The Chemistry of Exercise

Compound Interest has just released a new infographic regarding The Science of Exercise. As always, they make my favorite infographics! Just enough information for your average person, with the avenue for you to do further research via links.

The Science of Exercise

As Chemists, let’s talk about the chemicals involved:

Carbohydrates
Biomolecules consisting of Carbon, Hydrogen and Oxygen atoms, usually with a H:O ratio of 2:1 (as in water) and thus with the general formula Cm(H2O)n, where m may be different from n, and also with exceptions, such as deoxyribose*.

Another Bane of my existence… Lactose… which I am heavily intolerant of!

Carbohydrates serve numerous roles in living organisms. Polysaccharides (such as starch and glycogen) serve for storage of energy, as well as structural components (such as cellulose and chitin). Ribose is an important component of coenzymes and also the makes up the backbone of RNA while *Deoxyribose makes up the backbone of DNA. There are numerous other uses, as always, along with their derivatives.

Electrolytes
For this case, they would mean the substances that are used to balance fluid levels in the body via the use of semi-permeable membranes & concentration gradients (cf. Osmosis)

Adenosine Triphosphate (ATP)
Most take the energy value of foods literally. Rather, they should think in terms of the “molecular unit of currency” of intracellular energy transfer that is ATP.

Adenosine Triphosphate (ATP)

During many processes in living cells, e.g. muscle contraction, nerve impulse propagation, and chemical synthesis, ATP is converted to ADP or AMP. This process generates energy, as given by chemical energetics. (ATP is regenerated by other processes, most notably respiration, which us Biochemists have spent decades of our lives learning about)

Let’s say Person A wants to workout. First of all, 1 calorie is roughly 4.2 Joules of energy, so that would be about 4.2 kJ of energy. To cut the story very very short, for every 7300 calories (over 30kJ) stored, 1 mole of ATP is formed. That’s 6.0 x 1023 ATP molecules formed. Now 7300 calories is really high! Generally, the recommended daily calorie intake is 2000 calories a day for women & 2500 for men. This is, of course, subject to your body type, amount of physical activity per day, existing medical conditions, etc.

Now, I am supposing that Person A wants to play basketball. DISCLAIMER: These are just general estimates!
During a basketball game, about 85% of the athlete’s energy comes from the phosphagen system and 15% from the glycolytic system (anaerobic), and a small % comes from the oxidative pathway (aerobic).

-Rebounding is pretty intense and would likely use the ATP-CP for a quick burst of immediate energy. (phosphagen system)

-Fast breaks can be moderately to very intense depending on sustainability -by the athlete and usually would require the glycolytic system to supply energy. Anaerobic glycolysis releases ATP and produces lactic acid (also explains why you will be sore). These moderate-intensity activities also include full-court defensive pressure or motion offensive plays.

-what about the oxidative energy system (aerobic)?
Although it is the least used system in basketball during a match, it is one of the most important for basketball success (and most skills!)
During the entire game, the oxidative system is essential for continuous play as they replenish the energy stores while the phosphagen & glycolytic systems are releasing ATP and producing lactic acid.

Note that all the above processes require the use of ATP, NOT our carbohydrates, i.e. what we eat. For that, please look up the process of Respiration.

I have always been highly skeptical of “Calories burnt” calculators and similar ‘measures’. Looked up for basketball values and it reads that the average person ‘burns’ 575-775 calories per hour in a game of basketball. If they are shooting baskets, they will ‘burn’ 325-450 calories per hour. Of course, this is subject to the intensity of the player. Now what about metabolic state of Person A? High metabolic rate vs low metabolic rate?

I used this “Calories Burned Calculator” and input my data in. It seems, for my weight… I will only burn 236-488 calories per hour. Interesting to note is that basketball officiating would burn 368 calories per hour, which would be more than shooters! Also, you burn more calories per hour during TRAINING than you do in GAME. (THIS I APPROVE).

Let’s now look at Person B during our Quarantinewhile… doing nothing at home. Will Person B burn any calories? YES! Depending on our body weight, a person burns calories to sustain the body, e.g. repair… respiration… etc.

Person B weighs 150 pounds, and so might burn 46 calories an hour doing nothing. While sleeping, 322-414 calories will be burnt. The heavier you are, the more calories you will burn just by doing nothing. This is just relativity speaking (in a sense). Now the estimate figures for sleeping have immense significance! By having a full night of sleep, one can burn more calories than an hour of shooting basketball!

Finally, we come to Highs & Cramps. I love this section as it revealed to me a misconception that I’ve had my entire life! I even stated above that lactic acid may cause soreness but in the infographic above, it states that this is not proven and that there are other hypotheses. Very interesting, and will be digging further into anandamide as well as the other hypotheses for why we feel sore after workout.

Anandamide – apparently these contribute to that feeling of ‘high’ after you score a crucial basket during a match!

I hope this article was enjoyable to read. I honestly enjoyed looking up the individual aspects, and doing the personal calculation for my own calorific study. Maybe it’s time to focus less on just what you eat, but also your workout lifestyle. Working out should NOT be an event… it should be a habit instead.

Stay safe & healthy always everyone!


Ravenslark

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Molecule of the Month – May 2020 – Remdesivir

1024px-Remdesivir.svg.png

Remdesivir – Synthesis

800px-Synthesis_of_Remdesivir.png

By 盧樂 (Lu, Le) – Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=87311572

Yes, yes, I know… the drug trials for RDV have been inconclusive. But I found this synthesis pathway as credited above, and the Chemist in me just smiled evilly 😀

As I worked on my Masters in Pericyclic Chemistry, as well as other key areas of Organic Synthesis, most of the above is familiar to me. I suddenly recalled all those hours spent per week doing practicals with my Practical Partner from Russia. Oh Dr Yakovlev… be safe & healthy!

For my Chemistry students, please scrutinize each step. Predict the conditions where applicable, and imagine all the mechanisms that are in play in each step!

May the Fourth be with you all, always! ❤

 

Ravenslark

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Reactions of Amino Acids at a Glance

20-Common-Amino-Acids-v3.png

As always, I turn to the genius of Compound Interest! Here is an updated infographic depicting the Twenty Common Amino Acids, classified according to their side chain (-R group). Aliphatic, Aromatic, Acidic, Basic, Hydroxylic, Sulfur-containing and Amidic are the classes here, but even within some, there are further details. E.g. for tryptophan, the side chain is aromatic, but also has a secondary amine.

Today in class, we discussed four reactions of amino acids:

  1. Decarboxylation (loss of CO2; histidine becomes histimine, which is responsible for allergic response. As part of an immune response to foreign pathogens, histamine is produced by basophils and by mast cells found in nearby connective tissues. Histamine increases the permeability of the capillaries to white blood cells and some proteins, to allow them to engage pathogens in the infected tissues. Of course, this leads to quite a few problems and sometimes we take anti-histamine to reduce our allergic response.)
  2. Reduction (for cysteine; forming disulfide bridges that are important in maintaining the tertiary structure of a protein)
  3. Condensation reactions (between -COOH and -OH/-NH2 and vice versa, forming amide links & esters.)
  4. Dehydration by Phosphoric acid to form a phosphoester bond. (Yes, this looks a lot like the reaction between sugars and ATP; the chemistry is essentially the same, just an extension)

Then, we delved into the individual amino acids themselves to discern if they could do any other reactions, and found a LOT of possibilities!

Organic-Functional-Groups-–-Expanded-v2.png

To become adept at organic synthesis, one must first know all about the reactions of functional groups. Without this, one will find the entirety of Organic Chemistry a real pain. As a Biochemist, I used to make Flash Cards with functional groups and some brief descriptions whilst I was at O- & A-level. As I progressed to University, the cards became more and more numerous, as well as more and more detailed.

My procedure for answering Organic Reaction or Mechanism questions was usually as follows:

  1. Draw the skeletal formula (in 3D representation if needed)
  2. Highlight functional groups
  3. Label dipoles (so important!!!) & active lone pairs
  4. “Push electrons” (curly arrows or even half-curly arrows)
  5. Check intermediates / transition states
  6. Score more or less free marks 🙂

Some of the steps above can be skipped, but please do check the marks allocated for each question, as they would give you an idea of how much information you need to depict in your answer.

Personally, among Physical, Organic & Inorganic Chemistry, I found Organic Chemistry to be the easiest. I scored full marks for my Inorganic Papers whilst in A-level but that was simply because memorization is the EASIEST skill, hence BOTTOM of Blooms’ Taxonomy. Organic Chemistry required a deep level of understanding. But if you have that, you can even encounter NEW organic compounds, and predict their reactions! With the correct skillset, you can draw up synthetic pathways, design more efficient routes, etc!

I chose to read Organic Chemistry for my Masters, specifically Pericyclic Chemistry. Some of my work is still up on Oxford University’s website. Unfortunately, Flash Macromedia is obsolete, and my work cannot be viewed in full now. But I am proud to say that my work won the RSC Exemplarchem Prize in 2003, which netted me a plaque and 500 pounds. The money was donated to charity, and I must thank my Supervisor for recommending my work to RSC, and guiding me towards completing my MChem ❤

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Biotechnology has always been a very important field, as right now, with these dark times, my colleagues have stepped up for us. May they all remain safe & healthy… always.

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Molecule of the Month – Hydroxychloroquine

Hydroxychloroquine… oh hydroxychloroquine. If you were a figure on Instagram or Twitter… I am sure that you would have millions of followers by now. Doesn’t matter if it works or not (Yes, I believe it works, somewhat)… people need HOPE now. But do NOT self-dose if you are healthy. It will do more harm than good. Also, no matter what drug you are taking, ALWAYS get a prescription from a Doctor (MD or DO). Calculations need to be made! Critical things such as calculations need to be made, and also medical histories need to be reviewed in case of allergies or other complications from taking HCQ (or Plaquenil and other brand names).

Historically, when malaria plagued the world… Quinine was the first-line treatment for malaria as recommended by WHO. As a child, learning about malaria vs sickle-cell anemia from my Science teacher, I was fascinated and traveled to our BSB library to look up Quinine. Back then, there was no internet, so everything had to be learnt through books. I found out back then that in 1820, Quinine was isolated from the bark of a cinchona tree (yes, I still remember this from my childhood as it was like a mystical story for me). A piece of bark from a tree could cure such a deadly disease???? WOW!

Quinine-3D-balls.png

Quinine

I have featured Quinine as the Molecule of the Month before, in 2009. And then came Artimisinine, which is now the go-to drug for malaria, discovered in 1972. Tu Youyou, a Chinese Pharmaceutical Chemist & malariologist (I hope that’s not something I just made up -_-)  won the 2015 Nobel Prize in Medicine for her research and it saved millions of lives in South China, SEA, Africa, and South America.

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Artemisinine (qinghaosu)

Now back to hydroxychloroquine, which is an analogue of quinine. It is a derivative of chloroquine, which was discovered by Hans Andersag & coworkers at the Bayer laboratories, who named it Resochin. It was ignored for a decade, because it was considered too toxic for human use* (We will come back to this later).

Chloroquine.svgHydroxychloroquine.svg

Chemists will be able to immediately tell the difference between chloroquine (left) and hydroxychloroquine (right) by the additional hydroxy group on the top right of the molecule. The IUPAC name for hydroxychloroquine is… UGH is the word for it:
(RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol

Molecular formula: C18H26ClN3O
Molar mass: 335.872 g mol−1

DISCLAIMER!!! I do not endorse nor deny the applications of hydroxychloroquine. I merely chose the drug as it is a subject of heavy debate in the world at this very moment. But I am against self-dosing unless you are a doctor (even doctors will admit that when it comes to their own selves, they can be bad patients).

Now, as stated above, HCQ is a medication to prevent and treat malaria. Other uses include treatment of rheumatoid arthritis, lupus, and porphyria cutanea tarda.

Why is this drug so important now? It is being studied as an experimental treatment for COVID-19. A question that should pop into your mind right now should be: Eh?? Isn’t this drug for malaria?? How can it be used to treat COVID-19? This is a question that is too often NOT ASKED. But I am actually more concerned with *the toxicity of this drug that left it’s original form chloroquine untouched for a decade.

Even when used for treatment of malaria, common side effects include vomiting, diarrhea, headache, changes in vision, and muscle weakness. These are just the common side effects. Yes, this drug is listed on the WHO’s List of Essential Medicines. It is also the 128th most-prescribed medication in the United States, with more than five million prescriptions. Now, if you think about this figure right now… there should be a lot of supply in the USA.

Let’s talk about the more severe side effects. HEART PROBLEMS, LIVER FAILURE, MUSCLE ATROPHY. The risk of death from overdose is significant as well. Yes, what have we got to lose, right? I believe that compassionate use may outweigh this, but as always, it has got to be a case by case basis. Don’t self-dose with this if you are healthy or having mild symptoms of covid-19, especially for children and pregnant mothers!

As of 3rd April, 2020, there is limited evidence to support the use of HCQ to treat COVID-19. This is NOT a statement saying it does not work. What is means is that, there are many other factors to consider before they can place it a front-line drug. Safety evaluation in different age demographics of people, studies of other known complications in patients with existing medical conditions, dosage calculations, etc.

Antiviral effects:
It increases late endosomal and lysosomal pH, resulting in impaired release of the virus from the endosome or lysosome. This prevents a virus from releasing its genetic material into the cell and replicate. It also seems to act as a Zinc ionophore, that allows extracellular Zinc to enter the cell and inhibit viral RNA-dependent RNA polymerase. Sounds good right? But don’t go and drink alkaline concoctions. That will damage your stomach and cells along the way. This won’t help either! Also, don’t go and spam Zn tablets. Again, this is a reaction at the cellular level. What you do to your alimentary canal will have limited effects on the disease, if any.

On January 2020, Chinese medical researchers stated that exploratory research into chloroquine seemed to have “fairly good inhibitory effects” on the SARS-CoV-2 virus.

Chloroquine has been approved by Chinese, South Korean and Italian health authorities for the experimental treatment of COVID-19. These agencies noted contraindications for people with heart disease or diabetes. Here comes the IMPORTANT PART:

Chloroquine has a relatively narrow therapeutic index and it can be toxic at levels not much higher than those used for treatment!!!!!! EASE OF OVERDOSE ALERT!!!

On 28th March 2020, the FDA authorized the use of HCQ and chloroquine under an Emergency Use Authorization (EUA). The treatment itself has not been approved by the FDA. There is a key difference there. The experimental treatment is authorized only for emergency use for people who are hospitalized but not able to receive treatment in a clinical trial.

On 1st April 2020, the European Medicines Agency (EMA) issued guidance that chloroquine and HCQ are only to be used in clinical trials or emergency use programs.

So what brought humanity to HCQ to treat COVID-19? Well, in October 2004, a group of researchers at the Rega Institute for Medical Research published a report on chloroquine, stating that chloroquine acts as an effective inhibitor of the replication of the SARS-CoV virus. SARS-CoV… NOT SARS-CoV-2.

To gain a better understanding of where chloroquine & HCQ might be effective, please watch this video at this timestamp. I recommend watching the entire video, and the follow-up video regarding treatment etc. 1.5 hours well worth it!

Not all parts of the videos are accurate as of today, as new information is coming in every day. We are actually living this pandemic… no matter where we are… affected in a lot of ways.

Recommendation: Biochemists will be able to understand this better. A lot of the acronyms and jargon can be skimmed over, but it would be wise to actually learn some of them if you truly wish to know more about COVID-19.

Be hopeful. Many institutions and organizations are working very hard at vaccine development, repurposing of existing drugs, scrutinizing the blood of recovered patients to try to identify antigens, and actively testing existing and new drugs that may be used to treat the symptoms of COVID-19.

As always, be safe & healthy!

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Major Updates to Site!

As teachers all over the globe are beginning to go fully into Home-based Learning, I have finally decided to activate the links on the menu bar above. Students may download the files that I have used for supplementary notes. Will be adding more files in the coming weeks… exercises, worksheets, past paper compilations, etc.

The files come from other websites, and should be credited via the watermarks or footnotes in the files themselves.

Do not depend on these notes alone. Surf the web, visit Chemguide & other educational sites for Chemistry and acquire as much mastery as you can for your A-levels!

Happy Surfing!

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Doodly Mechanisms: Electrophilic Addition & Nucleophilic Substitution

The mood has been pretty grim in the past month, but we must press on. For my students who are preparing in advance for the November AS & A-Level Exams… here’s my latest Doodly Mechanism!

It’s been quite a while, but I’ve finally taken my Doodly Project off the shelf for one Mechanism. I’ve chosen Electrophilic Substitution of HBr to Ethene. Generally, this would the mechanism depicting attack by an electrophile (permanent or temporary) to an electron-rich C=C double bond.

For A-Level students, remember to display the molecules as required by the question. I’ve chosen to use skeletal formula as, personally, they are my favorite. Neat, and least clutter.

  1. Draw the molecules, ethene & HBr, in the correct alignment (with the H end facing the C=C double bond, specifically attacking the π-bond)
  2. Label the dipole
  3. Draw a full curly arrow from the C=C double bond to the H; Draw a full curly arrow from the H-Br bond to the Br
  4. Draw the carbocation that forms (Markovnikoff’s Rules may need to be applied in some questions)
  5. Draw a curly arrow from the Br anion to the carbocation. Some textbooks will insist on depicting trans-addition (personally I feel that it seems right, but mostly doesn’t matter since the C=C has become a freely rotatable C-C.

Feel free to email me regarding the Doodly video below to suggest improvements! Thank you so much!

As for Nucleophilic Substitution (specifically via Sn2), the ‘attacking’ species is a nucleophile, and the leaving group will end up becoming a nucleophile. Due to nucleophiles having higher electron densities, they will target the electron-deficient atom.

Remember the following:

  1. Draw the molecule of bromomethane & hydroxide ion (with the lone pair of the O facing the electron-deficient C)
  2. Label the dipole
  3. Draw a full curly arrow from the lone pair on the O to the electron-deficient C and draw a full curly arrow from the C-Br bond to the Br
  4. Sn2 has a transition state but NOT an intermediate, unlike for Sn1.
  5. A Walden inversion has occurred.

I hope this series of Doodly Mechanisms was helpful! Stay safe & be healthy!

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Keeping ourselves safe from COVID-19

Dear Readers,

After almost 3 weeks of staying at home… and the curb seems to be working. The curve is flattening… but it is not a time to relax. What will happen once COVID-19 goes away? Back to not practicing good hygiene… travelling all over and exposing ourselves to unknown invisible threats like this… I feel proud to be a Bruneian… as our Ministry of Health have really done an amazing job. It takes time to mitigate. It takes time to flatten the curve. A lot of pain has been felt collectively, and watching our own Minister of Health choking back emotions when he announced our first fatality from COVID-19… what can we do as people of Brunei… to help?

Stay at home as much as you can, but stay healthy. Work out. Eat clean. Boost your immune system. For more information, I ALWAYS turn to my favorite source of Scientific Infographics that are well-researched and well-made. Trusted source: Compound Interest.

Four-ways-to-destroy-coronavirus-v6

The Governor of California, Gavin Newsom has already started calling it physical distancing rather than social distancing. Similar principles… stay out of range if possible, but as life must go on… be mindful of what you touch… where you’ve been… THINK about what you may be bringing back home to your loved ones… this is an enemy that CANNOT be SEEN!

There won’t be a truly SAFE vaccine for this for a year or so… and there may be a chance that this may become seasonal as well, as in… recovered patients may not retain immunity for life.

Also, the amount of MISINFORMATION is staggering. The rate of spread rivals the spread of COVID-19. Seriously! We, as scientists, might as well just quit. It usually starts with a claim that the information comes from a Virologist… a Surgeon… a veteran Doctor… which catches our attention. Then, the pseudoscience comes. The fake news comes. The Conspiracy Theories come. #curbmisinformation #nomorefakenews

Trust the WHO. Trust the CDC. Trust those who have treated COVID-19 patients SAFELY.

  1. The Chemistry of Soap can be easily looked up. It can dissolve that fatty outside layer of SARS-CoV-2. The virus would be torn apart, and unable to continue wreaking havoc.
  2. What if we don’t have soap nearby? Hand sanitisers with a minimum of 70% alcohol concentration will be a quick fix. But they are in short supply these days… and also expensive. Go back to #1 as soon as possible!
  3. What about surfaces where the virus may have landed on? They need to be sanitized. But no, we cannot use #2 as it would simply cost too much. A more efficient way is bleach. NaClO is a strong oxidizing agent, and will destroy proteins and genetic material. But do take care! It is toxic to us too!
  4. An alternative to #3 would be hydrogen peroxide. Among the strongest oxidizing agents, a concentration of 3% and above will destroy the virus (and a LOT of other things too, including us… given the right amount, concentration & conditions)

Then comes videos of people lighting themselves up on fire due to usage of alcohol. Hello???? Alcohol is flammable. Basic science. Drinking bleach to kill the virus??? COME ON! Sniffing peroxide??? /facepalm

Apologies… being at home for 3 weeks… teaching from home… marking from home… there no longer is any ‘safe sanctuary’ for us Tutors. What day is it today? I am not totally sure. I had to ask!

Last, but not least, if we follow the infographic above… does it guarantee that we won’t catch the virus? Well… NO! Even hand sanitizers say they can clear 99.9% only. There always has to be a disclamer and caveat. Even Scientists always use that adage: Believe none of what you hear… and half of what you see. (Edgar Allan Poe)

PUT IT TO THE TEST. Or even better… let the REAL professionals test it. Don’t just listen to politicians or celebrities claim to have miracle cures in the works, etc. and believe it at face value.

If you truly wish to understand a lot more about COVID-19, I recommend this video on YouTube by Ninja Nerd Science. It will take 1.5 hours to view the movie. You will need to pause it if you aren’t a Biochemist like I am. (Even I had to look up so many of the acronyms they used!) Have another window open so you can do some research on each of those individual terms. Spend the weeks required to know them. Spend months learning how to understand them. Spend years putting the facts together. Spend a decade … oh wait… that’s what DOCTORS did! Now you know… leave the treatments to the doctors. They spent a DECADE or so and yet they cannot claim to fully understand COVID-19. What more can keyboard warriors do?

However, albeit being inherently realistic (some call it pessimistic) in nature… I will say that if you think something works to combat COVID-19, go put it to the test, get it peer-reviewed, specialist-reviewed, heck… put it forward to MOH, the CDCs of other countries… the WHO! They will run the necessary tests to ensure there aren’t harmful side effects. They will figure out how to ‘safely’ mass produce and ‘fairly’ distribute the cures & vaccines. Until then, be vigilant. Our country, no… our entire world depends on the actions of every single person. Be safe & healthy dear readers!

 

 

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How do the tests for Coronavirus work?

Firstly, the tests that are currently being used in diagnosis of infectious diseases is by no means a new testing method. Coronavirus itself, is not new, with the first human cases documented in the late 1960s. Thus, it is not a surprise to see the term coronavirus popping up on the back of various old disinfectants, claiming to be able to ‘kill’ it, along with other viruses.

However, the strain is new… with SARS-CoV-2 (previously known by the provisional name 2019 novel coronavirus (2019-nCoV). Now, this new virus strain causes COVID-19. As the name suggests, CO = corona, VI = virus & D = disease, and 19 as the year of designation by the World Health Organization (WHO). Unfortunately for our fellow humans in Wuhan, China, the original source of viral transmission to humans and WHEN the strain became pathogenic remains unclear. Virology is a huge topic that requires years and years of research but as a Chemist, I just know the basics (infection, reservoir, phylogenetics & taxonomy, and some structural biology), and so I’ll leave the explanation of the virus strain & disease that it causes to actual professionals.

However, the morphology of the coronavirus itself is fascinating. Below is a cross-sectional model of a coronavirus via By https://www.scientificanimations.com – https://www.scientificanimations.com/wiki-images/, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=864364461280px-3D_medical_animation_coronavirus_structure
As suggested by the single coil within, it is a single-stranded RNA. Furthermore, the lipid bilayer encircling it as a viral envelope is basically like the liposomes that we learn about in our A-Level Syllabus. If a large model was made, it would look like a soft toy that we might even use in ball sports. However, once the contents are attached to a host cell… we’ve already seen the results of that… sadly…

On the frontlines, the first thing that must be done is Testing. How-the-coronavirus-test-works
As always, my favorite source of infographics for Science is Compound Interest.

Now, as a Chemist, let’s break down the information in this wonderful infographic.

  1. From the swab, processing, etc, the virus RNA in the diagram shows exposed base pairs (RNA, so you know which bases they are ^_^)
  2. Reverse transcriptase is an enzyme, and serves to convert the RNA (single strand) to DNA (double strand). A good question now would be: “What holds the two strands together, and which bases pair up?”
  3. Replication of the virus DNA is done (safely in a controlled fashion). The primers will hold the virus DNA in specific places via the same forces as in 2. (and maybe other interactions too?)
  4. The fluorescent dye basically let’s the tester detect the presence of the virus.

Now, regarding the results… it’s just as obvious. If no viral RNA was present to begin with, there wouldn’t be a minimum level of fluorescence shown.

Moreover, the problems mentioned above are real. Supply, for starters, followed by the sheer amount of time it takes just to obtain the results. Furthermore, there is a possibility of false positives/negatives. Let’s say the tester used a contaminated sample. That would give rise to a false positive. And if the test was rushed, and too little time passed during step 3, there might be too low levels of the viral DNA, and hence, a false negative. The frontliners really have a lot to process. Not only are the numbers overwhelming, they cannot rush the testing too. So, please listen to your Minister of Health, and be thankful, yet have empathy for your frontliners. Stay at home. DON’T PUSH IT. Social distancing now, can save months (or even years) of pain. I pray that our frontliners, who can’t even afford to take leave now… will be rewarded accordingly after everything blows over… God bless them.

As for future tests, I’ve read about a few that are being developed in Japan (together with China). Don’t worry about a vaccine… this will take 12-18 months at least, and let the real experts deal with it. The SOP for developing a vaccine must be followed to prevent unnecessary loss of life. Not to mention that skipping steps is illegal. Then what about the issue of mass manufacture & distribution? Costs? Etc. Too many variables that are in the future. As a responsible member of society, the least we can do is just simply to stay at home. Our sacrifices now (it will be a short time compared to a lifespan) can greatly reduce the spread of COVID-19, and prevention is always better than a cure!

Disclaimer: I am not a virologist, nor am I a pathologist. When I was 13, I CHOSE to walk down the path to become an educator in Chemistry. I dodged the path of a doctor even though I was encouraged to walk down that path. It takes a special kind of mental & emotional strength to become one. Take this as a case in point. I reached out to one of my ex-students who happens to be on the front lines. Asked him to take care, etc, but what was his response? “It’s ok sir. I didn’t study so hard back when you taught me to falter now.” This touched me greatly, whilst at the same time breaking my heart and filling me with immense pride at our younger generation of Doctors. I am not ashamed to admit that I wouldn’t have had such a high level of empathy for my fellow humans. But what I CAN do is fact-check, and educate. And to those who created & spread ‘fake news’, shame on you.

Just my two cents. (not taxable)

Ravenslark

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Coronavirus: How Hand Sanitisers Protect Against Infections

“As coronavirus continues its spread, panic-buying has swept supermarket shelves of hand sanitisers. What’s in these sanitisers and how effective are they in comparison to hand washing? This graphic takes a look.”

Excerpt above taken from Compound Interest, one of my favorite sites!

Chemistry-of-hand-sanitiser-

As Scientists, we should be well-equipped with experience & knowledge to act responsibly. To be better prepared & react accordingly when faced with a crisis like this.

Anas ibn Malik reported: A man said, “O Messenger of Allah, should I tie my camel and trust in Allah, or should I leave her untied and trust in Allah?” The Prophet (pbuh) replied: “Tie her and trust in Allah.”

Source: Sunan al-Tirmidhi 2517

As Prophet Muhammad (pbuh) once advised his people to tie their camel & be faithful, we as scientists should urge caution to those who actually listen. “Don’t Push It” is the new slogan! Trust in your Ministry of Health & those who work within. Let us pray for those who work at the front lines, losing health & sleep… only to be constantly urged to go even further beyond their capabilities. Be as supportive of them as we can. If we are unable to help them directly, the least we can do is NOT to be negative.

Don’t spread false information; Don’t cultivate social stigma; Don’t become one who adds to the already numerous problems around; Don’t be an expert unless you truly are… as even highly acclaimed media outlets have already had to recant their news due to misquotes & errors; And even if you truly are an expert… work with those who are at the front lines directly or indirectly… don’t let your words be twisted unknowingly or knowingly by non-experts due to fear or worse…

Practice high levels of personal hygiene & don’t leave your waste behind as well. Put them in proper places designated for disposal. Avoid congregating… let us all play our part to reduce the burden on our front liners. 14 days seems long. It’s time for self-development! Online classes are already being setup by our hardworking tutors on Discord, Zoom & other platforms, despite it being their first time! Online yoga lessons, online calisthenics lessons, online tutorials, etc can be found! (check out my IG if you know me for an upcoming 14-day Core Strength tutorial!)

Trust to hope… but be prepared as you can be… without becoming too much of a burden to others. Stay safe & healthy everyone! God Bless!

Ravenslark Majere (rmajere)

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The Chemistry of Porridge

Gong Xi Fa Cai, readers! First of all, here’s a lovely infographic (as always) from Compound Interest!

The-science-of-making-porridge

CNY is almost over, but due to the binge eating of ‘heaty’ foods (hmm, we really should have some medical articles regarding the Chinese ‘heaty’ phenomenon), quite a number of people have sore throats, upset tummies, etc. Porridge becomes a staple for the duration! Now, making porridge is pretty easy. Add more water, heat, stir, heat stir, season, heat, stir. The more care you’ve put into the cooking, the better the texture and taste (as with most cooking). But it can be challenging to make it Porridge Perfect. So how can you make it better? Science, of course!

Oats are around 40-60% starch, which is a carbohydrate which forms granules made up of amylose and amylopectin. These are long molecules made up of glucose units. Amylose chains are linear, and tightly packed, whereas amylopectin is highly branched. This branching makes it more soluble than amylose.

So, when we heat our porridge, the starch granules absorb water, disrupting the hydrogen bonds between their chemical components. This causes the granules to swell. Over time, this swelling of granules causes the porridge to thicken. This process is starch gelatinisation.

As gelatinisation proceeds, the porridge gets thicker and thicker. This thickening is known as ‘pasting’. Now, here is where it becomes crucial for the cook. STIR the porridge! Do you want your porridge clumpy and lumpy (porridge cake facepalm), or do you want it finely distributed and seasoned evenly throughout?

Now, once the temperature gets high enough, the porridge thickness reaches its peak. Heating further only breaks down (slowly) the starch and lowers the thickness of the porridge. This is because the amylose starts leaking out of the starch granules.

So how do we prevent making poor porridge?

  1. Heat the porridge to high enough temperatures to gelatinise
  2. Stir the porridge at intervals
  3. Stop heating when it goes over around 95 degrees Celcius

Seasoning, adding other ingredients, garnishing, plating; all that adds value to the meal, but the gist of making good porridge is the balance between gelatinisation & pasting.

I personally use a 2:1 ratio of liquid to rice to make porridge. Sometimes, I even add a bit of Jasmine tea to disrupt the intermolecular forces further ^_^

Many say that porridge keeps you feeling fuller for longer after breakfast… sorry not in my case as someone with an OMEGA level Metabolic Rate. I feel weak in about 1-2 hours and I will need more ‘solid’ foods to satiate my hunger. But then again… if the porridge is ‘porridge cake’, I’d probably feel fuller for longer, BUT, it would be poor porridge!

Ravenslark

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