Unit 2 : Organotrophy Flashcards
What is the general formula for aerobic respiration? What type of reaction is it?
What little reactions is it made up of? What do these reactions do with the energy of glucose?
The general formula for aerobic respiration:
C6H12O6 —> 6CO2 + 6H2O + Energy
This is a combustion reaction, and therefore is exothermic and exergonic.
This combustion reaction is made of a series of coupled REDOX reactions that release the free energy of glucose so that it can be utilized in ways that are actually beneficial to the plant. The molecules it transfers to include: ATP, NADH, CO2, H2O, and heat. The latter 3 increase the total entropy of the universe (which is why it is exergonic).
What types of bonds in the reactants are broken? What types of bonds in the products are formed?
How do bonding electrons move from carbon atoms and oxygen atoms during this process, and how does this lead to REDOX? (Which molecules in the overall reaction are being reduced and oxidized?)
How is the production of CO2 important to the breakdown of glucose?
Non-polar covalent bonds are broken in the products (O=O, C-C, C-H), which all have their electrons equally shared between the molecules. Therefore those electrons are at high potential energy because they want to go towards the positive nuclei of each but cannot. So allowing them to do this should be exergonic. But activation energy is still needed to break these stable bonds in the first place.
In the products, polar-covalent bonds are formed, where electrons are not shared equally between atoms, and therefore they are at lower potential energy since they are allowed to be close to the positive nucleus, and hence Coulomb’s law indicates that they have a stronger force of attraction. So moving to this state should release energy.
Overall, carbon bonds go from C=C and C-H to C-O and O-H. The conversion for carbon leads to electrons moving away from it, as they move towards the more electronegative atom of oxygen. This causes carbon to be oxidized (lose electrons). At the same time, the addition of electrons closer to oxygen reduces oxygen. Therefore, from glucose to carbon dioxide (only places where carbon is), oxidation occurs. However, from oxygen to water, reduction occurs. This leads to a REDOX reaction overall.
Overall, as glucose is oxidized, it is losing potential energy of the electrons. When CO2 is released, this is the lowest energy form of carbon, and therefore is of no use to the cell. This means that the energy was released in other ways and added to NADH, starting the process of ATP reduction (turning that energy into a form that the cell can actually use).
What do these REDOX reactions generate? Where is that product that is generated stored?
REDOX reactions generate reduction potential, because electrons are released and these can be used to reduce and add energy to other molecules. Of course the net reaction does not generate reduction potential (because it has to be both oxidized and reduced so the number of electrons on each side are the same, but the individual reactions that lead to this net reaction DO generate reduction potential! That is how we generate ATP in the first place!
Where is this reduction potential stored? In electron carriers called NAD+, NADP+, and FADH, which are reduced to NADH, NADPH, and FADH2 when electrons (and hydrogen atoms) are added. This allows many oxidation reactions to occur within the cell over and over again, breaking down the high energy glucose molecules and releasing their energy to these carriers so they can do work to make ATP.
Give an overview of Chemoorganotrophy (the general pathway) and what the word means:
What happens when in low oxygen environments?
Chemoorganotrophy: When organisms eat organic molecules that have already been fixed by other organisms to produce the energy they need. These molecules have high potential energy, but not in a form that can be used.
Overview:
In high oxygen environments:
Glucose (or any hydrocarbon —> reduction potential by glycolysis)—> Pyruvate (—> reduction potential)—> Acetyl CoA (—> reduction potential) —> Krebs cycle (—> Reduction potential) —> Oxidative phosphorylation —> production of ATP using ATP synthase.
MAKES A LOT OF ATP! (around 32-36?)
In low oxygen environments:
Fermentation:
Glucose (—> reduction potential by glycolysis because gives electrons to NADH, and produces net 2ATP)—> Pyruvate —> Pyruvate reduction (NADH produced in earlier step gives electrons to Pyruvate and reduce it to byproduct (lactic acid in humans and most eukaryotes), which then restores NAD+ to do the glycolysis cycle all over again — and produce little ATP.
MAKES LITTLE ATP (2 NET).
Anaerobic respiration:
Glucose (—> reduction potential by glycolysis) —> pyruvate
—> acetyl-CoA (—> reduction potential) —> Krebs cycle (—> reduction potential) —> oxidative phosphorylation using an inorganic molecule as final electron acceptor (not O2) —> production of ATP through ATP synthase.
MAKES A LOT OF ATP! (around 32-36?)
Glycolysis overview:
Where does glycolysis occur? Why does this show that LUCA must have been able to carry out Glycolysis?
How many reactions are connected to do glycolysis? What does each reaction require? It is the partial ________ of ____________.
Glycolysis occurs in the cytosol (NOT IN THE MITOCHONDRIA), which highlights that this process can occur in prokaryotes which do not have membrane bound organelles. Because LUCA was a prokaryote, that means that it would have had glycolysis too.
There are 10 connected reactions, 5 of which require energy, and 5 of which produce energy. Overall, the process is exergonic as it releases a net of 2 ATP.
Each reaction requires a unique enzyme.
It is the partial oxidation of glucose, because the whole point of cellular respiration is to completely oxidize glucose so that all the energy present in its high Ep bonds can be utilized to produce energy that the cell can use to carry out its processes. This is just the first step in doing this.
Describe the process of glycolysis in a simplified manner. What are the net inputs and outputs, what is the net reaction, and what is the net energy change?
- Glycolysis starts with glucose, and then has two ATP molecules react with it to add a phosphate group to either end of the carbon chain. This makes the chain extremely unstable, so that it is willing to react.
- It then instantaneously splits into two 3 carbon molecules, each with an unstable phosphate still attached. These molecules are now called G3P.
- Each G3P is then oxidized by NAD+, (turning into NADH), and at the same time an inorganic phosphate is added.
This happens on each molecule, making them both have 2 phosphates attached each. - Because it is so unstable, one phosphate is released and added to ADP to form ATP from each molecule. This then leaves on phosphate, which will be removed after, forming ATP from ADP and the Pi, which produces another 2 ATP. This results in a net production of 4 ATP OVERALL!!
- The 3 carbon molecule that is left is pyruvate, which has produced some reducing power and ATP in its formation, but still has a lot of potential energy inside of it to be harvested.
Net reactants: Glucose + 2 ADP and 2 Pi + NAD+
Net Products: 2ATP + 2NADH + 2 Pyruvate
NET ENERGY CHANGE = 2 ATP!
Overall just simple statements of what goes in and what comes out for glycolysis:
Net equation of electrons and hydrogens gained for NAD+:
Glucose comes in, 4 ADP and Pi’s go in, and 4 ATP come out. 2ATP go in, and 2 ADP and Pi’s come out. This results in a net of 2 ATP. 2 NAD+ come in and take from G3P, 2 NADH are formed (1 for each 3 carbon molecule). This then results in 2 pyruvate overall.
2NAD+ + 4e- + 4H+ —> 2NADH + 2H+
-so 2 electrons and one hydrogen go to each electron carrier, and then one hydrogen for each is leftover.
Is NAD+ reduced or oxidized when reacting with glucose and other carbon molecules? How does this help and work for the electron transport chain?
NAD+ is reduced when it takes electrons from the carbon molecules, and hence it is oxidizing those molecules. This takes away some of their potential energy due to the position of the electrons, as those electrons want to move towards the more electronegative electron carrier. This generates reducing potential, as the NADH (reducing agent now) can bring those electrons elsewhere to reduce other substances.
This works for the e- transport chain because those reducing agents bring electrons to the chain, where more electronegative complexes take those electrons, and transport them down the chain via increasing electronegativity. As they fall to a lower and lower potential energy state, this produces energy, which pushes H+ across its gradient, and then powers the production of ATP through ATP synthase.
How is ATP generated when it is produced from glycolysis and acetyl CoA? What is this process called?
This process is called substrate-level phosphorylation, because the phosphates are coming from a substrate which they are bonded to, not an inorganic phosphate floating around in the cytoplasm.
This occurs by the use of an enzyme:
A phosphorylation substrate (donor molecule) is brought together with ADP, and the phosphate is taken off and attached to ADP to produce ATP. This then makes an unphosphorylated product molecule and ATP.
What are the three problems with glycolysis that indicate that it’s not enough for energy production?
1) Only 2 net ATP has been made, which is not enough to power the cell.
2) Most of the energy is still present in the pyruvate, and so it needs to be oxidized further because not much energy has been released.
3) NAD+ needs to be restored because there is no point in continuously generating it. Instead recycling it is much more efficient.
What is one way to regenerate NAD+ and continue producing energy when no oxygen is present (not using an electron transport chain?) How do the cells know if there is enough oxygen or not?
One way to regenerate this NAD+ is through fermentation, specifically lactic acid fermentation for humans. To know if there is enough oxygen, cells have receptors which measure oxygen tension in the environment around them.
This allows glycolysis to still occur, producing a net 2 ATP, making G3P and then making pyruvate. But instead of going off to the electron transport chain, NADH stays in the cytosol, and comes back to reduce pyruvate into a new organic acid called lactic acid or lactate. This is then a byproduct which allows pyruvate to be removed (so that the cell will keep producing it) and allows some energy to continuously be produced when no oxygen is present.
So essentially this method just oxidizes NADH to regenerate NAD+, but doesn’t really produce much energy.
What are the various membranes of the mitochondria called, and what occurs on each of them? Which membrane is convoluted to allow for increased ________ ___________?
What is the structure of pyruvate? Can it diffuse across the lipid bilayer?
The outer membrane is smooth, and not much occurs here. the inner membrane is convulsed and allows for increase surface area so that many electron transport chains can exist and produce a ton of energy.
Between these two is the inter membrane space, which will have high hydrogen concentration and low pyruvate concentration.
The inner membrane is where the electron transport chain occurs, and also is where ATP synthesis occurs via ATP synthase.
The matrix is then inside both membranes, and this is where pyruvate oxidation and the citric acid cycle occur.
Pyruvate is 3 carbons, 3 oxygens and 3 hydrogens. It has 2 oxygens attached to one carbon, and one oxygen has a partial charge. The other oxygen is double bonded. This charged structure cannot diffuse across the hydrophobic lipid bilayer. Therefore, it needs to pass though a carrier protein to get into the mitochondria for the next steps of cellular respiration.
What is pyruvate oxidation and what is its alternate name? What is its purpose? Where does this occur and what is produced here?
This is the same as removing electrons from pyruvate, and this is a bridge reaction which is also called Acetyl-CoA formation. The purpose of this is to produce further reducing power by oxidizing pyruvate, and also to oxidize it so much that it can produce a CO2 molecule and become a 2C molecule. This is required to enter the Krebs cycle and oxidize it further. Also, acetyl CoA essentially leads the carbons to the Krebs cycle so that they do not get lost in the matrix by simple diffusion.
This occurs in the mitochondrial matrix, as pyruvate enters this matrix after it is formed. First, 2 electrons and 2 protons are removed from the molecule (and collected by NAD+) and then that oxidized CO2 group is released, which increases the entropy of the universe. Then, CoA attaches to form acetyl CoA.
Acetyl CoA then moves to the Krebs cycle, which is also in the matrix.
Give the general facts we need to know about the citric acid cycle (how many reactions, what does each step require, and what is its purpose?)
The citric acid cycle completes the oxidation of glucose to CO2 (the lowest energy form of that carbon). It does this by oxidizing it through many steps, and hence releasing 2 carbon dioxide molecules in the process.
There are 8 connected reactions and 5 of them are coupled, and each step has a unique enzyme.
Simplified version of the Krebs cycle, what are the net products and reactants? How many times does the Krebs cycle occur for one glucose molecule?
Can the citric acid cycle break down other molecules (not just glucose?)
The Krebs cycle starts with oxaloacetate (a 4C molecule), and then gains the two carbons from the acetyl co-A molecule. This then forms citrate, a 6C molecule. To reduce it to a 5C molecule, first an NAD+ is reduced to NADH, stripping it of electrons and energy, and hence releasing a CO2 molecule in the process (decarboxylation step). This happens again to produce another carbon dioxide molecule, turning it into a 4C molecule. One ATP will also be made, and then a 3rd NAD+ will be reduced to NADH, removing as much reducing power from the hydrocarbon as possible. FAD is also reduced to FADH2, producing further reducing power, just in a different form.
The Krebs cycle occurs twice for each glucose molecule, as it has to release the two carbons that were added into it, and there are two acetyl CoA molecules that come from each glucose molecule.
Net inputs: 3NAD+, FAD, ADP and Pi, and Acetyl CoA
Net outputs: 2CO2, 3NADH, FADH2, ATP (everything else just continues in the cycle).
The citric acid cycle can break down other polysaccharides, such as lipids, nucleic acids and amino acids.
