Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 432

Biochemistry

Spring 2009

Lecture Notes: 28 January

© R. Paselk 2006
 
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The Dark Reactions

(Calvin Cycle), cont.

In the reaction catalyzed by Ribulose-1,5-bis phosphate carboxylase (RuBisCo), carbon dioxide is added to the keto-carbon, giving a six carbon sugar which can now be cleaved into the two three carbon PGA's. As shown in the figure, RuBisCo catalyses the addition of a carbon dioxide to ribulose-1,5-bis phosphate, which then splits to give two molecules of 3-PGA:

Reaction diagram for RuBisCo mechanism

Note that in the rearrangement resulting with the carboxylation, the final three carbons become essentially a PGA, in particular the keto carbon now has the same oxidation state as an acid carbon (recall that an alcohol elimination involves no formal oxidation, thus a C-C bond is formally the same oxidation as a C-OH bond). Of course the upper portion also now looks about like a PGA too. The attack by water and subsequent cleavage releases the first 3-PGA, leaving a carbanion on the enzyme. The enzyme constrains the addition of a proton to this achiral intermediate to give only the 3-PGA of the proper chirality.

FYI - RUBISCO Structure

The enzyme itself is large (MW= 560,000 daltons), consisting of 8 large (MW= 56,000) catalytic subunits and 8 small (MW= 14,000) regulatory subunits. The eight catalytic subunits form the core of the enzyme, with the interfaces between them forming eight catalytic sites. The enzyme requires magnesium for activity, and there is a copper in each oligomer.

Once 3-PGA is formed the reactions of glycolysis/gluconeogenesis interconvert it to Ga-3-P and F-6-P, intermediates of the pentose-P pathway, and DHAP. These intermediates are then interconverted to reform Ru-5-P. For every three carbon dioxides incorporated by RuBisCo, one extra 3-PGA is formed which can be used for the synthesis of glucose etc. The overall stoichiometry of the cycle is shown on the Calvin Cycle Flow Diagram. This diagram emphasizes recycling vs. incorporation. (packet)

C4 Plant Photosynthesis

Background on plant strategies under high heat/light low water conditions

C4 Plants: These plants thrive in environments with high temperatures and low humidities where the stomata in the leaves must be kept closed during much of the day in order to avoid water loss. Under these circumstances carbon dioxide concentrations fall in the leaves while oxygen rises, favoring photorespiration over photosynthesis and greatly reducing productivity. (In photorespiration oxygen binds competitively with carbon dioxide at the active site of RuBisCo: the net result is that Ru-1,5-bis P is oxidized and energy and carbon are lost instead of gained.) In C4 plants the photosynthesizing cells are protected from the atmosphere by a layer of mesophyll cells. In these cells the PEP carboxylase reaction is used to capture carbon dioxide, with the resulting oxaloacetate carbons transported to the photosynthesizing cell. [[text Figure 20-23] {overhead} The first compound incorporating the carbon dioxide thus has four carbons and hence the name (unlike in the Calvin cycle where the first labeled compound, PGA is C3). The carbon dioxide is then released and used in the Calvin cycle. Note that these plants are investing extra energy from ATP to concentrate carbon dioxide. However, they tend to live in high light environments where cyclic Photophosphorylation can be used to make up this extra ATP with little trouble. A variety of transport mechanisms exist in different plant groups. In another mechanism, CAM carbon dioxide is taken up at night and incorporated into malate. The malate is then used the next day to make PEP. Thus the plants can keep their stomata closed during the day.

Fatty Acid Biosynthesis

[Reference: Wakil, S. J., Stoops, J. K., and Joshi, V. C., Ann. Rev. Biochem. 52, 537-79 (1983).]

Chemically fatty acid biosynthesis is a review of of beta-oxidation and pyruvate carboxylation. Want to reverse the reactions of beta-oxidation. But beta-oxidation is highly favorable as is, and want synthesis to also be favorable - obviously some variations in the pathways are needed.

Two reactions enable the synthesis pathway:

The first step in fatty acid biosynthesis is to activate acetyl-CoA by the addition of a carbon dioxide using Acetyl-CoA carboxylase. This reaction is chemically identical to the Pyruvate carboxylase reaction seen in Chem 431 (Lecture 34, Gluconeogenesis):

reaction diagram foracetyl CoA activation by Pyruvate Carbozylase

This reaction is physiologically irreversible and is the flux generating or first committed step of fatty acid biosynthesis. As expected it is regulated. In mammals acetyl-CoA carboxylase is a large enzyme existing as inactive protomers (560,000 MW, 4 subunits, one biotin), which can assemble into active filaments (4 - 10 million MW).

Formation of the filaments (activation) is

As we shall see these are excellent indicators of the fuel status of the cell.

In addition to the activator/inhibitor controls of citrate and fatty acyl-CoA, the enzyme is also under hormonal control (note the similarities to glycogen control):

In mammals Fatty Acid Synthase (FAS) [overhead] catalyzes fatty acid synthesis on a homodimeric enzyme, each monomer of which has seven catalytic activities, and eight sites! (In bacteria such as E. coli there are seven separate enzymes plus an acyl-carrier protein. Plants also have individual proteins for the various activities which are associated in a quaternary complex. In eukaryotes other than plants the FAS are complexes of multifunctional proteins. Note: the numbers in the sites correspond to the numbered reactions of the FA Synthase reactions diagram, below.) The enzyme weighs approximately 500,000 Daltons. [Reference: Maier Timm, Simon Jenni and Nenad Ban. "Architecture of Mammalian Fatty Acid Synthase at 4.5 A Resolution." Science 311(3 March 2006) 1258; mini review comparing fungal and mammalian enzymes - Smith, Stuart. "Architectural Options for a Fatty Acid Synthase." Science 311(3 March 2006) 1251.]

There are two carriers on this complex.

Looking at the the Fatty Acid Synthase reactions (packet):
We now have a beta-ketoacyl group ready to go through the reverse of the reactions of beta-oxidation.


Pathway Diagrams

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Last modified 29 January 2009