Metabolism
Wednesday, June 3, 2020
9:19 AM
Glucose metabolism occurs in four different steps: Glycolysis, Pyruvate dehydrogenase complex, Krebs cycle, and
electron transport/oxidative phosphorylation.
Glycolysis happens in the cytoplasm.
PDC and Krebs happen in the mitochondrial matrix.
ETC happens in the inner mitochondrial membrane.
Glycolysis
The overall reaction of glycolysis is the conversion of glucose into 2 pyruvate molecules. Resulting in the production
of NADH, ATP and H2O.
Glucose + 2 ADP + 2 Pi + 2 NAD+ = 2 Pyruvate + 2 ATP + 2 NADH + 2 H2O + 2 H+
Gluconeogenesis
Reverse process of glycolysis which converts small molecules (pyruvates, ketones etc) into glucose. It is mainly
done in the liver and to a smaller extent in the kidney.
The first step is the conversion of pyruvate to oxaloacetate by the addition of CO2, which is catalyzed by
pyruvate carboxylase. Then oxaloacetate gets decarboxylated and phosphorylated to form Phoshphoenol
Pyruvate which is catalyzed by PEP carboxykinase. The rest of the steps up to F­1,6­P are done by the same
enzymes as glycolysis.
The conversion of F­1,6­P to F6P is catalyzed by Fructose 1,6­Bisphosphatease. Which is then isomerized to G6P.
The conversion of G6P to Glucose is done by Glucose 6 Phosphatase.
The full steps of gluconeogenesis are shown below:
1. The first step is converting Glucose to Glucose­6­Phosphate by Hexokinase. ­> Inhibited by G6P.
2. The second step is converting G6P to Fructose­6­Phosphate.
3. The third and most important step is converting F6P to Fructose­1,6­BisPhosphate by Phosphofructokinase. ­>
inhibited by ATP. Committed step.
4. The last step is the conversion of Phosphoenolpyruvate to Pyruvate by pyruvate kinase. (incorrectly named
pyruvate kinase before it was discovered that it is a phosphatase).
For glycolysis to occur, there needs to be NAD+ present, which get reduced to NADH. Without NAD+, there are no
molecules to reduce and glycolysis stops. In aerobic conditions, NAD+ is regenerated within the ETC. During
anaerobic conditions, the PDC, and Krebs cycles run out of NAD+ to reduce, and cease, as well as ETC having no O2
to donate electrons to, so it ceases as well.
Additionally, without any ATP present at the start (required for the addition of two phosphate groups to glucose),
glycolysis cannot start either.
The enzymes and pathway of glycolysis is shown below:
Regulation of Glycolysis and Gluconeogenesis
The regulation of the two opposite pathways occurs mainly at the start of each pathway. Therefore the main
enzymes which get regulated are PFK and F­1,6­Bpase. Both enzymes are regulated by intermediates of
glycolysis. For instance in a starved state, AMP gets produced, which activates PFK and inhibits F­1,6­BPase.
Fermentation
During anaerobic conditions, NAD+ needs to be regenerated for glycolysis to run, and ATP to be generated. To do so,
pyruvate gets reduced to lactate in human muscle cells, or to ethanol in yeast cells. Reducing pyruvate oxidizes
NADH, and regenerates NAD+.
Another enzymatic control factor is Fructose­2,6­Bisphosphate. Its intercellular concentration is regulated by
one large protein which either creates F­2,6­BP or degrades it. The large protein is controlled by insulin or
glucagon, where insulin stimulates the production of F­2,6­BP, and glycolysis, while glucagon causes the
breakdown of F­2,6­BP and the switch to gluconeogenesis.
Glycogen Metabolism
Glycogen is the main storage of glucose within the body and muscle cells. It is a polymer made of glucose
molecules.
The first step in the synthesis of glycogen is the conversion of glucose­6­phosphate to glucose­1­phosphate done
by phosphoglucosemutase. The next step is the activation of G­1­P by UTP into UDP­Glucose, which gets added
to a growing chain of glycogen by glycogen synthase.
The catabolism of glycogen is done by phosphorylating glycogen by Glycogen Phosphorylase which yields
glucose­1­P, which gets converted to Glucose­6­P, which can finally enter glycolysis.
Pentose Phosphate Pathway
The PPP converts glucose­6­P into NADPH and Ribose­5­P. The PPP diverts G6P from glycolysis for the
production of these elements, or the production of other glycolysis intermediates. The PPP is split into the
irreversible oxidative phase, and the reversible non­oxidative phase. Ribose­5P and NADPH get made during the
oxidative phase. In it G6P gets converted to R5P and NADPH by Glucose­6­P dehydrogenase yielding one R5P
and two NADPH. NADPH acts as a negative feedback inhibitor for G6P dehydrogenase.
NADPH serves primarily as a reducing agent for anabolic processes within the cell, while R5P either gets
converted to nucleotides or other glycolysis intermediates.
PDC
Once pyruvate is made in the cytoplasm it gets shuttled to the mitochondrial matrix, where it enters the pyruvate
dehydrogenase complex. Within the PDC lies a complex of three enzymes which oxidatively decarboxylate pyruvate
into an acetyl. To direct the transportation of acetyl into the Krebs cycle post PDC, it gets attached to Coenzyme­A
via a sulfur group. In the process, one NAD+ gets converted to NADH per pyruvate, or a total of 2 NADH for one
glucose molecule.
Krebs cycle
The main goal of the Krebs cycle is to oxidatively decarboxylate the pyruvate into two CO2 molecules, and
regenerate the starting materials of the cycle, as well as generating 3 NADH, 1 FADH, and 1 GTP molecule per
acetyl­CoA.
The Krebs cycle can be broken down into three stages:
Stage 1:
Β Oxidation
Is the main process by which fatty acids get metabolized. The first step in beta oxidation is the activation of a
fatty acid. A fatty acid is activated when it is bound to CoA, and the activation costs 2 ATP molecules. The
activation of fatty acids takes place in the outer mitochondrial membrane.
Once activated, they get transported to the matrix, where the beta oxidation takes place.
Beta oxidation is a series of steps which removes an acetyl­CoA from a fatty acid, and produces one FADH and
one NADPH. The initial cost of 2 ATP molecules is just at the start (activation) of the fatty acid.
Krebs cycle
The main goal of the Krebs cycle is to oxidatively decarboxylate the pyruvate into two CO2 molecules, and
regenerate the starting materials of the cycle, as well as generating 3 NADH, 1 FADH, and 1 GTP molecule per
acetyl­CoA.
The Krebs cycle can be broken down into three stages:
Stage 1:
The first step is the condensation of Acetyl­CoA with oxaloacetate to form citrate (citric acid) which is a
tricarboxylic acid.
Stage 2
In this stage, the oxidative decarboxylation occurs. First citrate is isomerized to isocitrate which is decarbonylated
to α­ketoglutarate which is then again decarboxylated into succinyl­CoA. During each decarboxylation step, CO2
gets released and NADH gets produced.
Stage 3
In the last stage of the Krebs cycle, oxaloacetate gets regenerated, with the production of NADH and FADH2, as well
as one GTP molecule which ends up converting ADP to ATP.
The acetyl­CoA from the oxidation gets sent to the Krebs cycle, where it gets converted to NADH, which then
goes into the ETC.
Ketogenesis
During starvation, blood glucose falls too low. To combat this, the liver creates ketone bodies, which can travel
past the blood brain barrier and enter the Krebs cycle within neuronal cells.
Ketone bodies are formed by combining two acetyl­CoA molecules initially, then adding a third and modifying it
to form Acetoacetate, which can get converted to Acetone and β­Hydroxybutyrate. All three act as ketone
bodies.
The full Krebs cycle is shown below:
The oxidation of Glucose before the ETC yields the following:
- Glycolysis: 2 ATP + 2 NADH per glucose
- PDC: 2 NADH per glucose (1 per pyruvate)
- Krebs: 6 NADH, 2 FADH2 and 2 GTP (2 ATP) per glucose
Compartmentalization
As mentioned before glycolysis occurs in the cytoplasm while PDC and the Krebs cycle occur in the mitochondrial
matrix. The ETC, which consumes NADH and FADH2 occurs in the inner mitochondrial membrane.
The mitochondria is composed of the following structures:
- Outer membrane which contains large transmembrane proteins called porins which let molecules and proteins
freely travel into and out of the intermembrane space. Therefore the intermembrane space is continuous with
the cytoplasm.
- Inner membrane is composed of many folded structures called cristae which contain the proteins of the ETC.
The inner membrane is very densely packed and does not allow even small ions (H+) to diffuse in or out of the
inner membrane space.
- Mitochondrial matrix is the inner most space within the mitochondria and is the location of the PDC and Krebs
cycle.
Because glycolysis occurs in the cytoplasm, NADH molecules made from glucose need to be transported into the
mitochondria. While the NADH and FADH2 molecules made through the PDC and the Krebs cycle do not as they are
made within the mitochondria.
Electron transport chain
Occurs on the inner membrane. The membrane contains a complex of five proteins, three large ones and two small
ones. The large proteins, also called cytochromes, are bound to the membrane, while the two smaller ones are
loosely bound to it.
In the first step of the chain, NADH donates two electrons to the first protein, called NADH Dehydrogenase or
Coenzyme­Q reductase. The NADH Dehydrogenase then passes the electrons to Coenzyme­Q also called
ubiquinone. The movement of electrons causes H+ ions to move against their gradient from the matrix into the
intermembrane space. Next the electrons are passed from ubiquinone to Cytochrome C reductase which then
passes the electrons to Cytochrome C. Cytochrome C passes them to Cytochrome C oxidase which finally passes
them to O2 forming H2O.
Fatty acid synthesis
The most important part is that it is synthesized by Fatty acid synthase, which first binds Acetyl­CoA. Then, each
time a new two carbon unit gets added to the growing fatty acid, it is first converted to malonyl­CoA, which
reacts with the bound acetyl­CoA, and gets decarboxylated back to acetyl­CoA.
Confusing I know.
Basically it proceeds like this.
1. Fatty acid synthase binds Acetyl­CoA
2. Somewhere else, another acetyl­CoA gets converted to malonyl­CoA (2 carbon ­> 3 carbon)
3. Then malonyl­CoA binds to a different site on the Fatty acid synthase.
4. The bound acetyl­CoA and the newly bound malonyl­CoA react, forming a 5 carbon unit.
5. The 5 carbon unit now gets decarboxylated to a 4 carbon unit, which gets moved to the original acetyl­CoA
site.
6. A new malonyl­CoA binds, and the extension continues.
It is important to know that fatty acid synthesis occurs in the cytoplasm (anabolic), and that the carboxylation of
acetyl­CoA to malonyl­CoA gets catalyzed by acetyl­CoA­carboxylase.
Additionally, the conversion of Acetyl­CoA to malonyl­CoA costs 1 ATP and one CO2, while the decarboxylation
of the 5 carbon unit costs 2 NADH molecules.
Once the gradient is made, ATP synthase, a transmembrane protein within the inner mitochondrial membrane,
pumps protons back into the matrix. The transfer of protons along their gradient powers the conversion of ADP +
Pi ­> ATP by ATP synthase.
The total energy production of glucose catabolism:
Glycolysis = 2 ATP
NADH Transport = ­2 ATP
PDC = 0 ATP
Krebs Cycle = 2 ATP
ETC = 34 ATP
Total = 36 ATP per Glucose