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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.

TCA-simple

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/

Villain Protein Becomes Hero!

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Growing up, I followed everything my big brother did, be it climbing mango trees or attempting to play football with my other male cousins (that did not work out well for me). I really look up to him so when he introduced me to the 1990’s  X-Men cartoon which you may or may not be familiar with, it held a special place in my heart forever. Looking back on those days of coming home from school to hear the epic theme song just brings back really fond memories. Have you ever thought of some of the X-Men heroes who actually started off as villains? I can think of a few:

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How about Gambit, who started off as a professional thief and had the ability to mentally generate, control and manipulate pure kinetic energy at his wish. He is of course an expert at card-throwing and hand-to-hand combat. He later joined the X-Men team where he met his love, Rogue.

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If you read the comics you might remember Emma Frost who changed from one of the X-Men’s most dangerous adversaries to one of its most dominant members and leaders. She was a mutant with massive telepathic ability, and also had the ability to transform into an organic diamond state which as we know, has amazing strength and toughness. This also overpowered her telepathy.

Just like these villains turned superheroes, a protein that has previously been blamed for causing cancer cells to spread around the body is now being praised for its brain repair and protection function.

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According to researchers at the University of Copenhagen mutations of a protein called S100A4 has forever been deemed a protein involved in metastasis (the spread of cancer from one organ to another). Scientists found that this protein is not typically found in our brain except when there’s shock or deterioration in the brain. However, after conducting experiments on mice where this protein was deleted, they found that the brains of the mice were not as protected and had a lesser ability to resist injury.

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So what happened?

The scientists discovered that the S100A2 worked by signaling pathways inside neurons in metastasis.

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When the protein S100A4 was deleted in the mice, it worsened the neuron loss after the brain trauma thus causing the oxidative cell damage to become greater and down regulating the neuroprotective protein metallothionein I + II. Two neurotrophic themes were identified in S100A4 which showed that they were neuroprotective in animal replicas of brain trauma. They found that S100A4 saves neurons via the Janus kinase/ STAT pathway and predominantly the inter-leukin 10 receptor. Their data introduced S100A4 as healing target in neurodegeneration, and thus the whole S100 family is currently being researched as a possibly significant aspect in central nervous system injury.

Research is being continued in the hope that they may be able to find an even better treatment for Alzheimer’s disease among other neurodegenerative diseases. Let’s keep our fingers crossed!

Article Reference: 

University of Copenhagen. 2012. “Reconsidering cancer’s bad guy.” ScienceDaily. Accessed March 24, 2013. http://www.sciencedaily.com/releases/2012/11/121116124644.htm

References:

http://www.sciencedaily.com/releases/2012/11/121116124644.htm

http://www.readcube.com/articles/10.1038/ncomms2202

http://www.sciencedirect.com/science/article/pii/S0002944010603665

http://www.beyondhollywood.com/rosamund-pike-as-emma-frost-in-x-men-first-class/

http://www.nailscars.com/2011/07/26/x-men-animated-1992-and-tv-sass/

http://www.tumblr.com/tagged/gambit

Jell-O Destroying Enzymes?! :O

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(Photo Credit:http://www.tumblr.com/tagged/jello%20gif)

I can never forget the time I ate my first bowl of jell-o. I was around 4 years old, quietly sitting in the classroom of my preschool, playing house with my favourite Barbie doll. It was snack time and my teacher brought each of us a small plastic bowl filled to the brim with a pretty, pink, wiggly and fruity smelling concoction. I had no clue what it was, but from the looks of it I knew I would like it! I took my first spoonful of the mysterious snack and I was in love! It tasted so sweet, like strawberries, and the texture was very squishy and slimy.

 jell_o_by_queen_spade-d4k1q5s

(Photo Credit: http://queen-spade.deviantart.com/art/JELL-O-275537584)

 I was so excited to go home and ask my mummy to make more of the delicious grub because I was convinced it was my new favourite snack.  She entertained my newly found obsession, so while we were preparing it in the kitchen, I became more and more fascinated with how jell-o was formed. I now know that the consistency of jell-o can be attributed to a protein called gelatin.

gelatin

I recently found an article claiming that when preparing jell-o, fresh fruits should not be used as they are unable to set the jell-o mold. This is because fresh fruits contain proteolytic enzymes also known as proteases. Proteases are a group of enzymes whose function is to break down protein. They do this by hydrolyzing the peptide bonds that connect the amino acids together in the polypeptide chain that forms proteins.

 hygel

Gelatin is derived from collagen which is a protein found in animals especially in connective tissue. When preparing jell-o, the gelatin is heated and mixed with water and the substance naturally gels. The proteases such as those found in fruits such as pineapples, peaches and pears, break down the collagen in the fruit thus preventing it from successfully gelling.

However, Mike Adams, the author of the article, suggested that canned fruits can be used instead or fresh fruits since their proteolytic enzymes have already been destroyed by heat. This makes gelling possible and your yummy jell-o can be made!

Now that I’m older, jell-o doesn’t interest as much, I’ve moved on to bigger and better deserts (Häagen-Dazs :p) but if you’re still obsessing over this delight, I must urge you to take it in small quantities as too much jell-o can negatively affect your health. Try to substitute peach jell-o with maybe a real fruit, like a real peach!

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Resist the tempatation! 😀

Article Reference:

Adams, Mike. 2012. “Weird food fact: Jell-O molds cannot be made with many fresh fruits, because they contain enzymes that eat away the gelatin”. Accessed March 19, 2013. http://www.naturalnews.com/034872_Jell-O_fresh_fruit_enzymes.html

References:

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

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

http://www.enzymeessentials.com/HTML/proteases.html

It’s….Quiz Time!!! :D

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Test your knowledge on amino acids and proteins

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1)      Which of the following amino acids is the smallest amino acid possible?

 A. Valine

B. Proline

C. Glycine

D. Leucine

E. Serine

2) Which three amino acids are essential amino acids?

A. Arginine, Leucine, Alanine

B. Histidine, Lysine, Valine

C. Cysteine, Proline, Tryptophan

D. Methionine, Phenylalanine, Asparagine

E. Serine, Isoleucine, Threonine

3)      Which test is used to test for amino acids?

A.  Benedict’s Test

B. Biuret Test

C. Iodine Test

D.  Ninhydrin Test

E.  Molisch’s Test

4)      By what process is Cystine formed as shown in the diagram?

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A. reduction

B. condensation

C. hydrolysis

D. hydration

E. oxidation

5)      What kind of bond is shown in the red circle on the diagram?

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A. covalent bond

B. disulphide bond

C. ionic bond

D. polar covalent bond

E. metallic bond

6)      What is the name of the bond highlighted in blue in the diagram?

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A. disulphide bond

B. peptide bond

C. metallic bond

D. ionic bond

E. hydrogen bond

7)      What is the name given to a molecule containing three amino acids joined by peptide bonds?

A. tripeptide

B. protein

C. polypeptide

D. dipeptide

E. peptide

8)      The primary level of structure in a protein is:

A. the regular folding of regions of the polypeptide chain.

B. the spatial arrangement of amino acids that are far apart in the linear sequence.

C. the composition and linear sequence of amino acids as joined together by peptide bonds.

D. the first level of the proteins structure

E. the alpha and beta folding of the protein structure

9)      What bonds are involved in stabilizing the tertiary structure of a protein?

A. Hydrogen bonds and covalent disulphide bonds

B. Hydrogen bonds, hydrophobic forces, electrostatic forces, covalent disulphide bonds

C.  Hydrogen bonds

D. Ionic bonds and covalent disulphide bonds

E. Hydrogen bonds, ionic bonds and electrostatic forces

10)   Name the chaotrope in the experiment below and state the role of the chaotrope.

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A. Mercaptoethanol; disrupts the hydrogen bonds in the protein structure

B. Urea; disrupts the hydrogen bonds in the protein structure

C. Mercaptoethanol; disrupts the hydrophobic interactions in the protein structure

D. Urea; disrupts the hydrophobic interaction in the protein structure

E. Mercaptoethanol; reduces the disulphide bond in the protein structure

 

Test your knowledge on Glycolysis

Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:

A. 1, 2 and 3 are correct

B. 1 and 3 are correct

C. 2 and 4 are correct

D. only 4 is correct

E. all are correct

Question 1: In the energy investment phase of glycolysis:

  1. There are 2 irreversible reactions
  2. There are 3 reversible reactions
  3. Phosphorylation of glucose occurs
  4. 4 ATP is used

Question 2: The purpose of converting pyruvate to lactate is:

  1. To regenerate ATP
  2. To regenerate ATP and NAD+
  3. To regenerate NADH
  4. To regenerate NAD+

Question 3: In the conversion of pyruvate to lactate:

  1. NADH is a cofactor
  2. The enzyme used in the reaction is lactate decarboxylase
  3. The reaction is reversible
  4. ATP is a cofactor

Question 4: In the conversion of pyruvate to Acetyl-CoA:

  1. TPP is a cofactor
  2. Lipoate is a cofactor
  3. FAD is a cofactor
  4. FADH is a cofactor

Question 5: In the energy generation phase of glycolysis:

  1. There are 2 irreversible reactions
  2. Therese are 4 reversible reactions
  3. 4 ATP used
  4. 2 NAD+ used

 

Question 6: In the payoff phase of glycolysis, which 5 enzymes catalyse the 5 reactions?

  1. Glyceraldehyde 3-phos[ate dehydrogenase
  2. Pyruvate kinase
  3. Phosphoglycerate mutase
  4. Enolase
  5. Phosphoglycerate kinase

Question 7:  Which enzyme(s) catalyses the conversion of acetaldehyde to ethanol?

  1. Pruvate decarboxylase
  2. Alcohol decarboxylase
  3. Pyruvate dehydrogenase
  4. Alcohol dehydrogenase

Question 8:  For every glucose molecule entering glycolysis:

  1. 2 ATP are used
  2. 4 NAD+ used
  3. 4 ATP generated
  4. 4 NADH generated

Question 9:  The net gain of glycolysis is:

  1. 2 ATP
  2. 4 NADH
  3. 2 NAD+
  4. 2 NADH

Question 10: The two ATP forming reactions (substrate level phosphorylation) are:

  1. Glucose>Glucose-6-phosphate
  2. Glyceraldehyde-3-phosphate> 1,3-Bisphosphoglycerate
  3. 3-phosphoglycerate> 2-phosphoglycerate
  4. Phosphoenolpyruvate> pyruvate

 

It’s a Bird, It’s a Plane, It’s Bromelain and Papain!

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a_lyrical_superhero_by_jmirman-d34pn6i

Amazing Artwork by: (http://jmirman.deviantart.com/)

I love my dog. There are no ifs, ands or buts about it. He makes me smile, cry, excited and scared at times but at the end of it all, he is one of my closest friends. How would you feel if one of your best friends was really sick? You would be worried and concerned and want to help them in any way you could right? That’s exactly how I felt when my family and I found out that my dog, Ares, had worms. Yes worms. Ew.

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Worms are one of pet owner’s worst nightmares but are also the most common health problem for dogs. How did we know he had worms? He habitually kept rubbing his butt on the ground also known as “scooting”. At first, watching him do it made me giggle a little but then I realized he wasn’t doing it for my amusement but rather he seemed to get some kind of relief from it, like he was getting rid of an itch. From that moment, there was no hesitation and straight to the vet we went.

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Ares’ favourite vet explained to us the various non-toxic worm remedies that we could use such as common herbs, ground pumpkin seeds as well as pureed carrots. But what fascinated me the most was that she suggested digestive enzymes such as bromelain and papain to take care of the problem.

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Figure 1 showing the structure of Bromelain

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Figure 2 showing the structure of Papain

In my Biochemistry class, we are learning more and more on the topic of enzymes which has always been interesting to me, especially since they are so amazingly powerful and efficient. In the lecture (http://www.youtube.com/watch?v=qcA57r2gBL8) my teacher defined enzymes as biological catalysts that speed up a chemical reaction by providing an alternative pathway with a lower activation energy.

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Bromelain and papain are proteolytic enzymes, this means that they break down proteins. Bromelain comes from pineapple while papain is derived from papaya plants. These enzymes can be taken as supplements to aid in the battle against intestinal worms as well as digestive issues. The supplemental enzymes are corrosive towards the outer coating of the worms thus making them weak and forcing their grip away from the intestines.  Once their protective outer “skin” is gone, they can then be burned by the body’s digestive juices. Yes, those parasites can turn into mush!

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Bromelain and papain are not only useful for getting rid of those intruders but they also promote muscle contractions, reduce inflammation from wounds and reduce swelling.

Once we finally gave Ares his meds, a week later he was back to his normal self again,  running, jumping biting O.O… but no more butt rubbing YAY! Once again, superheroes bromelain and papain save the day and all is well in the world of Ares.

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References:

http://www.natural-wonder-pets.com/non-toxic-worm-remedies.html

http://rhrplus.com/b2evolution/blogs/index.php/Articles/enzymes-help-to-kill-worms-part-3

http://www.livestrong.com/article/293141-the-effects-of-bromelain-on-parasites/

http://www.wisegeek.com/what-is-the-connection-between-bromelain-and-papain.htm

http://shaeward.tripod.com/parasite_prevent.html

http://www.cesarsway.com/heartworm-awareness/Symptoms-of-Worms-in-Dogs

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

http://jmirman.deviantart.com/art/A-Lyrical-Superhero-189313434