Showing posts with label ATP. Show all posts
Showing posts with label ATP. Show all posts

Monday, June 1, 2015

The Light Independent Reaction (and you thought we were done)

3:03 PM
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I'm actually serious. We are done. After this post, you will know the process of photosynthesis in its basics. Although, I might still write another couple, to sum it up a little more cohesively. Also if you can't learn in paragraph form, I sincerely apologize... On with the show! I should probably mention that the goal of photosynthesis is to make glucose... Yeah sorry about that.

We now move from the grana to the stroma of the chloroplast. Fun stuff. There we meet the Calvin Cycle. Not the Krebs Cycle. Don't get the two mixed up. I know I do. CALVIN CYCLE. Wonderful. Now we can move on. As we established with cellular respiration a cycle means it is continuous. This time, however, it is not oxaloacetate that we start off with, but a molecule called Ribulose Bisphosphate (RuBP). Unless unlike oxaloacetate it is a 5 carbon compound. Then in a process called carbon fixation, a CO2 molecule binds with RuBP. This reaction is catalyzed by enzyme RuBP carboxylase (Rubisco for short).

This creates a highly unstable 6 carbon molecule, which immediately splits into two 3 carbon molecules called glycerate-3 phosphate, GP (not G3P, which is glyceraldehyde 3 phosphate and what we made during glycolysis). GP is then reduced by NADPH and ATP (old friends from the light dependent reaction), which ultimately gives us a different 3 carbon molecule called TP (triose phosphate). TP now faces the most important decision of its life. To leave home (the cycle) and become a sugar phosphate (such as glucose), or follow in his father's footsteps and convert back to a RuBP molecule. Most TP molecules don't have the guts to leave the comfort of home and are thus converted back into TP with the help of ATP. And thus the cycle begins again.

Ta for now.

Sunday, May 31, 2015

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

4:00 PM
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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.

Saturday, May 30, 2015

The Link Reaction "Moving to a new world"

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 

Friday, May 29, 2015

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

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.