Theme Change

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Bleh, so wordpress says my old theme ‘ Rounded’ has retired
😦 so i had to change themes…
and everything looks so messy now. So to everyone, I apologize for the unkempt nature of my old posts since they were made to complement my old.
With a new theme comes a different arrangement.
🙂 I hope the info is still helpful.

 

I should be posting again soon,worry not.

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Tricarboxylic Acid Cycle by ~shonohime on deviantART

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As we mosey on along the yellow brick road of cellular respiration , let’s look back at how this stuff goes, shall we?

Cellular respiration

  • in our former post we saw the mechanics of GLYCOLYSIS where glucose was broken down to  2 molecules of 3-C pyruvate
  • pyruvate may befall 3 possible fates, depending on  AEROBIC or ANAEROBIC reactions.

Under AEROBIC conditions ( in the presence of oxygen ) , pyruvate is converted to a 2-C molecule : Acetyl Co-A.

This is know as the LINK REACTION …you know..because it link glycolysis to the Kreb’s cycle.. 🙂 very original naming 

The Link reaction is an  oxidation reaction 

where NAD+ gains a hydrogen to give NADH 

    • 2 NADH’s are generated (1 per pyruvate)
    • 2 CO2 are released (1 per pyruvate)
    • ******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************

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yay motivational flower…..

Acetyl Co-A is swept of into the Kreb’s cycle to continue cellular respiration.

Who knew producing energy is so much work :/ .
Alas, we have quite a bit to go yet.

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Tricarboxylic Acid Cycle by ~shonohime on deviantART.

Unfortunately, I cannot give a better view of the TCA cycle shown by the link but once you follow it it’s extremely fulfilling.
Lamentably I did not find this a month ago for my blog assignment, but I’ll share it now for the rest to see 🙂
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A little trip into the Kreb’s Cycle

The Acetyl Co-A produc in the link reaction now takes a Dosey Doe in the Kreb’s cycle ( you’ll also hear the names : Citric acid cycle, or tricitric acid cycle)

These brain scrambling reactions never end do they? =/

Climb on the Magic School Bus

 *****************************the***********************************************The **

Indeed it does look pretty confusing, but a few times reviewing it and it becomes  a piee of cake =).
Luckily, thanks to my friend , Inked Biochemist unearthing a great aide in studying the TCA cycle while prepping for our year 1 finals 🙂

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An interactive tutorial to the citric acid  cycle.

A Special Project for Pharmaceutical Chemistry 127 by Shonohime .

  • The tutorial offers details into the pathway :
    -enzymes which facilitate reach reaction
    -pointing out major co factors and inhibitors at each step allowing for understanding little at a time 🙂 accommodation
  • It also gives a wrap up of the products of this TCA cycle – very important to know in learning it.
  • The little notes at each reaction are quite helpful
  • there’s also a little surprise in there 😉

tca

  • the REGULATION  and RELATED DISEASES tabs also offer insightful information involving the TCA cycle
  • such as a deficiency of pyruvate dehydrogenase  a key enzyme forming Acteyl Co-A from pyruvate, furthering the glycolysis process and much more, also the effect of arsenic poisoning and how detrimental it can be to the TCA cycle and thus our bodies*******************************************************************************************************************************************************************************************************************************************************
  • Net Product of Citric Acid cycle :
    • 6 NADH’s are generated (3 per Acetyl CoA that enters)
    • 2 FADH2 is generated (1 per Acetyl CoA that enters)
    • 2 ATP are generated (1 per Acetyl CoA that enters)
    • 4 CO2‘s are released (2 per Acetyl CoA that enters)

    ************************************************************************************************************************************************************************************************************************************************************

In my view, the presentation was very well done 🙂 great work put into it and a very helpful studying tool.
Butttt, don’t click those shoes together just yet! We aren’t quite finished with cellular respiration. Next stop:  Electron Transport Chain !

Finals!!! (╯°□°)╯︵ ┻━┻)

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So finals are upon us university students. Gaining hard and fast on our heels and we’re scrambling helplessly to cram in those last few notes :/…
So all us students have been doing is studying… ♪♪all day…all night♪♪
Though, to be honest, biochemistry is actually one of the least of my worries for the exam, for 2 reasons :

  1. I’ve kept at studying Biochem all through the semester so i have most ( not all) of the stuff already in my pocket (assisted by this blog as well)
  2. It’s an entire week after all my other course exams ..lol 
    Of course all this preparation is largely owing to our lectuer,Jason Matthew, with his innovative methods for teaching us. 🙂 We highly likely couldn’t do it without him ( heh…the past few years would be testament to that). So credit to where it’s due.

There are a few topics I skipped out in posting but I’ll come back to those later or revisit the old topics while I’m reviewing my own work.
So that’s part of the reason the biochem posts have been on a low for a while :/…
BUT! in the spirit of avid studying, I shall share with you my faithful companion through the hours of arduous toil.
  Carpe Diem by lamusette

🙂 some of the best soundtracks to get you through your work without distracting you.

Good Luck everyone!

yoda

How Mircoorganisms Move

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so this may not necessarily be biochemistry, probably more cell biology really, but i found on tumblr, and looked fun to share 😀

 The Science Parody to How Animals Eat Their Food

Pretty cool tumblr blog where i found it : http://scinerds.tumblr.com/post/48543552850/comaniddy-how-microorganisms-move-this-weeks

vid can be found here : 🙂  http://www.youtube.com/watch?v=IboPemprk7A&feature=youtu.be

Amino acids – Legos of life

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From basic Biology we know the general structure of amino acids :

And that amino acids vary on  the single point of the R group. So, they go from  ^ , to:

Quite an array of amino acids exist, and only 10 of them are deemed essential amino acids ( amino acids which the body cannot synthesize and is required from diet).

All amino acids are important to life since they are the building blocks proteins and this life, but 3 of these bad boys are ‘special cases’ or so to say which stand out from all the rest :

amino acids special cases

  • CYSTEINE unlike other amino acids contain a sulfhydryl group ( -SH-) and thus forms disulphide bonds with other cysteine molecules. Disulphide bonds are the strongest of interactions found in proteins/amino acids, however they are woefully infrequent thus are not a main contributing force to protein structure.

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  • GLYCINE glycine is known for being the smallest amino acid,having an R-group of a single Hydrogen . 
    Being such a small amino acid, glycine has a tendency to be a bit…loose…so to say. That is, it moves around a lot, having a high conformational flexibity
  • Basically…like this >>>  and .
    Clearly because of that, in structure which require stability and rigity, glycine is most unwelcome, for example in the collagen α-helix,  since it will destabilize the helix.
    ****************************************************************************************************************
  • Therefore, glycine is cast out of the alpha group into the Outlands ( the end of the helix) where it function to regulate the turn of the helix   and terminate it.
  • Further more, glycine is the only amino acids which does not display optical activity.
    Recall, for a molecule to have a optical isomer, it must be chiral, and glycine here, has  2 hydrogen groups, not all 4 substituents are different. ********************************************************************************************************************************************************************************************************************************
  • PROLINE–  yet another one of the oddities of the amino acids since its R group is cyclic,  and therefore quite rigid. rotation about the N-C bond is not posssible
  •  thus forms a kink in the helix…not good, messy stuff.

    Proline

    Therefore it’s less welcomed in the helix.

  • Also, with the lack of hydrogen atoms on the N-atom, proline cannot readily form patterns of hydrogen bonding required in the alpha helix to achieve maximum stability.
  • ****************************************************************************************************************Alas, proline is often found at the end of the chain where it functions to alter the direction of the polypeptide chain and terminate the helix.

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I suppose in a sense cystine, glycine and proline can be viewed as the misfits of amino acids. Doesn’t mean they’re any less important !!

  • …not that kind…

Delving into Vortex The of Science News

When we look into the evolution of the Earth like in the earlier posts ‘Back to the Future of Cells‘ with postulations of the Primordial Soup Theory  we saw how the little biomolecules were key in birthing new life, and slowly…oh slowly and gradually evolution after painstaking evolution Earth and life on planet Earth has come to be as it is now.

Earth has thus far been deemed the sole planet for fully supporting life yet the search throughout the Universe continues. While finding amino acids in the Universe proves to be a trying task, recent discovery by West Virgina’s Green Bank Telescope has identified two precursor molecules, cyanomethanimin and ethanamine.

These two molecules are precursors to nucleobase and amino acid, adenine and alanine respectively earmarking prospective biomolecules integral to life, particularly DNA, and will continue to form more complex molecules by interaction with interstellar clouds. As a consequence, they may give rise to life as the Earth began with many billion years ago.

These little bites were found in dense interstellar clouds in the Milky Way’s core which has been  the prime region for the hunt for new molecules known as Sagittarius B2( Sgr B2). 

A few years back researchers came upon  glycoaldehyde, the simplest sugar, in a solar type young star and ethyl formate in Srg B2.
These were also accompanied by  DNA nucleobase adenine in meterorites and various other molecules scattered across the Universe in earlier years lay foundation of life beyond Earth .These discoveries stoke the curiosity to burrow deeper into space in search for answers in aspiration of understanding the Birth of Earth, other planets and the perspective for further life than on planet Earth which may unfurl in many years to come.

Who knows what else we can discover….

http://news.discovery.com/space/astronomy/icy-clues-for-lifes-origins-130307.htm#mkcpgn=rssnws1
http://news.discovery.com/space/alien-life-exoplanets/top-10-places-to-find-alien-life-130130.htm

 

Allons-y

Or who will take us there?

Galactic Core of Milky Way

Glycoysis MCQ

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Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:
A. (i), (ii)and (iii) are correct
B. (i) and (iii) are correct
C. (ii) and (iv) are correct
D. only (iv) is correct
E. all are correct

  1. Which of the following  lists enzymes all facilitate the removal or addition of phosphate groups?
    (i)phosphoglycerate kinase, enolase, glycerate-3-phosphate dehydrogenase
    (ii)aldolase, enolase, triose phosphate isomerase
    (iii) phosphofructokinase-1,triose phosphate isomerase, phosphoglycerate mutase
    (iv)phosphofructosekinase -1, pyruvate kinase, phosphoglycerate kinase

2.In which reaction is ATP used up?
(i) fructose -6- phosphate ——> fructose -6-bisphosphate
(ii)Phosphoenol pyruvate ——->pyruvate
(iii)glucose ——> glucose -6-phosphate
(iv)  dihydroxyacetone phosphate—–> glyceraldehyde -3-phosphate

3 Which reaction of glycolysis are irreversible reactions?
(i) fructose -6- phosphate ——> fructose -6-bisphosphate
(ii)phosphoenol pyruvate ——>pyruvate
(iii) glucose —-> glucose – 6- phosphate
(iv) dihydroxyacetone phosphate—–> glyceraldehyde -3-phosphate

4. For every glucose molecule metabolised, how many molecules  of dihydroxyaceton  phosphate is produced in glycolysis
(i)2
(ii)4
(iii) 0
(iv) 1

5.phase2_01

In the reaction above, what do A,B ,C and D  represent?

(i)( A) ATP ;( B)-  ADP
(ii)( A) NAD+ & Pi; (B) NADH & H+
(iii) (C) NADH2 + Pi   ;  (D) NADH
(iv) (C) ADP   ;   (D) ATP

Glycolysis : glucose munching

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Picking up from where Cindy introduced us( she’s got other things to do..running glycolysis is a lot of work), I’ll pick up from here 🙂

Glycolysis is the kickstart of cellular respiration 

  • Glycolysis is a metabolic pathway  which breaks down glucose ( this is where the carbs come in ) into pyruvate

  • The following video takes you through this process, step by step.

  • Yea, admittedly, it’s a bit mind boggling at first but This video would be one of my favorites 🙂
  • it’s probably because of how  neatly and simply he takes you through a complex process of glycolysis.
  • The aid of molecular structure helps us to see just what happens at each step: Where a phosphate may be taken away, or the splitting of a molecule.
  • The video publisher also makes key mention of the products of glycolysis ( that’s key info..pay attention to that ) , as well as the enzymes for each reaction, yet another necessity.
  • Not much further details were explained in the presentation but it indeed got the message across, emphasizing :
  1. The key steps where ATP is involved
  2. the enzymes for each reaction, denoted in their individual clouds on the right-hand-side.
  3. segmenting the process into the :investment phase and the payoff phase to make it simpler for understanding.

GLYCOLYSIS may be further explained in the following images,take apart and each step explained :

  • Quite a handful to take in huh?   For me, i had to draw this over …and over…and over  to get it fully stuck in my head. It  did work though 😀
  • use of the molecular structures help a lot, you may not necessarily have to remember them but it help in  understanding just what you’re doing 🙂

a few things that a good to know about what goes on in glycolysis:

  • HEXOKINASE the first enzyme in the glycolysis pathway, and like all other ‘-kinases’ it involves the removal or addition of a
    The glycolytic reaction catalyzed by hexokinase

    phosphate group. In this case, this guy uses ATP to add an phosphate group onto glucose,
    giving glucose-6-phosphate.

  • fun little ditty:  the addition of phosphate group onto glucose renders the molecule phosphorylated  to a negatively charged G3P which is unable to pass through the hydrophobic cell membrane, so this is glycolysis’ way of keeping glucose trapped in the pathway. Do or die O_O
    **************************************************************************************
  • ******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
  • PHOSPHOFRUCTOKINASE- 1 glycolytic enzyme which catalyses the irreversible reaction of
    fructose-6-phosphate + ATP  fructose-1,6-bisphosphate + ADP
    PFK is the key regulatory enzyme for glycolysis. When ATP levels are high in the cell, the cell no longer needs metabolic energy production to occur. In such an instance, PFK’s activity is inhibited by allosteric regulation by ATP itself, closing the valve on the flow of carbohydrates through glycolysis.
  • This allows it to act as  a modulator by lowering the affinity of PFK for its other substrate, fructose-6-phosphate for the time being.

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 And to polish it all off, how about a fun game to test your knowledge in Glycolysis.

The game isnt mine, it’s a Wiley Production, but fun and great for learning all the same
🙂
see the below link

http://www.wiley.com/college/boyer/0470003790/animations/glycolysis/glycolysis.htm
a snapshot to the game :
glycolysis game
The site carries a great number of games and quizzes of the biochemistry topics 🙂 I strongly you suggest you try them out.
Afterall, they are the people who make some of your textbooks 😛

Click on the name of the enzyme to select then click on the space you want to assign it to to answer 🙂

http://www.wiley.com/college/boyer/0470003790/animations/animations.htm

Cellular Respiration

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In our few posts back we reviewed Carbohydrates  known for being a large part of our diet.
But..just how does these carbohydrates fuel our living. why are they so important as food?
Annndd that’s where this fella comes in : CELLULAR RESPIRATION
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The wee comic below slightly brushes on what happens to our food and what it does for us ie. how it gives us energy
to live.
cellular respiration
cell res

Might seem a bit farfetched ( I mean ….that woman is eating cake….yet she’s got stick legs :/ )

now but we’ll soon delve into it. Nitpicking and figuring out the schematics of all this. 🙂

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As our lovely comic people mention, Cellular respiration begins with :

  1. GLYCOLYSIS

a process which we’ll see in our later post. We’ll now let our host, Cindy, introduce you 🙂