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What is the smallest number of amino acids required for life?

What is the smallest number of amino acids required for life?


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Is there any hypothesis on the minimum number of amino acids required for life?


You can divide the 22 (including selenocysteine and pyrrolysine) proteinogenic amino acids into broad groups of similar amino acids. There are the hydrophobic amino acids like trypthophane, valine and leucine, the charged amino acids like glutamate and arginine and the polar amino acids like serine and threonine. There are some amino acids with unique features like cysteine which can form disulfide bonds.

Some amino acids are very similar, for example isoleucine and leucine, it is plausible that one of those would suffice to create most protein folds.

There are several examples of proteins designed with a smaller alphabet of amino acids, one example is the E. coli orotate phosphoribosyltransferase (Akanuma et al., 2002). The simplified enzyme consists of only 13 different amino acids and 88% of it are composed of only nine different amino acids. Even after those drastic changes the enzyme still folds correctly and has enzymatic activity.

There is one study (Fan and Wang, 2003) that tried to answer exactly the question you asked. They came to the conclusion that around 10 amino acids are necessary to create properly folding proteins:

First, we study the minimum sequence complexity that can reserve the necessary structural information for detection of distantly related homologues. Second, we compare the ability of designing foldable model sequences over a wide range of reduced amino acid alphabets, which find the minimum number of letters that have the similar design ability as 20. Finally, we survey the lower bound of alphabet size of globular proteins in a non-redundant protein database. These different approaches give a remarkably consistent view, that the minimum number of letters required to fold a protein is around ten.


Akanuma, S., Kigawa, T. & Yokoyama, S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proceedings of the National Academy of Sciences 99, 13549 -13553 (2002).

Fan, K. & Wang, W. What is the minimum number of letters required to fold a protein? J. Mol. Biol. 328, 921-926 (2003).


If you allow for the "RNA world" hypothesis, then the minimum number of amino acids needed for life would be zero, because RNA in that context would be self-replicating and would not need proteins (or their amino acids).

Since this question was asked in 2012, with respect to modern life on Earth circa 2019, Craig Venter's lab put out a 2016 paper in Science about their engineered organism called JCVI-syn3.0.

This organism is engineered to contain the simplest, smallest set of genes required to sustain life, i.e., metabolism, reproduction, etc.

The latest version of its genome is 531 kb long and is made up of 432 protein-coding genes. In the Supplementary Materials of that paper, there is a file called Database S1, an Excel spreadsheet. The authors state that this spreadsheet contains the amino acid sequence of proteins coded for by genes in JCVI-syn3.0.

When we take this column and filter out non-protein-coding or untranslated genes, we get a listing of sequences, like so:

MSFNKLNQTYLDWINHPNLDQELKELLNKADDNELNAAFNLELKFGTAGIRGILGAGPGRFNVYTIKKVTIAYAKLLQTKYSNDLNKGVVIGHDNRHNSKKFAKLVADILTSFNIKAYLFKNNDLQPTPVVSFATKALNCIGGIVITASHNPAEYNGYKIYDPYGCQLMPHDTDVIANYMNEITNILDWTFISNNNLLEIVDQTVIDKYFEMIKNLEFYKDQDKSNLKIIYSAVNGTGSLYTPIVLKQSGYEVIEVKEHAFEDETFKNVINPNPEFDPAWKIPLEYAKKYDADIIILNDPDADRFGMAIKHNNEFIRLNGNQTGAILIDWKLSNLKRLNKLPKNPALYSSFVTSDLGDRIASETYNANVVKTLTGFKWMGQEMLKEPLNGLNFVFAYEESYGYVIDDSTRDKDGIQASIIAAEACWYYKNQNMTLVDYLNQLYEKYGYYYTTTYNLNFKPEEKDSKIAPIMKLLRTTGIKQINNLKVVKIEDYINGLYNMPSEDLLKIYLEDKSWIAIRPSGTEPKLKIYFVIVDSSLQKAENKAEKIYTELKTILNI MFKVKFADIGEGLTEGTVAEVLVKVGDVVKEGQSLYFVETDKVNSEIPAPVAGKIAVINIKAGQEIKVGDVVMEIDEGSGASVASEPKAEAKQEAKVEVVEENASVVGATPVSNDLIVRKQASTVTKSSTIKATPLARKVAADLNIDLSLVTPTGPNQRILVADIKNYHSSSAQPASQPAPTPTLVASQPAPAPTPAITPAIKVVEPSAPLSWDEVPMNGVRKATVKAMTKSHTEIAAFTGMKNTDITETHKMRTELKDHAAASGIKLTYLAFIIKAVAKSLRDMPNINVRGDFANNKIQFMHNINIGIAVDTPNGLMVPVIKGADHLSVFEIAIKISELANKAKDGKLTRAEMTEATFTVSNFGSVGLDYATPIINSPESAILGVGTMSQTPLYINGELQKRFIMPLSMTCDHRIIDGADAGRFLIKVQDYLSKPVLLFM MQIPIIKPKKAPPLTIEEINEIKQHSSYEKSYLKTFNKYKKKVEHRIYFKTSFWWDIFIIALAALANTITTDYFILATGDTGLFPGGTATIARFLSIVLNKHITSISTSSSFFIFLFIVNLPFFVFGFIKVGIKFTLTSLLYILLSIGWNQIITRLPIINPNEWSLIINYKLISSLPTEWSSKLWLFVFSIFGGFFLGITYSLTYRVGSSTAGTDFISAYVSKKYNKQIGSINMKINFTLLLIFVVLNTVIMPIYKIDSTAKLSVLNTLTDEQFTEIYNKAKDSGKFILDFNSHHHFYLPSNWSVSDQQIWTRQQIAQIIASNTNFTNYDNLTTIIKLKFVFGPSLFASFICFVIQGVVIDRIYPKNKLFTVLISTTKPREVKNYLFESGYRNNIHFLENQTAKKENGYIAQSVIMIHIGLMNWKPLQAGANNIDPDMMISFIRTKQVKGPWSYSLDTQKRELSLYKKVITDRRLMARIEKESILLTKQKITNDKKLKSKSKTF…

This text can be processed with a simple Python script to count the number of unique residues, e.g.:

#!/usr/bin/env python import sys import re with open(sys.argv[1], 'r') as f: a = f.read() b = re.sub('[
-]',", a) # strip out newlines and indels len(list(set(b))) # count the number of unique codes

This answer suggests a minimally-viable organism codes for proteins that, altogether, use 20 amino acids.

I did not create a frequency table to see what is most commonly used, or what is least used, and what might be hypothetical targets for substitution with other amino acids. But that might be an avenue for further exploration.

In the future, Venter or other labs may find that there are ways to engineer an organism to use fewer genes, or protein-coding genes that use fewer amino acids or which use synthetic amino acids that have redundant chemical features that could allow it to substitute multiple residues, while preserving the protein's function.


Figure 1. Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH4), depicted here.

Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom (Figure 1).

However, structures that are more complex are made using carbon. Any of the hydrogen atoms could be replaced with another carbon atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure 2a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 2b). The molecules may also form rings, which themselves can link with other rings (Figure 2c). This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and other atoms.

Figure 2. These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon atoms and the atoms of other elements. (a) This molecule of stearic acid has a long chain of carbon atoms. (b) Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.


Branched-Chain Amino Acids (BCAAs)

Branched-chain amino acids (BCAAs), which include leucine, isoleucine and valine, are essential amino acids that stimulate protein synthesis in the muscles.

Acidic and Basic Amino Acids

ACIDIC amino acids are aspartic and glutamic acid, and BASIC amino acids are arginine, histidine and lysine [25] .

Sulfur-Containing Amino Acids

Sulfur-containing amino acids include cysteine, homocysteine, methionine and taurine [23] .

  • Animal foods high in cysteine and methionine: chicken, turkey, fish (bluefish, yellowtail, tuna, salmon), pork (ham) beef, veal, lamb, bison, crabs, mollusks, cheese [20] .
  • Plant foods high in cysteine and methionine: nuts (butternuts, peanuts), seeds (pumpkin, sunflower), legumes (beans, soybeans, lentils) [20] .
  • Foods high in taurine include red meat and fish [21] and certain energy drinks.
  • Homocysteine is produced in the body during protein breakdown.

In individuals with celiac or Crohn’s disease or other disorders with impaired amino acid absorption, foods high in sulfur-containing amino acids can cause sulfur-smelling gas [24] .

Glucogenic and Ketogenic Amino Acids

In the human body, glucogenic amino acids can be converted to glucose in the process called gluconeogenesis they include all amino acids except lysine and leucine [3] .

Ketogenic amino acids, which can be converted to ketones: isoleucine, leucine, lysine, phenylalanine, threonine, thryptophan and tyrosine [3] . Ketones can be used by the brain as a source of energy during fasting or in a low-carbohydrate diet.


Contents

Essential Conditionally essential [3] [4] Non-essential
Histidine (H) Arginine (R) Alanine (A)
Isoleucine (I) Cysteine (C) Aspartic acid (D)
Leucine (L) Glutamine (Q) Asparagine (N)
Lysine (K) Glycine (G) Glutamic acid (E)
Methionine (M) Proline (P) Serine (S)
Phenylalanine (F) Tyrosine (Y) Selenocysteine (U)
Threonine (T)
Pyrrolysine* (O)
Tryptophan (W)
Valine (V)

(*) Pyrrolysine, sometimes considered the "22nd amino acid", is not used by humans. [5]

Eukaryotes can synthesize some of the amino acids from other substrates. Consequently, only a subset of the amino acids used in protein synthesis are essential nutrients.

Estimating the daily requirement for the indispensable amino acids has proven to be difficult these numbers have undergone considerable revision over the last 20 years. The following table lists the WHO and United States recommended daily amounts currently in use for essential amino acids in adult humans, together with their standard one-letter abbreviations. [6] [7]

Amino acid(s) mg per kg body weight
WHO USA
H Histidine 10 14
I Isoleucine 20 19
L Leucine 39 42
K Lysine 30 38
M Methionine
+ C Cysteine
10.4 + 4.1
(15 total)
19 total
F Phenylalanine
+ Y Tyrosine
25 (total) 33 total
T Threonine 15 20
W Tryptophan 4 5
V Valine 26 24

The recommended daily intakes for children aged three years and older is 10% to 20% higher than adult levels and those for infants can be as much as 150% higher in the first year of life. Cysteine (or sulfur-containing amino acids), tyrosine (or aromatic amino acids), and arginine are always required by infants and growing children. [6] [8]

Foodstuffs that lack essential amino acids are poor sources of protein equivalents, as the body tends to deaminate the amino acids obtained, converting proteins into fats and carbohydrates. Therefore, a balance of essential amino acids is necessary for a high degree of net protein utilization, which is the mass ratio of amino acids converted to proteins to amino acids supplied. [9]

Complete proteins contain a balanced set of essential amino acids for humans. Whole foods plant and natural animal sources provide all of the essential amino acids. [10] Near-complete proteins are also found in some plant sources such as quinoa. [11]

The net protein utilization is profoundly affected by the limiting amino acid content (the essential amino acid found in the smallest quantity in the foodstuff), and somewhat affected by salvage of essential amino acids in the body. It is therefore a good idea to mix foodstuffs that have different weaknesses in their essential amino acid distributions. This limits the loss of nitrogen through deamination and increases overall net protein utilization. [9]

Protein source Limiting amino acid
Wheat lysine
Rice lysine
Maize lysine and tryptophan
Legumes methionine/cysteine pair and tryptophan
Egg, chicken, milk none egg is the reference for complete protein

The amino acid distribution profile is less optimal in plant foods than in animal foods. [12] [13] but it is not necessary to consume plant foods containing complete proteins as long as a reasonably varied diet is maintained. [14] Numerous pairs of different plant foods can provide a complete protein profile. Certain traditional combinations of foods, such as corn and beans, or beans and rice, contain the essential amino acids necessary for humans in adequate amounts. [15] The official position of the Academy of Nutrition and Dietetics is that protein from an appropriate planned combination of a variety of plant foods eaten during the course of a day can be nutritionally adequate when caloric requirements are met. [14]

Protein quality Edit

Various attempts have been made to express the "quality" or "value" of various kinds of protein. Measures include the biological value, net protein utilization, protein efficiency ratio, protein digestibility-corrected amino acid score and complete proteins concept. These concepts are important in the livestock industry, because the relative lack of one or more of the essential amino acids in animal feeds would have a limiting effect on growth and thus on feed conversion ratio. Thus, various feedstuffs may be fed in combination to increase net protein utilization, or a supplement of an individual amino acid (methionine, lysine, threonine, or tryptophan) can be added to the feed.

Protein per calorie Edit

Protein content in foods is often measured in protein per serving rather than protein per calorie. For instance, the USDA lists 6 grams of protein per large whole egg (a 50-gram serving) rather than 84 mg of protein per calorie (71 calories total). [16] For comparison, there are 2.8 grams of protein in a serving of raw broccoli (100 grams) or 82 mg of protein per calorie (34 calories total), or the Daily Value of 47.67g of protein after eating 1,690g of raw broccoli a day at 574 cal. [17] An egg contains 12.5g of protein per 100g, but 4 mg more protein per calorie, or the protein DV after 381g of egg, which is 545 cal. [18] The ratio of essential amino acids (the quality of protein) is not taken into account, one would actually need to eat more than 3 kg of broccoli a day to have a healthy protein profile, and almost 6 kg to get enough calories. [17] It is recommended that adult humans obtain between 10–35% of their 2000 calories a day as protein. [19]

Scientists had known since the early 20th century that rats could not survive on a diet whose only protein source was zein, which comes from maize (corn), but recovered if they were fed casein from cow's milk. This led William Cumming Rose to the discovery of the essential amino acid threonine. [20] Through manipulation of rodent diets, Rose was able to show that ten amino acids are essential for rats: lysine, tryptophan, histidine, phenylalanine, leucine, isoleucine, methionine, valine, and arginine, in addition to threonine. Rose's later work showed that eight amino acids are essential for adult human beings, with histidine also being essential for infants. Longer-term studies established histidine as also essential for adult humans. [21]

The distinction between essential and non-essential amino acids is somewhat unclear, as some amino acids can be produced from others. The sulfur-containing amino acids, methionine and homocysteine, can be converted into each other but neither can be synthesized de novo in humans. Likewise, cysteine can be made from homocysteine but cannot be synthesized on its own. So, for convenience, sulfur-containing amino acids are sometimes considered a single pool of nutritionally equivalent amino acids as are the aromatic amino acid pair, phenylalanine and tyrosine. Likewise arginine, ornithine, and citrulline, which are interconvertible by the urea cycle, are considered a single group. [ citation needed ]

If one of the essential amino acids is not available in the required quantities, protein synthesis will be inhibited, irrespective of the availability of the other amino acids. [2] Protein deficiency has been shown to affect all of the body's organs and many of its systems, for example affecting brain development in infants and young children inhibiting upkeep of the immune system, increasing risk of infection affecting gut mucosal function and permeability, thereby reducing absorption and increasing vulnerability to systemic disease and impacting kidney function. [2] The physical signs of protein deficiency include edema, failure to thrive in infants and children, poor musculature, dull skin, and thin and fragile hair. Biochemical changes reflecting protein deficiency include low serum albumin and low serum transferrin. [2]

The amino acids that are essential in the human diet were established in a series of experiments led by William Cumming Rose. The experiments involved elemental diets to healthy male graduate students. These diets consisted of corn starch, sucrose, butterfat without protein, corn oil, inorganic salts, the known vitamins, a large brown "candy" made of liver extract flavored with peppermint oil (to supply any unknown vitamins), and mixtures of highly purified individual amino acids. The main outcome measure was nitrogen balance. Rose noted that the symptoms of nervousness, exhaustion, and dizziness were encountered to a greater or lesser extent whenever human subjects were deprived of an essential amino acid. [22]

Essential amino acid deficiency should be distinguished from protein-energy malnutrition, which can manifest as marasmus or kwashiorkor. Kwashiorkor was once attributed to pure protein deficiency in individuals who were consuming enough calories ("sugar baby syndrome"). However, this theory has been challenged by the finding that there is no difference in the diets of children developing marasmus as opposed to kwashiorkor. [23] Still, for instance in Dietary Reference Intakes (DRI) maintained by the USDA, lack of one or more of the essential amino acids is described as protein-energy malnutrition. [2]


Acid-base properties

Another important feature of free amino acids is the existence of both a basic and an acidic group at the α-carbon. Compounds such as amino acids that can act as either an acid or a base are called amphoteric. The basic amino group typically has a pKa between 9 and 10, while the acidic α-carboxyl group has a pKa that is usually close to 2 (a very low value for carboxyls). The pKa of a group is the pH value at which the concentration of the protonated group equals that of the unprotonated group. Thus, at physiological pH (about 7–7.4), the free amino acids exist largely as dipolar ions or “zwitterions” (German for “hybrid ions” a zwitterion carries an equal number of positively and negatively charged groups). Any free amino acid and likewise any protein will, at some specific pH, exist in the form of a zwitterion. That is, all amino acids and all proteins, when subjected to changes in pH, pass through a state at which there is an equal number of positive and negative charges on the molecule. The pH at which this occurs is known as the isoelectric point (or isoelectric pH) and is denoted as pI. When dissolved in water, all amino acids and all proteins are present predominantly in their isoelectric form. Stated another way, there is a pH (the isoelectric point) at which the molecule has a net zero charge (equal number of positive and negative charges), but there is no pH at which the molecule has an absolute zero charge (complete absence of positive and negative charges). That is, amino acids and proteins are always in the form of ions they always carry charged groups. This fact is vitally important in considering further the biochemistry of amino acids and proteins.


Avidin-Biotin Technical Handbook

Our 48-page Avidin-Biotin Technical Handbook brings together everything needed to biotinylate, purify or detect proteins. Featured products include cell-surface protein biotinylation and purification kits, antibody labeling and new photo-reactive biotinylation reagents. This handbook includes dozens of references along with protocols, troubleshooting tips, selection guides and a complete listing of available tools.

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Disadvantages of using the Avidin-biotin system

Although the Avidin-biotin system is simple to set up and use, it does have certain limitations. Because any biotinylated molecule will bind to any biotin-binding protein, these reagents must be used in combination with other detection-probe systems (i.e., primary-secondary antibodies) for multiplex experiments.

Also, because biotin is a biological molecule, endogenous biotin can cause background and specificity issues when performing assays with certain biotin-rich tissues and extracts (i.e., brain, liver, milk, eggs, corn). This also applies to samples containing endogenous biotin-binding proteins such as eggs (source of Avidin) or bacteria like Streptomyces avidinii (source of Streptavidin).

Chemical structure of HNS-Desthiobiotin. Note the modified ring structure on the right (native biotin has a double ring structure that fits into the binding site of Avidin, Streptavidin or NeutrAvidin).

For purification applications, the strength of the binding interaction between biotin and Avidin is a factor that limits its utility. This is because harsh conditions are required to break the Avidin-biotin bonds (i.e., to dissociate and elute), and these may denature target proteins. To overcome this limitation, modified versions of Avidin resins and modified forms of biotin labeling reagents are commercially available which make the interaction readily reversible. These include monomeric Avidin, cleavable disulfide biotin reagents, and iminobiotin and desthiobiotin derivatives (see discussion of Protein Isolation and Enrichment below).

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Autocatalytic Origami

Most of those elongated polymers merely continue on their way. But a few end up folding, and some even have a hydrophobic patch of their own, just like the original catalyst. When this happens, the folded molecules with landing pads not only continue to form long polymers in greater and greater numbers, but they can also end up constituting what&rsquos called an autocatalytic set, in which foldamers either directly or indirectly catalyze the formation of copies of themselves. Sometimes two or more foldamers can engage in mutual catalysis, by enhancing reactions that form one another. Although such sets are rare, the number of these molecules would grow exponentially and eventually take over the prebiotic soup. &ldquoIt&rsquos like lighting a match and setting a forest fire,&rdquo Dill said.

&ldquoThat&rsquos the whole magic of it,&rdquo he added, &ldquothe ability of a small event to leverage itself to much bigger events.&rdquo

And all that&rsquos needed to spark this process are particular sequences of hydrophobic and polar components, which his model can predict. &ldquoDill&rsquos model shows you need only those two properties,&rdquo said Peter Schuster, a theoretical chemist and professor emeritus at the University of Vienna. &ldquoThat&rsquos a beautiful theoretical result.&rdquo

&ldquoIt puts in doubt the vision of the origin of life that is based on the RNA world hypothesis,&rdquo said Andrew Pohorille, director of NASA&rsquos Center for Computational Astrobiology and Fundamental Biology. To him and some other scientists, proteins seem like a &ldquomore natural starting point&rdquo because they are easier to make than nucleic acids. Pohorille posits that the information storage system found in the earliest rudiments of life would have been less advanced than the nucleic acid-based system in modern cells.

&ldquoPeople didn&rsquot like the protein-first hypothesis because we don&rsquot know how to replicate proteins,&rdquo he added. &ldquoThis is an attempt to show that even though you cannot really replicate proteins the same way you can replicate RNA, you can still build and evolve a world without that kind of precise information storage.&rdquo

This fertile information-rich environment might then have become more welcoming for the emergence of RNA. Since RNA would have been better at autocatalysis, it would have been favored by natural selection in the long run. &ldquoIf you begin with a simpler model [like Dill&rsquos], something like RNA could appear later, and it would become a winner in the production game,&rdquo said Doron Lancet, a genomics researcher who has worked on his own simple chemistry-based model at the Weizmann Institute of Science in Israel.


The 20 amino acids and their main functions

1- Phenylalanine

Phenylalanine is an amino acid found in three forms: L-phenylalanine (naturally synthesized), D-phenylalanine (artificially synthesized) and DL-phenylalanine (a mixture of the two above).

Phenylalanine is necessary for the formation of chemicals used by the brain (neurotransmitters and hormones), such as dopamine , noradrenaline Y adrenalin . Similarly, phenylalanine is involved in the formation of thyroid hormones.

Phenylalanine deficiency can lead to depression , loss of appetite, cognitive problems (confusion, loss of memory), lack of energy, decreased alertness, among others.

Some foods rich in this amino acid are beef, pork and fish, eggs, yogurt , cheese, soy products and some nuts.

2-Tryptophan

Tryptophan helps in the formation of serotonin and melatonin, substances that regulate the sleep cycle. For this reason, said amino acid is used in pharmaceuticals antidepressants and in sedative and hypnotic pills.

It also intervenes in tolerance to pain, so it is used by athletes who undergo intense physical activities. Further, improves concentration . The deficit of this amino acid generates insomnia , depression and weightloss .

Foods rich in tryptophan are turkey, chicken, beef, fish, soy grains, rice, some nuts and cheese.

3-Lysine

Lysine intervenes in the formation of L-carnitine, which is a compound that allows the circulation of oxygen in muscle tissues. Lysine is involved in the metabolism of lipids, making them used as an energy source.

It also promotes the development of the immune system (thanks to the creation of antibodies), it is involved in the formation of hormones, enzymes and collagen (protein that creates bones, cartilage and connective tissues).

Foods rich in lysine are fish, eggs, cheese, soy grains, potatoes, yeast and dairy.

4-Methionine

Methionine is involved in metabolism and helps to burn fat, and to the formation of other amino acids, such as cysteine ​​and glutamine. It is used in the control of some pathogenic bacteria and to treat stones in the kidneys.

Other functions of this amino acid are reducing fat in the liver and muscle degeneration, keeping skin and nails healthy. The deficiency of methionine can lead to fat accumulation in the liver.

Some sources of methionine are lentils, red meats, fish, garlic, onions, eggs, yogurt, soy grains and some seeds.

5-Threonine

Threonine is involved in the formation of vitamin B12. On the other hand, it promotes digestion and prevents diseases of the liver (since it helps to lower the cholesterol level in that organ and in the blood).

Intervenes in the regeneration of collagen proteins and helps the body to recover from wounds at muscle level.

Foods that are a source of threonine are meats, grains, dairy products, mushrooms and truffles, and vegetables.

6- Isoleucine

Along with leucine and valine, isoleucine is important for protein development and for energy storage. It helps the body to recover after having performed intense physical activities.

In addition, isoleucine is necessary for the synthesis of hemoglobin and is one of the main elements of red cells. Isoleucine deficiency produces symptoms similar to those of hypoglycaemia.

Foods that are sources of isoleucine are seeds, nuts, red meats (lamb, pork and beef), fish (especially tuna), lentils, soybeans, dairy pecorino cheese and parmesan) and eggs.

7- Leucine

Leucine is important in the formation of muscle tissue, it helps maintain that tissue once it has been formed and is necessary to maintain nitrogen balance in the body.

In addition, leucine benefits the rebuilding of muscle tissues, skin and bones.

Foods rich in leucine are grains (soybeans, lentils and chickpeas), nuts (peanuts, walnuts and almonds), red meat (especially pork and beef), marine products salmon, crustaceans and shrimp), eggs and dairy.

8-Valine

Valine is the amino acid that promotes tissue repair. It participates in energy storage, regulates the level of sugar in the blood and contributes to the process of growth and development of the human body.

Because of its restorative properties and energy storage, valine is one of the most important amino acids for athletes, so they consume it as supplements (in shakes, in pills, among others). It is possible to emphasize that the excess of valine in the body generates hallucinations.

Foods with higher levels of valine are meats, dairy, soy, peanuts and mushrooms.

9- Glycine

Glycine is the second most common amino acid in the human body. It forms part of the hemoglobin structure and is one of the major inhibitory neurotransmitters in the human body.

On the other hand, it is related to the production of glycogen and is involved in the suppression of the desire to ingest sugar and is part of the enzymes responsible for producing energy.

Finally, glycine transforms toxic substances into the body into non-harmful substances.

People with hypoglycemia, anemia, chronic fatigue syndrome and viral infections are deficient in this amino acid.

10- Alanine

Alanine is one of the main sources of energy for muscles and one of the most important amino acids involved in sugar metabolism.

It helps in the production of antibodies, which strengthens the immune system and is part of the connective tissues of the body.

Alanine deficiency is seen in people with hypoglycemia, fatigue, levels of viral infections, and elevated insulin levels.

11-Serine

Serine helps maintain blood sugar levels. Intervenes in the creation of antibodies, so it helps to strengthen the immune system, promotes the growth of muscle tissue and helps maintain it.

Other functions include fat metabolism and brain protein formation.

12-Cysteine

Cysteine ​​is an antioxidant. Protects the human body against ultraviolet rays, radiation and pollution. Also, this amino acid plays an important role in the metabolism of some enzymes.

On the other hand, it involves repairing the skin tissue and keeping it healthy. It is one of the main components of hair.

13- Aspartic acid

The main function of aspartic acid is to generate resistance. This amino acid is involved in the metabolism of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Other functions include protecting the liver (eliminating excess ammonia) and boosting the immune system (through the creation of antibodies).

The deficiency of aspartic acid in the human body generates the decrease of the levels of calcium and magnesium.

14- Glutamic acid

Glutamic acid is one of the most important amino acids among non-essential amino acids. This is responsible for the transport of glutamamine and other amino acids through the blood.

The presence of this molecule decreases the need to consume sugar and alcoholic beverages. It also increases energy levels in the human body.

Other functions are to accelerate the healing process of wounds and ulcers, and to aid in the synthesis of DNA.

The excess of this amino acid in the brain tissue can generate cellular damage. It is considered that during the cardiovascular accidents the brain releases large amounts of this acid thus damaging the neurons.

15-Asparagine

Asparagine helps to remove ammonia from the body, increases resilience, decreases fatigue, detoxifies the body of harmful chemicals and intervenes in DNA synthesis.

It is found in large concentrations in the hippocampus and in the hypothalamus . It is necessary to maintain the homeostatic balance in the nervous system and plays an essential role in the short term memory .

16- Glutamine

Glutamine is important as it keeps the blood sugar level. It maintains the strength of the muscles and makes them able to withstand intense physical activities.

On the other hand, glutamine is important for the functioning of the digestive system. The small intestine uses glutamine as the primary source of energy, being the only organ in the human body to do so. This amino acid is also involved in DNA synthesis.

Glutamine deficiency is seen in people with chronic fatigue syndrome, alcoholism and anxiety.

17- Arginine

Arginine is essential for the immune system to function properly. It also intervenes in wound healing, regeneration of the liver and increases insulin release.

This amino acid is necessary for the production and release of growth hormones.

The deficiency of this amino acid generates muscle weakness, hair loss, skin irritations and slow healing of wounds.

18- Tyrosine

Tyrosine reduces appetite, therefore, helps to reduce adipose tissue. It increases energy levels and intervenes in mental processes, improving concentration and reasoning ability.

This amino acid is precursor of the neurotransmitters dopamine, adrenaline, noradrenaline and melanin. It is used as an antidepressant.

Tyrosine deficiency can lead to depression, chronic fatigue syndrome, and hypothyroidism. The Parkinson's disease and drug addiction are also related to the deficiency of this amino acid.

19-Proline

Proline affects nutrition in humans and is involved in the formation of cartilage . This amino acid is believed to act as a source of nitrogen.

Therefore, it is important to maintain the health of joints, tendons and ligaments.

Another function of this amino acid is to keep the heart strong and healthy. It also works together with vitamin C to protect the skin.

20-Histidine

This amino acid is essential in some stages of human development, for example: during childhood. For this reason, it is called semi-essential, since it is only required in special circumstances.

Histidine is involved in the formation of hemoglobin, which is why it is used to treat anemia. It is also used to treat rheumatoid arthritis and some allergies. It also helps maintain pH in the blood.

Histidine deficiency can cause skin diseases, and cognitive and speech problems in children. For its part, the excess of this amino acid reduces the level of zinc.


Contents

The following illustrates the structures and abbreviations of the 21 amino acids that are directly encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical zwitterion forms that exist in aqueous solutions.

IUPAC/IUBMB now also recommends standard abbreviations for the following two amino acids:

Following is a table listing the one-letter symbols, the three-letter symbols, and the chemical properties of the side chains of the standard amino acids. The masses listed are based on weighted averages of the elemental isotopes at their natural abundances. Forming a peptide bond results in elimination of a molecule of water. Therefore, the protein's mass is equal to the mass of amino acids the protein is composed of minus 18.01524 Da per peptide bond.

General chemical properties Edit

Amino acid Short Abbrev. Avg. mass (Da) pI pK1
(α-COOH)
pK2
(α- + NH3)
Alanine A Ala 89.09404 6.01 2.35 9.87
Cysteine C Cys 121.15404 5.05 1.92 10.70
Aspartic acid D Asp 133.10384 2.85 1.99 9.90
Glutamic acid E Glu 147.13074 3.15 2.10 9.47
Phenylalanine F Phe 165.19184 5.49 2.20 9.31
Glycine G Gly 75.06714 6.06 2.35 9.78
Histidine H His 155.15634 7.60 1.80 9.33
Isoleucine I Ile 131.17464 6.05 2.32 9.76
Lysine K Lys 146.18934 9.60 2.16 9.06
Leucine L Leu 131.17464 6.01 2.33 9.74
Methionine M Met 149.20784 5.74 2.13 9.28
Asparagine N Asn 132.11904 5.41 2.14 8.72
Pyrrolysine O Pyl 255.31 ? ? ?
Proline P Pro 115.13194 6.30 1.95 10.64
Glutamine Q Gln 146.14594 5.65 2.17 9.13
Arginine R Arg 174.20274 10.76 1.82 8.99
Serine S Ser 105.09344 5.68 2.19 9.21
Threonine T Thr 119.12034 5.60 2.09 9.10
Selenocysteine U Sec 168.053 5.47 1.91 10
Valine V Val 117.14784 6.00 2.39 9.74
Tryptophan W Trp 204.22844 5.89 2.46 9.41
Tyrosine Y Tyr 181.19124 5.64 2.20 9.21

Side-chain properties Edit

Amino acid Short Abbrev. Side chain Hydro-
phobic
pKa § Polar pH Small Tiny Aromatic
or Aliphatic
van der Waals
volume (Å 3 )
Alanine A Ala -CH3 - - Aliphatic 67
Cysteine C Cys -CH2SH 8.55 acidic - 86
Aspartic acid D Asp -CH2COOH 3.67 acidic - 91
Glutamic acid E Glu -CH2CH2COOH 4.25 acidic - 109
Phenylalanine F Phe -CH2C6H5 - - Aromatic 135
Glycine G Gly -H - - - 48
Histidine H His -CH2-C3H3N2 6.54 weak basic Aromatic 118
Isoleucine I Ile -CH(CH3)CH2CH3 - - Aliphatic 124
Lysine K Lys -(CH2)4NH2 10.40 basic - 135
Leucine L Leu -CH2CH(CH3)2 - - Aliphatic 124
Methionine M Met -CH2CH2SCH3 - - Aliphatic 124
Asparagine N Asn -CH2CONH2 - - - 96
Pyrrolysine O Pyl -(CH2)4NHCOC4H5NCH3 N.D. weak basic - ?
Proline P Pro -CH2CH2CH2- - - - 90
Glutamine Q Gln -CH2CH2CONH2 - - - 114
Arginine R Arg -(CH2)3NH-C(NH)NH2 12.3 strongly basic - 148
Serine S Ser -CH2OH - - - 73
Threonine T Thr -CH(OH)CH3 - - - 93
Selenocysteine U Sec -CH2SeH 5.43 acidic - ?
Valine V Val -CH(CH3)2 - - Aliphatic 105
Tryptophan W Trp -CH2C8H6N - - Aromatic 163
Tyrosine Y Tyr -CH2-C6H4OH 9.84 weak acidic Aromatic 141

§: Values for Asp, Cys, Glu, His, Lys & Tyr were determined using the amino acid residue placed centrally in an alanine pentapeptide. [5] The value for Arg is from Pace et al. (2009). [6] The value for Sec is from Byun & Kang (2011). [7]

N.D.: The pKa value of Pyrrolysine has not been reported.

Note: The pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein. Protein pKa calculations are sometimes used to calculate the change in the pKa value of an amino-acid residue in this situation.

Gene expression and biochemistry Edit

Amino acid Short Abbrev. Codon(s) Occurrence Essential‡ in humans
in Archaean proteins
(%)&
in Bacteria proteins
(%)&
in Eukaryote proteins
(%)&
Occurrence
in human proteins
(%)&
Alanine A Ala GCU, GCC, GCA, GCG 8.2 10.06 7.63 7.01 No
Cysteine C Cys UGU, UGC 0.98 0.94 1.76 2.3 Conditionally
Aspartic acid D Asp GAU, GAC 6.21 5.59 5.4 4.73 No
Glutamic acid E Glu GAA, GAG 7.69 6.15 6.42 7.09 Conditionally
Phenylalanine F Phe UUU, UUC 3.86 3.89 3.87 3.65 Yes
Glycine G Gly GGU, GGC, GGA, GGG 7.58 7.76 6.33 6.58 Conditionally
Histidine H His CAU, CAC 1.77 2.06 2.44 2.63 Yes
Isoleucine I Ile AUU, AUC, AUA 7.03 5.89 5.1 4.33 Yes
Lysine K Lys AAA, AAG 5.27 4.68 5.64 5.72 Yes
Leucine L Leu UUA, UUG, CUU, CUC, CUA, CUG 9.31 10.09 9.29 9.97 Yes
Methionine M Met AUG 2.35 2.38 2.25 2.13 Yes
Asparagine N Asn AAU, AAC 3.68 3.58 4.28 3.58 No
Pyrrolysine O Pyl UAG* 0 0 0 0 No
Proline P Pro CCU, CCC, CCA, CCG 4.26 4.61 5.41 6.31 No
Glutamine Q Gln CAA, CAG 2.38 3.58 4.21 4.77 No
Arginine R Arg CGU, CGC, CGA, CGG, AGA, AGG 5.51 5.88 5.71 5.64 Conditionally
Serine S Ser UCU, UCC, UCA, UCG, AGU, AGC 6.17 5.85 8.34 8.33 No
Threonine T Thr ACU, ACC, ACA, ACG 5.44 5.52 5.56 5.36 Yes
Selenocysteine U Sec UGA** 0 0 0 >0 No
Valine V Val GUU, GUC, GUA, GUG 7.8 7.27 6.2 5.96 Yes
Tryptophan W Trp UGG 1.03 1.27 1.24 1.22 Yes
Tyrosine Y Tyr UAU, UAC 3.35 2.94 2.87 2.66 Conditionally
Stop codon† - Term UAA, UAG, UGA†† ? ? ? N/A N/A

* UAG is normally the amber stop codon, but in organisms containing the biological machinery encoded by the pylTSBCD cluster of genes the amino acid pyrrolysine will be incorporated. [8]
** UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a SECIS element is present.
† The stop codon is not an amino acid, but is included for completeness.
†† UAG and UGA do not always act as stop codons (see above).
‡ An essential amino acid cannot be synthesized in humans and must, therefore, be supplied in the diet. Conditionally essential amino acids are not normally required in the diet, but must be supplied exogenously to specific populations that do not synthesize it in adequate amounts.
& Occurrence of amino acids is based on 135 Archaea, 3775 Bacteria, 614 Eukaryota proteomes and human proteome (21 006 proteins) respectively. [9]

Mass spectrometry Edit

In mass spectrometry of peptides and proteins, knowledge of the masses of the residues is useful. The mass of the peptide or protein is the sum of the residue masses plus the mass of water (Monoisotopic mass = 18.01056 Da average mass = 18.0153 Da). The residue masses are calculated from the tabulated chemical formulas and atomic weights. [10] In mass spectrometry, ions may also include one or more protons (Monoisotopic mass = 1.00728 Da average mass* = 1.0074 Da). *Protons cannot have an average mass, this confusingly infers to Deuterons as a valid isotope, but they should be a different species (see Hydron (chemistry))

Amino acid Short Abbrev. Formula Mon. mass§ (Da ) Avg. mass (Da )
Alanine A Ala C3H5NO 71.03711 71.0779
Cysteine C Cys C3H5NOS 103.00919 103.1429
Aspartic acid D Asp C4H5NO3 115.02694 115.0874
Glutamic acid E Glu C5H7NO3 129.04259 129.1140
Phenylalanine F Phe C9H9NO 147.06841 147.1739
Glycine G Gly C2H3NO 57.02146 57.0513
Histidine H His C6H7N3O 137.05891 137.1393
Isoleucine I Ile C6H11NO 113.08406 113.1576
Lysine K Lys C6H12N2O 128.09496 128.1723
Leucine L Leu C6H11NO 113.08406 113.1576
Methionine M Met C5H9NOS 131.04049 131.1961
Asparagine N Asn C4H6N2O2 114.04293 114.1026
Pyrrolysine O Pyl C12H19N3O2 237.14773 237.2982
Proline P Pro C5H7NO 97.05276 97.1152
Glutamine Q Gln C5H8N2O2 128.05858 128.1292
Arginine R Arg C6H12N4O 156.10111 156.1857
Serine S Ser C3H5NO2 87.03203 87.0773
Threonine T Thr C4H7NO2 101.04768 101.1039
Selenocysteine U Sec C3H5NOSe 150.95364 150.0489
Valine V Val C5H9NO 99.06841 99.1311
Tryptophan W Trp C11H10N2O 186.07931 186.2099
Tyrosine Y Tyr C9H9NO2 163.06333 163.1733

Stoichiometry and metabolic cost in cell Edit

The table below lists the abundance of amino acids in E.coli cells and the metabolic cost (ATP) for synthesis of the amino acids. Negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell. [11] The abundance of amino acids includes amino acids in free form and in polymerization form (proteins).

Amino acid Short Abbrev. Abundance
(# of molecules (×10 8 )
per E. coli cell)
ATP cost in synthesis
Aerobic
conditions
Anaerobic
conditions
Alanine A Ala 2.9 -1 1
Cysteine C Cys 0.52 11 15
Aspartic acid D Asp 1.4 0 2
Glutamic acid E Glu 1.5 -7 -1
Phenylalanine F Phe 1.1 -6 2
Glycine G Gly 3.5 -2 2
Histidine H His 0.54 1 7
Isoleucine I Ile 1.7 7 11
Lysine K Lys 2.0 5 9
Leucine L Leu 2.6 -9 1
Methionine M Met 0.88 21 23
Asparagine N Asn 1.4 3 5
Pyrrolysine O Pyl - - -
Proline P Pro 1.3 -2 4
Glutamine Q Gln 1.5 -6 0
Arginine R Arg 1.7 5 13
Serine S Ser 1.2 -2 2
Threonine T Thr 1.5 6 8
Selenocysteine U Sec - - -
Valine V Val 2.4 -2 2
Tryptophan W Trp 0.33 -7 7
Tyrosine Y Tyr 0.79 -8 2

Remarks Edit

Amino acid Abbrev. Remarks
Alanine A Ala Very abundant and very versatile, it is more stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, and can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.
Asparagine or aspartic acid B Asx A placeholder when either amino acid may occupy a position
Cysteine C Cys The sulfur atom bonds readily to heavy metal ions. Under oxidizing conditions, two cysteines can join together in a disulfide bond to form the amino acid cystine. When cystines are part of a protein, insulin for example, the tertiary structure is stabilized, which makes the protein more resistant to denaturation therefore, disulfide bonds are common in proteins that have to function in harsh environments including digestive enzymes (e.g., pepsin and chymotrypsin) and structural proteins (e.g., keratin). Disulfides are also found in peptides too small to hold a stable shape on their own (e.g. insulin).
Aspartic acid D Asp Asp behaves similarly to glutamic acid, and carries a hydrophilic acidic group with strong negative charge. Usually, it is located on the outer surface of the protein, making it water-soluble. It binds to positively charged molecules and ions, and is often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine.
Glutamic acid E Glu Glu behaves similarly to aspartic acid, and has a longer, slightly more flexible side chain.
Phenylalanine F Phe Essential for humans, phenylalanine, tyrosine, and tryptophan contain a large, rigid aromatic group on the side chain. These are the biggest amino acids. Like isoleucine, leucine, and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule. Phenylalanine can be converted into tyrosine.
Glycine G Gly Because of the two hydrogen atoms at the α carbon, glycine is not optically active. It is the smallest amino acid, rotates easily, and adds flexibility to the protein chain. It is able to fit into the tightest spaces, e.g., the triple helix of collagen. As too much flexibility is usually not desired, as a structural component, it is less common than alanine.
Histidine H His His is essential for humans. In even slightly acidic conditions, protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However, only a few histidines are needed for this, so it is comparatively scarce.
Isoleucine I Ile Ile is essential for humans. Isoleucine, leucine, and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule.
Leucine or isoleucine J Xle A placeholder when either amino acid may occupy a position
Lysine K Lys Lys is essential for humans, and behaves similarly to arginine. It contains a long, flexible side chain with a positively charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., DNA-binding proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids prone to be located on the outer hydrophilic surfaces of the proteins when they are found inside, they are usually paired with a corresponding negatively charged amino acid, e.g., aspartate or glutamate.
Leucine L Leu Leu is essential for humans, and behaves similarly to isoleucine and valine.
Methionine M Met Met is essential for humans. Always the first amino acid to be incorporated into a protein, it is sometimes removed after translation. Like cysteine, it contains sulfur, but with a methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule.
Asparagine N Asn Similar to aspartic acid, Asn contains an amide group where Asp has a carboxyl.
Pyrrolysine O Pyl Similar to lysine, but it has a pyrroline ring attached.
Proline P Pro Pro contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. It can disrupt protein folding structures like α helix or β sheet, forcing the desired kink in the protein chain. Common in collagen, it often undergoes a post-translational modification to hydroxyproline.
Glutamine Q Gln Similar to glutamic acid, Gln contains an amide group where Glu has a carboxyl. Used in proteins and as a storage for ammonia, it is the most abundant amino acid in the body.
Arginine R Arg Functionally similar to lysine.
Serine S Ser Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophilic, so the outer regions of soluble proteins tend to be rich with them.
Threonine T Thr Essential for humans, Thr behaves similarly to serine.
Selenocysteine U Sec The selenium analog of cysteine, in which selenium replaces the sulfur atom.
Valine V Val Essential for humans, Val behaves similarly to isoleucine and leucine.
Tryptophan W Trp Essential for humans, Trp behaves similarly to phenylalanine and tyrosine. It is a precursor of serotonin and is naturally fluorescent.
Unknown X Xaa Placeholder when the amino acid is unknown or unimportant.
Tyrosine Y Tyr Tyr behaves similarly to phenylalanine (precursor to tyrosine) and tryptophan, and is a precursor of melanin, epinephrine, and thyroid hormones. Naturally fluorescent, its fluorescence is usually quenched by energy transfer to tryptophans.
Glutamic acid or glutamine Z Glx A placeholder when either amino acid may occupy a position

Catabolism Edit

Amino acids can be classified according to the properties of their main products: [12]


Conclusion

Probability arguments can present a strong argument for the existence of a Creator God. However, even when such evidence is presented to an evolutionist there is no guarantee that he or she will be persuaded. The real issue is not about evidence it is a heart issue. As Christians we are called to have ready answers and break down strongholds that act as stumbling blocks to the unbeliever. It is the Holy Spirit that changes lives.

But sanctify the Lord God in your hearts, and always be ready to give a defense to everyone who asks you a reason for the hope that is in you, with meekness and fear ( 1 Peter 3:15 ).

For the weapons of our warfare are not carnal but mighty in God for pulling down strongholds, casting down arguments and every high thing that exalts itself against the knowledge of God, bringing every thought into captivity to the obedience of Christ ( 2 Corinthians 10:4–5 ).


Watch the video: Circle the smallest number UKG (June 2022).


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