can we visualise these structures?
The files that describe the atomic structure of a macromolecule are stored in an international database that is open to everyone: the Protein Data Bank.
To find out if you know what a three-dimensional (3D) structure is and how the files used to describe it are made, you can start by answering a few questions in the quiz below.

What is a three-dimensional structure?

1 / 13

What information can be found in the international database of biological macromolecule structures?

2 / 13

When was the R-free factor introduced to assess the quality of a structure solved by X-ray crystallography?

3 / 13

Which of these words correspond to modes of representation of a three-dimensional model?

4 / 13

What does the PDB acronym stand for?

5 / 13

Which 3D structures must have their coordinates deposited in the PDB before publication in a scientific journal?

6 / 13

What file tool(s) can be used to visualise a molecular structure in 3D?

7 / 13

Which file format(s) is (are) a standard format for saving the 3D coordinates of molecules?

8 / 13

Which of these extensions corresponds to a standard format for coordinate files used by software for visualising the structures of biological macromolecules?

9 / 13

What parameters are used to assess 3D structure quality?

10 / 13

Which level of structure involves interactions between the side chains of amino acid residues?

11 / 13

Which command below is used to import a PDB structure file into ChimeraX?

12 / 13

When editing a coordinate file for a three-dimensional macromolecule structure, what information can be found in a line that begin with the keyword ATOM:

13 / 13

What functions are available in ChimeraX?

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What is a protein?

Proteins are responsible for virtually all the functions of living organisms, including enzymatic functions, cytoskeletal structure, cell signalling, regulation of gene expression, etc. etc.
Find out if you know what a protein is by answering the questions below

What is a protein?

1 / 5

Enzymes are proteins whose function is to ...

2 / 5

Proteins are made up of atoms of:

3 / 5

Ribosomes, responsible for protein synthesis, are made up of ...

4 / 5

The sequential covalent linkage of amino acids makes up the ...

5 / 5

Haemoglobin is a protein that enables the ...

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Experimental methods in structural biology

There are three main experimental methods in structural biology. On what basis should you choose one method over another?
Find out if you are familiar with these methods by answering these questions before watching the videos at the end of the quiz.

The experimental methods

Introduction to experimental methods in structural biology

1 / 6

What experimental methods can be used to determine the three-dimensional structure of a macromolecule at the atomic scale?

2 / 6

Associate the experimental method with the corresponding property that this method exploits.

Cryo-Electron microscopy
X-ray crystallography
Nuclear Magnetic Resonance

3 / 6

The proteins studied by crystallography are generally :

4 / 6

What is the size unit associated with the three-dimensional structure of a biological macromolecule?

5 / 6

Protein crystals :

6 / 6

Crystal diffraction analysis is carried out using :

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Prerequisites

Biological sample preparation

Choosing the right expression system

How do you choose the best expression system for your structural biology project?
Take the quiz below to find out if you already know about the different expression systems and their advantages and disadvantages.

Choosing an expression system

1 / 5

True or false, when it comes to producing recombinant proteins of eukaryotic origin, mammalian CHO cells are good tools for the industrial production of complex proteins with specific post-translational modifications.

2 / 5

Tick each box whose statement corresponds to an advantage of the cell-free expression.