OpenLLM-France/wikimedia huggingface dataset:
# Definition

Electron affinity is the energy change or gain that is accompanies an atom when an electron is added to it. When a neutral chlorine atom in the gaseous form picks up an electron to form a Cl- ion, it releases an energy of 349 kJ/mol or 3.6 eV/atom. It is said to have an electron affinity of -349 kJ/mol and this large number indicates that it forms a stable negative ion. Small numbers indicate that a less stable negative ion is formed. Groups VIA and VIIA in the periodic table have the largest electron affinities. Alkali earth elements (Group IIA) and noble gases (Group VIIIA) do not form stable negative ions.
The sign of the electron affinity is associated with the potential energy that is created with the addition of the electron. If the addition of the electron were to create stability within the atom, it is considered to have higher electron affinity, which decreases the potential energy and this energy gained is negative. If the addition of the electron were to make the atom less stable, the potential energy increases, and the energy gained is found to be negative.
Electron affinity is essentially the opposite of the ionization energy. Instead of removing an electron from the element, we add an electron to the element to create an anion. Also, the noble gases, alkali metals and alkali earth metals have electron affinity.

# Trends
### Across the Period

Typically, electron affinity increases from left to right across the period, but it is definitely not a regular or steady increase. Factors such as charge and the atomic size both affect electron affinities, hence the trend across the period is not as regular as the other periodic table trends.

### Across the Group

Electron affinity tends to decrease down a group, but as mentioned previously, it is not a regular trend, and there are several exceptions to this rule of thumb down the group.

# References

* Silberberg, Martin S. Principles of General Chemistry. Boston: McGraw-Hill Higher Education, 2007. Print.
# Structural Biochemistry/Edwin G. Krebs
## Introduction

Edwin G. Krebs, an American biochemist, was awarded the Nobel Prize for his work with Edmond H. Fischer in finding how protein phosphorylation functions as a regulatory mechanism.

## Personal Life

Edwin G. Krebs was born on June 6, 1918 in Lansing, Iowa. After his undergraduate studies at University of Illinois, he started his study in medicine at Washington University School of Medicine in St. Louis. There, he was licensed as a physician and gained experience in medical research and later became a medical officer in the Navy. After the Navy, he decided to study biochemistry rather than returning to hospital work. He decided to continue as a biochemist and became an assistant professor at University of Washington, Seattle. There, he met Edmond H. Fischer, who he worked with to discover how protein phosphorylation functions as a regulatory mechanism. Afterwards, he became the founding chairman of the Department of Biological Chemistry at University of California, Davis. He also became the Chairman of the Department of Pharmacology at the University of Washington.

## Nobel Prize in 1992

After becoming an assistant professor at University of Washington, Seattle in 1948, Krebs met Edmond H. Fischer, who arrived there in 1953. Together they worked on how phosphorylase functions as an enzyme. Through their research, they observed the mechanism of phosphorylation and saw the interconversion that phosphorylase goes through, called the reversible protein phosphorylation. This mechanism works by having a kinase add a phosphate group from ATP to a protein. The protein conforms to begin its function in a biological process. After the protein finishes its function, a phosphatase removes the same phosphate group and the protein conforms to its idle form. Because Krebs and Fischer were able to describe this process that occurs in numerous metabolic processes, they were awarded the 1992 Nobel Prize.

## Reference

"AN ACCIDENTAL BIOCHEMIST." Annual Reviews. 21 Nov. 2012. Web. 21 Nov. 2012. <http://www.annualreviews.org/doi/full/10.1146/annurev.biochem.67.1.0?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed>
"Edward G. Krebs." Wikipedia. Wikimedia Foundation, 21 Nov. 2012. Web. 21 Nov. 2012. <http://en.wikipedia.org/wiki/Edwin_G._Krebs>
# Structural Biochemistry/Duchenne Muscular Dystrophy
## Overview

Duchenne Muscular Dystrophy is a fatal genetic disorder that affects the X-chromosome and is commonly found in men. It is found across all cultures and races. Duchenne occurs in approximately 1 in every 3,500 male births. It is caused by a mutation in the X-chromosome were a gene encodes for dystrophin.

## Effects

Duchenne Muscular Dystrophy results in a loss of strength. This is due to the lack of dystrophin, which allows for muscle cells to be damaged easily. The heart and lungs are affected the most since muscles become progressively weaker.
http://www.childrensnational.org/files/Images/research/ResearchCenters/CGMR/Duchenne_MuscularDystrophy.jpg

## Cause

Dystrophin acts as a glue, which holds muscles together and maintains the structure of cells. It is also known to carry signals inside and outside of muscle fibers. Since dystrophin is carried on the X-chromosome, and boys only carry one X-chromosome, they are more susceptible to damage. Boys is considered diagnosed with Duchenne when they are unable to produce dystrophin at all. Duchenne is normally passed from parent to child but mainly occurs spontaneously.

## References

1. "About Duchenne." Muscular Dystrophy. N.p., n.d. Web. 07 Dec. 2012.
# Structural Biochemistry/Eat your Fruits and Veggies! How Vitamin C combats scurvy

Scurvy is a disease that causes degeneration of connective tissue. It is caused if there is a deficient amount of Vitamin C found in the body. Scurvy if left untreated can cause small hemorrhages, tooth loss, poor wound healing, the reopening of old wounds, bone pain and degeneration and heart failure. To regain the deficient vitamin C level one must eat fruits and vegetables.
How consuming vitamin C combats Scurvy
Collagen is in the repeated tripeptide unit Gly-X-Y where X and Y are generally Pro or 4-Hyp. It is necessary that the Pro residue in the Y position to be in the Carbon-gamma exo conformation and requires the Pro residue in the X position to have the Carbon-gamma endo conformation. The 4-Hyp if introduced can destabilize the helix. When vitamin C is absent t leads to collagen instability because the molecule can not hydroxylate the Pro at the Y position. A special enzyme is required to hydroxylate the Pro residue in procollagen, the enzyme is called prolyl 4-hydroxylase. Prolyl 4-hydroxylase is a alpha2Beta2 tetramer in all vertebrate. The alpha subunit was found to be the site of proline-hydroxylating activity. Vitamin C is essential in hydroxylating the proline to stabilize the collagen. Vitamin C is found in high abundance in fruits and veggies, particularly in lemons.

## Reference

1. Nelson, David L., Michael M. Cox, and Albert L. Lehninger. "Why Sailors, Exploeres, and College Students Should Eat Their Fresh Fruits and Vegetables." Lehninger: Principles of Biochemistry. New York: W. H. Freeman and, 2005. N. pag. Print.
# Structural Biochemistry/Carbohydrates/Breaking Down of Carbohydrates
## Overview

All cells require energy for continual survival and operation. This energy comes from energy-containing compounds such as sugars, starch or lipids. The breakdown and interconversion of these energy-containing compounds in living organisms is a biochemical process coined Carbohydrate metabolism.

## Humans

Carbohydrate metabolism is carried out by aerobic respiration where glucose and oxygen are metabolized releasing water and carbon dioxide. In cellular respiration metabolic reactions in order to convert the energy stored in the carbohydrate into ATP (adenosine triphosphate). ATP is created and is often referred to as "the molecular unit of currency" for intracellular energy transfer. ATP stores the now broken down energy and transports it to different areas of the cell when needed.
Carbohydrates are stored as polysaccharides consisting of longer polymers of glucose(monosaccharides) by glycosidic bonds. When energy is needed or to be stored, these polysaccharides are cleaved into their smaller monosaccharides units in preparation for catabolism. Carbohydrate catabolism is this breakdown of larger carbohydrates into smaller pieces in order to retrieve the energy within the bonds.
There are also other types of Carbohydrate metabolism such as glycolysis, anaerobic respiration, glycogenesis and more.
For the human body, glucose is used as the main source of energy. The breaking down of the glucose carbohydrates takes place during metabolism, thus releasing energy to the body. The chemical formula for the breakdown of glucose is the following:
C$_6$H$_{12}$O$_6$ + 6 O$_2$ → 6 CO$_2$ + 6 H$_2$O + energy

## Plants

Plants utilize many of the same metabolic reactions to metabolize Carbohydrates. .
Carbohydrates are compounds that bring energy to living cells. In order to provide energy to the cells, the enzyme needs to distribute and metabolize in a certain manner. One type of carbohydrate is starch, a compound that stores energy until it is needed within the living organism. Starch can break down its carbohydrates into glucose units, which can then disperse into the blood stream of a living organism and provide energy to its cells.

## References

Capri, Anthony. "Nutrients and Biochemistry". http://web.jjay.cuny.edu/~acarpi/NSC/11-nutrients.htm. Last accessed: 30 Nov. 2011.
* ↑ G Cooper, The Cell, American Society of Microbiology, p 72
* ↑ Stetten, DeWitt Jr. and Topper, Yale J. Seminars on Carbohydrate Metabolism: "The Metabolism of Carbohydrates, A Review", American Journal of Medicine. Bethesda, Maryland
# Structural Biochemistry/Carbohydrates/Chitin
## Introduction

Chitin is a nitrogen modified polysaccharide made up of N-acetylglucosamine, bound together in beta 1, 4 glucosidal bonds. Chitin is very similar in structure of cellulose; it has the additional amine component and hydroxyl substituent on each monomer. Chitin has an overall positive charge, making it great at binding to negatively charged objects, such as skin and proteins. It is insoluble in water and organic solvents. There are alpha, beta, and gamma forms of chitin. Alpha chitins are composed of alternating antiparallel polysaccharide strands mostly found in crustacean. Beta chitins are composed of parallel strands of polysaccharides, often found in squid. 2 parallel chains alternating with an antiparallel strand constitute gamma chitin and are found in fungi. One chitin derivative is chitosan, which is soluble in water and is made when chitin is placed in a chemical solution and well heated. Chitin has extensive medical uses, chitin when used during sutures increase healing by 50%, making the process shorter and less painful. Chitin can also be used for artificial blood vessels, antibacterial sponges, and dressings. Chitin can also act as a water purifier, it contains internal hooks which can remove impurities in water. In farming, chitin treated seeds tend to be resistant to fungus. In its unmodified form, chitin appears to be translucent, hard, and flexible. It mainly functions as the hard exterior of arthropods, and does a good job of protecting the soft interiors of these organisms from their harsh environment. It acts as structural support for organisms and prevents fluid loss in these organisms.
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/chitin.jpg
# Structural Biochemistry/Carbohydrates/Aldoses
## General information

An Aldose contains an aldehyde with two or more hydroxyl groups attached; one of the hydroxyl groups is at end opposite to the aldehyde. An Aldose is a type of monosaccharides, which is a chiral molecule that plays a key role in the development of nucleic acids. The two simplest forms of Aldoses are L- and D-Glyceraldehydes, which are three-carbon structures that each contain one aldehyde and two hydroxyl groups. The L and D symbols apply to the two different configurations of the asymmetric carbon farthest from the aldehyde group.
In the figure below, the common D-aldose sugars are shown:
Family Tree of D-Aldoses.jpg

## Hemiacetal

The carbonyl group in aldehydes and ketones may react with one molecule of alcohol to form a hemiacetal. The ‘-OR’ group in alcohol attacks the carbonyl carbon in aldehydes or ketones, thus breaking the ‘C-O’ double bond. Proton transfer either intramolecularly or via solvent completes the reaction. Hemiacetal formation may be either acid or base catalyzed. Under acidic condition, however, the carbonyl group may react one more time when alcohol is in excess to form an acetal. The following two diagrams depict an example of hemiacetal and acetal found in carbohydrates.
The red arrows shown in the Fischer projection of a glucose molecule demonstrate the brief overview of mechanism for the hemiacetal formation. The (*) mark on the oxygen of aldehyde indicates the position of the oxygen after the ring formation, while the numbers on each stereocenters indicate the position of each carbon.

## Ring formation

Most of the sugars form cyclic rings, which are more stable than the open chain form. To enable ring formation, the aldehyde can react with an alcohol to form a hemiacetal. Carbohydrates may form either five or six membered rings depending on which hydroxyl group undergoes the hemiacetal formation. A five membered ring is called furanose, while a six membered ring is called pyranose. Furanoses form when the hydroxyl group on C4 reacts with the carbonyl group, while pyranoses form when the hydroxyl group on C5 reacts. This forms the intramolecular hemiacetal in the ring structure. In carbohydrates, the hemiacetal/acetal carbon (C1) in cyclic form is called the anomer. This carbon may be labeled as α or β depending on the position of the (*)-labeled oxygen in the figure. If the (*)-labeled oxygen in the picture is above the ring, the anomeric carbon is labeled as β. If below, it is labeled as α. The following is the formation of a five membered ring by a glucose molecule:
# Structural Biochemistry/Carbohydrates/Carbohydrate Structure Elucidation through Periodic Acid Cleavage

One important method of elucidating the structure of carbohydrates is using periodic acid degradation. Periodic acid (HIO4) is a reagent that cleaves the carbon-carbon bonds in a sugar through oxidation. Periodic acid attacks the vicinal diols in carbohydrates and oxidizes these groups to form carbonyl compounds. The mechanism of this reaction involves a cyclic periodate ester that reacts with two neighboring alcohol functional groups which are oxidized to carbonyl functional groups.

## How is a sugar degraded through periodic acid degradation?

When a sugar is reacted with excess periodic acid, each carbon-carbon bond is broken, forming a characteristic composition of one-carbon compounds that can provide some information about the structure of that carbohydrate. A quick rule of thumb for this reaction is that for any given carbon atom in the carbohydrate, for each carbon-carbon bond that is broken, that carbon atom will be oxidized once. Therefore, each broken bond will be replaced with an OH group. If there is a any carbon with two OH groups, it will lose water and become a carbonyl group. The final product will be either a ketone or an aldehyde.
For example, an aldehyde has one carbon-carbon bond and will react to form formic acid. Secondary alcohols will break 2 carbon-carbon bonds and will be oxidized twice, also forming formic acid. Primary alcohols will break one carbon-carbon bond and will be oxidized once to formaldehyde. Ketones will break two carbon-carbon bonds and form carbon dioxide (CO2).

## Evidence that can be elucidated from periodic acid cleavage

This method can provide several clues to elucidate the structure of an unknown carbohydrate. By analyzing the ratios of the products mentioned above, some information about the types of functional groups present can be obtained. Specifically, because ketones oxidize to carbon dioxide when they are reacted with periodic acid, this method can provide clues as to whether the carbohydrate in question is an aldose or a ketose. Also, the size of the carbohydrate can be revealed by the amount of periodic acid that is consumed. One equivalent of periodic acid corresponds to one carbon-carbon bond cleavage. For example, a six-carbon carbohydrate would consume 5 equivalents of periodic acid.

## Examples of periodic acid cleavage

One example of periodic acid cleavage involves the degradation of one equivalent of D-glucose into five equivalents of formic acid and one equivalent of formaldehyde.
Another example of periodic acid cleavage involves the degradation of one equivalent of D-fructose to three equivalents of formic acid, two equivalents of formaldehyde, and one equivalent of carbon dioxide.
# Structural Biochemistry/Carbohydrates/Carbohydrates and Proteins/proteoglycans

Introduction
Proteoglycans, often recognized for their role in connective tissue, are proteins which have carbohydrates covalently bound to their structure which are important for their function. They are found in extracellular matrix side of cell membranes and are significant in intercellular communication.
Structure and Function
Examples
# Structural Biochemistry/Christian de Duve

Christian de Duve is a renowned biochemist and cytologist. De Duve was born on October 2, 1917 near London but being of Belgian descent, moved back to Antwerp,Belgium where he was educated by the Jesuits and later went to school at the Catholic University of Leuven. He is most well known for his studies in subcellular biochemistry and cell biology. He was attracted to studying medicine because of the appeal of having an occupation in the field of medicine.
He first started off his career in a laboratory under Professor J.P. Bouckaert, who greatly influenced his later career. De Duve's work in the laboratory was focused on discovering the effects of insulin upon glucose uptake in the body; therefore, by the time he graduated, de Duve's main primary goal was to elucidate insulin's mechanism of action. From that point on, his career was focused on the biochemical study of insulin.
He eventually became a professor in 1951 at Louvain, and headed a small research laboratory to answer the broader questions concerning insulin. In this lab, he accidentally discovered the "latency" of acid phosphatase while investigating carbohydrate metabolism in the liver. He abandoned his insulin focus, and decided to focus on his new discovery instead. Following this new focus in his career, de Duve was coined for discovering lysosomes and peroxisomes, cell organelles where digestive and metabolic processes take place. He found that lysosomes are the cell's digestive system, while peroxisomes are where crucial cell metabolism takes place.
In 1962, de Duve became a professor at Rockefeller University in New York and started another laboratory with the same general research interests as the first laboratory in Belgium. In 1974 he was awarded the Nobel Prize with his colleagues Albert Claude and George Palade for describing the structure and function of organelles in cells. In addition to contributing to the discovery of the structures inside cells, he studied the enzyme activity in rat liver cells using a process called rate-zonal centrifugation. These studies helped pave the way for further discovery into the function of cell structures.
# Structural Biochemistry/Chromatography

Chromatography is a laboratory technique used for separation of mixtures. It is called chromatography because it was used for separation of plant pigments for the first time and resulted in separation of colors. It consists of a column with the stationary phase, that is immobile, and a mobile phase that passes through the stationary phase. This will result in separation of different chemicals present in the mixture. The moving phase may be
Several types of chromatography include:
* Affinity Chromatography
* Column Chromatography
* Planar Chromatography
** Paper Chromatography
** Thin Layer Chromatography
* [Chromatography]
* Liquid Chromatography
* Ion Exchange Chromatography
* Size Exclusion Chromatography
# Structural Biochemistry/Cholesterol 24-hydroxylase

Some interesting facts about Cholesterol 24-hydroxylase:
1. It converts cholesterol to 24S-hydroxycholesterol. It then diffuses out from the brain and is metabolized in the liver.
2. It is a P450 enzyme is located in the endoplasmic reticulum, an organelle in all eukaryotic cells. It is an enzyme that is expressed in some but not all neurons of the brain.
# Structural Biochemistry/Chromatography/Vandeemter
## Van Deemter Plot
#### General information

The plot
* Van Deemter plot
The Equation
H= A+ (B/u)+ C$_s$u +C$_M$u
| Variables | Meaning |
| H | Is the theoretical Plate Height (cm) |
| u | Velocity of mobile phase (cm/s) |
| A | Multipath effects ( also known as eddy diffusion) |
| B | Longitudinal Diffusion coefficient |
| C$_s$ | Mass Transfers for stationary phase |
| C$_m$ | Mass Transfers for Mobile phase |
The point of the Van Deemter plot is to gauge the column efficiency under gas (GC) or liquid chromatography (LC).$^1$
Multipath Effect(A)
Zone broadening in the mobile phase is caused by the multiple pathways a molecule can go through a packed column. Diffusion can take place anywhere a molecule transfer from a stream following one pathway to another pathway. At lower velocities, the molecule transfers streams multiple times so the effects are minimal. However, band broadening is more obvious at lower velocities.$^1$
Longitudinal Diffusion(B/u)
Diffusion is the movement from a concentrated portion of the mobile phase to a dilute region. The rate of diffusion is proportional to the concentration difference as well as the diffusion coefficient. The diffusion coefficient varies from species to species as well as the medium. Longitudinal diffusion goes towards and against flow of the mobile phase. This is not as prevalent in LC as it is in GC$^1$
C$_S$ and C$_M$
Not much is know about the complex nature of these two variables. However, theories have been formed.
How to Reduce Band Broadening
The diameter of the packing is important. If you refer to the Van Deemter plot, greater velocities equate to higher theoretical plate height (lower column efficiency). By lowering the temperature, it is diffusion will occur at a less prominent rate in gas chromatography. However, the effect is less pronounced in LC once again.$^1$

### References

$^1$ Skoog, Holler, & Nieman. Principles of Instrumental Analysis, 6th Ed., 2007.