Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2010

Lecture Notes: 5 April

© R. Paselk 2006



In order to provide glucose for vital functions such as the metabolism of RBC's and the CNS during periods of fasting (greater than about 8 hrs after food absorption in humans), the body needs a way to synthesis glucose from precursors such as pyruvate and amino acids. This process is referred to as gluconeogenesis. It occurs in the liver and in kidney. Most of Glycolysis can be used in this process since most glycolytic enzymes are operating at equilibrium. However three irreversible enzymes must be bypassed in gluconeogenesis vs. glycolysis: Hexokinase, Phosphofructokinase, and Pyruvate kinase. Phosphofructokinase, and/or hexokinase must also be bypassed in converting other hexoses to glucose.

Pyruvate carboxylase

Let's begin with pyruvate. How is pyruvate converted to PEP without using the pyruvate kinase reaction? Formally, pyruvate is first converted to oxaloacetate, which is in turn converted to PEP. In the first reaction of this process Pyruvate carboxylase adds carbon dioxide to pyruvate with the expenditure of one ATP equivalent of energy. Biotin, a carboxyl-group transfer cofactor in animals, is required by this enzyme:

Diagramatic Pyruvate Carboxylase reaction

The reaction takes place in two parts on two different sub-sites on the enzyme. In the first part biotin attacks bicarbonate with a simultaneous attack/hydrolysis by bicarbonate on ATP, resulting in the release of ADP and inorganic phosphate (note the coupling by the enzyme of independent processes in this reaction):

Molecular mechanism of part 1 of Pyruvate carboxylate reaction

Note that the 14 Angstrom arm of biocytin allows biotin to move between the two sites, in this case carrying the activated carboxyl group. In the second site a pyruvate carbanion then attacks the activated carboxyl group, regenerating the biotin cofactor and releasing oxaloacetate:

Molecular mechanism of part 2 of Pyruvate carboxylate reaction

Phosphoenolpyruvate carboxykinase (PEPCK)

Pyruvate carboxylase is followed by the Phosphoenolpyruvate carboxykinase (PEPCK) reaction. In this reaction oxaloacetate is decarboxylated with a simultaneous phosphorylation by GTP to give GDP:


In eukaryotes the transformation of Pyruvate to Phosphoenol pyruvate (PEP) is further complicated by the fact that oxaloacetate is generated from pyruvate and TCA Cycle intermediates only in the mitochondria, while PEP is converted to glucose in the cytosol. And oxaloacetate cannot cross the mitochondrial membrane efficiently (it is present at concentrations way below the KM of the carrier, so it must be converted into malate or aspartate in order to cross as summarized in the diagram: gluconeogenesis in the liver.

Fructose-bisPhosphatase (F-bisPase)

The glycolytic reactions from PEP to F-1,6-bisP are fully reversible, but a second bypass is required to get around PFK. This is accomplished by Fructose-bisPhosphatase (F-bisPase):

diagram of F-bisPase

Glucose-6-Phosphatase (G-6-Pase)

And finally the third irreversible reaction, Glucokinase, is bypassed by Glucose-6-Phosphatase (G-6-Pase):

Diagram of G-6-Pase reaction

Note that by hydrolyzing off the phosphates in these two reactions rather than recovering ATP they are made energetically favorable. Thus both glycolysis and gluconeogenesis can be favorable processes, even though they proceed in opposite directions: For Glycolysis, free energy= about - 80 kJ, and for Gluconeogenesis, free energy= about -36 kJ due to differences in ATP. Or another way: if take glucose to pyruvate and then back to glucose again, 4 ATP's are lost.

In order to accomplish gluconeogenesis reducing equivalents in the form of NADH must be provided to the GA-3-P DH enzyme and ATP must be provided to PGA Kinase. The obvious source for these is the Mitochondria, but then there are transport problems. Examples of two possible balanced gluconeogenesis are shown in the handouts: Gluconeogenesis from Lactate and Gluconeogenesis form Pyruvate. Other systems can also be involved, but we will not look at them.


Let's turn now to the fate of pyruvate in aerobic tissues. Pyruvate must first be transported into the mitochondria, where it can then be oxidized to give acetyl CoA, which can then be used to make fat for storage or it can be further oxidized to carbon dioxide via the Kreb's TCA Cycle.

FYI - DH Complex Protein Structure

Structure of Pyruvate DH Complex from bovine kidney: MW = 7 x 106 (without associated Phosphatase)

  1. Transacetylase: 60 subs x 52,000 = 3.1 x 106 arranged as a pentagonal dodecahedron
  2. Dihydrolipoyl DH: 5 dimers x 110,000 = 5 x 105 on faces of dodecahedron
  3. Pyruvate DH: 10 tetramers x 154,000 = 1.54 x 106 on edges of dodecahedron

The oxidation of pyruvate to acetyl CoA is accomplished by the Pyruvate Dehydrogenase complex, a large, multi-component enzyme with three main enzyme subunits. The reactions of the Pyruvate DH Complex are outlined in the diagram.

The first enzyme of this complex, pyruvate dehydrogenase (note that, unusual for the DH appellation, there is no direct NAD+ or FAD involvement), catalyzes two sequential reactions. In the first reaction, catalyzed by the alpha subunit of the enzyme, the coenzyme Thiamine Pyrophosphate (TPP), with a highly acidic carbon (a stable carbanion), attacks pyruvate at C-2 with the loss of carbon dioxide to give a covalent coenzyme-substrate intermediate. In the second reaction, catalyzed by the beta subunit, the ketol group is oxidatively transferred to one of the sulfurs of the lipoyl coenzyme on the second enzyme of the complex, dihydrolipoyl transacetylase, to give an acetyl-lipoamide intermediate.

The lipoamide of dihydrolipoyl transacetylase constitutes a long arm which may now move the acetyl group from the active site of pyruvate DH to its own active site where the lipoamide is exchanged for Coenzyme A-SH. (On the mammalian enzyme the 60 subunits of the transacetylase seem to form a pool of lipoyl groups among which the acetyl groups are freely exchanged.)

structure of lipoate

Note that in the reactions of dihydrolipoyl transacetylase the lipoamide has been reduced from a disulfide to two sulfhydryl groups. In order to continue operation lipoamide must be reoxidized and that is accomplished by the final enzyme of the complex, dihydrolipoyl dehydrogenase. The reactions catalyzed by this enzyme are complex, but the net result is the transfer of two electrons from the lipoamide to NAD+ to give NADH.

Overall then the Pyruvate DH Complex converts pyruvate into acetyl CoA in a physiologically irreversible reaction with the release of carbon dioxide and the capture of an electron pair as a hydride ion on NADH. Note the cofactors involved for this reaction sequence: TPP, FAD, Mg2+, lipoamide, Coenzyme A, and NAD+.

Pathway Diagrams

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Last modified 5 April 2010