Title: Jack Sparrow Biochem / Biochemistry / Biochemistry Chapter 10
Tags: #JackSparrow::#B/B::#Biochemistry::#Chapter.10

Q: What is the citric acid cycle?
A: The Citric acid cycle (AKA Krebs Cycle) is a series of metabolic reactions that occurs in the mitochondria.  The main function of this cycle is to produce high-energy electron carriers (NADH FADH2) by oxidizing Acetyl-CoA to CO_2 and H_2O.

Q: What about Acetyl-CoA makes it such an archetypal metabolic molecule?
A: Acetyl-Coa contains a high-energy thioester bond that can be used to drive a multitude of other reactions when hydrolysis occurs.

Q: What is Pyruvate Dehydrogenase Complex and what are its 5 components?
A: Pyruvate Dehyrogenase Complex is a 5 enzyme complex in the mitochondrial matrix that produces acetyl-CoA and NADH.  PDH is also inhibited by acetyl-CoA and NADH.
It is comprised of the following 5 enzymes.
1.  Pyruvate Dehydrogenase
2.  Dihydrolipoly transacetylase
3.  Dihydrolipoyl dehydrogenase
4.  Pyruvate Dehydrogenase Kinase
5.  Pyruvate Dehydrogenase Phosphatase

Q: What is Pyruvate Dehydrogenase's role in the PDH complex?
A: Pyruvate Dehydrogenase oxidizes pyruvate, creating CO_2.  It requires Thiamine and Mg2+ to function.

Q: What is Dihydrolipoyl Transacetylase's role in the PDH complex?
A: After pyruvate has been oxidized, Dihydrolipoyl transacetylase oxidizes the remaining two-carbon molecule using lipoic acid and transfers the resulting acetyl group to CoA, forming Acetyl-CoA.

Q: What is Dihydrolipoyl Dehydrogenase's role in the PDH complex?
A: Dihydrolipoyl Dehydrogenase uses FAD to reoxidize lipoic acid so it can be used again.  Doing so forms FADH_2, which can trade hydrogens with an NAD+ later down the road to form NADH.

Q: What is Pyruvate Dehydrogenase Kinase's role in the PDH Complex?
A: Pyruvate Dehydrogenase Kinase phosphorylates PDH when ATP or acetyl-CoA levels or high, which turns it off.

Q: What is Pyruvate Dehydrogenase Phosphatase's role in the PDH complex?
A: Pyruvate Dehydrogenase Phosphatase dephosphorylates PDH when ADP levels are high, which turns it on.

Q: How do fatty acids (in the cytoplasm) increase the levels of Acetyl-Coa in the mitochondria?
A: 1.  CoA is coupled with a fatty acid (acyl group) in the cytoplasm.
2.  The acyl group is transferred to carnitine to form acyl-carnitine, which crosses the inner membrane of the mitochondria.
3.  The acyl group is then transferred to a mitochondrial CoA to reform the CoA-fatty acid, which can undergo B-oxidation in the mitochondria to form acetyl-CoA.

Q: Other than fatty acids, how can the concentration of Acetyl-CoA be increased in the cell?
A: 1.  Amino Acids can be broken down into ketone bodies, which can be turned into acetyl-CoA
2.  Ketone bodies can be converted to Acetyl-CoA using the reverse reaction of the PDH complex.
3.  Alcohol can be converted into acetyl-CoA by alcohol dehydrogenase and acetaldehyde dehydrogenase.

Q: The citric acid cycle is [anaerobic or aerobic?]
A: aerobic
Extra: So, the citric acid cycle doesn't technically use Oxygen, but it won't occur without the presence of oxygen due to NADH build up, so it is considered aerobic.

Q: The citric acid cycle occurs in [the matrix of the mitochondria or the cytoplasm?]
A: the matrix of the mitochondria

Q: Describe the first step of the Citric Acid Cycle
A: Acetyl-CoA and Oxaloacetate undergo a condensation reaction with the help of Citrate Synthase to form Citrate and a free CoA.

Q: Describe the second step of the Citric Acid Cycle
A: Citrate is isomerized to Isocitrate in two quick steps by Aconitase.  Aconitase is a metalloprotein that requires Fe^2+ to work.

Q: What are the products of the citric acid cycle, in order?
A: 1.  Citrate
2.  Isocitrate
3.  a-Ketoglutarate
4.  Succinyl-CoA
5.  Succinate
6.  Fumarate
7.  Malate
8.  Oxaloacetate
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Q: Describe the third step of the Citric Acid Cycle
A: Isocitrate is oxidized to a-Ketogluturate by Isocitrate Dehydrogenase, releasing NADH and CO_2.  This is the rate limiting step of the citric acid cycle!!

Q: Describe the fourth step of the Citric Acid Cycle
A: a-Ketoglutarate is oxidized to Succinyl-CoA by a-ketoglutarate dehydrogenase complex, which liberates a NADH and a CO_2

Q: Describe the fifth step of the Citric Acid Cycle
A: Succinyl-CoA is converted into Succinate by Succinyl-CoA synthetase which also converts a GDP to GTP.  This GTP will transfer its phosphate to ADP to form ATP.  This is the only step of the citric acid cycle that results in substrate level phosphorylation.

Q: Describe the sixth step of the citric acid cycle
A: Succinate is converted into Fumarate by Succinate Dehydrogenase, which also converts FAD to FADH_2.  This step is unique in that it does not occur in the mitochondrial matrix.  Instead, Succinate Dehydrogenase is an integral protein on the inner mitochondrial membrane, and this reaction occurs within the membrane.

Q: What is a flavoprotein?
A: A flavoprotein is a protein that is covalently bonded to FAD.

Q: Describe the seventh step of the Citric Acid Cycle
A: Fumarate is converted to Malate by Fumarase.

Q: Describe the eighth step of the Citric Acid Cycle
A: Malate is oxidized to Oxaloacetate by Malate Dehydrogenase, which releases an NADH

Q: Generally speaking, how can you predict the inhibitory and activatory actions of the Kreb's cycle?
A: Remember that the Kreb's Cycle's purpose is to generate ATP energy, and so it will generally be activated in times of energy need and high and deactivated in times of energy surplus.
Also, remember the Kreb's Cycle is an equilibrium and therefore expect le'chatlier effects to manifest themselves.

What is the net reaction of the Pyruvate Dehydrogenase Complex?

What is the net reaction of the Citric Acid Cycle?

Q: What is the total energy and carbon dioxide output of the conversion of Pyruvate to Oxaloacetate?
A: In this step, 1 CO_2 and 1 NADH are produced per 1 molecule of Pyruvate (remember, Glycolysis creates 2 Pyruvates that both fall down this pathway).

Q: What is the total energy and carbon dioxide output of one turn of the citric acid cycle?
A: For each Pyruvate molecule that completes the citric acid cycle, there will be produced 3 NADH, 1 FADH_2, 2 CO_2 and 1 GTP.

Q: NADH is used in the ETC to generate [2.5 or 1.5 ATPs?]
A: 2.5 ATPs

Q: FADH_2 is used in the ETC to generate [2.5 or 1.5 ATPs?]
A: 1.5 ATPs

Q: What are the three main control points of the citric acid cycle?
A: 1.  Citrate Synthase (step 1)
2.  Isocitrate Dehydrogenase (step 3)
3.  A-Ketoglutarate Dehydrogenase Complex (step 4)

Q: Describe the regulation of Citrate Synthase
A: ATP and NADH (energy products) function as allosteric inhibitors of Citrate Synthase.  This makes sense, because if you already have energy products, why bother running the citric acid cycle to make more?  Succinyl-CoA and Citrate are also negative feedback inhibitors.

Q: Describe the regulation of Isocitrate Dehydrogenase.
A: ATP and NADH (energy products) are allosteric inhibitors of Isocitrate Dehydrogenase.  ADP and NAD+ on the other hand (low-energy signals) activate Isocitrate Dehydrogenase.

Q: Describe the regulation of a-Ketoglutarate Dehydrogenase Complex
A: ATP NADH and Succinyl-Coa (energy products) inhibit a-ketoglutarate dehydrogenase complex.  ADP and calcium ions stimulate it.

Q: What is the electron transport chain?
A: The electron transport chain is a series of enzymes in the inner membrane of mitochondria that uses high energy electron carriers (NADH and FADH_2) to generate ATP.

Q: What is the proton motive force?
A: The proton motive force refers to the electrochemical gradient of hydrogen ions from the intermembrane space into the matrix.  The force of hydrogens flowing down this gradient, much like the flow of water that turns a water wheel, is used to generate ATP from ADP's and P's.

Q: How do NADH and FADH_2 interact with the enzymes in the ETC to generate a proton gradient?
A: The energy and electrons in NADH and FADH_2 are used to drive a series of redox reactions that push hydrogen ionds into the innermembrane space.
This is why NADH has a higher ATP conversion than FADH_2.  NADH literally just pushes more hydrogen ions into the inner membrane space than FADH_2.

Q: How do electrons know to go down the Electron transport chain and not up it?
A: The electron transport chain is a series of redox reactions that have increasingly high reduction potentials until you hit Oxygen, which has the highest reduction potential of the ETC and is the last step.
Remember, reduction potential is kind of like how bad that reaction wants to GAIN electrons, and so the increasing reduction potentials of the reactions spontaneously pull the electrons through the chain.

Q: What are the main components of the ETC?
A: 1.  Complex 1 (NADH-CoQ oxioreductase)
2.  Complex 2 (Succinate-CoQ Oxioreductase)
3.  Complex 3 (CoQH_2 -cytochrome c Oxioreductase)
4.  Complex 4 (Cytocrhome c Oxidase)
5. ATP Synthase (technically its own thing, but extremely closely linked to the ETC and often referred to as the 5th complex.)

Q: Describe Complex I of the ETC
A: Complex I uses an iron-sulfur cluster to transfer electrons from NADH to FMN and then Coenzyme Q (CoQ).  This results in the pumping of 4 protons and the conversion of CoQ to CoQH_2
This is where NADH's start their journey through the ETC.
_

Q: Describe Complex II of the ETC.
A: Complex II uses an iron sulfur cluster to transfer electrons from succinate (in the krebs cycle!) to FAD to form FADH_2, which then transfers electrons to CoQ, forming CoQH_2.  FAD is not as high energy of a molecule as NADH and so even though CoQH_2 is formed here, no protons are pumped into the inner membrane space.
This is where FADH_2's start their journey through the electron transport chain.  Very important to note that Complex II is actually physically connected with the Krebs cycle through succinate dehydrogenase.

Q: What is ubiquinol?
A: Ubiquinol is just the chemical/common name for CoQH_2.  Because of the extra bonds to hydrogen, this is a reduced molecule.

Q: What is Ubiquinone?
A: Ubiquinone is just the chemical/common name for CoQ.  Because of the extra bonds to oxygen, this is an oxidized molecule.

Q: What is the Q Cycle?
A: The Q cycle is the 2 step transferring of electrons from CoQH_2 to a CoQ molecule within the ETC that then reduces cytochrome c's in the inner membrane space.
This is a little complicated, but basically the reason it happens is because CoQH_2 has 2 electrons but can only transfer 1 at a time.  The important thing to remember here is that the electrons provided by complex I and II are going to end up reducing cytochrome c.

Q: Describe Complex III of the ETC.
A: Complex III uses an iron sulfur cluster to transfer electrons from CoQH_2's to heme, reducing cytochrome c through the Q cycle.  Four protons are pumped into the inner membrane space at this point.

Q: Describe Complex IV of the ETC.
A: Complex IV uses Cu^2+ to transfer electrons from reduced cytochrome c in the forms of hydride bonds to oxygen, forming water and completing the journey of electrons through the electron transport chain.  This step pumps 2 hydrogen ions into the inner membrane space.

Q: Describe the issue with the NADH's generated by glycolysis as they relate to the ETC.
A: Glycolysis generates NADH in the cytoplasm, but NADH needs to get to the matrix of the mitochondria to actually interact with the ETC.  This is accomplished through the existence of two NADH shuttles.
1.  Glycerol 3-phosphate shuttle
2.  Malate-Aspartate Shuttle

Q: Describe the Glycerol 3 - Phosphate Shuttle
A: In the cytosol, a version of Glycerol-3-phopshate dehydrogenase (G3PD) oxidizes DHAP to Glycerol-3 Phosphate using a cytosolic NADH.
The Glycerol-3 Phosphate can then interact with a special version of G3PD that exists in the inner membrane of the mitochondria.  This version of G3PD uses an FAD as the electron acceptor.
This causes Glycerol-3 Phosphate to be converted back into DHAP in the cytosol, but this time the high energy electrons end up in the inner membrane as FADH_2 which can enter the ETC at complex II.

Q: Describe the Malate-Aspartate Shuttle
A: Cytosolic Oxaloacetate is converted to Malate, which uses up a cytosolic NADH.
But malate can cross the mitochondrial membrane.  It does so, and is converted back into oxaloacetate in the matrix, which produces an NADH.
Oxaloacetate can then be converted into aspartate, which can exit the mitochondria.
As you can see from the figure, this allows one to shuttle NADH's into and out of the mitochondria as needed.

Describe the total ATP production of Aerobic Respiration

Q: Describe ATP synthase
A: ATP synthase is responsible for generating ATP from ADP using the proton gradient.  It has two main portions
The F_0 portion is an ion channel that allows protons to flow down the gradient from the intermembrane space to the matrix.
The F_1 portion is the part that actually uses the energy released by the gradient to phosphorylate ADP into ATP.

Q: Is aerobic metabolism 100% efficient?
A: No!  A good chunk of the energy from the proton gradient actually ends up getting dissipated as heat instead of making ATP.