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Alrighty, round two of sugar metabolism: the Citric Acid Cycle, also known as the Krebs Cycle or the Tricarboxilic Acid Cycle.  Just like my previous post, we’ll run through the cycle stepwise, indicating enzymes and reversibility as well as any other notable information.  Lets get crackin’!

The TCA Cycle: An Overview!

Its a lovely circle!

Big sucker, yeah?Step 0: First, before the cycle can begin, we must take pyruvate (from the results of our glycolysis) and transform it into acetyl-CoA in order for the cycle to legitimately begin.  To do so, pyruvate dehydrogenase takes CoASH and NAD+ (with the help of the coenzyme TTP) and binds CoASH as acetyl-CoA, while giving off NADH and H+. (The NAD+ is used as a cofactor to return the enzyme to its original state) Now we can begin the TCA cycle.

Citrate Synthase in action!Step 1: Acetyl-CoA is added to oxaloactetate to make citrate, which adds a carbon to the chain, making it 5 carbons (instead of oxaloacetate’s 4), as well as transforming several of the groups on the carbons.  I will not go into detail here to spare you all the pain, but instead provided an image of the transformation. CoAsH is removed. This is irreversible.

Step 2: Citrate is then transformed into isocitrate by moving the OH group on C3 to C4.  Aconitase catalyzes the reaction and it is reversible.

Step 3: Isocitrate then has the newly moved OH group dehydrogenated to a carbonyl group, as well as has the COO- group from C3 removed entirely (with two H’s added in its place).  This compound is called a-ketoglutarate and it is catalyzed via isocitrate dehydrogenase.  The reaction is not reversible as NAD+ is reduced to NADH and CO2 is formed.

Step 4: A-ketoglutarate then has CoASH added yet again, this time to replace the COO group at C5 to form an SCoA group (Succinyl CoA the whole compound is called).  A-ketoglutarate dehydrogenase catalyzes the reaction, which is irreversible.  It takes NAD+ and CoASH and releases NADH and CO2.

Step 5: Succinyl CoA then passes through Succinyl CoA synthase, which removes the CoA group, while adding an O(H) group to the C4 carbon, making Succinate.  GDP and Pi are used, while GTP and CoASH are products.  This reaction is reversible (hence the misleading name “Succinyl CoA synthase”!)

Step 6: Succinate is then dehydrogenated via succinate dehydrogenase (duh) to form fumarate.  H2 is eliminated (one from C2 and one from C3) to form a double bond between the two carbons.  The H2 (and its subsequent electrons) are transfered to Q to make Q2(in the ETC) or FAD to FADH2. This enzyme is the only membrane bound enzyme in the cycle and is also known as Complex II of the electron transport chain and the reaction is reversible.

Step 7: Fumarate is then hydrated into malate. The double bond formed in the last step then gains an OH group and a hydrogen (C2 gets OH C3 gets H, though it doesn’t matter, since the molecule is not chiral and either addition would produce the same product.)  Fumarase catalyzes the reaction and water is consumed; the reaction is reversible.

Cute lil fellaStep 8: Malate is then dehydrogenated such that the OH group becomes a =O group, while NAD+ is reduced to NADH and H+ via malate dehydrogenase.  Oxaloacetate is formed and thus the circle is complete.  The reaction is reversible.

Overall, the TCA cycle produces 4 NADH, 1 FADH2 (or QH2) and 1 GTP.  If we take into account that two pyruvates are formed via glycolysis, the total comes to 8 NADH, 2 FADH2 and 2 GTP.  Granted, this isn’t alot of energy, but the payoff from both of these cycles comes as we enter the electron transport chain, our next topic.

Stay tuned, as this study session crams forward!

The Alchemist Kitten


Hey you masses of scientists!  Today, since I feel rather prepared for my biochemistry exam tomorrow, I felt like reviewing what I learned with you all.  This post (and the *hopefully* two subsequent) will overview the topics of my exam and help both myself and you!  Ah, what a symbiotic relationship we have!  Anyways, lets get down to buisness.

Glycolysis–The cycle in overview!

In Overview.

Ahhh, sugar. <3Step 1: Phosphate (-OPO3-2 in our case) is added onto the sixth carbon of glucose to form Glucose-6-Phosphate.  This reaction occurs via the O- (formerly OH) group of C6’s nucleophilic attack on ATP’s third phosphoryll group.  Hexokinase aids the reaction (via a Lys group) and thusly ADP and H+ (from the -OH group) are formed as products.

**Gluconeogenesis–glucose-6-phosphatase catalyzes the reverse reaction, since this step is IRREVERSIBLE**

Step 2: Glucose-6-Phosphate is then isomerized to fructose-6-phosphate.  Via two His groups from phosphoglucose isomerase, the 6 membered ring of G6P is opened up and then reclosed as a 5 membered fructose ring; the phosphate group remains unchanged.  This reaction is reversible (and works backwards for gluconeogenesis).

Step 3: Fructose-6-phosphate picks up another phosphate group via the same mechanism as step 1.  The C1 carbon of F6P then picks up a phosphate group via nucleophilic attack on ATP.  Phosphofructokinase catalyzes the reaction to form Fructose 1,6 bisphosphate.  ADP and H+ are released as side products.

**Gluconeogenesis–The reverse is catalyzed by fructose bisphosphate since this reaction is IRREVERSIBLE!**

Note the action center in the center of the enzyme.Step 4: Fructose 1,6 bisphosphate is then cleaved at the third carbon to produce D-glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Fructose bisphosphate aldolase catalyzes the reaction.  It leaves two, three carbon chains–one aldehyde and one keytone.  The reaction is reversible.

Step 5: The keytone (C1) in Dihydroxyacetone phosphate is reduced to an alcohol, while the alcohol (C2) is oxidized into a keytone, thusly making a second glyceraldehyde-3-phosphate.  Triosephosphate isomerase catalyzes the reaction and it is reversible.

Step 6: (From here on out, there are two equivalents of each molecule *i.e. G3P). The two glyceraldehyde-3-phosphates then pick up a second phosphate group (from Pi, not ATP) onto C3.  The aldehyde (=O) is moved to C1 and the OH on C2 becomes out instead of in (to the page).  This forms 1,3-bisphosphoglycerate and is catalyzed by glyceraldehyde phosphate dehydrogenase (GAPDH).  NAD+ is reduced to NADH and H+.  This reaction is reversible.

Step 7: 1,3 Bisphosphoglycerate then has its C1 phosphate group removed leaving just the oxygen (O-).  3-phosphoglycerate is formed as is ATP via the catalyst phosphoglycerate kinase.  This reaction is reversible.

Step 8: 3-phosphoglycerate then has its C3 phosphate group moved to C2, forming 2-phosphoglycerate.  Phosphoglycerate mutase is the catalyst and the reaction is reversible.

Step 9: 2-phosphoglycerate is then dehydrogenated at the C3 carbon to form a double bond between C3 and C2, forming phosphoenolpyruvate. The OH group on C3 is removed and pulls a proton off of C2 in the process, forming the double bond.  Enolase catalyzes the reaction, which is reversible.  Water is formed.

Pyruvate with its Na ion, balancing the negative charge on O.Step 10: Phosphoenolpyruvate then has its phosphate group (C2) removed to form ATP via pyruvate kinase. This leaves a keytone group on C2 while fully hydrogenating C3 (methyl group) called Pyruvate. ADP and H+ are consumed, while ATP is produced.

**Gluconeogenesis–this step is catalyzed via two enzymes, pyruvate carboxylase and phosphoenolpyruvase.  Pyruvate carboxylase turns pyruvate to oxaloacetate which is then transformed into phosphoenolpyruvate by phosphoenolpyruvase.  This reaction, obviously, is IRREVERSIBLE!**

The net gain of glycolysis is 2 ATP (4ATP were formed but 2 were consumed initially) and 2 NADH.

That’s glycolysis in a nutshell.  Hopefully, the step wise explanation of the reactions (minus mechanisms, sorry!) will aid you all in your studies of biochemistry.  NOW! On to the Citric Acid Cycle!


The Alchemist Kitten

I feel that I must write an entry on Star Trek—it is an obligation that my geeky innards require me to speak on.  It is hardly a secret that I am a huge gamer and sci-fi nerd, so I suppose it is almost my specialty to speak on sci-fi and fantasy in general.

Not exactly a god, but its got a damn computer that talks to you!The one particular thing I found interesting in my travels through the universe was that of the “god-like” figures that appear frequently in Star Trek.  Having watched every movie, seen part of the original tv series, most of The Next Generation, all of Voyager and a majority of Enterprise, I must say that these god-like figures can be found in every which direction and in every shape and size.  Each and every one of them is inherently flawed in some way.

For example, the Caretaker, a god-like entity who is the catalyst for the entire plot of Voyager, finds himself at the end of his life.  Granted, it is implied that his life has lasted millennia and shouldn’t be ending, he is, nevertheless, dying.  The reason?  His “life” partner had left him in some sort of relationship-trauma huff and never returned.  Unable to return to his home and unable to continue living, the Caretaker has been searching the galaxy for a means of power to keep his subjects alive.  Oh yes, did I mention that he created a race, placed them on the planet, and provided for their every whim?  Now that he is dying, the Caretaker belatedly realizes that his little race will soon die after him, since he had been their only source of sustenance.

Flawed?  Totally.  Almost human?  Yep.  Are the writers of Star Trek attempting to make an underhanded comment?  Oh yeah.

What?  I have no idea.

Whether they are just reinforcing the idea that the God on earth is supreme or making a comment on evangelist Christianity is beyond me.  What is apparent is that flawed god-like figures has become a staple in Star Trek lore.

Another interesting point, while on the topic of flawed gods, is that of the deities in the popular role-playing game Dungeons and Dragons.  Each and every one, like the Greek or Roman pantheon, has a specific realm of worshipers and jurisdiction.  They also have their stories about how they rose to god-hood.  Some fell through the depths of hell and emerged the glorious victor.  Others corrupted nations and defeated lich empires to steal the throne.  Each have their own story of failures and triumphs.

In fact, that’s the whole point of the “game” called D&D!  You, as a player, must conquer your enemies and your own personal issues in order to rise above and become whatever you (or your alignment, at least) are destined to be come.  A very fine example comes from the last campaign that I played with the guys.  In order to flesh out our DM’s homespun setting, we aspired to play fully in the “asian” empire, whose name I cannot spell for the life of me at the moment.  The entire game started out with the emperor slain at the feet of a once player character, Malek.  We then found ourselves running from the rather corrupt law and joining forces with the once-Shogun to take back what was our country.

After many battles and negotiations with other nations, we defeat Malek and his minions and take back the country that rightfully belongs to the people.  Kero Kuma, our silently designated leader, was then vocally promoted to the position of Emperor, after proving his worth as an apt and competent “Commander In Chief”.  It was perfect for a character that rose from nothing and became one of the most powerful men in the nation.

From what I've been told, this is how one of the guy's character became a saint.  Single handedly defeating a dragon.As it turns out, most of the deities in the current D&D pantheon weren’t even gods to begin with, but were raised to the title after their death (Even though Kuma-sama may never reach god-hood, we have several past player characters who have at least achieved sainthood.  My own character, Rosalynd, is quite on her way to being a god.  It all depends on who you become when you don the dice.).  Hence, one must redefine what they consider god/god-like.  If our flawed gods in Star Trek were placed in the D&D realms, would they have been given deity-hood?  I have to wonder.

My apologies for the rambling rant, I just wanted to examine the differences in god-like figures while waiting for my electrophoresis DNA run to be done.  And it is!


The Alchemist Kitten

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