OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Pyrimidines
## What is a Pyrimidine?

A pyrimidine is a 6-membered heterocyclic organic compound made up of 4 carbon atoms and 2 nitrogen atoms at positions 1 and 3. It is one of three isomers of diazine, the other two being pyridazine (1,2-diazine), and pyrazine (1,4-diazine). Pyrimidines are aromatic and planar. The nucleobases Cytosine(C), Uracil(U), and Thymine(T) are all examples of pyrimidines; each with different chemical groups. Pyrimidines can attach to a phosphate sugar group such as a ribonucleotide(which have a hydroxy group positioned axially at carbon-2) or deoxyribonucleotide(which have a hydrogen atom at C-2) through a glycosidic linkage at the 1st Nitrogen to form a nucleotide, the monomeric building block of nucleic acids (DNA and RNA).
Correct mistake: 2. It needs carbonyl phosphate synthetase, which is located in the cytoplasm.

## Pyrimidine Biosynthesis

1. Unlike in purine, the ring is synthesized first then conjugated after.
2. It needs carbamoyl phosphate synthetase, which is located in the cytoplasm.
3. It also needs an enzyme in order for the reaction to work, but the enzyme should be controlled in 2 steps:
* controlled level at where the reaction occurs & transcriptions must be reduced
* the pyrimidine nucleotides which produces the feedback inhibition level also must be controlled
4. The ring then closes.
5. The C-C bond is formed when the ring oxidizes.

## Chemical Properties

Pyrimidine has similar properties to that of pyridines. One similarity is that as the number of nitrogen atoms in the ring increase, the ring pi electrons become less energetic and, as a result, electrophilic aromatic substitution gets more difficult while nucleophilic aromatic substitution gets easier. One example is the displacement of the amino group in 2-aminopyrimidine by chlorine and its reverse reaction. Reduction in resonance stabilization of pyrimidines leads to the addition and ring cleavage reactions, and not substitutions. An example of this is in the Dimroth arrangement. Pyrimidines are less basic than pyridines and the N-alkylation and N-oxidation are more difficult in pyrimidines as well.
* ↑ https://www.sciencedirect.com/science/article/pii/B9780128144534000194
* ↑ https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1016&context=physicsuiterwaal
# Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Purines/Thymine
## Thymine

Thymine is one of the five bases that form nucleic acids, along with adenine, guanine, cytosine, and uracil. The formula of thymine is C$_5$H$_6$N$_2$O$_2$. Thymine is always paired up with adenine through two hydrogen bonds only in DNA to stabilize the nucleic acid structure. Thymine is not present in RNA. Instead, uracil takes place of thymine and binds with adenine. It is a derivative of pyrimidine and can be derived by methylation of uracil at the 5th carbon, hence the other name of thymine, 5-methyluracil. Uracil takes its place in RNA, which also binds to adenine. Thymine is a single ring planar molecule. Thymine combined with deoxyribose yields deoxythymidine while Thymine with ribose makes thymidine.
Thymine binds with deoxyribose to form the nucleoside deoxythymidine, which is the same thing as thymidine. This compound can be phosphorylated with one, two, or three phosphoric acid groups creating thymidine mono-, di-, or triphosphate, respectively.
Thymine is a part of one of the most common mutations of DNA, which involves two adjacent thymines or cytosines. In the presence of UV light, this may form thymine dimers, causing "kinks" in the DNA molecule, interfering with normal function.
Uses of thymine include cancer treatment where it serves as a target for actions of 5-fluorouracil (5-FU). Substitution of this compound to thymine (in DNA) and uracil (in RNA) allows inhibition of DNA synthesis in actively-dividing cells.

## Tautaumerization

Thymine may go through tautaumerization, interchanging from the keto to the enol functionality by intermolecular proton transfer.
# Xanthine

Xanthine is a purine base that's an antecedent of uric acid and is generally found in muscle tissue, blood, urine and some plants. It is a water insoluble toxic yellowish white powder and acids that's soluble in caustic soda; it sublimes when heated. It is involved in purine degradation and is converted from hypoxanthine and converted to uric acid by xanthine oxidase. Some of its derivatives are widely known as mild stimulants, which include caffeine, a sleep-inhibiting methylated xanthine found in coffee, and theobromine, a bitter alkaloid found in cacao.

## Diseases

There is a genetic disease of xanthine metabolism, xanthinuria, due to deficiency of an enzyme, xanthine oxidase. Xanthinuria is a rare genetic disorder where individuals are unable to convert xanthine into uric acid because of the lack of enzyme xanthine oxidase resulting in an accumulation of xanthine. Symptoms include renal failure and kidney stones. There is currently no treatment available to cure this disease.

## Clinical Use

Xanthine derivatives are collectively known as xanthines, which are a group of alkaloids used as stimulants and bronchodilators. As a result of widespread side effects, many of these derivatives have been treated as second-rate asthma treatment medication.

## References

Berg, et al. Biochemistry, 6th Ed. 2007.
# Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Purines/Guanine
## Guanine

Guanine is among the five nucleobases that is found in DNA and RNA. The formula of guanine is C$_5$H$_5$N$_5$O, and is a planar and bicyclic molecule. Guanine has two forms, keto and enol forms. The keto form is the major form. Guanine, like adenine, is a derivative of purine and binds to cytosine through 3 hydrogen bonds. The amino group in the cytosine is the hydrogen donor and the C2 carbonyl and the N3 amine are the hydrogen-bond acceptors. In Guanine, the group at C6 acts as the hydrogen accepter, and the group at N1 and the amino group at C2 act as the hydrogen donors. The related nucleoside containing guanine and ribose is called guanosine and guanine bound to deoxyribose sugar is called deoxyguanosine.
Guanine is capable of being hydrolyzed by strong acids to form ammonia, carbon monoxide, carbon dioxide, and glycine. Guanine oxidizes more readily than adenine, another purine-derivative nitrogenous base in nucleic acids. Guanine has a high melting point of 350°C due to the intermolecular hydrogen bonds between the oxo and amino groups in the crystal of the molecule. Also because of this intermolecular bonding, guanine is relatively insoluble in water as well as in weak acids and bases.

## DNA base pair bonding

From the image on the left, it can be seen that Guanine and Cytosine bond together through noncovalent hydrogen bonding at three distinct sites. Since Cytosin to Guanine has 3 H-bonds and Adenine to Thymine has 2 H-bonds, a higher CG content leads to higher melting point when compare with AT content. An interesting note is that Watson and Crick first hypothesized that Guanine and Cytosine bonded together through hydrogen bonding at two distinct sites.

## Tautomerization

Guanine may go through tautomerization, interchanging from the keto to the enol functionality by intermolecular proton transfer.

## Miscellaneous

Guanine is also the name of the white amorphous substance found in fish scales. It serves as an additive to various products such as shampoos, metallic paints, and simulated pearls and plastics providing a pearly iridescent effect. Also, it adds a shimmering luster to eye shadow and nail polish. This pearly luster is produced by the crystalline form of guanine which are rhombic platelets composed of multiple transparent layers that have a high index of refraction that partially reflects and transmits light from layer to layer. To provide this effect, it can be applied by spraying, painting, or dipping.

## References

* ↑ Crick, Francis H. (1953). "Molecular Structure of Nucleic Acids". Nature. 171: pp. 737-738. {{cite journal}}: |pages= has extra text (help); Unknown parameter |month= ignored (help)
Berg, Jeremy M. John L. Tymoczko. Lubert Stryer. Biochemistry Sixth Edition. New York: W.H. Freeman and Company, 2007.
# Hypoxanthine

Hypoxanthine (6-Hydroxypurine) is a naturally occurring purine derivative and deaminated form of adenine. It is an intermediate in the purine catabolism reaction and is occasionally found as a constituent in the anticodon of tRNA as the nucleosidic base inosine. It is also utilized as a nitrogen source in bacteria and parasite cultures for energy metabolism and nucleic acid synthesis.

## Reactions

Hypoxanthine exists as an intermediate in the biodegradation of AMP (adenosine monophosphate). It is first converted to xanthine with xanthine oxidase before it is excreted as urate.
A deleterious reaction that can occur is a spontaneous deamination of adenine to form hypoxanthine. This is a mutagenic process because the result is a pairing of hypoxanthine with cytosine rather than thymine, due to hypoxanthine’s guanine-like form. This could lead to an error in DNA transcription and replication.

## References

Berg, et al. Biochemistry, 6th Ed. 2007.
# Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Purines/Pyrimidine

Pyrimidine is a heterocyclic aromatic organic compound. Its structure is similar to benzene and pyridine. It contains two nitrogen atoms at position 1 and 3 of the six-member ring. Pyrimidine is isomeric with two other forms of diazine.
# Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Purines/Purine

Purine is a heterocyclic aromatic organic compound. Purine consists of a pyrimidine ring fused to an imidazole ring. Purines and pyrimidines make up of two groups of nitrogenous bases. The name was invented by the German chemist Emil Fischer in 1884. Below are the DNA bases.
DNA Bases
# Theobromine

Theobromine (xantheose) is a xanthine derivative and bitter alkaloid commonly found in cacao plants. Its name is derived from the name of the genus of the cacao tree. It doesn’t contain bromine, as its name might indicate. It shares a similar structure to that of another well-known purine and xanthine derivative known as caffeine, except it contains one more methyl group. It was first discovered in the cacao plant in 1841, isolated in 1878, and synthesized from xanthine by Hermann Emil Fischer shortly thereafter. In its pure form, it is a water-insoluble, crystalline white powder that has a milder effect than caffeine. Since dark chocolate has higher concentrations of theobromine than milk chocolate, its beneficial effects are better attained from the less diluted dark chocolate.

## Therapeutic uses

Theobromine is known as a diuretic, which promotes the removal of excess fluids accumulated in the body from edema, or the flushing of excess salts through the increase production of urine.
It is also widely used as a vasodilator, which widens blood vessels and improves blood flow. This, in turn, helps reduce blood pressure, although it is reputed that flavanols have a bigger role in promoting that effect.
A 2004 patent on the future use of theobromine for cancer prevention was granted due to recent research that revealed anti-carcinogenic activity.

## Effects
### Humans

Theobromine has a weaker effect on the human central nervous system than caffeine because of its weaker inhibition effects on cyclic nucleotide phosphodiesterases and its antagonism of adenosine receptors. As for its effect on the heart, theobromine stimulates it to a much greater degree than caffeine. It is cited as being involved in contributing to chocolate’s role as an aphrodisiac.
Since theobromine is a myocardial stimulator, it increases the heartbeat. As stated above it also dilates blood vessels and reduces blood pressure by enlarging the vessels. It is possible that theobromine might be able to treat cardiac failure since it has properties which allowing draining. Ingesting too much theobromine could lead to some adverse effects. Since it is a diuretic, it will increase the amount of urine produced in the person. It could also possible cause nausea, restlessness, sleeplessness, and anxiety.

### Poisoning

A helpful hint in responsible pet-keeping is to not feed dogs or cats cacao containing products. This is because they metabolize theobromine much more slowly than humans. Complications that arise from doing such an action is succumbing your pet to theobromine poisoning, which causes digestive issues, dehydration, excitability, and a slow heart rate. Larger quantities of theobromine can result in epileptic-like seizures and even death.
# Structural Biochemistry/Nucleic Acid/Nitrogenous Bases/Pyrimidines/Cytosine
## Cytosine

Cytosine is part of the pyrimidine family, and it is one of the 5 nucleotide bases found in both DNA and RNA. The molecular formula of cytosine is C$_4$H$_5$N$_3$O. Cytosine consists of a heterocyclic aromatic ring, an amine group at C4, and a keto group at C2. Cytosine binds with ribose to form the nucleoside cytidine and with deoxyribose to form deoxycytidine.
The molecule is of planar geometry and cytosine forms 3 hydrogen bonds with Guanine in the DNA double helix. The nucleoside of cytosine is cytidine in RNA, which consists of cytosine and ribose. In DNA, it is called deoxycytidine, which consists of cytosine and deoxyribose. The nucleotide of cytosine in DNA is deoxycytidylate which consists of a cytosine, ribose and phosphate.

## History

In 1894, Cytosine was discovered by the hydrolysis of the calf thymus tissue. The first structure for cytosine was published in 1903 and the structure was validated when it was synthesized that same year.(The Columbia Encyclopedia)

## Chemical Activity

From the image on the left, it can be seen that Guanine and Cytosine bond together through noncovalent hydrogen bonding at three distinct sites. An interesting note is that Watson and Crick first hypothesized that Guanine and Cytosine bonded together through hydrogen bonding at two distinct sites.
Cytosine is found in DNA and RNA or as a part of a nucleotide. When the nucleoside cytidine binds with three phosphate groups, it forms cytidine triphosphate (CTP). This molecule can act as a co-factor to enzymes and it aids in transferring a phosphate to convert adenosine diphosphate (ADP) to adenosine triphosphate (ATP) to prepare the ATP to be used in chemical reaction.
In DNA and RNA, cytosine binds with guanine through 3 hydrogen bonds. However, this unit is unstable and can change into uracil. This process is called spontaneous deamination. This can possibly lead to a point mutation if DNA repair enzymes such as uracil glycosylase does not repair it by cleaving uracil in DNA.

## Tautomerization

Cytosine may go through tautomerization, interchanging from the amino to the imino functionality by intermolecular proton transfer.

## References

* ↑ Crick, Francis H. (1953). "Molecular Structure of Nucleic Acids". Nature. 171: pp. 737-738. {{cite journal}}: |pages= has extra text (help); Unknown parameter |month= ignored (help)
Berg, Jeremy M. John L. Tymoczko. Lubert Stryer. Biochemistry Sixth Edition. New York: W.H. Freeman and Company, 2007.
CYTOSINE. The Columbia Encyclopedia, Sixth Edition
# Structural Biochemistry/Organic Chemistry/Organic Functional Group/Carbonyl/Aldehyde

The aldehyde is a functional group underneath the general group known as carbonyls. An aldehyde is a compound which contains a terminal carbon that is bound to any generic “R” group, doubly bonded to an oxygen, and single-bonded to a hydrogen. The “R” group is normally a simple aliphatic chain. When the “R” group is hydrogen, the resulting aldehyde is the simplest one, and is known as formaldehyde.
The carbon doubly bound to the oxygen is labeled as the alpha-carbon. Thus, the hydrogen bound to that carbon is the alpha-hydrogen. Because of the resonance stabilization from the carbonyl oxygen, the hydrogen is more acidic and has a pKa around 17. Of course, this pKa varies on the “R” group that the carbon is bound to.

## Nomenclature

When naming aldehydes use the IUPAC rules. For some aldehydes, it is much easier to use their common name.
IUPAC rules: 1. The carbonyl carbon is designated as carbon #1.
2. The longest alkyl chain including the carbonyl carbon is designated and named according to normal alkyl rules.
3. The suffix for an aldehyde is –al. The “e” in the alkane chain is replaced with “-al” to designate that the molecule is an aldehyde.
4. Exception: If the carbonyl carbon of an aldehyde is part of a ring, the compound is now a cycloalkane carbaldehyde. The carbon of the ring to which the aldehyde is attached is now carbon #1.
5. An aldehyde takes higher priority than an alcohol group.
6. If an aldehyde is a substituent because there are multiple carbonyl groups present, the carbonyl with the longer alkyl chain predominates and then presence of the other carbonyl group is designated by –oxo.
Several Common Names:
In some cases, the aldehyde can be named by removing the suffix and replacing it with aldehyde. For example:
HCHO is named formaldehyde.
CH$_3$CHO is named acetaldehyde. C$_6$H$_5$CHO is named benzaldehyde.

## Reactivity

Like all the carbonyl compounds, the carbonyl carbon in the aldehyde is positively charged due to the electronegative atom. Thus, the carbonyl carbon is an electrophile.
Nucleophilic Attack: Because of the polarity of the carbonyl carbon, nucleophilic attack is a typical reaction aldehydes undergo. Thus, the carbon is subject to nucleophilic attack from other excellent nucleophiles such as cyanide and hydroxide ions. In nucleophilic attack, the lone pair of electrons on the nucleophile attacks the positively charged carbon, which moves one of the two bonds shared between the carbon and oxygen onto the oxygen. Now the oxygen bears a full negative charge. This oxygen can be worked up with acid resulting in the alcohol.
Reducing and Oxidizing Aldehydes
1. Aldehydes can be reduced to primary alcohols by using reducing agents such as sodium borohydrate and lithium aluminum hydride. For example, ethanol is reduced to ethanol by using one of those two reducing agents.
2. Aldehydes can also be oxidized to carboxylic acids using reducing acids such as permanganate or nitric oxide.
# The Computer Revolution/Entertainment/Manipulation of Digital Data

The digital age has benefited society in many ways. A decline in production and distribution costs for film and music companies are a couple of good examples. Faster more reliable transfer and storage of information is also noteworthy. However, not all agree changes ushered in by the digital age have been positive. As with the advent of most technology there are detractors.
The manipulation of digital sound, photo,video and television are under intense scrutiny because of the efficiency and seamlessness with which they can be manipulated digitally.
When country music star Anita Cochran recorded a duet with long since deceased county legend Conway Twitty, Newspaper columnist William Safire called it (and other similar recordings) "a series of artistic frauds". The recording was made with software called Pro tools which pulled snippets from Twitty's recording sessions put them on a hard drive and patched them together with Cochran's recording.
With photos a procedure called morphing is used to morph two (or more) images seamlessly to create a different and misleading image. A notable example of this is the recent presidential election in US, where John Kerry's opposition morphed images of Kerry and anti Vietnam actress Jane Fonda in order to discredit Kerry's commitment to the Iraq war. Morphing takes a quantum leap in the world of television and video where digital technology is so prevalent the final product is more the result of sophisticated technology rather than pure and raw talent of actors or actresses.
Detractors argue these artistic frauds are misleading and in the wrong hands can be used with malicious intent. Proponents say sound, photos and television quality is better than ever.
# The Computer Revolution/Entertainment/Digital Video Quality

Digital Video basically is better visual picture quality, which comes from higher pixel resolution. The more the pixels there are the smoother the picture will be.
Digital video is widely used today. There are digital camera recorders, digital television recorders, digital dvd recorders and pretty much most of the electronics today are digital.
In smaller visual device the resolution can not be noticed between analog and digital quality, but when the visual is larger, the pixels in analog video are clearly noticed, because they can only be stretched so far and the actual pixel blocks are no longer smooth. In digital video quality, the resolution is better because there are more pixels, and when enlarged they have the capability to be stretched. For example in digital cameras, 3-megapixel camera can develop photos up to 5X7, if you would like to get clear 8X10 photos, then a 5-megapixel camera is needed, and poster size photos a 8 to 10-megapixel camera is required. The pixels can stretch so much before the picture becomes blurry.
Also, for example an analog TV would have 680 megapixels, where as digital TV would have 1680 and up, which gives a clear and smooth picture in larger TV screens.
# The Computer Revolution/Firewall
## What a firewall is

A firewall is a type of security for computers both personal and business. A firewall is produced as software or hardware and can be installed onto a computer. The main purpose of a firewall is to examine all the information entering a computer. If the information entering a computer fails to meet a certain criteria the information will not pass through into the computer. The entire purpose behind a firewall is, in the easiest words "to keep the bad out and the good in." It monitors the traffic of your computer. What is going out and what is coming in. It makes sure that you do not have to many vulnerabilities and that the information that is coming in is nothing malicious and that the information that is going out is not your essential information that needs to be kept on your computer. Although firewall is made for this purpose, firewall cannot always keep out all viruses and is not fool proof so it is still important to practice safe browsing. Firewalls are often built into your computer operating system but many times, it is just the basic. It is always good to browse around for a good firewall program, as many of them are set up to do different things and have different levels of security. Upon choosing the firewall that you feel is good for you, it is always important to uninstall the one that you have, as two firewalls running at once can cause major damage to your computer.

## How a firewall works

There are many techniques used by a firewall to monitor and sort the information accessing your computer. Some of these techniques are packet filters, application gateways, circuit gateways and proxy servers. All of these techniques work off a different characteristic to sort through potential dangerous files to safe files. But the most common aspect found between these techniques is the principle of checking the data through the information which is available. This includes a user defined criteria, a process of monitoring and checking FTP as well as TCP. And in some cases once a firewall has established a secure line to receive information from a server, information can freely flow without being checked.

## How you obtain a firewall

You can purchase software which will have a firewall built into it. Other firewalls can be purchased independently and installed along with other anti-virus software. Some of the main company’s which produce firewall software are McAfee, Norton, Microsoft and Apple. After purchasing firewall software you then follow the installation instructions provided and configure the firewall to your criteria for safe files and potential dangerous files.