Tag Archives: biochemistry

Protein Symphony!

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music_by_dante_mk  Amazing artwork by:(http://browse.deviantart.com/art/music-106660536)

One good thing about music, when it hits you, you feel no pain.

-Bob Marley

This is one of my most favourite quotes. Music is an important part of my life. Even though I may not be musically talented per say (does singing in the shower count?), I enjoy listening to it daily as it helps me forget about life’s problems instantly. For those few minutes I’m in a zone where nothing else matters except how the music makes me feel in that moment; be it happy, sad, calm you name it, music can take you on an emotional roller-coaster.

So when I read an article talking about assigning musical notes to each amino acid in different proteins to create a melody I was beyond thrilled!

This has been an ongoing project by Rie Takahashi and Jeffrey Miller, colleagues at the University of California at Los Angeles, in which their aim is to “musicalise” the amino acid sequences in various proteins. Although this idea has been thought of before, Takahashi and Miller have found a way to make the tunes richer and more rhythmic compared to earlier efforts that resulted in jumpy notes.

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Rie Takahashi

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Jeffrey H. Miller

So, how is this done?

It’s really simple actually. Each of the 20 amino acids is allocated a specific musical note, be it middle C or D sharp, until each one has their own note. Then a protein is chosen and a musical score is made just by transcribing the amino acids of the protein’s sequence into musical notes.

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Remember I told you that previous attempts at making “musical proteins” failed because of notes “jumpy notes”? This was because sometimes notes would leap 20 notes at a time, thus making it hard/ unmelodious to the ear. But Takahashi and Miller overcame this obstacle by giving each amino acid not just one note but three notes, also called a triad chord. These triad chords were played successively and the harmonies were easier on the ears and just overall nicer to listen to. They did cheat a little bit though because they made minor changes to the chords already used in the first 13 amino acids and then gave them to the remaining 7, but it was all to make the highest tunes more favourable.

They also discovered a way to put in timings to each triad so rhythm could be introduced into the music.  By using the changes in the codon (triplets of DNA bases in the gene) frequencies, they allotted time values to the chords for each of the amino acids in the protein sequence.  Since an amino acid can have up to 4 different codons, the more common the codon is in the DNA, the longer the time value it has. That means the longest note in the melody would have a semibreve enduring 4 beats! Cool right?

protein music

I’m sure you just want to hear what it sounds like by now, so listen here!! On their website, they have numerous other creations here. Even though it’s not Beethoven, I still think it’s an ingenious idea and I’m excited to see and hear what becomes of this as Takahashi would like to add other instruments to the protein music as well!

Other vids can be found on Youtube as well showing how others convert each amino acid sequence of different proteins into music 🙂


Article Reference:  Coghlan, Andy. 2007. “Music made to measure from nature’s proteins” Accessed April 6, 2013. http://www.newscientist.com/article/dn11775-music-made-to-measure-from-natures-proteins.html

References:

http://www.mimg.ucla.edu/faculty/miller_jh/gene2music/home.html

http://www.newscientist.com/article/dn11775-music-made-to-measure-from-natures-proteins.html

http://www.youtube.com/watch?v=kIZ_mMC9OqY

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Krebs in the Army?

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This is Krebs. Sir Hans Adolf Krebs to be precise. Who is he you may ask?

Sir Hans Adolf Krebs was a German-born British physician and biochemist. Krebs is well known for his Nobel Prize winning research in the citric acid cycle or what we usually call it, the TCA cycle/ Krebs cycle.

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The Krebs cycle is a series of metabolic chemical reactions used not only by us, but also by all aerobic organisms, to produce energy through the oxidization of acetate into carbon dioxide.

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Yeah, you may have heard of him before but I bet you didn’t know this about him.

Krebs was Jewish and he joined the German army in 1932, and was also appointed to the 13th Mechanized Infantry Division. You’re probably confused. How could a Jew be a part of the German army at that time? Well the Nazi party was not in power as yet so German Jews were welcome in the German army.

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Afterwards, Krebs returned to clinical medicine at the hospital of Altona and then at the medical clinic of the University of Freiburg, where he conducted studies and discovered the urea cycle. Yup, the Krebs cycle wasn’t the only cycle he discovered!

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Unfortunately, because he was Jewish, he was prohibited from practicing medicine in Germany when the Nazis took power, and he emigrated to England in 1933.  He then worked in the biochemistry department under Sir Frederick Gowland Hopkins in Cambridge. So… the guy who discovered the essential amino acid Tryptophan and the guy who discovered the TCA cycle were buddies! Two great minds working together for the love of biochemistry! I love it! 🙂

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References:

http://www.nndb.com/people/619/000129232/

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

http://www.nobelprize.org/nobel_prizes/medicine/laureates/1953/krebs-bio.html

http://inoxx.net/?tag=citric-acid-cycle

http://pictureshistory.blogspot.com/2009/12/men-of-wehrmacht-german-soldiers-part-1.html

http://www.corbisimages.com/stock-photo/rights-managed/SF8172/chemist-hans-adolf-krebs-and-assistant-in

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

The Sound of Glycolysis!

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Do you remember the musical “The Sound of Music”? I was really young the first time I watched it and I remember thinking “Wow, this movie is really…long.” I watched it again a few months back and absolutely loved it! Not only were the characters loveable but the songs they sang such as “The Sound of Music” and “My favourite things” were catchy and melodious. So you could imagine how excited I felt when I found this vid on YouTube that sang the steps of glycolysis in the same tune that Maria and the children sang “Do-Re-Mi”. Take a look!

 

 

Glycolysis is the metabolic pathway that converts glucose into pyruvate and it occurs in the cytosol of the cell. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

There are 10 enzyme reactions in total and two phases, the energy investment phase and the energy generation phase. In the energy investment phase, there are 2 irreversible reactions and 3 reversible, while in the energy generation phase there is only 1 irreversible and 4 reversible enzyme reactions.

Here is a pic I found that may help you remember the structures if you learn better with food in mind! 🙂

Glycolysis_before_lunch_by_llifi_kei

Photo Credit (http://llifi-kei.deviantart.com/art/Glycolysis-before-lunch-101607430)

The first time I found this vid was when I was learning glycolysis for my CAPE examinations and now it can still help me with my university studies as well! When learning the song, I found myself swaying from side to side and closing my eyes while singing (I was really into it XD). It really was a life saver for me because I always used to have trouble learning the steps of any chemical process if there were more than 5 steps involved lol. I have terrible memory. I’ve come to realize that my love for music can aid in my school work, I mean, if I can remember all the lyrics to Rihanna’s “Pour it Up” then why can’t I learn these steps in the same way right?

The video layout is creative with colourful drawings and diagrams plus the singer, Jenny Scoville Walsh, had a lovely voice that complemented the song very well. The steps were all in the correct order and the intro to the video explained very well some of the steps in the process of digestion.

The only things that I wish the video included in the song were the enzymes associated with each step of the breakdown of glucose for example, glucose >glucose 6-phosphate is catalyzed by the enzyme Hexokinase. I also would’ve liked that the step in which dihydroxyacetone phosphate is quickly converted to glyceraldehyde 3-phosphate would’ve been musically added to the song instead of just being put into brackets in the video. Other than that, the video is very well made and I recommend that you share it with others who would like a fun and easy way to remember the steps in glycolysis. Who knows, you might find yourself rocking out to the song just like this:

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Have a safe and happy Easter!

References:

http://llifi-kei.deviantart.com/art/Glycolysis-before-lunch-101607430

http://www.cnikky.com/carrie-underwood-will-star-in-the-re-make-of-the-sound-of-music/

Turkey Coma?

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I know Christmas may be long gone but it is and will forever be my most favourite holiday. The season brings joy, cheer and a spirit of giving, as well as those chilly nights when you just want to snuggle up in your bed. Although I love all of these things, the highlight of the season is…you guessed right, the food! Ham, pastelles, sorrel, ginger beer, you name it, I love it. Sadly my brother is allergic to pork ham so since mummy doesn’t want him to feel left out, she cooks a whole turkey just for him. He’s so spoiled. But that doesn’t mean I don’t have my fair share of turkey as well 🙂  Have you ever felt like you were in a food induced coma after eating your belly’s full at Christmas lunch? You know, when you’ve just finished eating a plate like this:

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And after you’re just like:

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What if I told you that there just might be an amino acid found in turkey and ham that induces drowsiness in human beings. That amino acid is called Tryptophan.

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In my amino acids and proteins lecture, I learnt that Tryptophan is one of the 20 amino acids and an essential amino acid that is required for a healthy diet. An essential amino acid is one which the body cannot make on its own thus has to be supplied in the diet. Only the L-stereoisomer of tryptophan is used in enzyme proteins. Since tryptophan is not found in the body, we have to consume different food sources and the tryptophan then converts into serotonin in the body. Serotonin, which in turn is the precursor of hormone melatonin, is a chemical found in the brain that maintains calmness and composure in humans.

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Different scientific studies have been done, even by the Oxford University, into the truth of whether or not tryptophan does in fact calm nerves and induce sleep. Interestingly enough, some studies go so far as to show that excessive consumption of the amino acid tryptophan actually affects the human sense of trust.

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Here is an excerpt from an article (Country Facts 2010) which explains how their study was conducted:

A very interesting research was conducted by Oxford University through a two member game titled the “Prisoners Dilemma”. The two options given to the teams were to make moves which would allow a player to earn money by taking it from another player or make moves where both of the players could make money. The idea was for both players to co-operate. Under normal situations, without any tampering, this occurred approximately 75% of the time.

 However in the second stage a chemical serotonin inhibitor was introduced. Before the players began the game half of the group of volunteers was made to drink a concoction which reduced their tryptophan levels thereby reducing the total amount of serotonin in the brain. This group of volunteers was less cooperative than the others who were not given any chemicals and also doubted the trustworthiness of others.

 The study activity reveals that a lack of serotonin or tryptophan in the human body could lead to lack of cooperative behavior in all age groups.

Since mutual cooperation always enhances brain activity and promotes positive reinforcement it is interesting to note that human beings who lack this chemical at optimum levels in the brain suffer from behavioral imbalances.”

You would think that if someone was consuming large numbers of turkey and ham they would have a large amount of tryptophan in the body right? That is not the case because there are many other factors that may contribute to post-meal drowsiness such as:

  • Carbohydrates

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L-tryptophan may be found in turkey and other protein rich foods, but it’s actually a carbohydrate-rich (as opposed to protein-rich) meal that raises the level of this amino acid in the brain and leads to serotonin synthesis. Carbohydrates stimulate the pancreas to secrete insulin. When this occurs, some amino acids that compete with tryptophan leave the bloodstream and enter muscle cells. This causes an increase in the relative concentration of tryptophan in the bloodstream. Serotonin is synthesized and you feel that familiar sleepy feeling.

  • Fats

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Fats slow down the digestive system, giving Christmas dinner plenty of time to take effect. Fats take a good amount of energy in order to digest, so the body will redirect blood to your digestive system to handle the job. Since you have less blood flow elsewhere in your body, you will feel less energetic after eating a meal high in fats.

  • Alcohol

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Alcohol is a central nervous system depressant. If alcoholic beverages are part of the Christmas celebration, then they will add to the sleep-factor.

I had no idea that this topic was an ageless debate with many persons claiming this as either fact or fiction. But nevertheless, I will continue to gobble my turkey and ham with a big smile on my face and then to my bed I will go.

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My apologies if this post made you hungry…or sleepy….or both :p. What do you think? Do you believe that the turkey coma is a myth?

Article Reference:

Country Facts. 2010. “Turkey Enzyme” Accessed March 1, 2013. http://www.kwintessential.co.uk/articles/turkey/Turkey-Enzyme/3446

References:

http://www.tumblr.com/tagged/sleep%20gif

http://circadiana.blogspot.com/2005/11/does-tryptophan-from-turkey-meat-make.html

http://scienceblogs.com/clock/2006/11/22/does-tryptophan-from-turkey-me/

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

http://trinichow.com/2013/01/02/holiday-christmas-food-trinidad-tobago/

http://www.loopbarbados.com/loop-blog/santas-got-sunburn-ponche-de-creme

http://naparimagirls.edu.tt/09/index.php?option=com_content&view=article&id=61&Itemid=66

http://www.uncommoncaribbean.com/2011/12/19/taste-of-the-caribbean-tis-the-season-for-sweet-bread/

http://science.howstuffworks.com/innovation/edible-innovations/question519.htm

Ninhydrin Starring in CSI!

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Every family has their own special traditions. For my mummy and I, we enjoy curling up on the couch on a Friday evening to watch marathons of our favourite TV-shows. One such show is CSI, specifically CSI Miami. I love Horatio’s character the most! He’s just so badass.

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If you’re an avid CSI fan such as me, you may have noticed that in the field of forensics, fingerprint work makes an appearance in every episode. Have you ever wondered what they use in forensics to develop fingerprints?

 

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Ninhydrin has become the most common method used to reveal prints on porous surfaces. Nearly all forensics labs use ninhydrin for this purpose, and some seldom use anything other than ninhydrin. Ninhydrin is cheap, sensitive, and commercially available in disposable spray cans. The developed prints are a high-contrast purple that’s readily visible on most paper backgrounds.

 

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Ok, so how does the ninhydrin work exactly?

Dusting the crime scene is the commonest, simplest and oldest latent print developing technique. A white powder composed of the chemical ninhydrin is used to develop latent prints (prints invisible to the eye). Latent prints are formed by sweat, either from the hands themselves or by unconscious contact between the fingers and the face or other parts of the body. Even the swiftest of criminals find it difficult to escape without leaving behind the trace of a single fingerprint. The traces of amino acids present in perspiration bind with the ninhydrin and the prints begin to appear in about an hour. In the pH range of 4-8, all α- amino acids react with ninhydrin; a powerful oxidizing agent to give a purple colored product (diketohydrin) termed Rhuemann’s purple.

 

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Ninhydrin degrades amino acids into aldehydes, ammonia, and CO2 through a series of reactions; the net result is ninhydrin in a partially reduced form hydrindantin. Ninhydrin then condenses with ammonia and hydrindantin to produce an intensely blue or purple pigment, sometimes called Ruhemann’s purple.

ninhydrin reaction

In our last lecture, we made a clear distinction between the two tests : Biuret test and Ninhydrin test. Mr. Matthew (my lecturer) made a video that clearly differentiates between the two tests in a clear understandable manner so if you are having trouble understanding their differences, I urge you to watch the vid! It’s really helpful and not too long.

Apparently students mix up their uses all the time, and if my lecturer didn’t stress on this I’m 99.9% sure I would’ve been one of those careless students as well.The Biuret test is used to test for proteins while the Ninhydrin test is used to test for amino acids.  Don’t forget!!!!

Mr. Matthew also posed a question to us. Do all amino acids give that lovely purple colour when the ninhydrin test is performed? From his tone I knew there had to be some exception.

Here’s what I found:

The color produced when the ninhydrin test is performed varies slightly from amino acid to amino acid, probably because the unreacted acids complex with the pigment.

Proline and hydroxyproline give a yellow color.  Proline has aliphatic side chains with a distinctive cyclic sturcture. The secondary amino (imino) group of proline  residues is held in a rigid conformation that reduces the structural flexibility of polypeptide regions containing proline. Proline does not give the ninhydrin reaction as this reagent requires free alpha amino group (-NH2) but proline has an imino group (-NH).  For the amino acids which have a free -NH2 (amino) group, ninnydrin test is positive but is negative for proline because it only has -NH (imino) group.

I hope this post was helpful! Can you find any more amino acids that don’t give the purple colour when the ninhydrin test is performed?

 

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References:

Information:

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

http://antoine.frostburg.edu/chem/senese/101/organic/faq/amino-acid-test.shtml

http://amrita.vlab.co.in/?sub=3&brch=63&sim=1094&cnt=1

http://www.bxscience.edu/publications/forensics/articles/fingerprinting/r-fing01.htm

http://www.chemistry.ccsu.edu/glagovich/teaching/316/qualanal/tests/ninhydrin.html

http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch27/ch27-3-3.html

http://pharmacol.weebly.com/uploads/3/7/8/8/3788687/pharmaglimps_biochemistry.pdf

Pictures:

http://www.gov.im/dha/police/csi/fingerprint.xml

http://ars.els-cdn.com/content/image/1-s2.0-S0379073806003720-gr8.jpg

http://www.harpercollege.edu/tm-ps/chm/100/dgodambe/thedisk/food/ninhy/ninhy.htm

http://www.tumblr.com/tagged/csi:miami

http://thenata.deviantart.com/art/finger-print-color-58102348

Did You Know…?

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Now that we are onto the topic of amino acids and proteins in my biochemistry course, I found it only appropriate to share some interesting facts about protein that I discovered . I’m sure at least one will interest you!

  • Proteins can have really weird names. For example, the protein Pikachurin is a retinal protein that was named after a Pokémon character Pikachu and the protein Sonic Hedgehog was named after Sonic the Hedgehog. There is also a blue protein that is named Ranasmurfin, after the Smurfs.

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  • Protein is found in each of the trillions of cells in the human body. Life would not be possible without proteins. Water is the only other substance which is as abundant in the body. Approximately 18-20% of the body is protein by weight.

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  • In 2010, 20-year-old athlete Ben Pearson tried to increase his protein intake to boost muscle development. However, no one knew he had a rare genetic disorder that prevented his body from breaking down protein.

AthlteThe increased protein intake increased ammonia levels in his blood that caused brain swelling and death. (Read more of his story here: http://abcnews.go.com/Health/w_DietAndFitness/high-protein-diet-linked-hockey-players-death/story?id=11815908)

  • Hair is made up of a protein called keratin, which forms a helical shape. This protein has sulfur bonds, and the more sulfur links it has, the curlier a person’s hair will be. I guess my hair has A LOT of sulfur links!curly_by_jessicaxyl-d4q8gau
  • One of the smallest countries in the world, Luxembourg, is per capita the biggest meat eater. Luxembourgers eat on average about 300 pounds of meat annually per person. The U.S. comes in second with about 276 pounds of meat—mostly beef—per year. Austria is third with about 267 pounds of animal protein per person.

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  • Cow used to be the global leader in meat eaten. The pig is now the most popular.

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  • Without a protein called Albumin, the entire human body would swell.

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  • Cataracts are caused by the denaturation of proteins in the lenses of the eyes.

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  • Insects are more nutritious than many other common forms of protein. For example, 100 grams of top sirloin beef contain 29 grams of protein and 21 grams of fat. However, 100 grams of grasshopper contain 20 grams of protein and just 6 grams of fat.

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  • A protein in semen acts on the female brain to prompt ovulation.

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  • The human body has about 100,000 different types of protein. The body needs protein to grow, heal, and carry about nearly every chemical reaction in the body.

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  • Protein deficiency can cause serious health problems. For example, children with a protein deficiency could develop a condition known as Kwashiorkor. The symptoms include a protruding belly, thin hair, overall weight loss, and discolored skin and hair. Left untreated, it can lead to stunted growth, mental impairments, and death

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  • Middle- aged and elderly people have more extensive body breakdown than a younger person, which means they need more protein. However, as people enter middle age, hydrochloric acid, which helps digest protein in the stomach, drops to half its regular level. Because protein is crucial in cell regeneration, some researchers suggest that most of aging is due to this drop alone.

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  • Eating too much protein can be dangerous for the body. For example, high levels of protein can stress the livers and kidneys because they have to work extra hard to dismantle and dispose of the extra protein. Excess protein can result in weight gain.

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  • Proteins in the human body have many jobs. For example, a protein called rhodopsin in our eyes helps us see light. Hemoglobin in red cells carries oxygen from the lungs to the body’s cells and takes away their harmful waste product, carbon dioxide. A series of chemical reactions involving proteins makes the blood clot. Additionally, proteins give the body structure, help regulate body processes, defend against disease, maintain the body’s internal environment, and give us energy

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  • While human meat is a good source of high-quality protein, cannibalism was not historically motivated by diet or starvation. Rather it was a symbolic gesture, usually as a way to commune with the gods.

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Well, if you didn’t know any of these things..

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References:

Information:http://facts.randomhistory.com/protein-facts.html

Pictures:

http://www.geocaching.com/seek/cache_details.aspx?guid=284daf6f-7755-44a2-b233-8419294a66fe

http://magazine.benettiyachts.it/2010/03/the-smurfs/

http://lazearscience.blogspot.com/2007/12/food-protein.html

http://www.unchainedfitness.com/blog/how-often-should-an-athlete-train

http://jessicaxyl.deviantart.com/art/Curly-285929094

http://www.wort.lu/en/view/luxembourg-tops-world-meat-eater-ranking-4fa11824e4b00f68fa034f72

http://www.dailyspeculations.com/wordpress/?m=200901

http://www.kdweye.com/for-patients/disease-information/cataracts-and-intraoclar-lenses

http://www.livestrong.com/article/552388-how-nutritious-are-insects/

http://www.ppi-wageningen.org/edible-insects-high-nutrients/

http://www.irbbarcelona.org/index.php/en/news/irb-news/scientific/scientists-reveal-the-key-mechanisms-for-affinity-between-transient-binding-proteins

http://phenomena.nationalgeographic.com/2013/01/30/gut-microbes-kwashiorkor-malnutrition/

http://www.carnipure-for-you.com/why_is_it_difficult_for_elderly_people_to_get_sufficient_l_carnitine.html

http://blog.friendseat.com/do-you-eat-too-much-protein-infographic/

http://www.amazing-trinidad-vacations.com/cannibal-stories.html

http://publications.nigms.nih.gov/structlife/chapter1.html

http://www.justjenniferblog.com/2012/10/did-you-know-get-your-lattelove-on.html

Bombshell… “Bumshell”?

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Lactose_intolerance_by_eternalsaturn

For many years I have been the unfortunate witness to the passing of pungent gas from a person whose name I shall not call, for they might slap me silly for posting this on the World Wide Web. These occurrences usually present themselves at birthday parties, Christmas limes or just our monthly trip to an ice-cream parlour.

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When I was younger, I used to accuse this anonymous person of being lactose intolerant. I was young, I didn’t really know what this meant, I had only heard of the term occasionally in primary school when teachers would huddle around the teacher’s desk discussing their “old people” problems, you know, high blood pressure, menopause, the usual. Yes, I was a maco :D.

At the time I didn’t know all the science behind the term, only that the wind that would be passed would be quite unpleasant and accompanied by complaints about bloating and tummy aches from the anonymous. When I would make the accusations, that certain person would strongly agree with my diagnosis yet still the spoon of ice-cream and the slice of cheesecake would make no attempt to detour from her mouth. It was honestly like waiting for a volcano to erupt. Oh the joy.

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This never fails to be my reaction:

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In the last lecture, we discussed carbohydrates more in detail and along the way we talked about the science behind being lactose intolerant. I learnt a lot of new information and I plan to use it in a letter to convince the anonymous that maybe its about time that she switch to soya.

Here is how my letter will begin.

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Wish me luck!

Just had to include this, LOL!

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Don’t forget to check out my lecturer’s vid below! Super informative 🙂

References:

Information:

http://www.medicinenet.com/lactose_intolerance/article.htm

http://www.univie.ac.at/nutrigenomics/teaching/vo_integr_nutr/11_Hypolactasia.pdf

http://www.mymultiplesclerosis.co.uk/hypolactasia.html

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

Pictures:

http://eternalsaturn.deviantart.com/art/Lactose-intolerance-163763333

http://www.tumblr.com/tagged/fart%20gif

http://www.tumblr.com/tagged/who%20farted

http://www.amyoops.com/2012/09/sometimes-its-obvious.html#.URro-KVX299

http://spidergypsy.deviantart.com/art/letter-paper-VII-264405343