A guide to the twenty common amino acids

Have you ever thought about what makes up your body? Only 20 amino acids! Take a look at the graphic below, to discover the structure of each of these, plus information on the notation used to represent them.

Source: Compound Interest. Click to enlarge.

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, although other elements are found in the side chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side chain"); often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics. 

Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The other two ("non-standard" or "non-canonical") are selenocysteine (present in many noneukaryotes as well as most eukaryotes, but not coded directly by DNA), and pyrrolysine (found only in some archea and one bacterium). Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts) is generally considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.

Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid ("GABA", non-standard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters. Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells. Carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be created from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.

Because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts.

For more information visit:-

http://www.compoundchem.com/2014/09/16/aminoacids/

https://en.wikipedia.org/wiki/Amino_acid

http://www.prlabs.co.uk/lab-supplies.php?N=l-arginine-for-biochemistry&Id=22533

The chemistry of the environmental effects of fireworks

Who doesn’t love fireworks at New Year? Yet whilst fireworks are undoubtedly a spectacle, they can also have a negative effect on the environment. Take a look at the graphic below, to discover some of the issues that they can cause.

Source: Compound Interest

So that’s the science, but what about the history? Who first invented the firework?

The earliest documentation of fireworks dates back to 7th century China (time of the Tang Dynasty), where they were invented. The fireworks were used to accompany many festivities. It is thus a part of the culture of China and had its origin there; eventually it spread to other cultures and societies.

The art and science of firework making has developed into an independent profession. In China, pyrotechnicians were respected for their knowledge of complex techniques in mounting firework displays. Chinese people originally believed that the fireworks could expel evil spirits and bring about luck and happiness.

During the Song Dynasty (960–1279), many of the common people could purchase various kinds of fireworks from market vendors, and grand displays of fireworks were also known to be held. In 1110, a large fireworks display in a martial demonstration was held to entertain Emperor Huizong of Song (r. 1100–1125) and his court. A record from 1264 states that a rocket-propelled firework went off near the Empress Dowager Gong Sheng and startled her during a feast held in her honor by her son Emperor Lizong of Song (r. 1224–1264). 

Rocket propulsion was common in warfare, as evidenced by the Huolongjing compiled by Liu Bowen (1311–1375) and Jiao Yu (fl. c. 1350–1412). In 1240 the Arabs acquired knowledge of gunpowder and its uses from China. A Syrian named Hasan al-Rammah wrote of rockets, fireworks, and other incendiaries, using terms that suggested he derived his knowledge from Chinese sources, such as his references to fireworks as "Chinese flowers".

With the development of chinoiserie in Europe, Chinese fireworks began to gain popularity around the mid-17th century. Lev Izmailov, ambassador of Peter the Great, once reported from China: "They make such fireworks that no one in Europe has ever seen." In 1758, the Jesuit missionary Pierre Nicolas le Chéron d'Incarville, living in Beijing, wrote about the methods and composition on how to make many types of Chinese fireworks to the Paris Academy of Sciences, which revealed and published the account five years later. His writings would be translated in 1765, resulting in the popularization of fireworks and further attempts to uncover the secrets of Chinese fireworks.

For more information visit:-

http://www.compoundchem.com/2017/01/05/fireworks-environment/

https://en.wikipedia.org/wiki/Fireworks

http://www.prlabs.co.uk/lab-supplies.php?N=lead-1000ppm-for-icp&Id=60146

The chemistry behind the aroma of coffee

The Aroma of Coffee (Compound Interest) 

What is it about that delicious smell of coffee? Or, more specifically, what lies behind it? The graphic above takes a look at a selection of the chemical compounds behind this aroma. 

So that's the chemistry, but what about the biology of coffee?

Several species of shrub of the genus Coffea produce the berries from which coffee is extracted. The two main species commercially cultivated are Coffea canephora (predominantly a form known as 'robusta') and C. arabica. C. arabica, the most highly regarded species, is native to the southwestern highlands of Ethiopia and the Boma Plateau in southeastern Sudan and possibly Mount Marsabit in northern Kenya. C. canephora is native to western and central Subsaharan Africa, from Guinea to Uganda and southern Sudan. Less popular species are C. liberica, C. stenophylla, C. mauritiana, and C. racemosa.

All coffee plants are classified in the large family Rubiaceae. They are evergreen shrubs or trees that may grow 5 m (15 ft) tall when unpruned. The leaves are dark green and glossy, usually 10–15 cm (4–6 in) long and 6 cm (2.4 in) wide, simple, entire, and opposite. Petioles of opposite leaves fuse at base to form interpetiolar stipules, characteristic of Rubiaceae. The flowers are axillary, and clusters of fragrant white flowers bloom simultaneously. Gynoecium consists of inferior ovary, also characteristic of Rubiaceae. The flowers are followed by oval berries of about 1.5 cm (0.6 in). When immature they are green, and they ripen to yellow, then crimson, before turning black on drying. Each berry usually contains two seeds, but 5–10% of the berries have only one; these are called peaberries. 

Arabica berries ripen in six to eight months, while robusta take nine to eleven months.

Coffea arabica is predominantly self-pollinating, and as a result the seedlings are generally uniform and vary little from their parents. In contrast, Coffea canephora, and C. liberica are self-incompatible and require outcrossing. This means that useful forms and hybrids must be propagated vegetatively. Cuttings, grafting, and budding are the usual methods of vegetative propagation. On the other hand, there is great scope for experimentation in search of potential new strains.

In 2016, Oregon State University entomologist George Poinar, Jr. announced the discovery of a new plant species that's a 45-million-year-old relative of coffee found in amber. Named Strychnos electri, after the Greek word for amber (electron), the flowers represent the first-ever fossils of an asterid, which is a family of flowering plants that not only later gave us coffee, but also sunflowers, peppers, potatoes, mint — and deadly poisons.

For more information visit:-

http://www.prlabs.co.uk/lab-supplies.php?N=acetaldehyde-for-synthesis&Id=28877

http://www.compoundchem.com/2015/02/17/coffee-aroma/

https://en.wikipedia.org/wiki/Coffee

Vitamins!

Ever wondered about the vitamins we need or that we eat as part of our breakfast cereal.  What they do?  How they help us?

A vitamin is an organic compound and a vital nutrient that an organism requires in limited amounts.  An organic chemical compound (or related set of compounds) is called a vitamin when the organism cannot synthesize the compound in sufficient quantities, and must be obtained through the diet; thus, the term "vitamin" is conditional upon the circumstances and the particular organism. For example, ascorbic acid (vitamin C) is a vitamin for humans, but not for most other animal organisms. Supplementation is important for the treatment of certain health problems, but there is little evidence of nutritional benefit when used by otherwise healthy people.

 

 

 

There are 13 recognised vitamins from A to E and K.  The reason that the set of vitamins skips directly from E to K is that the vitamins corresponding to letters F-J were either reclassified over time, discarded as false leads, or renamed because of their relationship to vitamin B, which became a complex of vitamins.

The German-speaking scientists who isolated and described vitamin K (in addition to naming it as such) did so because the vitamin is intimately involved in the coagulation of blood following wounding (from the German word Koagulation).

Again, the excellent Compound Interest has produced a detailed image of the chemical structures of vitamins as below.  Click on the image to enlarge.



Click to enlarge

 

Well-known human vitamin deficiencies involve thiamine (beriberi), niacin (pellagra), vitamin C (scurvy), and vitamin D (rickets). In much of the developed world, such deficiencies are rare; this is due to an adequate supply of food and the addition of vitamins and minerals to common foods, often called fortification.

For more information visit:-

http://www.compoundchem.com/2015/01/13/vitamins/#more-3479

http://en.wikipedia.org/wiki/Vitamin

 

pH Indicators

A pH indicator is a colour changing (or halochromic) chemical compound that is added in small amounts to a solution so that the pH (acidity or basicity) of the solution can be determined visually.

A pH indicator is a chemical detector for hydronium ions (H3O+) or hydrogen ions (H+).  Normally, the indicator causes the colour of the solution to change depending on the pH.

pH (potential of hydrogen) is a scale of acidity from 0 to 14. It tells how acidic or alkaline a substance is. More acidic solutions have lower pH. More alkaline solutions have higher pH. Substances which are not acidic or alkaline (neutral) usually have a pH of 7. Acids have a pH less than 7. Alkalis have a pH greater than 7.

pH indicator solutions are themselves weak acids or bases.  As one chemical is added it changes the arrangement of the electrons in the molecule causing it to absorb different wavelengths of light and therefore appear different in colour.

Different chemicals can be used for different pH ranges as shown in the diagram below.

 

pH indicators are frequently employed in titrations in analytical chemistry and biology to determine the extent of a chemical reaction. Because of the subjective choice (determination) of colour, pH indicators are susceptible to imprecise readings. For applications requiring precise measurement of pH, a pH meter is frequently used.

Many plants or plant parts contain chemicals from the naturally-coloured anthocyanin family of compounds. They are red in acidic solutions and blue in basic. Anthocyanins can be extracted with water or other solvents from a multitude of coloured plants or plant parts, including from leaves (red cabbage); flowers (geranium, poppy, or rose petals); berries (blueberries, blackcurrant); and stems (rhubarb). Extracting anthocyanins from household plants, especially red cabbage, to form a crude pH indicator is a popular introductory chemistry demonstration.

For more information visit:-

http://en.wikipedia.org/wiki/PH_indicators

http://www.compoundchem.com/2014/04/04/the-colours-chemistry-of-ph-indicators/

 

The Microscope

The optical microscope, often referred to as the "light microscope", is a type of microscope which uses visible light and a system of lenses to magnify images of small samples. Optical microscopes are the oldest design of microscope and were possibly designed in their present compound form in the 17th century. Basic optical microscopes can be very simple, although there are many complex designs which aim to improve resolution and sample contrast. Historically optical microscopes were easy to develop and are popular because they use visible light so that samples may be directly observed by eye.

Binocular Microscope

 

There are two basic configurations of the conventional optical microscope: the simple (single lens) and the compound (many lenses). The vast majority of modern research microscopes are compound microscopes while some cheaper commercial digital microscopes are simple single lens microscopes. A magnifying glass is, in essence, a basic single lens microscope. In general, microscope optics are static; to focus at different focal depths the lens to sample distance is adjusted, and to get a wider or narrower field of view a different magnification objective lens must be used. Most modern research microscopes also have a separate set of optics for illuminating the sample

It is difficult to say who invented the compound microscope. Dutch spectacle-makers Hans Janssen and his son Zacharias Janssen are often said to have invented the first compound microscope in 1590.

Christiaan Huygens, another Dutchman, developed a simple 2-lens ocular system in the late 17th century that was achromatically corrected, and therefore a huge step forward in microscope development. The Huygens ocular is still being produced to this day, but suffers from a small field size, and other minor problems.

In August 1893 August Köhler developed Köhler illumination. This method of sample illumination gives rise to extremely even lighting and overcomes many limitations of older techniques of sample illumination. Before development of Köhler illumination the image of the light source, for example a lightbulb filament, was always visible in the image of the sample.

For more information on microscopes visit:-

http://en.wikipedia.org/wiki/Optical_microscope

Or visit http://www.prlabs.co.uk/news/article.php?Id=207 and read all about our range of Visiscope Microscopes.

See also http://www.prlabs.co.uk/news/article.php?Id=208