5.

0 Glycolysis
Glycolysis is a method of anaerobic glucose degradation that is possessed by nearly all organisms.
Overall, this process yields 2 moles of ATP per mole of glucose oxidized to either lactate or ethanol.
This process represents a rapids means in generating ATP in the absence of oxygen and a process
that prepares glucose for aerobic oxidation to produce additional energy. Click the enzyme or
substrate labels for more information.
5.01 Hexokinase
Hexokinase initiates glycolysis by attaching a phosphate group from ATP to position 6 on glucose.
The attachment of a phosphate group traps glucose by making it a charged molecule and therefore
unable to pass through the cell membrane. This reaction is irreversible under physiological
conditions, and is inhibited by glucose 6-phosphate.

5.02 Phosphoglucose Isomerase

Phosphoglucose Isomerase catalyses the reversible conversion of Glucose 6-Phosphate to Fructose
6-Phosphate. This enzyme is not regulated.

5.03 Phosphofructokinase
Phosphofructokinase catalyzes the committed step in glycolysis, converting Fructose 6-Phosphate to
Fructose 1,6-Bisphosphate at the expense of 1 ATP. This is the rate limiting step in glycolysis and
is inhibited by citrate, ATP, and low pH. Phosphofructokinase can be activated by AMP, fructose
2,6-bisphosphate, and inorganic phosphate. This enzyme can inactivated by phosphorylation by
cAMP dependent protein kinase in response to the hormone glucagon. High insulin levels cause
phosphoprotein phosphatase to activate phosphofructokinase by dephosphorylation.

5.04 Aldolase
Aldolase cleaves Fructose 1,6-Bisphosphate into Dihydroxyacetone Phosphate and Glyceraldehyde
3-Phosphate. Aldolase can also catalyze the reverse reaction.
5.05 Triose Phosphate Isomerase
Triose Phosphate Isomerase converts Dihydroxyacetone Phosphate to Glyceraldehyde 3-Phosphate.
The reverse reaction is also catalyzed by the same enzyme.

5.06 Glyceraldehyde 3-Phosphate Dehydrogenase

Glyceraldehyde 3-Phosphate Dehydrogenase reduces NAD+ to NADH while converting
Glyceraldehyde 3-Phosphate to 1,3-Bisphosphoglycerate. The reverse reaction that oxidizes NADH
to NAD+ is carried out by the same enzyme. The 1,3-Bisphosphoglycerate produced by this
reaction is a high energy compound that can be readily used to make ATP. The delta G of this
reaction is +1.5 kcal/mol, and is therefore freely reversible under physiological conditions.

5.07 Phosphoglycerate Kinase

Phosphoglycerate Kinase produces 1 ATP during the conversion of 1,3-Bisphosphoglycerate to
3-Phosphoglycerate, and is capable of catalyzing the reverse reaction. The 1,3-Bisphosphoglycerate
is a high energy compound that can be easily used to power substrate level phosphorylation to
produce ATP.

5.08 Phosphoglycerate Mutase

Phosphoglycerate Mutase introconverts 3-Phosphoglycerate with 2-Phosphoglycerate.
5.09 Enolase
Enolase liberates water during the reversible conversion of 2-Phosphoglycerate to
Phosphoenolpyruvate. The phosphoenoyl pyruvate generated by this reaction is a high energy
compound that can be used to produce ATP via substrate level phosphorylation.

5.10 Pyruvate Kinase

Pyruvate Kinase irreversibly converts Phospoenolpyruvate to Pyruvate while producing 1 ATP by
substrate level phosphorylation. This reaction is not reversible under physiological conditions and
is inhibited by ATP and alanine. Pyruvate Kinase is activated by fructose 1,6-bisphosphate. This
enzyme can inactivated by phosphorylation by cAMP dependent protein kinase in response to the
hormone glucagon. High insulin levels cause phosphoprotein phosphatase to activate pyruvate
kinase by dephosphorylation.

5.11 Lactate Dehydrogenase

Lactate Dehydrogenase oxidizes NADH to NAD+ while converting Pyruvate to Lactate. The
reverse reaction is catalyzed by the same enzyme. This is the terminal step in glycolysis in
mammalian and most other eukaryotic cells. In many bacteria and some eukaryotes, Alcohol
Dehydrogenase is used to convert Pyruvate to Ethanol.

5.12 Pyruvate Decarboxylase

Pyruvate Decarboxylase converts Pyruvate to Acetaldehyde while releasing CO2. This reaction is
irreversible, and occurs when low oxygen levels inhibit the TCA cycle.
5.13 Alcohol Dehydrogenase
Alcohol dehydrogenase oxidizes NADH to NAD+ while converting Acetaldehyde to Ethanol. This
is the terminal anaerobic step in glucose metabolism for many bacteria and some eukaryotes.

5.14 ATP
ATP is a nucleotide triphosphate that serves as a link between energy producing and energy utilizing
processes in all organisms. The beta and gamma phosphate groups are linked to the alpha
phosphate group by high energy bonds. If the gamma-beta bond is hydrolyzed, -7.3 kcal of energy
is released per mole of ATP. Further hydrolysis of the resulting ADP (adenosine diphosphate) to
produce AMP will release additional energy. The energy released by the hydrolysis of ATP can be
coupled to a reaction by an enzyme to allow reactions to occur at faster rates. Other nucleotide
triphosphates such at GTP play a similar role in specific metabolic processes.
5.15 NADH
NADH is the carrier of reducing equivalents that are used for energy generating processes in cells.
NADH can serve as an electron donor for enzymatic reactions and the electron transport chain. The
electrons carried by NADH can be used to generate 3 ATP. NADH is produced via the enzymatic
reduction of NAD+.

5.15.1 Glucose
5.15.2 Glucose 6-Phosphate

5.15.3 Fructose 6-Phosphate

5.15.4 Fructose 1,6 Bisphosphate

5.15.5 Glyceraldehyde 3-Phosphate

5.15.6 Dihydroxyacetone Phosphate

5.15.7 1,3 Bisphosphoglycerate

5.15.8 3-Phosphoglycerate

5.15.9 2-Phosphoglycerate

5.15.10 Phosphoenoylpyruvate
5.15.11 Pyruvate

5.15.12 Lactate

5.15.13 Acetaldehyde
5.15.14 Ethanol

5.15.15 H2O

5.15.16 CO2

5.15.17 cAMP
5.15.18 Pi

8.0 TCA Cycle

The Tricaroboxylic Acid or Kreb’s Cycle is a biochemical cycle that generates reducing equivalents
such as NADH and FADH2 from pyruvate (glycolysis) or fatty acids. The reducing equivalents can
then be used to generate ATP in the electron transport chain. A complete turn of the TCA cycle will
produce two CO2, 1 GTP, 3 NADH, and 1 FADH2 from an Acetyl-CoA. Click the enzyme or
substrate labels or for more information.
8.10 Pyruvate Dehydrogenase
Pyruvate Dehydrogenase is a large multisubunit complex that converts Puryvate and CoASH to
Acetyl CoA while reducing NAD+ to NADH. This enzyme requires thiamin pyrophosphate, lipoic
acid, coenzyme A, FAD, and NAD+ to be functional. This reaction has a delta G of -8 kcal/mol,
making this reaction irreversible under physiological conditions, making the net conversion of fatty
acids to glucose impossible. The activity of this enzyme is inhibited by acetyl CoA and NADH.
This enzyme is also deactivated by phosphorylation in response to high levels of acetyl CoA and
NADH. Dephosporylation in response to high levels of NAD+ and CoASH activates the enzyme.
This regulatory scheme makes pyruvate dehydrogenase responsive to the NADH/NAD+ and acetyl
CoA/CoASH levels in the cell.

8.20 Citrate Synthase

Citrate synthase combines oxaloacetate, acetyl CoA, and H2O to form citrate. The delta G of this
reaction is -9 kcal/mol and therefore irreversible under physiological conditions. The activity of
citrate synthase is inhibited by ATP, NADH, succinyl CoA, and fatty acyl CoA molecules.

8.30 Aconitase
Aconitase reversibly converts citrate to isocitrate, and requires ferrous iron (Fe2+). The ferrous iron
is bound in an iron-sulfur center which is essential for the activity of this enzyme.
8.40 Isocitrate Dehydrogenase
Isocitrate Dehydrogenase is an enzyme that reversibly converts Isocitrate to Alpha-ketoglutarate
while reducing NAD+ to NADH. CO2 is also released by this reaction. The delta G of this reaction
is -5 kcal/mol, favoring the forward reaction. The activity of isocitrate dehydrogenase is stimulated
ADP and AMP. ATP and NADH inhibit this enzyme.

8.50 Alpha-ketoglutarate Dehydrogenase

Alpha-ketoglutarate Dehydrogenase is a multisubunit enzyme that converts Alpha-ketoglutarate and
CoASH to Succinyl CoA while reducing NAD+ to NADH. This enzyme requires thiamin
pyrophosphate, lipoic acid, coenzyme A, FAD, and NAD+ to be functional. The delta G of this
reaction is -8 kcal/mol, making it irreversible under physiological conditions. This enzyme is
inhibited by ATP, GTP, NADH, and succinyl CoA. Alpha-ketoglutarate dehydrogenase is activated
by calcium (Ca2+) ions.

8.60 Succinyl CoA Synthase

Succinyl CoA Synthase reversibly converts Succinyl CoA to Succinate and CoASH. This
conversion also produces a GTP. This reaction has a delta G of -0.7 kcal/mol.
8.70 Succinate Dehydrogenase
Succinate Dehydrogenase reversibly converts Succinate to Fumarate accompanied with the
reduction of FAD to FADH2. Succinate dehydrogenase has a number of non-heme iron atoms and
acid-labile sulfur atoms that are incorporated into iron-sulfur centers. This enzyme is inhibited by
oxaloacetate and is stimulated by ATP, inorganic phosphate, and succinate.

8.80 Fumarase
Fumarase reversibly converts Fumarate and H2O to Malate.

8.90 Malate Dehydrogenase

Malate Dehydrogenase reversibly converts Malate to Oxaloacetate while reducing NAD+ to
NADH. The delta G of this reaction is +7 kcal/mol, and is therefore endothermic in the forward
direction. Because the oxaloacetate produced by this reaction is rapidly removed by citrate
synthase, the reaction progresses under physiological conditions.
8.90.1 FADH2
FADH2 is a carrier of reducing equivalents that are used for energy generating processes in cells.
FADH2 serves as a electron donor for the electron transport chain and can be used to produce 2
ATP. FADH2 is produced via the enzymatic reduction of FAD.

8.90.2 GTP
GTP is a nucleotide triphosphate that serves as a link between energy producing and some energy
utilizing processes in all organisms. Though ATP serves as the primary energy currency of the cell,
GTP is the energy donor in translation and several other critical cellular processes. The beta and
gamma phosphate groups are linked to the alpha phosphate group by high energy bonds. If the
gamma-beta bond is hydrolyzed, -7.3 kcal of energy is released per mole of GTP. Further
hydrolysis of the resulting GDP (guanosine diphosphate) to produce GMP will release additional
energy. The energy released by the hydrolysis of GTP can be coupled to a reaction by an enzyme to
allow reactions to occur at faster rates.
8.90.3 Acetyl-CoA

8.90.4 Citrate

8.90.5 Isocitrate
8.90.6 Alpha-ketoglutarate

8.90.7 Succinyl-CoA

8.90.8 Succinate
8.90.9 Fumarate

8.90.10 Malate

8.90.11 Oxaloacetate
8.90.12 CoASH

10.0 Beta Oxidation

Beta oxidation is used to sequentially remove two carbon unity from fatty acyl-CoA’s to produce
Acetyl-CoA that is further oxidized in the TCA cycle. During each round of beta oxidation a
FADH2 and an NADH is produced. These reduced coenzymes can then donate their electrons to
the electron transport chain. Click the blue enzyme labels for more information.
10.10 Acyl CoA Dehydrogenase
Acyl CoA Dehydrogenase converts a fatty acyl CoA to a trans-delta2-Enoyl CoA while reducing
FAD to FADH2.

10.20 Enoyl CoA Hydratase

Enoyl CoA Hydratase hydrates trans-delta2-Enoyl CoA to convert it to 3-L-hydroxyacyl CoA.

10.30 3-L-Hydroxyacyl CoA Dehydrogenase

3-L-Hydroxyacyl CoA Dehydrogenase converts 3-L-hydroxyacyl CoA to Beta Ketoacyl CoA while
reducing NAD+ to NADH.

10.40 Beta Ketothiolase

Beta Ketothiolase converts beta ketoacyl CoA and CoASH to acetyl CoA and a fatty acyl CoA that
is 2 carbons shorter than the starting fatty acyl CoA.
11.0 Electron Transport Chain
Reducing equivalents such as NADH and FADH2 that were generated by glycolysis, the TCA cycle,
or beta oxidation donate their electrons to the electron transport chain. Through a series of
sequential electron carriers, protons are pumped across the membrane to create a proton gradient.
This gradient can be harnessed to generate ATP.

11.1 NADH Dehydrogenase Complex

This complex accepts electrons from NADH and pumps a proton across the membrane. The
electron passes through a flavin and 5 iron-sulfur centers before being transferred to ubiquinone.

11.2 Ubiquinone
Ubiquinone is a lipid soluble quinolone that can transport and electron from the NADH
Dehydrgenase Complex to the B-C1 Complex. Ubiquinone is a mobile electron carrier, and it can
accept electrons from FADH2.

11.3 B-C1 Complex

The B-C1 complex accepts electrons from Ubiquinone and passes them to Cytochrome C after
pumping a proton across the membrane. The B-C1 Complex contains 9 heme-derived cytochromes
and three iron-sulfur centers.

11.4 Cytochrome C
Cytochrome C is a heme containing protein that carries electrons from the B-C1 Complex to
Cytochrome Oxidase.

11.5 Cytochrome Oxidase

Cytochrome oxidase, also known as Cytochrome AA3, accepts electrons from Cytochrome C. After
pumping a proton across the membrane, Cytochrome Oxidase passes the donated electron to oxygen
to form H2O.
11.6 F1F0 ATPase
The F1F0 ATPase, also known as ATP synthetase, can harness the potential energy in the proton
gradient that is established by the electron transport chain. Protons are allowed to flow down their
concentration gradient, and the energy generated from this process is used to produce ATP from
ADP and Pi. This ATPase can work in reverse to pump protons out of the mitochrondiral matrix at
the expense of ATP.

12.0 Glycogen
Glycogen is branched chain polymer of glucose that serves as a readily mobilizable
reserve of glucose for the body. The glucose monomers are linked together by a-1,4
linkages and the chain branches are linked together by a-1,6 linkages. A single
glycogen molecule has a single reducing end and multiple non-reducing ends. It is at
these non-reducing ends that glucose monomers are added and removed from the
glycogen molecule as the cells energy needs change
12.1 Glycogen Synthesis
Glycogen is produced from glucose in the cytosol. The process of glycogen
synthesis requires ATP, UTP, glucose, and an existing glycogen molecule (or the
protein glycogenin to form a new glycogen molecule). Glucose is polymerized on
the non reducing ends of the glycogen molecule. Branches are introduced in the
glycogen polymer every 8 to 10 monomers to produce a highly branched molecule.
Click on the enzyme or substrate labels for more information.

12.11 Glucokinase
Glucokinase catalyzes the addition of a phosphate group to glucose to form glucose
6-phosphate.

12.12 Phosphoglucomutase
Phosphoglucomutase introconverts glucose 6-phosphate with glucose 1-phosphate.
This reaction is freely reversible under physiological conditions.
12.13 UDP-Glucose Pyrophosphorylase
UDP-Glucose pyrophosphorylase catalyzes the addition of UDP to glucose
1-phosphate. The delta G of this reaction is nearly zero but inorganic
pyrophosphatase rapidly degrades the PPi, thus forcing the reaction to proceed in the
forward direction.

12.14 Glycogen Synthase

Glycogen synthase attaches UDP-glucose to a non-reducing end of a glycogen
polymer. The delta G of this reaction is -13.4 kJ/mol making the reaction
spontaneous under physiological conditions. Glycogen synthase forms alpha 1-4
glycosidic bonds between the individual glucose residues.

12.15 Branching Enzyme

The branching enzyme adds a chain of glucose monomers to another chain of
glucose monomers by forming an alpha 1-6 glycosidic bond. The 7 monomer chain
is produced by glycogen synthase and cleaved from the chain of monomers by the
branching enzyme. The branching enzyme links the 7 monomer chain to another
monomer chain by a alpha 1-6 glycosidic bond. The branches are spaces 11 residues
apart, giving a glycogen molecule a highly branched structure.
12.2 Glycogenolysis
Glycogenolysis is the process of breaking down the glycogen molecule into glucose
monomers. This process occurs rapidly and is used as a store of energy in many cell
types. Glucose monomers are removed singly from the non-reducing ends of the
glycogen polymer. This process requires H2O, Pi, and a glycogen molecule. Click
on the enzyme or substrate labels for more information.

12.21 Glycogen Phosphorylase

Glycogen phosphorylase removes a glucose monomer from a non-reducing end of
glycogen by phosphorolysis to produce glucose 1-phosphate. This enzyme exists in
two forms, phosphorylase A and phosphorylase B. Phosphorylase A is a
phosphorylated form of this enzyme and is insensitive to allosteric effectors except
glucose. The conversion of phosphorylase B to phosphorylase A is mediated by
phosphorylase kinase which is activated by cAMP dependent protein kinase. The
phosphate group can be removed by phosphoprotien phosphatase-1 to restore full
activity. ADP is a positive effector for phosphorylase B, and ATP and glucose
6-phosphate inhibit the activity of this enzyme.
12.22 Phosphoglucomutase
Phosphoglucomutase reversibly introconverts glucose 1-phosphate with glucose
6-phosphate.

12.23 Glucose 6-phosphatase

In liver cells, glucose 6-phosphatase removes the phosphate group from glucose
6-phosphate so glucose can leave the cell and enter circulation. This enables the
liver to store glucose in the form of glycogen and release glucose as required by
other organs.

12.24 Debranching Enzyme

The debranching enzyme removes chains of glucose monomers that are 5 residues or
less in length and attaches them with an alpha 1-4 glycosidic bond to a longer
glucose polymer.

13.0 Amino Acid Metabolism

In addition to their roles in protein structure, amino acids can also serve as precursors
for glucose, fatty acids, and ketone bodies. This conversion of structural materials
to energy occurs in two major steps: Deaminiation and carbon skeleton metabolism.
13.10 Deamination
The alpha amino group is removed from the amino acid by an aminotransferase
specific for that amino acid. The liberated nitrogen is then channeled into the urea
cycle for detoxification. Click on the blue enzyme labels and substrate labels for
more information.

13.11 Aminotransferase
Aminotransferase moves the alpha-amino group from an amino acid to alpha-ketoglutarate to form
glutamate and a alpha-keto acid. Aminotransferases require PLP and PMP as cofactors.

13.12 Glutamate Dehydrogenase

Glutamate dehydrogenase deaminates glutamate to produce alpha-ketoglutarate and ammonia. This
reaction produces an NADPH from NADP+ (or NADH from NAD+) and consumes one H2O.
This enzyme is inhibited by GTP and ATP with a delta G of 30 kilojoules/mol.
13.13 Glutamate-Aspartate Aminotransferase
Glutamate-Aspartate Aminotransferase moves the alpha-amino group from glutamate to
oxaloacetate to form alpha-ketoglutarate and aspartate. Glutamate-aspartate aminotransferase
require PLP and PMP as cofactors.

13.20 Carbon Skeleton Metabolism

The carbon skeletons from amino acids are shuttled to the TCA cycle where they are used to
generate energy in the form of NADH or used to produce glucose via gluconeogenesis. Mammalian
cells often generate as much as 20% of their energy by this method. Two fates await the carbon
skeletons once they enter the TCA cycle - they are either gluconeogenic (green) or ketogenic (blue).
Click on the substrate labels for more information.
13.30 Urea Cycle
The urea cycle is utilized to detoxify ammonia by generated by deamination and other biochemical
processes in land animals. The ammonia is converted to urea which is then excreted by the kidneys.
Without the urea cycle, or the ability to excrete ammonia as do fish, toxic levels of this nitrogenous
waste would soon accumulate. Organisms that live in very arid environments will excrete uric acid
because it requires less water for excretion. The urea cycle is illustrated below. Click on the blue
enzyme labels and the substrate labels for more information.

13.30.1 Carbamoyl Phosphate Synthetase

Carbamoyl Phosphate Synthetase combines NH4 and HCO3, accompanied by the hydrolysis of 2
ATP, to form carbamoyl phosphate. This reaction is irreversible.
13.30.2 Ornithine Transcarbamoylase
Orinthine Transcarbamoylase transfers the carbamoyl group from carbamoyl phosphate to ornithine
to form citruline. This reaction occurs in the mitochondria and liberates inorganic phosphate.

13.30.3 Argininosuccinate Synthetase

Arginiosuccunate Synthetase transfers the amino group from aspartate to citrulline to form
argininosuccinate. This reaction occurs in the cytosol and consumes an ATP.

13.30.4 Arginiase
Arginine cleaves arginine to form urea and ornithine. This reaction occurs in the cytosol.