OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Enzyme/Radical-SAM Enzyme
### Introduction

The diversity of proteins and nucleic acids is much due to the many mechanisms that allow site-specific additions of chemical groups into macromolecules. These modifications done to macromolecules were considered to be only nucleophilic, such has in DNA methylation. However, after the discovery of the Radical-SAM (S-Adenosylmethionine) enzyme family, a lot of protein and RNA modification reactions were found to be done through radical mechanisms rather than nucleophilic mechanisms. Because free radicals are very reactive, it allows any site of the target substrate to be activated for modification. So, this free radical mechanism discovery expanded the number of modified monomers, creating diversity. However, these reactions are more difficult to control. The study of these radical-based mechanisms through Radical-SAM enzymes are still at the beginning stages. These mechanisms require detail structural characterization of enzymes in complex polymers, which is a problem since the 3-D structures for many of these polymers are unknown still.

### Radical-SAM enzymes

Many modifications can occur through radical mechanisms. Protein modifications, the simplest being the glycyl radical, can occur via radical mechanisms. In addition, these radical-based mechanisms are also at work in post-transciptional modifications of nucleosides. These Radical-SAM enzymes creates a radical in a specific polymer, and this radical can bind to methyls, thiols, and other groups, creating more complex molecules. Glycine radicalization done by converting a glycine into the radical form, generated by a "Radical-SAM" activase. This process causes a conformational change in the structure. Radical-SAM enzymes also are involved in the addition of methylthio (CH3 and SH) groups into proteins and transfer RNAs. First, there is a hydrogen atom abstraction by the 5'-deoxyadenosyl radical. Then, there is a sulfuration of the substrate radical to make an intermediate thiol. Lastly, there is a nucleophilic methylation by SAM. Then, two different activities happen, both SAM dependent. First, the catalyze radical C-H to C-S. Second, they function as SAM-dependent methyltransferases.

### Structural organization of Radical-SAM enzymes

These SAM enzymes have a conserved core with a mixture of alpha and beta structure forms. A six-stranded parallel B-sheet binds SAM and a [4Fe-4S] cluster at equivalent positions for all the radical enzymes. SAM binds at the groove formed between adjacent B-strands connected to alpha helices that pack on opposite surfaces of the B-sheet. This specific packing geometry produces a concave surface that has different degrees of curvature based on the specific Radical-SAM enzyme family. These different degrees of curvature are very important because it contributes to their specificity for diverse substrates ranging from small molecules to macromolecules.

## Reference

Atta, Mohamed, Mulliez, Etienne, etc. "S-Adenosylmethionine-dependent radical-based modification of biological macromolecules." Current Opinion in Structural Biology. 2010.
# Structural Biochemistry/Enzyme/Reaction intermediates

The transition state is the highest energy intermediate of a reaction and thus tends to be the shortest-lived intermediate along a reaction coordinate. Upon formation of the transition state, the intermediate can spontaneously proceed to product formation.
This transition state of intermediates are indicated by double dagger. Transition state has a higher free energy or delta G than reactants and products. Therefore, the intermediates are less stable than reactants and products.
The energy difference between reactant and transition state is called activation energy. The activation energy determine the rate of reactions. Since the activation energy is the difference in energy between the reactant and the intermediate, it acts as a barrier for the reactant to overcome. As a result, enough energy must be added to the reactants in order to overcome the activation energy and transform into product. Therefore, the higher the activation energy, the harder it will be for the reactant to be converted into product. The rate limiting step, which is sometimes related to formation of the highest energy intermediate determines the rate of the reaction. The activation energy depends on a number of factors including temperature, the specific reaction involved and the presence of catalysts.
An enzyme generally accelerates the rate of reaction by stabilizing the transition state intermediate. Enzymes simply lower the activation energy of the intermediates by changing the conformation of the intermediates into a more favorable and stabilized conformation. A stabilized intermediate means lower activation energy and as mentioned above, lower activation energy means lower activation barrier so the reactants can form products at a faster rate. The result is generally a very large increase in reaction rates on the order of millions of times.
Enzymes do not alter reaction equilibrium because they do not change the potential energy of either starting material or products. Furthermore, the rates of the forward and reverse reactions are changed equally, meaning that the ratio of k$_{forward}$ and k$_{reverse}$ is the same at all times.
# Structural Biochemistry/Enzyme/Pre-steady state

The pre-steady state is the first few milliseconds in a reaction before anything significant happens (aka before it reaches its steady state). This occurs during the moment when the enzyme is mixed with the substrate, but products have not yet been formed. It concerns the kinetics for the reaction to reach the steady-state.
# Structural Biochemistry/Enzyme/Rates and constants
## Enzyme Rates and Constants

Enzyme Thermodynamics
For enzyme thermodynamic, the most important constant is probably ∆G. ∆G is the free-energy difference between products and reactants, also known as the amount of energy required to convert reactants to products. More importantly, it can tell whether a reaction will occur spontaneously, which are what enzymes are concerned with.
If ∆G is negative then the reaction will occur spontaneously (exergonic). If ∆G is zero, the system is at equilibrium and no net change can take place. If ∆G is positive, energy is required for the reaction to occur (endergonic).
A thermodynamic explanation of this starts with the definition of Gibbs free energy, which says
∆G = ∆H - T∆S,
where ∆H is the change in enthalpy (joules) and ∆S is the change in entropy (joules/Kelvin). As we can see, if the energy due to entropy (disorder of a system) exceeds the enthalpy (thermodynamic potential of a system), the Gibbs free energy will be negative and thus no energy is needed for the reaction to occur.
Enzyme Kinetics
Enzyme Kinetics contain a few more constants and rates; starting with V$_{max}$, this is the maximal rate when all the catalytic sites on the enzyme are saturated (bounded) with substrates. Another constant is K$_m$, which is the substrate concentration when it is half the V$_{max}$. Their relationship to each other can be seen through the Michaelis-Menten equation.
Enzyme Kinetics is measuring rate of enzyme reaction. One way to measure of rate of reation is by using spectroscopy change, absorb light at different wavelength. Another way to study enzyme kinetics is through the graph that has substrate concentration (x-axis) vs. reaction velocity (initial velocity). km(michaelis constant) is substrate concentration at which our enzyme reacts half of maximum velocity.
V$_o$ = V$_{max}$([S]/([S]+ K$_M$))
where [S] is the substrate concentration and V$_o$ is the initial rate of the reaction (t=0). Finally, there is the rate of k$_{cat}$/K$_M$ which measures the catalytic efficiency. k$_{cat}$ is the turnover number of an enzyme, which is the number of substrate bounded to an enzyme in a unit of time when the enzyme is fully bounded. Given this, the higher the k$_{cat}$/K$_M$ rate is, the more efficient it is at binding substrates.
# Structural Biochemistry/Enzyme/Prosthetic Group
## Prosthetic group

A prosthetic group is a tightly bound, specific non-polypeptide unit required for the biological function of some proteins. The prosthetic group may be organic (such as a vitamin, sugar, or lipid) or inorganic (such as a metal ion), but is not composed of amino acids. Prosthetic groups are bound tightly to proteins and may even be attached through a covalent bond, as opposed to cosubstrates, which are loosely bound. In enzymes, prosthetic groups are often involved in the active site, playing an important role in the functions of enzymes.
Vitamins are another common prosthetic group. This is one of the reasons why vitamins are required in the human diet. Inorganic prosthetic groups, however, are usually transition metal ions such as iron. The Heme group in hemoglobin is a prosthetic group located in the porphyrin, which is a tetramer of cyclic carbon groups. It contains an organic component called a protoporphyrin made up of four pyrrole rings and an iron atom in the ferrous state (Fe2+). The red color of blood and muscles is attributed to the Heme groups. The difference between a prosthetic group and a cofactor depends on how tightly or loosely bound to the enzyme they are. If tightly connected, the cofactor is referred to as a prosthetic group.

## Heme group

A heme group is a prosthetic group consisting of a protoporphyrin ring and a central iron (Fe) atom. A protoporphyrin ring is made up of four pyrrole rings linked by methine bridges. Four methyl, two vinyl, and two propionate side chains are attached.
Heme of hemoglobin protein is a prosthetic group of heterocyclic ring of porphyrin of an iron atom; the biological function of the group is for delivering oxygen to body tissues, such that bonding of ligand of gas molecules to the iron atom of the protein group changes the structure of the protein by amino acid group of histidine residue around the heme molecule.
The iron lies in the center is an organic component called protoporphyrin, which is bound to four pyrrole nitrogen atom linked by a methine bridge that forms a tetrapyrrole ring. The iron can either be in the ferrous (Fe$^{2+}$) or the ferric (Fe$^{3+}$) oxidation state. However, it is only able to bind to oxygen when in the ferrous state. The iron can form two additional bonds in fifth and in sixth coordination which on both side of heme plane. The fifth coordination sites is linked to a distal histidine while the sixth coordination site can, not always, bind to oxygen. Upon binding, the Heme group will actually shrink in size and descend further into the plane of the porphyrin ring. Along with it, the distal histidine will follow, and this histidine is attached to the alpha-Beta interface thus resulting in local to complete conformational change.
A conjugate protein combined with its specific prosthetic group is termed a holoprotein, while a protein in its absence is called an apoprotein. Prosthetic groups have varying functions, such as oxidizing-reducing reactions (redox), methylation reactions, oxygenation reactions, and so forth.
The heme group gives muscles and blood their distinctive red color.
# Structural Biochemistry/Enzyme/Rate equation

The rate equation of a reaction maps out the rate of disappearance/appearance of a compound over time.
rate = k[A]
Where [A] is the molar concentration of compound A, and 'k' is the rate constant. Rates can have a certain order to them. They can be zero, first, second, etc. depending on the reaction. First order reactions (like the one above) are directly proportional to the concentration, so its 'k' value has a unit equal to (1/s) so as to make the rate (M/s).
Second order reactions could look like so:
rate = k[A]$^2$
where the constant 'k' units are (1/M•s).
Though reaction orders are often whole numbers, they may also be fractions or negative in value.

## Zero Order Reaction

A zero-order reaction is independent of the concentration of the reactants, in which even a higher concentration of reactants will not speed up the rate of the reaction. This kind of reaction if found when a catalyst or other material required for the reaction is saturated by the reactants. Zero-order reactions frequently have to occur first in order to provide reactive substances for the higher order reactions.
The rate equation of this reaction is illustrated as: Rate = K
Furthermore, a plot of concentration versus time should yield a straight line.
File:Order0.gif

# First Order Reaction

A first-order reaction depends on the concentration of only one reactant. This order occurs mostly in the reactions where there is only one reactant.
The rate equation of this reaction is illustrated as: Rate = K[A]
Furthermore, a plot of the natural log of concentration versus time should yield a straight line.

# Second Order Reaction

A second-order reaction is characterized by the property that their rate is proportional to the product of the concentrations of two reactants.
The rate equation of this reaction is illustrated as: Rate = K[A][B]
This means that if you double the concentration of the reactants, it will result in a four time increase in rate.
Furthermore, a plot of the inverse of concentration versus time should yield a straight line.
File:Orderx.gif
# Structural Biochemistry/Cell Organelles/Endoplasmic Reticulum/ER Stress & Type 2 Diabetes
## Endoplasmic Reticulum Stress and Type 2 Diabetes
### Introduction

The Endoplasmic Reticulum (ER) is an important organelle in the cell that performs a wide variety of tasks including and not limited to protein folding, modification, and transfer of membrane proteins to and from Golgi apparatus. Also, the maintenance of ER homeostasis in insulin-secreting beta-cells is extremely important, because when the ER’s homeostasis is disrupted, the ER generates an unfolded protein response (UPR), to maintain homeostasis of this organelle. However, if homeostasis is not restored, the ER promotes death signal pathways. Observations have shown that type 2 diabetes is an important causal factor in the disruption of ER homeostasis and subsequent death of insulin secreting beta cells.
The frequency of Type 2 diabetes in society has dramatically increased due to unhealthy living and eating lifestyles with the consumption of foods rich in fat. Type 2 diabetes consists of a mixture of metabolic conditions characterized by increased levels of blood glucose. The disease develops in areas of the body that are resistant to insulin. Also it is important to note that the disease develops only when beta-cell dysfunction appears. Blood glucose and fatty acids that cannot be properly stored or excreted can overload the cell and disrupt ER and mitochondrial functions. High glucose and saturated fatty acids cause beta cell failure and subsequent oxidative stress through its metabolism.

### ER Stress by Lipotoxicity

Elevated levels of plasma free fatty acids (FFA) are associated with high fat diets and obesity in humans. Free fatty acids are considered to be vital mediators of apoptosis and dysfunction of pro insulin beta cells in type 2 diabetes. It is known that both unsaturated and saturated FFas inhibit proinsulin synthesis. The precise mechanism of Beta cell dysfunction and apoptosis is not yet fully understood. There is great evidence of long saturated fatty acid chains being responsible for the induction of ER stress and subsequent beta cell failure.

### ER Stress by Glucotoxicity

Insulin deficiency associated with insulin resistance is known to cause blood glucose levels to remain high (hyperglycemia). Over stimulated beta cells show a gradual decrease of glucose-induced insulin secretion and insulin gene expression and eventually impaired beta-cell function and survival. This phenomenon is known as gucotoxicity. As blood glucose levels continue to remain high, the glucose that originally served as fuel is now used to generate detrimental metabolites for beta cells.

### References

1. Endoplasmic reticulum stress and type 2 diabetes. Back SH, Kaufman RJ.
# Structural Biochemistry/Cell Organelles/Nucleolus
## Overview

The nucleolus, or plural nucleoli, is normally a circular structure composed of proteins and nucleic acids. Nucleoli are not typical organelles for the reason that they have no lipid membrane, making it with of the few non-membrane bound organelles in the cell. The nucleolus is located within the nucleus of eukaryote cells and is in charge of producing ribosomal RNA and the arrangement of ribosomes. The structure of the nucleoli can be seen using electron microscopy and fluorescent protein tagging can be used to view the dynamics of the nucleoli.

## Structure

The nucleolus has three components:
* Fibrillar Centers (FC): FC is the place where ribosomal proteins are made.
* Dense Fibrillar Components (DFC): It has new transcribed RNA which binds to ribosomal proteins to form rRNA
* Granular Components (GC): Before ribosomes are formed, GC has rRNA that binds to ribosomal proteins.

## Function

The nucleolus is the nuclear subdomain that assembles ribosomal subunits in eukaryotic cells. The nucleolar organiser regions of chromosomes, which contain the genes for pre-ribosomal ribonucleic acid (rRNA), serve as the foundation for nucleolar structure. The nucleolus disassembles at the beginning of mitosis, its components disperse in various parts of the cell and reassembly occurs during telophase and early G1 phase. Ribosome assembly begins with transcription of pre-rRNA. During transcription ribosomal and nonribosomal proteins attach to the RNA. Subsequently, there is modification and cleavage of pre-rRNA and incorporation of more ribosomal proteins and 5S rRNA into maturing pre-ribosomal complexes. The nucleolus also contains proteins and RNAs that are not related to ribosome assembly and a number of new functions for the nucleolus have been identified. These include assembly of signal recognition particles, sensing cellular stress and transport of human immunodeficiency virus 1 (HIV-1) messenger RNA.

## Reference

http://en.wikipedia.org/wiki/Nucleolus
# Web App Development with Google Apps Script/Data to spreadsheets
## Basic gist

If you collect some data from a user (maybe from an input tag or something) that you want to save to your spreadsheet, you have to send it to the server-side, even though you're using the client-side for all the user interface.
The steps are:
* Grab data from the html element that the user adjusts
* Possibly massage the data a little (trim any trailing or leading spaces, for example)
* use the magic sauce: google.script.run!
* Deal with any response from the server

## Get data from input

Here's a simply way to get the data from a textarea element when the user hits "send":

## Sending to the server

Once you have some information to send to the server, you have to somehow get it there. That's where the magical google.script.run comes in!
Basically you can send some data to the server by calling a function **on the server** that can do stuff there and then return some response.
Here's an example that builds on the one from above. We grab whatever the user enters and we add it to a sheet on the (attached) spreadsheet:
Meanwhile on the server (so in code.gs instead of javascript added to main.html):

## Hearing back from the server

Often you'll want to hear something back from the server. That's what withSuccessHandler is all about. Basically you tell javascript both the server function you want to run **and** the client-side function that should run when something comes back. The syntax is weird, but it works.
Here's an example that augments the last one letting the user know the data has been saved in the spreadsheet:
Meanwhile on the server (so in code.gs instead of javascript added to main.html):
# Web App Development with Google Apps Script/Templated html
## Putting variables into html pages

As noted in the Hello World chapter, you can have a basis of an html page by creating one and using it as a template. Normally you'd want to tailor that page with information from the server (ie usually one of your Google Sheets). You can use the various templating tools to do that.
You send a variable to the template with t.coolvariable="whatever" and you put it in the html document with <?= coolvariable ?>.

### doGet code

from "code.gs":

### html code

From "main.html":

### Web result

hi there

## More complex variables

If you want to send something more complex than a string, there are a few options:
* <?!= somevariable ?> will print things with special characters in it. This is useful, for example, for strings that contain html tags in them.
* var pagevariable = <?!= JSON.stringify(somevariable) ?>; inside a <script> tag on the html page will then let the local javascript deal with it as a global variable.
* If you have a bunch of variables that you want to have as global variables in the html document:
** t.globals={"var1":var1, "var2":var2}; in the code.gs doc
** var globals = <?!= JSON.stringify(globals) ?>; Object.keys(globals).forEach(key=>window[key]=globals[key]);
** this works because the window object is the global so-called "namespace" for the html document. That just means it's where global variables sit.

## Passing functions

The Google Apps Script editor doesn't work very well when checking for syntax errors in javascript code that's embedded in an html file. Here's a trick to let you write javascript functions in the server code spaces (which lets them be syntax checked) and then pass them to the client. The trick is to use function expressions.
In the server side you'd do this:
and in the client html file you'd do this:
# Web App Development with Google Apps Script/Data from spreadsheets
## Structure overview

Google Apps Script lets you have access to Google Sheets. You do it by making a connection first to the Google Drive Sheet. There are two ways to do this:
* ss = SpreadsheetApp.openById(id) where "id" is the typical google drive id (the long string of characters usually right after "https://docs.google.com/spreadsheets/d/" in the url of a sheet).
* ss = SpreadsheetApp.getActive if your script is tied to a Spreadsheet (see below)
Once you have the spreadsheet variable (ss in those examples), you can access the various sheets (some people call them tabs) in that doc and any data inside them.

## Script tied to spreadsheet

If you want you can tie your script to a spreadsheet. Then the script doesn't live as a stand-alone google drive file but rather is stored with the Google Sheet. You can access the script by going to Tools->Script editor. It'll then look just like any other script. Oddly it still needs a name, but it'll prompt you to name it when you try to run something.
If you have it connected to a spreadsheet you definitely want to use the second approach mentioned above. Interestingly, the first method always works. There are some subtleties to access control when you tie it to a spreadsheet. Personally I do this a lot because if I want to edit the script I usually want access to the data at the same time. This way they're all stored together.

## Read the data from a spreadsheet

If you have the spreadsheet variable, let's say you wanted to get all the data in a sheet called "Sheet1", which is the default name for the first sheet in a brand new Google Sheet document. You'd do that like this:
This usually takes a second or two, even for large (500+ row) spreadsheets. Once you have the data you can do all sorts of things. Let's say you have a spreadsheet that looks like this:
| Name | email | age |
| Andy | andy@myschool.edu | 48 |
| Ash | ash@myschool.edu | 20 |
| Char | char@myschool.edu | 18 |
Assuming it's in "Sheet1", you could augment the above code to create an html list to be displayed on the main.html page like this: