Cellular Respiration: Substrate-Level Phosphorylation, Glycolysis, Pyruvate Oxidation, and Citric Acid Cycle part 3

Substrate-level phosphorylation: Phosphate group comes directly from an organic molecule and is transferred to ADP to make ATP.
- Example: Step 10 of glycolysis.
- Occurs in glycolysis and the Krebs cycle.
Oxidative phosphorylation: ATP generated by phosphorylating ADP with inorganic phosphate.
- Enzyme: ATP synthase.
- Driven by a proton concentration gradient set up by electron transport.
- Inorganic phosphate (no carbon involved) is attached to ADP to create ATP.
ATP synthase generates the bulk of ATP, but it doesn't use substrate-level phosphorylation; it uses inorganic phosphate.

Starting molecule: Glucose (C6).
End product: Two pyruvate molecules (each C3).
For every one glucose molecule, two pyruvate molecules are produced.
Other products include water.
ATP Production:
- Investment phase: 2 ATP hydrolyzed.
- Payoff phase: 4 ATP formed.
- Net gain: 2 ATP (4 ATP formed - 2 ATP hydrolyzed).
Other energy-storing molecules:
- Two NADH (electron carrier).
- Pyruvate molecules (can be further broken down).
Stored energy forms:
- Electrons held by NADH.
- ATP (powers endergonic reactions directly).
- Pyruvate (bulk of remaining energy).

Cells regulate enzymes based on metabolic needs.
Enzyme regulation often occurs at the beginning of metabolic pathways via product inhibition.
In glycolysis, phosphofructokinase is the rate-limiting enzyme, dictating the speed of glycolysis.
Phosphofructokinase is allosterically regulated by ATP.
High ATP levels inhibit phosphofructokinase, slowing down glycolysis.
The steps between fructose-1,6-bisphosphate and pyruvate generation signify other enzymatic reactions of glycolysis.

Stored energy in pyruvate is tapped into in the next stage of cellular respiration.
Pyruvate oxidation occurs on the way into and within the mitochondrion.
Pyruvate is oxidized to get a molecule ready for the citric acid cycle.
Requires the presence of oxygen because the electron transport chain uses oxygen as a final electron acceptor; without oxygen, processes back up.
In the presence of oxygen, pyruvate enters the mitochondrion.
Pyruvate is converted to acetyl coenzyme A (acetyl CoA) which links glycolysis and the citric acid cycle.

Pyruvate oxidation is carried out by a multi-enzyme complex that catalyzes three reactions.
Pyruvate decarboxylase (first enzyme, in blue) removes a carbon from pyruvate, releasing it as carbon dioxide, going from a three-carbon molecule to a two-carbon molecule.
Dihydrolipoyl dehydrogenase (second enzyme, in green) works on the product of the first enzyme.
A final enzyme (in red), present in multiple copies, processes the product of the second enzyme.
The arrangement facilitates the sequence of reactions by passing the intermediate directly from one enzyme to the next, speeding up the pathway.
Pyruvate, a three-carbon molecule, loses a carbon as carbon dioxide.
The remaining two-carbon molecule attaches to coenzyme A, forming acetyl CoA.
Electrons stripped from pyruvate are picked up by $NAD^+$ , reducing it to NADH.
The acetyl CoA proceeds into the citric acid cycle.

The citric acid cycle completes the energy-yielding oxidation by extracting the remaining energy from pyruvate.
Pyruvate must be converted into acetyl CoA before entering the cycle.
The result of the citric acid cycle is ATP, NADH, and FADH2 (another high-energy electron carrier).
NADH has been the primary electron acceptor up to the Citric Acid Cycle, where FAD also accepts electrons becoming FADH2.
ATP can be used directly, while NADH and FADH2 pass off their electrons to the electron transport chain.

Two pyruvate molecules for every glucose molecule.
As a result of oxidation, one carbon is lost as carbon dioxide.
Stripped electrons are picked up by $NAD^+$ to generate NADH.
Remaining two-carbon molecule (acetyl) attaches to CoA, forming acetyl CoA.
Acetyl CoA enters the citric acid cycle by combining with oxaloacetate (four-carbon molecule) to form citrate (six-carbon molecule).
CoA is released to facilitate the reaction.

Two carbons from the acetyl group combine with the four carbons of oxaloacetate to make citrate.
Through the citric acid cycle, two more carbons will be lost as carbon dioxide.
The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, and citrate is formed.
During the cycle, $NAD^+$ is reduced, becoming NADH; ATP is made directly, and FAD is reduced, forming FADH2.
The molecules FADH2 and NADH pass off their electrons to the electron transport chain.
The ATP generated is produced via substrate-level phosphorylation that can be used directly.

The citric acid cycle can be called the Krebs cycle after Hans Krebs or the tricarboxylic acid cycle (TCA cycle).
Krebs performed his work in England in the 1930s and won the Nobel Prize in the 1950s.
The name Tricarboxylic Acid cycle comes from the three carboxylic acid groups found in citrate.
The citric acid cycle involves eight steps, each catalyzed by a specific enzyme.
The cycle takes place in the mitochondrial matrix where all the enzymes are located.
Molecules such as FADH2 and NADH can pass their electrons directly to carriers embedded in the inner mitochondrial membrane.

The citric acid cycle is a cycle because, after the generation of citrate, seven steps decompose it but regenerate oxaloacetate.
The primary purpose of the cycle is to produce the high-energy electron carriers NADH and FADH2 and a little ATP.
The acetyl group, derived from pyruvate, is processed to extract the last bits of energy and trap them in these high-energy molecules.
ATP can be used directly, while high-energy electron carriers must pass off their electrons for further ATP production.

Following the carbons, the carbons from acetyl remain in the cycle for at least one turn, whereas the carbons from oxaloacetate are lost as carbon dioxide. Right?
Two carbon dioxide molecules are generated in the conversion of isocitrate to alpha-ketoglutarate and from alpha-ketoglutarate to succinyl CoA.
These two carbon atoms are lost in the turn of the citric acid cycle. Right?

The citric acid cycle consists of eight steps that can be regulated at certain positions.
The purpose of the cycle is to generate ATP directly and to trap the remaining energy stored in the acetyl group by transferring it to high energy currency molecules for use in the electron transport chain.
The citric acid cycle finishes the oxidation of the original glucose molecule.