OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Enzyme Catalytic Mechanism/Enzyme Classification/Ligases
## Overview

A ligase helps to form a bond between smaller molecules in order to form one large joined molecule by catalytic methods. This reaction usually involves the hydrolysis of a minor group branching off from one of the smaller molecules and usually needs ATPase, or some form of energy in order to carry out the reaction. This can be illustrated by the following reaction:
Aa + Bb --> Aa-B + b
Where [A] and [B] denote large molecules, [a] and [b] denote smaller molecules, and the dash [-] represents a new bond formed.
A page with a list of Ligases can be found here

## DNA ligase

DNA ligases are vital enzymes that function in important cellular processes, such as: DNA replication, repair of damaged DNA, and recombination. The enzyme forms phosphodiester bonds between adjacent 3'-OH and 5'-phosphate terminals to link the double stranded DNA. However, ligases may also repair and restore the nicks and cuts between double stranded DNA, double stranded RNA, or hybridized DNA/RNA strands.
Ligases can be classified into two groups depending on their requirement for ATP or NAD+ as the cofactor. All eukaryotic and viral enzymes require ATP, and most prokaryotic enzymes require NAD+ for their activity.

## Ligase mechanism

Ligases are a type of enzyme that can catalyze ligation of two substrates through ATP hydrolysis. Ligases are seen in DNA and RNA ligation, where they bind two nucleotides by forming covalent phosphodiester bonds between 3'-OH ends of one nucleotide with the 5' phosphate end of another. The catalysis mechanism involves three steps:
1. The lysine residue of the enzyme is covalently linked to the adenylyl group from ATP and form an enzyme-AMP intermediate. The reaction is driven by the hydrolysis of the pyrophosphate in ATP. The ATP is the larger molecule in the graph shown below.
2. The adenynyl group of the enzyme-nucleotide intermediate is transferred to the 5’ phosphate group on the DNA strand.
3. The 3’-OH of the DNA strand attacks the phosphorus atom to displace the adenynyl group and form a phosphodiester bond in the DNA. By forming a pyrophosphate linkage and a good leaving group in the previous step, the 3’-OH of one nucleotide is readily bonded through nucleophilic attack.
# Structural Biochemistry/Enzyme Catalytic Mechanism/Enzyme Classification/Transferases

A transferase is an enzyme that aids in the transferring of a functional group from one molecule to another. The functionl group detaches from the donor molecule and forms a bond with the acceptor through catalytic pathways. The donor molecule is usually small non-protein molecules known as coenzymes.
As the name states, transferases transfer functional groups, such as amino group, acyl group, phosphate group, and glycosyl group, between donors and acceptors.
A page with a list of transferases can be found here
File:Example of Aminotransferase.jpg

## Nomenclature and Classification

Transferases are commonly labeled as acceptor transferases or donor transferases depending on the target transfer. Functional groups can also be found in the name describing the functional group that the transferase transfers. There is also a classification system in which transferases are organized. This system is called the EC system. In this system there are 9 subgroups each beginning with EC 2. They are mainly organized by the functional groups that they transfer.
# Structural Biochemistry/Enzyme Catalytic Mechanism/HindIII
## HindIII

HindIII is a type II restriction enzyme derived from Haemophilus Influenzae. HindIII is site specific and cleaves the DNA sequence AAGCTT through hydrolysis when the cofactor Mg2+ is present. The cleavage of this sequence results in 5' sticky ends:
5'-A |A G C T T-3'
3'-T T C G A| A-5'
This type II restriction enzyme is composed of four β-sheets and one α-helix. As a type II restriction enzyme, HindIII protects the host genome against foreign DNA.

### Proposed Mechanism and Usage

HindIII first binds to the DNA backbone through hydrogen bonds and weaker forces such as Van der Waals. When arrived at the specific sequence, it was suggested that HindIII hydrolyses the DNA by having the Lys-92 stabilizes the nucleophilic water while the leaving hydroxide anion is stabilized by the Asp90.
As a type II restriction protein, HindIII is useful in that it cleaves DNA at very specific sites, different than those of type 1, which cleaves randomly at sites other than the specific site. As such, HindIII is used for genetic engineering and molecular biology. It becomes possible to add, delete, or change specific genes, which is very important when trying to change an organism's genome.
It is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the palindromic DNA sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis. The cleavage of this sequence between the AA's results in 5' overhangs on the DNA called sticky ends.

### References

Tang, D et al. (2000). "Mutational analyses of restriction endonuclease-HindIII mutant E86K with higher activity and altered specificity". Protein Engineering Horton, N., Newberry, K. Perona, J. (1999). "Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases". Proc Natl Acad Sci U S A.
# Structural Biochemistry/Enzyme Catalytic Mechanism/Enzyme Classification/Hydrolases

Hydrolases are a class of enzymes that catalyzes the hydrolysis of a chemical bond. The enzymes disrupt the chemical bond by adding water; this step is known as the acylation step. The following scheme is indicative of a hydrolase enzyme: A–B + H2O → A–OH + B–H.
File:Hydrolase.jpg
Hydrolases reactions can be used to cleave many types of chemical bonds. They can be used to cleave peptide bonds to break down proteins and polypeptides. Such reaction involve protease. Other hydrolase reactions can be used to cleave phosphodiester bonds to degrade DNA molecules. Such reaction is performed by restriction enzymes, also known as restrictive endonuclease.
In terms of free energy, it is found that hydrolases forms more entropy and is typically an exergonic reaction.
Hydrolases help induce degradative reactions in the body. For example, during digestion lipases hydrolyze lipids and proteases convert proteins to amino acids. Hydrolases also cleave large molecules into fragments used for synthesis, the excretion of waste materials, or as sources of carbon for the production of energy. In each of these reactions, biopolymers are converted to monomers. Some hydrolases also expel a considerable amount of energy as they act.
One of the most important hydrolases is cholinesterase. Acetylcholine is a potent neurotransmitter for voluntary muscle. Nerve impulses travel along neurons to the synaptic cleft, where acetylcholine stored in vesicles is released, carrying the impulse across the synapse to the postsynaptic neuron and propagating the nerve impulse. After the nerve impulse moves on, the action of the neurotransmitter molecules must be stopped by cholinesterase, which hydrolyzes acetylcholine to choline and acetic acid. Dangerous toxins exist such as the exotoxin of Clostridium botulinum and saxitoxin that interfere with cholinesterase, and a considerable number of nerve agents such as tabun and sarin act by blocking the hydrolytic action of cholinesterase.
# Structural Biochemistry/Enzyme Catalytic Mechanism/Enzyme Classification/Isomerases

Isomerases are a class of enzymes that catalyze the conversion of one isomer into another. Isomerases catalyze reactions of the form A to B. Triose phosphate isomerase (TPI) is a prime example of an isomerase. TPI catalyzes the isomerization of a ketose into an aldose by catalying the transfer of a hydrogen atom from carbon-1 to carbon-2. Isomerases can also be used to catalyze the isomerization of aldoses to ketoses.
TPI uses glutamate as a base to abstract a proton from the carbon-1. Histidine is used as an acid to donate a proton to the oxygen bonded to carbon-2, this intermediate is known as the enediol intermediate. The glutamic acid then donates a proton to carbon-2 while histidine removes a proton from the hydroxyl group on carbon-2, forming an aldose.
Examples of Isomerases
A page with a list of Isomerases can be found here
# Structural Biochemistry/Unique Properties/Structure of Water
## Structure of Water

1. A water molecule is composed of two hydrogen atoms and one oxygen atom
2. Two lone-pair electrons from the oxygen atom make two lobes of negative density in the overall molecule 3. Large dipole moment—gives 33% ionic character to O-H bonds 4. Large polarizability 5. The H-O-H angle is 104.3 degrees

## Quick Brief about the importance of the structure of water

The structure of water contributes tremendously to its unique properties. Water has two Hydrogen atoms attached to an Oxygen atom give it some partial charges due to Oxygen's great electro-negativity. These partial charges are what make it possible for water to form hydrogen bonds.
It is also due to its bent shape, due to the two lone pairs of electrons, which allow it to have this dipole moment. If it was linear, then it would not contain a dipole because both individual dipole's would be pulling against each other, thus canceling. Thanks to the electron pairs and their repulsions, water is in a bent shape, and the polarity is allowed to exist.

## More about water molecule structure

Water molecule is composed of one Oxygen and two Hydrogen atoms. Together with its two lone electron pairs, the Oxygen atom bonding to two Hydrogen atoms nearly forms a 3D tetrahedral structure. X-ray and neutron diffraction has been used to confirm liquid water tetrahedral structure. The nearly tetrahedral structure of the orbitals around the oxygen atom allows one liquid water to form three Hydrogen bonds with four other water molecules. The Hydrogen bonds that are formed between a Hydrogen on one water molecule and the oxygen of another water molecule are not as strong as the covalent bonds between a hydrogen and oxygen atom on the same water molecule. Hydrogen bonds are longer and weaker than covalent O-H bonds
* A water molecule forms H-bonds with 4 other molecules.

## References

* ↑ Viadiu, Hector. "Water." UCSD, 5 October 2011.
* ↑ Viadiu, Hector. "Water." UCSD, 3 October 2011.
* ↑ Viadiu, Hector. "Water." UCSD, 3 October 2011.
* ↑ http://pubs.rsc.org/en/content/articlepdf/1981/f1/f19817702053
* ↑ Viadiu, Hector. "Water." UCSD, 5 October 2011.
# Structural Biochemistry/Unique Properties/Polarity and Hydrogen Bonding
## Polarity

One defining characteristic of the water molecule is its polar nature. Polarity occurs when there is an uneven distribution of charges on the two ends of any molecule. In water, the oxygen atom is much more electronegative than each of the two hydrogen atoms covalently bonded to it. As a result, electrons are more highly attracted to the oxygen atom due to the oxygen's high affinity for the electrons, resulting in a net negative charge on the oxygen atom and a net positive charge on each of the hydrogen atoms. This unequal distribution of charges on each atom produces a net dipole moment in all water molecules, creating the basis for hydrogen bonding.

## Hydrogen Bonding

When the negatively charged oxygen atom in the water attracts surrounding positively charged hydrogen atoms, a weak intramolecular force arises called the hydrogen bond. This interaction between water molecules accounts for the various unique properties of water.
A water molecule is capable of forming a maximum of four hydrogen bonds due to its four bonding sites. Each hydrogen atom is able to form a hydrogen bond with surrounding oxygen atoms, and each oxygen atom is able to form two hydrogen bonds with surrounding hydrogen atoms because of the two lone pairs on the oxygen atom.
Although hydrogen bonds are weaker than the covalent bonds that hold the structure of the water molecule together, they are nonetheless responsible for various unique physical properties of water. Such properties include its relatively high melting and boiling point temperatures, accounted for by the collection of intermolecular forces between water molecules. Thus the hydrogen bonds require a high input of energy in order to break the bonds between molecules. Such weak bonds are crucial to biochemical systems; they are weak enough to be reversibly broken in biochemical processes, yet they are strong enough, when many forms simultaneously, to help stabilize specific structures such as the double helix.
# Structural Biochemistry/Unique Properties/High Heat of Vaporization
## General Information

One unique property of water is its high heat of vaporization.
Heat of vaporization refers to the energy required to convert one gram of liquid into a gas at boiling point. This required energy will break down the intermolecular attractive forces in water. At 100oC, which is the boiling point of water, water has a heat of vaporization equal to 2260 J/g. This means that 2260 J of heat is needed in order to convert 1 gram of water into 1 gram of steam at boiling point. When water is converted from liquid to steam, 2260 J of heat will be absorbed into the water. But when 1 g of steam is converted back into 1 g of liquid, 2260 J will be released into the water's surroundings.
The dominant intramolecular force that leads to this high heat of vaporization in water is hydrogen bonding. Because liquid water consists of numerous H$_2$O molecules, a great amount of hydrogen bonds are formed between the water molecules. Although hydrogen bonds are not the strongest forces (especially when considering ionic or covalent bonds, which are much stronger), the great multitude of hydrogen bonds that need breaking leads to the high heat of vaporization because so much energy can be released. When water changes its physical state during vaporization, there is a large change in volume for the water molecule. For example, one mole of water contains 18 grams of liquid; but in the gas phase, the same mole of water would amount to 22.4 liters of gas.

## References

* ↑ http://www.kentchemistry.com/links/Energy/HeatVaporization.htm
* ↑ http://hyperphysics.phy-astr.gsu.edu/hbase/thermo/phase2.html#c3
# Structural Biochemistry/Unique Properties/Phase States of Water
## General Information

The temperature at which a substance will change phase is a physical, not a chemical, property because it is due to the breaking and forming of intermolecular bonds (the identity of the substance remains the same.) To melt or vaporize a substance, energy must be inputted to break these intermolecular bonds (such as hydrogen bonds or Van Der Waals forces). This means that the energy used to melt or vaporize does not cause molecules to vibrate more vigorously or to travel at higher velocities. In other words, temperature remains constant during a phase change, as seen in the third diagram on the right.
Notice that the heat of vaporization is much higher than the heat of fusion. This is because only a few hydrogen bonds must be broken to melt ice. Each water molecule still maintains between 3-4 hydrogen bonds with its neighbors. On the other hand, ALL hydrogen bonds must be broken to evaporate liquid water to water vapor. Thus a greater input of energy is needed.
H$_2$O has three different phases in which it can exist: Solid, Liquid, and Gas.
As shown on the phase diagram on the right, as the temperature is increased, the state begins to change. The temperature at which ice begins to melt is 0°C. At room temperature, 25°C, the ice becomes a liquid. Finally, at a temperature of 100°C, water begins to boil, turning into steam.
The ΔH value is enthalpy which can be summarized by the amount of energy/heat needed to convert unit mass of a substance from one phase state to another. To each phase state its own denotation.
Solid phase to liquid phase is enthalpy of fusion, also known as heat of fusion. It's a measure of how much energy needs to be put into the system in order for melting to occur. Going backwards, from liquid to solid, this is called freezing, and the value of the heat of freezing is negative the heat of fusion.
Liquid phase to gas phase is enthalpy of vaporization, also known as heat of vaporization. It's a measure of how much energy needs to be put into the system in order for the vaporization to occur. Going backwards, from gas to liquid, this is called condensation, and the value of the heat of condensation is negative the heat of vaporization.
| ΔH Values for H$_2$O | (kJ/mol) |
| ΔH$_{fusion}$ | 6.01 kJ/mol |
| ΔH$_{vaporization}$ | 40.65 kJ/mol |
| ΔH$_{freezing}$ | -6.01 kJ/mol |
| ΔH$_{condensation}$ | -40.65 kJ/mol |
# Structural Biochemistry/Unique Properties/Surface Tension
## Surface Tension of Water

Surface tension is caused by the cohesive intermolecular forces of water with other water molecules at the surface of liquid water. This property can be observed when water forms droplets on a surface, when a curvature forms on the top of a filled cup of water, and when reptiles walk on the surface of water. Surface tension is usually measured in units of force per length (dynes/cm) or units of energy per area (ergs/cm^2).

## The Physics of Surface Tension

In the molecular view, water can be separated into two groups - free water molecules in the bulk and water molecules that are interacting with each other on the surface. Because water molecules at the surface can only interact with water molecules underneath and to the side of them, a resulting force exists and points towards the interior of the bulk, indicating that the energy of water molecule at the surface of water is higher than that of water molecules in the bulk. Therefore, water must receive energy to move from the interior to the surface. In another point of view, surface tension of water can be seen as the energy distribution on the surface of water. Since energy is required to create a large surface area, liquids such as water tend to reduce their surface by forming spheres, which has the lowest surface/volume ratio.

## Examples

The Water Strider is a typical example that reveals the life sustaining ability of surface tension. The Strider has three pairs of long hydrophobic legs that are covered with wax. Since hydrophobic substances do not form interaction with water, the hydrophobic legs of the Water Strider prevent it from sinking. This hydrophobic property allows water to exert an opposite force on the Strider and to support its weight. This opposite force comes from surface tension. Another example in which plants transport water from roots to stems is also strong evidence that surface tension and cohesion help sustain life on earth.

## Reference

Timothy A. Isgro, Marcos Sotomayor, and Eduardo Cruz-Chu. "Case Study: Water and Ice"
# Structural Biochemistry/Unique Properties/Versatility as a Solvent
## Overview

Water is a polar solvent that tends to not react with the solute. Since many biomolecules are either polar or charged, water readily dissolves these hydrophilic compounds. Water is an inert solvent that solvates salts by separating the cations and anions, therefore reducing their electrostatic interactions and abilities to form crystals. This may occur because the water-water hydrogen bonds are replaced with water-solute bonds. On the other hand, water is a poor solvent for hydrophobic molecules such as lipids. The non-polar molecules in water undergo hydrophobic interactions; the water changes its hydrogen bonding patterns around the hydrophobic molecules. The bonding patterns that form constrains the water molecule which decreases entropy.
The need for water to have high entropy helps to promote protein folding. When the hydrophobic portions of the protein are exposed to the water, more of the water needs to be organized around it, decreasing entropy. When the protein is folded (a decrease in entropy that is overcome by favorable non-covalent bond formation and increased water entropy), the hydrophobic parts have less surface area in contact with water, freeing up the water to favorably make and break hydrogen bonds.
•Molecules such as butanol have a polar hydroxyl group and thus can from intermolecular hydrogen. Alcohols, aldehydes, ketones and compounds containing N-H bonds all form hydrogen bonds with water molecules and tend to be soluble in water. •Water is effective in screening the electrostatic interactions between dissolved ions because it has a high dielectric constant, a physical property that reflects the number of dipoles in a solvent. •The strength of the ironic force F= (Q1 Q2)/ er ², for water at 25 ºC, e is 78.5. Ionic interactions between dissolved ions are much stronger in less polar environments. •Oxygen and nitrogen and carbon dioxide gases are all nonpolar. they are not very soluble in water. •Non polar compounds force energetically unfavorable changes in the structure of water.

## Hydration Process

Water involves the hydration process. The “positive ends” of H$_2$O are attracted to the negatively charged anion and that the “negative ends” are attracted to the positively charged cations. Salt dissolves in water by the hydration process. The strong water-ion interaction takes over the force of the positive and negative ions of the solid. When ionic substances (salts) dissolve in water, they break up into individual cations and anions. For example, when sodium chloride (NaCl) dissolves in water, the resulting solution contains Na$^+$ and Cl$^-$ ions moving freely.

## Reference

Zumdahl/Zumdahl, Chemistry, 7ed. Houghton Mifflin Company, Boston New York
# Robotics/Types of Robots/Entertainment Robot

These are robots that have no real useful application. They're build for fun and practice but little else more. Most homebuilt robots would fall in this category.
They can be simple robots that use simple sensors (light sensor, sound, bumper switches) and have simple behavior, but they could as well have complex sensors and extensive programming.
One other category of robots that's very close related to this category are robot build as "tech-demos". For example the Asimo robot.
# Robotics/Stepper Motors
### Stepper Motor Basics

* Degree of Rotation - Every stepper motor has a degree of rotation. This value indicates how far the rotor will spin around its axis for each signal sent.
* Number of Coil - These motors drive coils in a pattern to advance the rotor position
* Driving a Coil - This is done by passing current through the coil. In stepper motors, all coils must be driven in both directions over a complete revolution.
* Sequencing - These motors require the electronic control to change which coil in being driven at the correct time. Without this the motor will hold in one position.
* H-Bridge Style Driver - ...
What's a stepper motor?
In robotics stepper motors are primarily used in stationary robots as they tend to consume quite a lot of power. They are ideal for movements that have to be accurate and are larger than 180°.

### Common Uses/Part Sources

* Floppy, hard disk, or CD/DVD-ROM drives - The heart of most these is the stepper motor. In most of these drives, there are two stepper motors. They position the read/write heads and they spin the medium.
* Printers, scanners, plotters, and copy machines - Most of these devices utilize stepper motors. They are used primarily to position the print head or optics on an (X,Y) coordinate system. One motor positions on the X axis and the other positions on the Y axis.
* CNC machines, routers, scanners, lathes etc - Used for X/Y/Z positioning of heads.