Explaining Dragons

Sunday, May 31, 2015

Here we go again: step 1, light dependent reaction.

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As the name implies, in this stage of photosynthesis, light is needed. Duh.

Alrighty, well this process takes place in the chloroplasts of cells. You don't have chloroplasts, just a little by the way. Unless you're a plant... In which case, I guess I was under a rock when we figured out how to communicate with plants. Welcome fellow living things.

So this process takes places in the grana of the chloroplasts, which are stacks of thylakoids. These thylakoids have electron transport chains embedded into their membranes. The system gets kicked off in photosystem II of the electron transport chain. Yes. Photosystem II. Not one. It's not a typo. Photosystem II has two chlorophyll a molecules, which are a type of pigment. They also have a primary electron acceptor. Here's where the sun comes into play. A photon of light from the sun is captured by one of the pigment molecules inside Photosystem II, it is then passed along (like a hot potato) from one pigment molecule to the next, until it reaches one of the chlorophyll a molecules. The photon then proceeds to excite the electron of chlorophyll a to a higher energy level.

Backstep. The chlorophyll molecule's electron comes from a process called photolysis. Whereby water is split (using light), this results in two hydrogen ions and one oxygen atom. The two electrons on the hydrogen ions are handed over to two chlorophyll a molecules in photosystem II. The oxygen atom waits until this process happens one more time, bonds with the resulting oxygen, and leaves as a waste product.

Back to our negative friend the electron. This excited electron is captured by what is called the primary acceptor. From there it moves down the electron transport chain, first to a plastoquinone (PQ), then a cytochrome complex, and then another PQ. As the electron moves down the chain it loses energy, this energy is then used to undergo chemiosmosis. i.e. hydrogen ions are pumped into the thylakoid space, building up a high concentration of hydrogen ions in the thylakoid. These hydrogen ions then want to get out of the thylakoid to the lower concentration, they can only do this through the ATP synthase channel. Where they pass through and the energy released by them going through there is used to phosphorylate (photophosphorylate) ADP into ATP.

The electron then enters photosystem I, and is once again excited. It is once again captured by a primary electron acceptor. This electron is once again passed along another electron transport chain, and there ferrodoxin is used as the energy carrier. The energy created by passing along this electron is now used to reduce NADP+ to NADPH. An enzyme called NADP reductase catalyzes the movement of the electron from ferrodoxin to NADP.

Essentially, the whole point of this yet another lengthy process was to end up with ATP molecules and NADPH to be used in the light independent reaction.

Science

Finally, we've made it. The electron transport chain, and chemiosmosis

Hakuna Matata 3:40 PM

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Just one more stretch. You can do it. Take a big breath. Open your mind. And grab a cup of tea (I had Lipton camomile).

So this is where the big guns are taken out, this is were 32 of the 36 ATP molecules are produced. The electron transport chain also occurs in the mitochondria, however, it doesn't occur in the matrix it takes place in the inner mitochondrial membrane and cristae membranes.

These membranes have carriers within them, which have the property of being easily reduced and oxidized. So that's kind of neat. For the sake of simplicity all of these carriers are known as cytochromes, except for CoEnzyme Q. The electrons are passed along the electron chain from one carrier to another, due to an increasing electronegativity.

The electrons that are passed down this chain are donated by our electron carriers NADH and FADH2.

FADH2 enters the electron chain at a later stage, and the does not produce as much ATP.

Each NADH molecule will produce 3 ATP molecules

Each FADH2 molecule will produce only 2 ATP molecules

As the electrons are passed along the chain they lose energy. Oxygen is the last electron acceptor, this is due to it's relatively high electron negativity. Thai oxygen molecule then bonds with two hydrogen atoms to form water.

As the electrons are passed along they release energy. This energy is used to pump hydrogen ions out of the matrix into the intermembrane space. This results in a very concentrated area of hydrogen ions in this intermembrane space.

This process involving the movement of hydrogen ions is called chemiosmosis.

These hydrogen ions then want to move from this high concentration back to into the matrix, however they can only do so through ATP synthase. The hydrogen ions passively move through this channel (facilitated diffusion). As they move through the channel the enzyme uses this energy to phosphorylate ADP to ATP. This type if phosphorylation is called oxidative phosphorylation, because it utilizes the electron transport chain.

And thus ends our journey through cellular respiration. Up next. Photosynthesis. Yup. There's more.

Science

The Krebs Cycle (it's a never ending one too)

Hakuna Matata 3:36 PM

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We've finally arrived. Well technically we were already in the matrix during the link reaction. But anyway. We're back!

As is implied by the name this is a cycle. And what does that mean? Well, it repeats itself... I'm hoping you have a pretty clear idea of what a cycle is... If not, well I can't really help you.

Alrighty then, moving around this cycle is a 4 carbon molecule called, oxaloacetate (I'll be quite surprised if that's spelled correctly...). So one of the two Acetyl CoA molecules we made during the link reaction will enter the Krebs cycle. There it will combine with an oxaloacetate molecule to form a 6 carbon compound called, citrate.

Citrate will then be oxidized and decarboxylated. The decarboxylation will create a CO2 molecule, and a resulting 5 carbon compound. The oxidation will cause the reduction of another NAD+ molecule to form NADH.

This will happen one more time, to create a 4 carbon compound, another NADH, and another carbon dioxide molecule.

The 4 carbon compound will now undergo further modification and oxidation. This will result in another NADH molecule, the reduction of coenzyme FAD to form FADH2, and the reduction of ADP to form ATP.

All these steps help us bring this 4 carbon compound back to the original oxaloacetate.

The cycle then begins again.

Also keep in mind that this cycle will run twice for every one glucose molecule, because we produce two molecules of Acetyl CoA.

So with this in mind, these are the products of the Krebs Cycle:

2 ATP molecules

6 molecules of electron carrier NADH

2 molecules of electron carrier FADH2

4 molecules of CO2

In total we have a net gain of 4 ATP molecules, out of the 36 total.

We have 10 NADH molecules (2 from glycolysis, 2 from the link reaction, and 6 from the Krebs cycle)

And finally we have 2 FADH2 molecules.

Hope this was informative. Sorry if it wasn't. Next step, the electron transport chain and chemiosmosis.

PS: You'll get the featured image if you know german :)

Saturday, May 30, 2015

Science

The Link Reaction "Moving to a new world"

Hakuna Matata 5:29 PM

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Excuse the dramatic and nonsensical title.

Now many people might neglect our friend the link reaction, but lucky for you, I am not one of those people. So yay. I guess.

Let's get started shall we? Well our two friends pyruvate now enter the mitochondria of your cell, fun stuff right? There they decarboxylated (lose a carbon), to form a 2 carbon acetyl group.

This carbon bonds with O2 to form CO2. This waste gas is released, to wreak havoc on our atmosphere. Also fun stuff. Yeah. Not really... But I digress, the acetyl group is now oxidized.

Oops, side note. Redox reactions. They are more complex than I'm about to describe them, but for now this is all you have to know. Or all I'm going to tell you. Remember these two words, OIL RIG. Got it? Good.

Oil stands for: oxidizing is losing

And rig stands for: reduction is gaining.

Now what do I mean by that? Well oxidizing is losing hydrogens and electrons and gaining oxygen, and reduction is gaining hydrogens and electrons, and you guessed it, losing oxygen. Also important to note, if something is reduced something else was oxidized. In other words, they always happen together.

Back to the link reaction. The acetyl group is oxidized forming reduced NAD+. And reduced NAD+ is NADH.

Finally the acetyl group combines with coenzyme A (CoA) to form Acetyl CoA.

Also, remember this process happens twice, because there are two pyruvate molecules produced for every one molecule of glucose.

In summary (what is produced in the link reaction)

No ATP produced

2 NADH molecules

2 Acetyl CoA

In summary (what have we produced in total thus far)

4 NADH molecules

2 ATP

2 Acetyl CoA

yeast

Aerobic vs. Anaerobic Respiration (I realize you probably don't care)

Hakuna Matata 3:07 PM

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Hello again. Back to the world of biology. Whether or not that pleases you, I don't know. Anywho. My last post introduced you to the fine-art of glycolysis. If you still don't understand it, well, reread the blogpost? Otherwise Khan Academy is pretty darn amazing.

Anyway. As I said earlier glycolysis occurs in both aneorobic and aerobic respiration. I should probably clarify that with aneorobic respiration there is no available oxygen, with aerobic respiration there is. So as we all now know, the products of glycolysis are: 2 pyruvate molecules, 4 ATP (for a net gain of 2), and 2NADH molecules.

In aerobic respiration the two pyruvate molecules and the NADH will proceed to the link reaction, then Krebs cycle, and finally the electron transport chain. I did warn you it was a complex process...

In aerobic respiration there will (in an ideal world- which isn't often the case) be a net production of 36 ATP molecules. 38 if you don't subtract the two ATPs needed to start the process during glycolysis.

However, in anaerobic respiration only 2 ATP molecules total will be produced. Nonetheless, the pyruvate molecules will be further modified, for no additional ATP. Don't ask me why. I'm sure there's a valid reason... Anyway, if you happen to be a yeast cell, which would be interesting to say the least, you will convert the 3 carbon pyruvate into ethanol. Since ethanol is a 2 carbon compound, we know that pyruvate was decarboxylated to create ethanol. All in all you produce ethanol and CO2, because of the decarboxylation. I kind of like that word.

If, by the off chance that you are not a yeast cell, but an animal of some sort, you will convert pyruvate into lactic acid (also known as lactate). This is also a 3 carbon compound, so no carbon dioxide is produced. This tends to happen if you have insufficient oxygen during a period of intense exercise. This process also occurs in the cytoplasm, and also results in a net gain of two ATP.

Hehem. Part 2, of the very long, and laborious process of cellular respiration. Also, might I add that the process I am describing is a simplified one. There's actually even more to this than I'm explaining... So yeah. Next step, the link reaction.

Friday, May 29, 2015

Science

Glucoregulation: The Basics

Hakuna Matata 9:48 PM

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Homeostasis. Here we go again. So another aspect of our blood also needs to be kept in a narrow range of conditions. Blood glucose levels. Like many things, blood glucose is regulated by your hypothalamus. Good on you hypothalamus.

Controlling blood glucose is an example of negative feedback. No it's not insulting the way the pancreas looks. Goodness, we're not in middle school. Sheesh. Okay so negative feedback is when the body has to change conditions to keep something in a narrow field. So it corrects things, it stops processes from continuing. Whereas positive feedback compliments your new scarf. Hehem. It encourages a process to continue.

High levels of blood glucose

Glucose levels cannot go higher than around 110 something or others (I can't remember test units if you can't tell...). So your hypothalamus carefully monitors this. If it senses too much glucose it signals the pancrease's beta cells to produce insulin. The insulin encourages the muscles and the liver to take up glucose. The glucose can then be used for cellular respiration. The glucose absorbed by the liver is converted in to the storage polysaccharide glycogen.

Low levels of blood glucose (sugar)

On the flip side, too low blood sugar is also undesirable. So your hypothalamus signals your pancreas again (it's a busy little fellow). This time it makes the alpha cells, in the pancreas, produce glucagon. Glucagon then stimulates the liver to break down some of its glycogen storage into glucose. This glucose can then be released into the blood stream, thus increasing blood sugar. Problem solved.

Be nice to your pancreas, it works hard. Every day. You should try it sometime. Kidding. But seriously try and do something productive, we'll all thank you.

Keep reading folks

Tea: Lipton's caffeine free Mint tea (pretty good, need to get a new box this is my last tea bag)

Science

Glycolysis (the first step in the all too laborious process of cellular respiration)

Hakuna Matata 12:28 PM

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Cellular Respiration. First things first, breathing is not cellular respiration. Drill that into your head. Please. If you start talking about lungs when referring to cellular respiration, you are wrong on so many different levels. Never ever ever think cellular respiration as breathing. If you do, mentally slap yourself in the face with a biology textbook. I hope I've made myself clear. I do believe I have.

I should probably give you a brief overview of the entire process of cellular respiration. Here you go: starts off with glycolysis, followed by the link reaction, then the Krebs Cycle, and finally the electron transport chain. Oh, please keep in mind only glycolysis will occur in a case of no oxygen.

Glycolysis reactants
1 glucose molecule
2 ATP molecules
4 ADP molecules

Glycolysis products
2 pyruvate molecules (pyruvic acid)
2 NADH (reduced NAD+ molecules)
Total ATP = 4
Net gain ATP = 2

Alrighty then. Let us begin. Glycolysis occurs in the cytoplasm of your cells. Not the mitochondria. Cytoplasm. Glycolysis occurs in all organisms, whether or not they undergo aerobic or anaerobic respiration, so that's cool.

It starts off with glucose, which is a 6 carbon molecule.
Glucose is then phosphorylated by two ATP molecules, making fructose 1,6 bisphosphate (still a 6 carbon molecule).
This is a highly unstable molecule and thus splits into two 3 carbon molecules called glyceraldehyde-3-phosphate (G3P for short).
This splitting process is called lysis.
Once all this has occurred there is an even more wordier and lengthier process whereby the two G3P molecules are oxidized, involving ATP synthesis and the reduction of NAD+ (coenzyme).
Both of the G3P molecules are oxidized forming a NADH (reduced NAD+).
The released energy of the forming of this coenzyme is used to add another phosphate to each of the G3P molecules.
Leaving us with a G3P molecule with two attached phosphates each.
Our busy friends, the enzymes, now remove all four of the phosphate groups and add them to four ADP molecules, to form ATP.
We are now left with pyruvate, whoopee.

This is only the beginning... Brace yourselves, it's going to get more complicated.

Science

Inspiration and Expiration

Hakuna Matata 8:31 AM

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Yes. Indeed this is another post about science. Human anatomy to be specific. If you don't find it interesting, well there's an easy solution. I'm sure you can work it out. In any case, if you don't want to read this, I hope to see you soon!

Now on to those who need to know this for school, or this is a controversial idea, actually find this interesting, I will try to explain inspiration and expiration.

Hint: Itty-bitty blood vessel makes another appearance. Again, if you haven't read my past article about this, let me reiterate that I actually mean capillary. Please don't call capillaries, itty-bitty blood vessels on anything of importance.

Moving on. So inspiration and expiration are absolutely vital (and I don't mean this in the hyperbolic way that this word is often used), without these two processes, you would be dead. Literally. Not figuratively. Literally. Why? Well these are the two mechanisms involved in breathing. You know the thing you do so you get oxygen? Kind of important when you think about it. Another use? Well during cellular respiration (I will cover this later) we produce CO2 (sorry I don't have a subscript key). You should know carbon dioxide is kinda toxic to your body. So it's a tad necessary to get rid of it. This is also accomplished by our friend expiration. I just noticed how similar the word friend and fiend are. I better remember my r's...

I'm sure you are all dying to know how it works at this point. *crickets*

Anyway. There are five (I believe) mechanisms that are involved in inspiration. Yes, there are also five in expiration, but patience young grasshopper. Hold your horses, etc. etc.

Numero uno. Your external intercostal muscles (located near the ribs) contract, stretching out, thus pushing out your rib cage. At the same time your diaphragm contracts. This means that it extends downwards. Finally one set of abdominal muscles also contract.

So what does all this contracting accomplish? No. It does not accomplish overpopulation. Goodness. It means the volume in your lungs has increased. And what do we know about the relationship between volume and pressure?

Come on people. Say it all together. They are inverse to each other. So as the volume in the thoracic cavity increases the pressure decreases. Good. I'm glad we've gotten this sorted.

And since pressure has decreased, well, surprise surprise, so has the pressure on the lung tissue. Gasp. Yes I know. It's true. Radical.

What happens next you ask in fascination? Well. I'll tell you. Maybe. Yes. Okay. Well, a partial vacuum is created. No not the thing you clean your floor with, trust me I've had a 20 minute conversation with someone about vacuums, all the while they thought I was talking about the household appliance, when in reality I was talking about black holes... Anywho, partial vacuum created.

Now, with this partial vacuum created, air from the outside world with flood in through your nasal passages, and/or mouth. Because, well gases moves from areas of high pressure to low pressure. And as I hope I've made clear, there is a lower pressure in the lungs.

Pfew. We're done. I think I neglected numbers after número uno. Well, I'm hoping you can figure it out... More to come soon.

Monday, May 18, 2015

the ogre

Gotham: the ogre

Hakuna Matata 9:42 PM

So I was watching Gotham the other night, and the entire time I was staring at the ogre. The actor seemed very familiar to me. I will mention now quick, that his character is despicable. And not in the cute despicable me type of despicable. The type that makes you gag a little. Or a lot.

Anyway, I was watching this character, and I could not for the life of me figure out why I recognized him. Suffice it to say my aha moment was quite fufilling. Slowly I thought to myself, Gilmore Girls. Then I thought, Dean? Then I thought, no way. Then I thought oh that other guy! I believe his name was Jess? Well. That's that. Just thought I'd share.

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Tuesday, May 5, 2015

thea queen

Arrow: recent episodes...

Hakuna Matata 5:05 PM

Well. That was unexpected. And more than a little disturbing.

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Spoilers FYI.

Honestly though, if your looking this stuff up, you must realize there will be spoilers. So in the future expect no warnings from me. Not going to happen. We are mature enough to predict the consequences of clicking on articles/blog posts about series.

So since everything is sort of muddled in my brain, forgive me if this is covering multiple episodes. Well, what are you gonna do?

First we find out Thea dies.

And then she doesn't...?

But so she didn't die, Oliver becomes Raz...

Well. I guess it was unexpected, then again it's the league of assassins. If they want someone, they get them. No matter what the cost.

So now that Oliver is in training with the league he has essential become a cold hearted animal. Pleasant. The latest episode (that I have watched) was painful to watch, to put it lightly. We see a character with dark undertones, become that very darkness itself.

I'll be interested to see where he ends up.

Sunday, May 3, 2015

thrombin

Blood clotting: Uncle Platelet and Itty-Bitty Blood Vessel

Hakuna Matata 3:06 PM

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I'm sure many of you have heard of the royal disease. Well this disease is the very absence of what I'll be talking (writing) about. When they bleed, they bleed out.

In most of the population (unless you have haemophilia) when you cut yourself, eventually your blood clots and you stop bleeding. This is quite a vital mechanism, considering how valuable our blood is. Without the process of blood clotting, you could literally die from a papercut (yes I mean literally, not figuratively).

So, how does it work? Well first you need a cut. If you bleed, that means some of the itty-bitty blood vessels (called capillaries) have been damaged. Side not: please don't call them itty-bitty blood vessels on a formal assessment. These itty-bitty blood vessels will send chemical messages, essentially shouting to your body that they have a boo-boo. Uncle platelet, will soon hear their screaming and make his way to the damaged blood vessels. Uncle platelet, is made up of fragmented cell parts produced in the blood marrow. These little cell parts with then try and create a plug to stop blood from exiting your body. Uncle platelet and itty-bitty blood vessel will then continue screamin (via chemical messages), letting your body that it still needs help. The chemical messages with cause prothrombin (protein) to break down into thrombin (enzyme). Thrombin is an enzyme for the transformation of fibrinogen to fibrin. So, as enzymes like doing, they will catalyze this reaction. Fibrin can then float on over to your boo-boo, and create a mesh. Viola, you are no longer dying from a paper-cut. Unless you have haemophilia, in which case, sorry...

Friday, May 1, 2015

marine biology

Hope is not lost

Hakuna Matata 4:24 PM

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An article about a 1.5 ton Sunfish, was recently published on the Dailymail. Some Indonesian fishermen found the animal stranded on the shore, and promptly tried to rescue it, by returning it to the see. It soon swept back in with the tide, dead.

Although this story may not have a happy ending, it gives me great hope. While reading it I couldn't help feeling the utmost respect and admiration for these fishermen. Unfortunately there aren't too many people out there, like them. But their actions mean all is not lost.