Tag Archives: proteins

Protein Symphony!

Standard

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.

RTpic

Rie Takahashi

JHMpic

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.

protein music2

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

Advertisements

Villain Protein Becomes Hero!

Standard

 xmen_animated-1024x798

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:

 tumblr_mi7rrw3a3V1rsltyyo1_1280

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.

emma-frost-pike

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.

 250px-Protein_S100A4_PDB_1m31

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.

 download

So what happened?

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

1-s2.0-S0002944010603665-gr1

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

It’s….Quiz Time!!! :D

Standard

Test your knowledge on amino acids and proteins

504244577_a5c1dc6d8b_o

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?

 pic4

A. reduction

B. condensation

C. hydrolysis

D. hydration

E. oxidation

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

pic3

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?

pic2

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.

 pic1

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