Student and teacher of reality in all its forms.
I self-published my personal experience of discovering and trying to understand and use a model of reality based on the Many Worlds Interpretation of Quantum Mechanics:
Surfing the Multiverse: Finding Happiness One Universe at a Time
Available on Kindle and from Amazon, and found in blog post form at:
I walked around the neighborhood with Katie this morning and found some interesting tree life along the path. The neighborhood of old homes is giving way to new construction.
L is for Leucine, an essential, non-polar, aliphatic, branched-chain amino acid. It is the most important ketogenic amino acid important for the generation of acetyl-CoA and acetoacetate.
Leucine is encoded by the codons UUA and UUG and all 4 codons starting with CU. The nearby codons starting with GU encode the similar branch-chain amino acid Valine. And the other BCAA Isoleucine is encoded by nearby codons AUA, AUC, and AUU.
Just a fun fact – during the 1970’s and 1980’s, the price of a barrel of oil was never cheaper than 1 gram of gold and was sometimes as high as 3 grams of gold. The recent “oil price cap at $USD 60” is about 1.03 grams of gold. I found it synchronistic that when I wrote down the prices and calculated the oil price in gold, that the end of the paper results in a oil price of 1.01 grams gold per barrel of oil, very, very close to the oil price cap when converted to gold. When China opens back up after they have their COVID case wave like other countries, then demand for oil will very likely push the price of oil higher.
K is for Lysine, which is essential, basic, charged, and aliphatic. Some important functions of Lysine are cross linking collagen polypeptides and histone modifications. Lysine was isolated from the milk protein casein in 1889. Lysine is encoded by the codons AAA and AAG.
A week ago, I noticed a feeling of exiting a wormhole and begin writing about it. I hadn’t written since 20210922W Day 631: Holding the Tension between the Head and the Heart and I had some concerns that I would write only a day or two. I don’t remember what led me to blog about amino acids. I think it was a synchronicity. Amino acids had been on my mind because I’ve been engrossed in studying tarot and I had noticed a correspondence between the number of amino acids encoded in the number of cards in the tarot’s major arcana. I knew if I committed to write about each genetically encoded amino acid, then there was a high priority I would write at least 20 posts. Then, to increase the probability of writing daily, I thought of a milestone 20 days in the future and realized that the winter solstice was Dec. 21. The synchronicity was when I realized that there were 20 days until the winter solstice. I use synchronicities as trail markers that let me know I’m “flowing with the stream”. In this case it gave me more confidence that the universe would support me if I write an initial blog post that day on amino acids and continue until the winter solstice.
Confession, I’m writing this post a day late on Saturday. The trip to the ER on Thursday morning put me off my schedule. I hope to catch up this weekend.
I is for Isoleucine. Isoleucine is an isomer of leucine, having the same chemical formula but different structure. Isoleucine is an essential amino acid. It is in the group of branch chain amino acids, which are sold as BCAA supplements. As might be expected, Isoleucine is one nucleotide mutation away from Leucine, with Isoleucine encoded by AUA, AUC, and AUU and Leucine encoded by all codons beginning with CU. Another BCAA, Valine, is also one nucleotide mutation away from Isoleucine, being encoded by all codons beginning with GU. BCAAs, being carbon chains, are good sources of energy in the body and BCAA supplements are sold with the promise of additional energy and to assist with muscle recovery. However, before taking BCAAs, please read “Branched-chain amino acids and muscle protein synthesis in humans: myth or reality?“. One argument made in the paper is that muscles are made up of all amino acids, not just BCAAs, so supplementing only these will not have any positive effect on muscle protein synthesis. A recent article in Men’s Health, “BCAAs Supplements Do a Whole Lot of Nothing“, is consistent with this argument and supports the recommendation to just eat enough protein in your diet so you get all the amino acids you need.
20221207W – After taking a 10mg Lisinopril yesterday afternoon and another 10mg before bed last night, I awoke with a low-for-me BP of 126/84. Dinner last night was steak, potatoes, and red wine. I cooked steak&potatoes and then, synchronistically, my Aunt invited me over for steak&potatoes. The meaning for this for me is alignment. I had pondered being elsewhere and decided to stay home and cook. So, this coincidence of common meals gave me a centered and grounded feeling.
H is for L-Histidine, not to be confused with the signaling molecule histamine, which mediates vasodilation and inflammation in response to allergens, such as insect bites or foreign substances. Histamine is formed from the removal of the carboxyl group of Histidine (by HDC). EGCG, a catechin found in green tea, has been shown to inhibit HDC and thereby reduce histamine and inflammation.
Histidine is an essential amino acid with a daily requirement of 8-12 mg/kg of body weight per day in adults. The average diet of Europe, USA and Japan has been reported to be 30-35 mg/kg of body weight per day.
The positively charged imidazole functional group of Histidine is commonly used in enzyme catalyzed reactions. It can serve as a base or an acid, acting as a proton buffer. Histidine is also important in stabilizing folded structures of proteins.
Histidine is encoded by the codons CAC and CAU. Histidine is often found in metal binding sites of proteins. In these cases, it is sometimes replaced by Cysteine (codons UGC and UGU), which by looking at the PAM250 substitution matrix, it seems to most often get there via Tyrosine (codons UAC and UAU).
20221208h-1644 I just got back from eating with my Aunt V. We went to Eastside Tavern which has quite a bit of Christmas decoration up. The arugula salad with salmon was my choice, cooked by Morgan wearing a birthday gift apron from Hedley and Bennett.
I had just woken up from sleeping all day because last night I spent from 3am onward in the ER after developing a rapid 160bpm heart rate around 2am.
I also talked to my Mom today and found out her best friend’s husband passed yesterday from heart issues.
In other news, Mars played hide-n-seek with the Moon last night.
G is for Glycine. Glycine is the simplest proteinogenic amino acid and the simplest stable amino acid. It has no side chain (having only a hydrogen where the side chain would be). It is encoded by all the codons that start with GG (GGA, GGC, GGG, and GGU). How synchronistic that G is for Glycine and G is also for Guanine, the only nucleotide of the first two positions of the codons encoding Glycine. The absence of a side chain makes Glycine the only achiral proteinogenic amino acid, with all others having L-chirality.
Glycine was named by the Swedish chemist Berzelius, who discovered the element selenium (in 1817) and also cerium (in 1803). He also discovered how to isolate silicon in 1824, which the entire computer chip industry is dependent upon for silicon wafers. He coined the term “protein” in 1838, meaning “of the first rank”, because proteins were fundamental to living organisms. Berzelius also developed a system of chemical notation (e.g. H2O, FE2O3) still used today with the only difference being that Berzelius used superscripts instead of subscripts.
Glycine makes up a third of collagen, which is the main structural protein the the extracellular matrix in various connective tissues. Collagen is the most abundant protein in mammals, making up 1/4th to 1/3rd of the whole-body protein content.
Glycine is also an inhibitory neurotransmitter in the central nervous system.
The best food sources for Glycine are red meat, seeds, turkey, chicken, pork, peanuts, caned salmon, granola, quinoa, hard cheese, pasta, soybeans, bread, almonds, eggs, and beans. Also, Gelatin being cooked collagen, it is quite high in Glycine.
It’s now time for some Glycine here at Café Crème…
Over 5 years ago, I painted an interpretation of the genetic code using symbols for the amino acids that I created to help me memorize the amino acid residues. Today, I drew these symbols again with a few modifications and different versions.
F is for Phenylalanine, which is named after it’s structure of Alanine with a Phenyl group attached. Phenyl is derived from “pheno”, which means “I bear light” in Greek. Phenylalanine assists in the production of two important neurotransmitters, norepinephrine and dopamine, through an intermediate amino acid Tyrosine. Because norepinephrine has antidepressant properties, Phenylalanine is theorized to treat depression. An estimated 1 in 15,000 people have PKU, a rare genetic disorder resulting in a non or poorly functioning enzyme used to convert Phenylalanine to Tyrosine. This results in a reduction of norepinephrine and dopamine and a buildup of Phenylalanine. Individuals with PKU need to avoid Phenylalanine, which is most easily done by avoiding protein-rich foods such as meat, nuts, milk, cheese, and grains bread/pasta. Also, the artificial sweetener aspartame found in Equal and NutraSweet breaks down into Phenylalanine (and Aspartate).
Phenylalanine also stimulates the production of melanin, the pigment that gives color to skin, eyes, and hair.
Humans are not able to synthesize Phenylalanine and must get it from foods. High sources of Phenylalanine are found in the following foods, in priority order: powdered milk, hard cheese, soy, veal, lamb, chicken, pig, cod fish, oats, eggs, bread, rice, cow milk, and mushrooms. For reference, hard cheese has 10 times the Phenylalanine per gram than mushrooms.
Phenylalanine is encoded by the codons UUU and UUC. Notice that these codons are one mutation away from the codons UAU and UAC which encode the metabolically related amino acid Tyrosine.
… Four hours later, I got to the dishes. In the mean time, we pulled out all the under sink plumbing we could to find the source of the clog that was stopping up the sink. Each piece of plumbing had some nasty black mold. We got in all cleaned out and put back together.
Meanwhile my post on Glutamate is waiting until now. I wondered if Glutamate and mold were related and a quick search showed that they were. According to online sources, mold releases mycotoxins that cause oxidative stress and glutathione (a tripeptide of Glutamate, Cysteine, and Glycine) helps to counteract this effect through it’s antioxidant function. These sources seem to base their claims on papers like “Deficient Glutathione in the Pathophysiology of Mycotoxin-Related Illness” (doi: 10.3390/toxins6020608).
This morning I measured my bp and found it to be slightly elevated at 145/95. Two days ago it had been 165/115 and I decided to take a half pill of Lisinopril 20mg (so 10mg) to see what effect that had. The Lisinopril just happened to be in a multiyear old prescription bottle on my dresser. I haven’t taken bp meds in many years. The 10mg of Lisinopril didn’t lower my bp that night, but in the morning my bp was 135/85, which for me feels quite good as I have rarely measured the classic 120/80 or below, which would likely have me faint if I exercised. In fact, I stopped taking Lisinopril before because it would make me light headed after exercise. That, and I also blamed it for contributing to my tinnitus that developed after I started taking it 10 yrs ago. It seems that the initial 10mg I took 2 days ago is still active a bit in my body. This morning I found the half-pill I bit and bit it again to give myself a 5mg dose. I’m curious to see if this is effective. Lisinopril acts a a diuretic. I’ve been wondering the last two days what else would naturally act as a diuretic.
D is for Aspartic Acid (ASP). Sometimes in sequences it is indistinguishable from Asparagine (ASN) and is given the one letter code B to code for the ambiguous amino acid (ASP/ASN). Aspartic Acid is non-essential in humans and is important in the synthesis of other amino acids, including Isoleucine, Lysine, Methionine, Arginine, and it’s sometimes substituter Asparagine. I happened to have pubchem open on Asparagine (https://pubchem.ncbi.nlm.nih.gov/compound/Asparagine) and was just reading that Asparagine (a beta-amido derivative of Aspartic Acid) is a “nontoxic carrier of residual ammonia to be eliminated from the body” and acts as a diuretic.
A quick google search finds the “duh” vegetable with Asparagine … Asparagus! Webmd says:
While I can’t find any information on Aspartic Acid’s role as a diuretic, it seems as a precursor to Asparagine, it would be important as well. When I learned the amino acids with a song I wrote, I referred to Aspartic Acid by it’s conjugate base form Aspartate because it rhymed better 🙂 I’ll use Aspartate and Glutamate for the rest of this post.
Aspartate is encoded by the codons GAC and GAU. The other two codons beginning with GA (GAA and GAG) encode Glutamate, which is structurally and chemically similar to Aspartate. The Aspartate codons GAC and GAU are also a single mutation of the first nucleotide (G to A) to codons AAC and AAU which encode previously mentioned Asparagine, which is often substituted for Aspartate.
Aspartate and Glutamate are both neurotransmitters that stimulate NMDA receptors.
Aspartate, along with Phenylalanine, are used in the sweetener aspartame.
Food sources of Aspartate are asparagus, avocado, molasses, sausage meat, oysters, and wild game. I have an avocado in the fridge that needs to be eaten. I wonder what it taste like with molasses… pretty good!
Last night I went to a “first Friday” open-house at The Odin in north Austin and met some people working on some very interesting projects. I met one of the co-founders of trilobio, a startup company working on “revolutionizing synthetic biology by changing the way synthetic biologists do science”.
Yesterday, I wrote about Alanine, the first common amino acid assigned a letter by IUPAC for bioinformatics research. The letter B is not assigned to a single amino acid but is instead used for both Aspartic Acid (Asp-D) and Asparagine (Asn-N) when it is either unclear or either amino acid may be found in a peptide sequence. Notice that the 3-letter codes for Asp-D are GAC and GAU and the 3-letter codes for Asn-N are AAC and AAU, so these two amino acids that are very close in molecular weight and size are separated in the genetic code by only a single nucleotide mutation between A and G in the first position.
C is for Cysteine, which is also abbreviated by Cys. It is sometimes abbreviated by the symbol Cyz when acting as a deprotonated catalytic residue. Cym also refers to the deprotonated form. Cyx is sometimes used to refer to Cysteine when the thiol is oxidized to form a disulfide derivative. The two sulfur-containing amino acids are more easily oxidized than the other amino acids.
Cysteine is the smallest and simplest of the two sulfur-containing proteinogenic amino acids (encoded by the genetic code). The other sulfur-containing amino acid is Methionine-Met-M.
Cysteine is encoded by the codons UGC and UGU. Notice that these codons are a single first position mutation (U to A) from the codons AGC and AGU which encode the similarly sized amino acid Serine-Ser-S. Also notice that the nearby UGA codon, which is normally described as a stop codon in the standard genetic code, can also encode for the “21st proteinogenic amino acid”, Selenocysteine-Sec-U, which is a modification of Cysteine in which Selenium replaces Sulfur. Additionally, Cysteine codons UGC and UGU are a single second position mutation (G to A) from the codons UAC and UAU which encode the slightly more acidic amino acid Tyrosine-Try-T, which is somewhat hydrophobic like Cysteine.
Of interest, “Cysteine has been proposed as a preventive or antidote for some of the negative effects of alcohol, including liver damage and hangover” is a quote from the wikipedia article on Cysteine. From the same article, Cysteine is important for flavoring food, breaking disulfide bonds in hair perms, and in detecting protein structure or investigating protein folding processes using site-directed spin labeling techniques.
It’s been a while since I have regularly posted and I would like to document daily the exit of the wormhole that I’m feeling in my own timeline. To increase the probability of doing this, today I’m going to talk about Alanine, one of the amino acids encoded by the genetic code that has a heritage shared by all life forms known to exist.
Amino acids are fundamental to all known life. Through their amine and carboxyl ends, they link together to form a chain of amino acids that folds up into a dynamic 3-D functional shape called a protein. These proteins can be enzymatic and catalyze reactions or they can be structural.
In bioinformatics, latin letters have been assigned to each of the common amino acids for standardization of storing protein sequence data. The Latin alphabet becomes then a reasonable choice for ordering the amino acids.
A is for Alanine. Alanine has a very simple side chain, or residue, of a single methyl group (CH3). It is the second smallest amino acid after Glycine, which has no residue. The methyl group results in it being non-polar and aliphatic. It is ambivalent, meaning it does not have a strong preference for being inside or on the surface of a protein. It is non-essential in humans and can be synthesized from pyruvate or branched chain amino acids such as Leucine, Isoleucine, and Valine. The largest common amino acid, Tryptophan, is a derivative of Alanine.
Alanine is encoded by all codons starting with GC (GCA, GCC, GCG, and GCU).
The “Alanine World” hypothesis (ref: https://doi.org/10.3390/ijms20215507) proposes that ancestral proteins predominantly relied on Alanine to provide the basic scaffold and secondary structure of the protein.
I haven’t heard of the Alanine World hypothesis before today. I do remember reading about the RNA World hypothesis. It makes sense to me that some amino acids were here along with RNA in the beginning. I imagine that future computer simulations will provide convincing evidence for how and when our unique genetic code came into existence.
Another death in my circle today – my friend just texted that her mother passed away this morning. I am grateful that I was able to visit her and her Mom earlier this year.