OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Enzyme/Cysteine Proteases
## Cysteine Protease

This is part of a large family of peptide-cleaving enzymes or proteases. Cysteine Proteases is one of proteases enzyme that cleave protein by cleave the peptide bond. The strategy used by the cysteine proteases is most similar to that use to be chymotrypsin family that is to generate a nucleophile that attack the peptide carbonyl group. Also similar to chymotrypsin, it polarizes the peptide carbonyl group to get it activated for attack, and upon attack by the nucleophile, a stabilizing tetrahedral intermediate is generated. But different from chymotrypsin enzyme, in this enzyme, a cysteine residue, activated by histidine residue play a nucleophilic attack the peptide bond.

## Most common Cysteine Proteases

Papain is a protein-cleaving enzyme derived from papaya fruit (Carica papaya) and certain other plants. Papain is used as a meat tenderizer and in medicine as a digestive aid. Cathepsins are members of the lysosomal cysteine protease (active site) family and the cathepsin family name has been synonymous with lysosomal proteolytic enzymes. In actuality, the cathepsin family also contains members of the serine protease (cathepsin A,G) and aspartic protease (cathepsin D,E) families as well. These enzymes exist in their processed form as disulfide-linked heavy and light chain subunits with molecular weights ranging from 20-35 kDa. Cathepsins have a vital role in mammalian cellular turnover, e.g. bone resorption. They degrade polypeptides and are distinguished by their substrate specificity
# Structural Biochemistry/Enzyme/Characteritics of enzyme

Enzymes are proteins (some may be catalytic RNA) that act as catalysts in chemical reactions. They function via a variety of mechanisms, but all increase the rate of reaction by lowering the activation energy of the reaction. Some characteristics of enzymes are as follows:
* Enzymes are highly specific for a particular substrate. The active site of an enzyme has a strong affinity for a specific substrate, and will slightly change its conformation, known as an "induced fit" to accommodate the target substrate. This induced fit allows for a stabilized transition state, which lowers the activation energy of the reaction.
* Enzymes remain unchanged during the reaction itself. While the enzyme's amino acid residues may break or form covalent bonds with the substrate, it will typically reform those bonds, enabling the enzyme to react with more substrates.
* Enzymes are very efficient, catalyzing about 1-10,000 molecules of substrate per second. Therefore, only a small number of enzymes are typically created under normal cellular conditions.
* Enzymes do not affect the equilibrium constant, or K$_{eq}$. While the rate of conversion from substrate to product is increased, the vice versa is true.
* Enzymes can be allosterically controlled by a variety of means. There are cofactors and coenzymes that are necessary for enzymatic catalysis. Furthermore, there are also molecules that can allosterically inhibit protein function by modifying the conformational shape of the enzyme.
* Enzymes are affected by pH (acidity or alkalinity) of their surroundings. They are destroyed by strong acid or alkali.
# Structural Biochemistry/Enzyme/Covalent Catalysis
## Definition

Covalent Catalysis is one of the four strategies that an enzyme will employ to catalyze a specific reaction. Covalent catalysis occurs when the substrate(s) in an enzymatic reaction become temporarily covalently attached to the enzyme during the catalytic reaction. In this reaction the enzyme contains a reactive group, usually a nucleophilic residue which reacts with the substrate through a nucleophilic attack. This is usually carried out by pyridine, which is a better nucleophile than water that has a pKa of 15.7. The charge loss in the reaction during transitional state will then cause hydrolysis to accelerate. The residue becomes covalently attached to the substrate throughout the catalytic reaction adding an additional intermediate which helps stabilize later transition states by lowering the activation energy. The covalent bond is then broken to regenerate enzymes.

## Examples of Enzymes that Participate in Covalent Catalysis

Examples of enzymes that participate in covalent catalysis include the proteolytic enzyme Chymotrypsin and trypsin in which the nucleophile is the hydroxyl group on the serine. Chymotrypsin is a degradative protease of the digestive system. It catalyzes the cleavage of peptide bonds that are adjacent to large aromatic or nonpolar residues. It cleaves the peptide bond on the carboxyl terminus side of the protein. The chymotrypsin has three main catalytic residues termed as the catalytic triad. These are His 57, Asp 102 and Ser 195. Upon deprotonation the serine residue becomes a powerful nucleophile due to its alkoxide that will attack the relatively unreactive carbon of the carbonyl in the protein. The figure shows the catalytic triads in neutral and deprotonated form. Courtesy of Kiongho; www.nsm.buffalo.edu/~kiongho/
Typical residues used in covalent catalysis are Lys, His, Cys, Asp, Glu, and Ser and some other coenzymes.
An example of covalent catalysis is shown below:
For more information, see Covalent Catalysis

## Reference

Berg, Jeremy M. John L. Tymoczko. Lubert Stryer. Biochemistry Sixth Edition. New York: W.H. Freeman, and Company 2007.
# Structural Biochemistry/Enzyme/Catalytic Triad and S1 Pocket
## Catalytic Triad

A catalytic triad is a group of three amino acids that are found in the active sites of some proteases involved in catalysis. Three different proteases that have catalytic triads are: chymotrypsin, trypsin and Elastase. In chymotrypsin, the catalytic triad is made from serine 195, histidine 57, and aspartate 102. The side chain of serine is bonded to the imidazole ring of the histidine residue which accepts a proton from serine to form a strong alkoxide nucleophile in the presence of a substrate for attack. The aspartate residue orients histidine to make it a better proton acceptor via hydrogen bonding and electrostatic reactions. The combined cooperation results not only in better orientation and stabilization, but also in a sufficient nucleophile that is capable of attack.
Retrieved from "http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Catalytic_Triad"

## Catalytic Dyad

In contrast to the catalytic triad described above, the catalytic dyad comprises only two amino acid residues, usually one acting as nucleophile and the other one representing a proton donor to stabilize the product(s). A well known example is the HIV-1 Protease, in which the active site is formed by two aspartic acid residues (Asp25 and Asp25'), one residing in its deprotonated carboxylate form while the other one is protonated to the corresponding carboxylic acid.

## S$_1$ Pocket

The S$_1$ pocket helps to explain why chymotrypsin, trypsin, and elastase cleave certain peptide binds. The S$_1$ pocket is a deep hydrophobic pocket that allows long, uncharged amino acids like phenylalanine and tryptophan to fit in chymotrypsin. Binding in the S$_1$ pocket positions the adjacent peptide bond at the active site for cleavage. Trypsin cleaves peptide bonds after arginine and lysine which are amino acids with long and positively charged side chains because its S$_1$ pocket contains an aspartate that is negatively charged which attracts and stabilizes the positively charged side chains of arginine and lysine in the substrate. Elastase cleaves peptide bonds after amino acids like alanine and serine which have small side chains because its S$_1$ pocket has two bulky valine residues that decreases the size of the pocket opening so only small chains can enter.
In the figure to the right, it shows that some proteases can have more complex specificity patterns. there are more pockets on their surface to recognize other groups on the substrate. the substrate with the enzyme is the P group that is colored in red and these bind to enzymes labeled in blue. The sessile bond is the red bond between the carbon and nitrogen is also known as the reference point.
# VCE History Revolutions/Chinese Revolution

The Communist Revolution in 1949 was perhaps one of the most significant events of the 20th century. In this History Unit there are two Areas of Study:
* Area of Study 1: Revolutionary Ideas, Movements, Leaders and Events This Area of Study covers the time from the Hundred Days' Reform in 1898 until the Communist Revolution in 1949. Topics will include ideas such as Marxism, Maoism, and Sun Yat Sen's Three Principles; movements such as the Guomindang and the Chinese Communist Party; events such as the Boxer Rebellion and the Long March and leaders such as Sun Yat Sen, Mao Zedong, Chiang Kai Shek and Zhou Enlai.
* Area of Study 2: Creating A New Society This Area of Study covers the time from the Communist Revolution in 1949 through to the death of Mao Zedong in 1976. Topics include the Great Leap Forward, the Hundred Flowers Campaign and the Great Proletarian Cultural Revolution.
First we must note that because the Chinese language [Mandarin] uses a writing system radically different to our own, various methods of transliterating Chinese sounds have emerged. The two used most commonly are the Wades-Giles (WG) system and the Pinyin system. This textbook, in explanations, will use the Pinyin system (therefore we shall say Mao Zedong and not Mao Tse-tung), except for those names who have become widely known under a different - often Cantonese - form (e.g., we shall say Sun Yat Sen and not Sun Yixian). Rather than changing names in primary sources, however, we shall merely state which system of transliteration is used, to avoid confusion. For more detail, consult this table of Chinese names

### Revolutionary Ideas, Movements, Leaders and Events

The Old Régime
* Background to Chinese History
* The Qing Dynasty
* The Hundred Days' Reform
* The Boxer Rebellion
# VCE History Revolutions/Chinese Revolution/The Boxer Rebellion

From China and the Manchus by Herbert Allen Giles [out of copyright]:
There was great unrest, especially in Shantung, due, it was said, to ill-feeling between the people at large and converts to Christianity, and at any rate aggravated by recent foreign acquisitions of Chinese territory. It was thus that what was originally one of the periodical anti-dynastic risings, with the usual scion of the Ming dynasty as figure-head, lost sight of its objective and became a bloodthirsty anti-foreign outbreak. The story of the siege of the Legations has been written from many points of view; and most people know all they want to know of the two summer months in 1900, the merciless bombardment of a thousand foreigners, with their women and children, cooped up in a narrow space, and also of the awful butchery of missionaries, men, women, and children alike, which took place at the capital of Shansi. Whatever may have been the origin of the movement, there can be little doubt that it was taken over by the Manchus, with the complicity of the Empress Dowager, as a means of getting rid of all the foreigners in China. Considering the extraordinary position the Empress Dowager had created for herself, it is impossible to believe that she would not have been able to put an end to the siege by a word, or even by a mere gesture. She did not do so; and on the relief of the Legations, for a second time in her life—she had accompanied Hsien Fêng to Jehol in 1860—she sought safety in an ignominious flight. Meanwhile, in response to a memorial from the Governor of Shansi, she had sent him a secret decree, saying, "Slay all foreigners wheresoever you find them; even though they be prepared to leave your province, yet they must be slain." A second and more urgent decree said, "I command that all foreigners, men, women, and children, be summarily executed. Let not one escape, so that my empire may be purged of this noisome source of corruption, and that peace may be restored to my loyal subjects." The first of these decrees had been circulated to all the high provincial officials, and the result might well have been an indiscriminate slaughter of foreigners all over China, but for the action of two Chinese officials, who had already incurred the displeasure of the Empress Dowager by memorializing against the Boxer policy. These men secretly changed the word "slay" into "protect," and this is the sense in which the decree was acted upon by provincial officials generally, with the exception of the Governor of Shansi, who sent a second memorial, eliciting the second decree as above. It is impossible to say how many foreigners owe their lives to this alteration of a word, and the Empress Dowager herself would scarcely have escaped so easily as she did, had her cruel order been more fully executed. The trick was soon discovered, and the two heroes, Yüan Ch`ang and Hsü Ching-ch`êng, were both summarily beheaded, even though it was to the former that the Empress Dowager was indebted for information which enabled her to frustrate the plot against her life in 1898.
# VCE Chemistry/Spectroscopy

AAS (atomic absorption spectroscopy) UV light and visible wavelengths are analysed. Works only with metals (most cations, some anions). Results obtained are qualitative.
# VCE Chemistry/Stoichiometry
## Particles and the Mole
### Particles

You may remember that the matter of which the universe is composed is itself made up of particles. Chemistry deals with many particles: all molecules and the atoms that make them up are specific types of particle, we may also need to understand the behaviour of smaller subatomic particles, such as the electron or proton.
In general, the particles which we will encounter will all be of minuscule size and mass, and in vast numbers - a single carbon atom weighs and there are more than 5×10$^{22}$ of them in a single gram of graphite.

### The Mole
#### Problems with Size

It can become very cumbersome to deal with such large and small numbers, especially during calculations. To overcome this impracticality, chemists deal with multiples of particles, instead of individually. A chemist will avoid calculating directly the number particles in a given sample - if the sample is of everyday proportions and the particles are on a molecular scale, then the number of particles will be immense whilst the mass of each particle will be infinitesimal. If instead the chemist calculated the number of multiples of a large, fixed number of particles, then, with clever selection of the specific number, the number of multiples present and the mass of each multiple would be much simpler and managable numbers. This can be compared to the sale of tiny items: if for instance, a grain merchant was to sell kernels of grain individually, then the price of each kernel would be frustratingly small and the merchant would need to painstakingly count out each kernel in order to make a sale. It is much more practical for the merchant to sell the kernels in intervals of some enormous number (by the kilogram, or even the ton) as they would be both easier to price and measure.

#### Atomic and Molecular Mass, the Mole

Theoretically, scientists could have chosen any large number and used it as a standard multiple. It would seem convenient to select a power of ten, like 10$^{23}$ or 10$^{24}$ as this would simplify calculations. Instead, scientists have chosen the mole, which is defined as approximately 6.02252×10$^{23}$ particles of the specific type in question.
Why 6.02×10$^{23}$? From first glance, this additional number seems to complicate rather than simplify matters. This number was however selected carefully and deliberately. The secret to its advantage lies in the mass of the particles under scrutiny.
Recall that each atom of a single chemical element has a specific atomic mass that is unique to that element, and measured in atomic mass units (AMU). Each AMU is defined as one twelfth the mass of a specific isotope of carbon, but an AMU can also be expressed in grams - it is about
# VCE History Revolutions/Chinese Revolution/Table of Chinese names

| Wade Giles System/Cantonese dialect form | Pinyin System |
| Mao Tse-tung | Mao Zedong |
| Sun Yat Sen [Cantonese dialect form] | Sun Yixian |
| Ch'iang Kai-shek | Jiang Jieshi |
| Chou En-lai | Zhou Enlai |
| Yuan Shi-kai | Yuan Shikai |
| Peking | Beijing |
| Ch'ing | Qing |
| Tsu-hsi | Cixi |
| Kuomintang (KMT) | Guomindang (GMD) |
| Chungking | Chongqing |
| Chianghsi | Jiangxi |
# VCE History Revolutions

The Victorian Certificate of Education (Australia) contains several history courses both at Units 1/2 and Units 3/4. One such sequence is the History of Revolutions (Units 3 & 4) which provides for the detailed study of two of the four following Revolutions: the American Revolution, the French Revolution, the Russian Revolution and the Chinese Revolution. The two Revolutions are to be chosen by the school, and may be studied in any order (one Revolution for each Unit). Both Units comprise two Areas of Study: Area of Study 1 - Revolutionary Ideas, Leaders, Movements and Events; and Area of Study 2 - Creating a New Society. Both Areas of Study must be covered for each Revolution.
This textbook aims to provide another source of general information, activities, questions, help and primary sources.

## Table of contents

    Chinese Revolution
    Russian Revolution
    American Revolution
    French Revolution
# VCE Mathematical Methods/Differentiation from First Principles
## Theory
### Formula

Given a function f, the rule of the derivative (sometimes called the "gradient") function is defined as $f'(x)=\lim _{h\to 0}{\frac {f(x+h)-f(x)}{h}}\,$.

### Method

Remember that in order to evaluate a limit, we usually substitute the value given into the expression. However, with the above formula, substituting $h=0$ will result in a division by zero, which is mathematically impossible. Therefore,in order to make use of this formula, you need to substitute the rules $f(x+h)$ and $f(x)$, then simplify to eliminate the fraction, and only then substitute $h=0$. This is called differentiation from first principles.
For example:
Let $f:\mathbb {R} \to \mathbb {R} ,f(x)=2x$
Let us differentiate f from first principles.
${\begin{aligned}f'(x)&=\lim _{h\to 0}{\frac {f(x+h)-f(x)}{h}}\\&=\lim _{h\to 0}{\frac {2(x+h)-2x}{h}}\\&=\lim _{h\to 0}{\frac {2x+2h-2x}{h}}\\&=\lim _{h\to 0}{\frac {2h}{h}}\\&=\lim _{h\to 0}2\\&=2\\\end{aligned}}$. Therefore, we can define the gradient function as $f':\mathbb {R} \to \mathbb {R} ,f'(x)=2$

## Exercises

Question One Differentiate the following functions from first principles.
(a) $f(x)=4x$ (b) $f(x)=7x$ (c) $f(x)=2x+1$ (d) $f(x)=3x+3$
Question Two Differentiate the following functions from first principles.
(a) $g(x)=x^{2}$ (b) $f(x)=5x^{2}$ (c) $f(x)=2x^{2}+3$ (d) $f(x)=(x+3)(x+4)$
# VCE Mathematical Methods/Exam One Practice One
## Instructions

Reading Time: 15 minutes
Writing Time: 60 minutes
* Students are permitted to use: pencils, pens, highlighters, erasers, sharpeners, rulers, protractors, set-squares, aids for curve sketching
* Students are NOT permitted to use: blank sheets of paper, white-out, any type of technology
* Any diagrams used are NOT drawn to scale unless otherwise indicated
* Students must answer all the questions in the space provided
* In questions where more than one mark is available, appropriate working MUST be shown
* When instructed to use calculus, an appropriate derivative or anti-derivative MUST be shown

## Questions
### Question 1

(a) Given $e^{3x+1}-1=0\,$, solve for x.
(b) If $f(x)=e^{3x+1}-1\,$ and $g(x)=e^{x}\,$ state the transformations required to change g into f
[1 + 2 = 3 marks]

### Question 2

Let $P(x)=x^{4}+2x^{3}-9x^{2}-2x+8\,$ and $Q(x)=x-1\,$.
(a) Evaluate ${\frac {P(x)}{Q(x)}}$
(b) Hence factorise P(x) given that $P(2)=0$.
(c) Hence sketch the graph of P
[2+2+2 = 6 marks]

### Question 3

Let $f:[0,\pi )\to \mathbb {R} ,f(x)=-cos(x)-x$. Use calculus to find the co-ordinates of the stationary point.
[3 marks]

### Question 4

A garden path can be modelled with the equation $y=sin(2x)+1\,$ where $x\in [0,2\pi ]$.
(a)Sketch the garden path over the domain specified.
(b) If the x-axis represents a fence, use calculus to determine the area between the path and the fence.
[2+2 = 4 marks]

### Question 5

State the equations of the tangent and the normal of the function $h:(-\infty ,-2)\cup (-2,\infty )\to \mathbb {R} ,h(x)=log_{e}(x+2)+3\,$ when $x=1\,$
[2 marks]

### Question 6

Shirley either eats lamingtons or a muesli bar for morning tea. If Shirley eats lamingtons one day, then the probability she will eat lamingtons the next day is 0.5. If Shirley eats a muesli bar one day, the probability that she will eat a muesli bar the next day is 0.3. If Shirley eats a muesli bar on Tuesday, what is the probability she will eat lamingtons on Thursday?
[2 marks]
# VCE Chemistry/Unit 3 Area of Study: Analytical Chemistry

Primary standard
These are substance that are pure enough, that the amount of substance in mole can be calculated accurately from their mass.
It is essential that primary standards
* be pure
* have a known molecular formula
* not react with the atmospheres
* have a high molar mass
* be easily obtainable
Suitable Primary standards are
acidic: Hydrated oxalic acid, potassium hydrogen phtalate
basic: Anhydrous Sodium Carbonate, sodium Oxalate
# The World of Peer-to-Peer (P2P)/Networks and Protocols/VoIP
## VoIP

Voice over IP can also be seen like an extension of a IM were text is substituted by live audio or video, the technological challenges are very similar, if not considering the type data of data that needs to be transfered and specific considerations due to timings. It is not uncommon for IM applications to also support VoIP or video conferencing.
Security on VoIP faces the same vulnerabilities and security threats of other P2P protocols and applications, including fuzzing, floods, spoofing, stealth attacks and VoIP spam.
# External Links

* Chord lookup service
* PAST distributed storage utility
* CoopNet cooperative content distribution system
* More peer-to-peer research resources
* Advanced Peer-Based Technology Business Models - P2P Industry Model from M.I.T.
* FailSafeWiki
* The Peer To Peer Foundation site with discussion of the philosophy/economics behind peer-to-peer networks.
* Various Papers(Research & Practical) on P2P (GOBO)
* P2P Networking 4 Science A review of the current and potential uses of peer-to-peer networks in scientific research
* Annual IEEE International Conference on peer-to-Peer Computing
* Conferences and Resources on peer-to-peer computing
* IBM Developer Works: The practice of peer-to-peer computing
* Internet2® peer-to-Peer Working Group
* Microsoft peer-to-peer networking
* OpenP2P peer-to-peer development resources
* Introduction to Windows Peer-to-Peer Networking from MSDN.
* Study: P2P effect on legal music sales "not statistically distinguishable from zero"