Pathways

anabolism and catabolism

Anabolism, as in ‘anabolic steroids’, refers to those metabolic processes that utilize energy to biosynthesize complex molecules and to generate growth.

The reverse process is catabolism, whereby nutrients are broken down to release energy. Catabolic processes provide intermediates for synthetic or further catabolic pathways and release energy, usually as the energy carrier molecules ATP and NADPH.

The following mnemonic may help in remembering the difference: "A B C D" : Anabolism = Biosynthesis ; Catabolism = Degradation

anabolic pathways : for a complete list see topics or sidebar • acetyl CoA pathway • Calvin cycle • C-3 • C-4 • CAM • HMG-CoA-reductase pathway • Isoprenoid biosynthesis in plants methylerythritol phosphate & HMG-CoA-reductase pathway • Light-reactions • MVA independent • Nonoxygenic photosynthesis • Oxygenic photosynthesis • Photosynthesis Overview • Photophosphorylation •

catabolic pathways: for a complete list see topics or sidebar • anaplerotic reactions • beta-oxidation • glycolysis • glyoxylate cycle • Krebs cycle • oxidative phosporylation •

Labels: anabolism, catabolism, mnemonic

catabolism

(Image at left - click to enlarge) Catabolic processes provide intermediates for synthetic or further catabolic pathways and release energy, usually as the energy carrier molecules ATP and NADPH.

In the first stage of catabolism, the storage forms of proteins, triacylglycerols, and polysaccharides are broken down in the cell's cytoplasm into amino acids, fatty acids, and glucose, respectively (1).

Within the mitochondrion, the intermediates generated by catabolism of proteins, fats, and sugars (2) are delivered to the Krebs tricarboxylic (citric) acid cycle (3). The catabolism of proteins delivers pyruvate, acetyl-CoA, and oxaloacetate to the Krebs TCA cycle. Beta-oxidation of fatty acids ultimately delivers acetyl-CoA. Glycolysis generates acetyl-CoA via pyruvate.

Products of the Krebs cycle are then processed by oxidative phosporylation (4).

electron donor

An electron donor passes an electron from one molecule to a second chemical compound, an electron acceptor. An electron donor is a reducing agent that is itself oxidized in the process of donating an electron

.............Donor –e^-→ Acceptor
...reducing agent –e^-→ oxidizing agent
..........oxidized –e^-→ reduced

Often the organic molecule that provides a source of electrons (donor molecule) will also serve as a source of cell carbon.

Oxidation Involves Loss of electrons, and Reduction Involves Gain of electrons (mnemonic 'oilrig').

Carbon dioxide is the most abundant form of carbon on earth and many microbes are capable, provided with enough ATP and NADH, of incorporating CO2 into cell carbon. This process is termed CO2 fixation. Organisms capable of fixing CO2 are classified as autotrophs and these include phototrophs and lithotrophs. The bacterium Pseudomonas cepacia is capable of growth on benzene (an organic molecule) alone, generating energy, via respiration and synthesizing all needed carbon molecules from it.

There are four pathways that are used for the fixation of CO2:
1. the Calvin cycle or ribulose bisphosphate pathway (RuBP),
2. the reverse tricarboxyclic acid cycle or reductive tricarboxylic acid pathway (rTCA),
3. the reductive acetyl CoA pathway (rACA),
4. the 3-Hydroxypropionate cycle.

Electron donors transfer electrons to electron acceptors during cellular respiration, resulting in the release of energy for utilization in metabolic pathways. Microorganisms, such as bacteria, obtain energy by transferring electrons from an electron donor to an electron acceptor, releasing energy for use by cellular machinery.

electron transfer chain

Electron transport chains
Electron transport chains (electron transfer chains) are biochemical reaction sequences that ultimately utilize ATP synthase to produce ATP, the energy currency of life.

Only two sources of energy are available to living organisms: oxidation-reduction (redox*) reactions and photic energy (photosynthesis). Chemotrophic organisms employ redox reactions to produce ATP. Phototrophic organisms employ light as their initial energy source. Both chemotrophs and phototrophs utilize electron transport chains to convert energy into ATP.

Table Electron Transport vs Oxidative Phosphorylation :

Oxidation involves loss of electrons, and reduction involves gain of electrons (mnemonic 'oilrig').

Redox reactions
*Because electrons may not be transfered in redox reactions, oxidation is better defined as an increase in oxidation number, and reduction as a decrease in oxidation number. Oxidants are typically highly electronegative molecules. Redox reactions are chemical reactions in which electrons are transferred from a donor molecule to an acceptor molecule. The reductant (electropositive metal, hydride) transfers electrons to the electronegative oxidant. The Gibbs free energy of the reactants compared to the products provides the chemical potential energy for redox reactions.

The Gibbs free energy is the energy available (“free”) to do work. Any reaction that decreases the overall Gibbs free energy of a system (reactants → products) will proceed spontaneously with release of that energy. The transfer of electrons from a high-energy donor molecule to a lower-energy acceptor molecule can be spatially separated into a series of intermediate redox reactions within an electron transport chain. The spatial separation permits biological control of the reactions.

Many metabolic reactions involve the storage and release of biological energy by means of redox reactions. Photosynthesis involves the reduction of CO2 into sugars along with the oxidation of H2O into O2. The carbon fixing, light-independent reactions of photosynthesis employ the Calvin cycle ( C-3) in most organisms, though carbon fixation may also employ the 3-hydroxypropionate cycle, the reductive acetyl CoA pathway, or the reverse tricarboxyclic acid cycle. The reverse reaction, respiration, oxidizes sugars to produce CO2 + H2O.

In intermediate steps, reduction of oxygen accompanies the employment of reduced carbon compounds to reduce nicotinamide adenine dinucleotide (NAD+ → NADH), which then contributes to the creation of a proton gradient, which in turn drives the synthesis by ATP synthase of adenosine triphosphate (ADP + Pi → ATP).

Within animal cells, mitochondria perform similar functions to the photophosphorylation reactions within the chlorosomes of prokaryotes, the phycobilin studded thylakoid membranes of Cyanobacteria, or the chloroplasts of plant cells.

The term redox state is often used to describe the balance of NAD+/NADH and NADP+/NADPH in a biological system such as a cell or organ. The redox state is reflected in the balance of several sets of metabolites such as lactate and pyruvate, and beta-hydroxybutyrate and acetoacetate whose interconversion is dependent on these ratios. An abnormal redox state can develop in a variety of deleterious situations, such as hypoxia, shock, and sepsis.

Within mitochondria, a complex series of transmembrane proteins perform the overall reaction of oxidative phosporylation:

NADH → Complex I → Q → Complex III → cytochrome c → Complex IV → O2
.................................. ↑
...........................Complex II

Within chloroplasts, the membrane-bound pigment-protein complexes of photosystem I perform cyclic photophosphorylation, and the sequence of photosystem I & photosystem II perform noncyclic photophosphorylation (image - Z-scheme).

anaplerotic reactions

Anaplerotic reactions form intermediates for the Krebs, TCA, citric acid cycle.

Two major types of anaplerotic reactions have been observed:
1. Anaplerotic carbon dioxide fixation such as the pyruvate carboxylase reaction.
2. Glyoxylate cycle used by acetogens, microorganisms that can grow on acetate as a sole carbon source in this modified TCA cycle. The enzymes isocitrate lyase and malate synthase, which convert isocitrate into succinate and malate (via glyoxylate) into the glyoxylate cycle.

Four reactions are classed as anaplerotic, although the production of oxaloacetate from pyruvate is probably the most important physiologically. The anaplerotic reactions are:

1. carboxylation of pyruvate to oxalocetate (malate can be formed similarly, though thermodynamics favour the reaction malate to pyruvate)

pyruvate + CO2 + H2O + ATP →pyruvate carboxylase→ oxaloacetate + ADP + Pi + 2H⁺

2. transamination of aspartate to oxaloacetate by aspartate aminotransferase, which allows incorporation of acetyl CoA into citrate via citrate synthase in glyoxysomes.

3. hydration of glutamate to α-ketoglutarate

glutamate + NAD⁺ + H2O →glutamate-dehydrogenase→ NH4⁺ + α-ketoglutarate + NADH + H⁺

4. β-oxidation of fatty acids to succinyl-CoA

acetyl CoA pathway

The acetyl CoA pathway is also called the Wood Ljungdahl Pathway. The acetyl-CoA pathway comprises two reductive branches, the methyl branch and the carbonyl branch, both of which reduce CO2 and fix CO2-derived carbon into covalently bonded forms.

The pathway allows bacteria to grow on sugars or on H2/CO2 :
4H2 + 2 CO2 = CH3COOH + 2 H2O
4H2 + 2 CO2 = CH3COOH + 2CO.

Althought the acetyl-CoA pathway can be presented in a cyclic form (Wood and Ljungdahl), it is a linear process that does not depend on multi-carbon intermediates to which CO2 is fixed in a cyclic fashion. For example, the Calvin (C-3) cycle is a CO2-fixing processes that depends upon ribulose biphosphate for the initial fixation of CO2, and the reductive (reverse) tricarboxylic acid cycle depends upon oxalacetate for the initial fixation of CO2. Although the cofactors and electron carriers of the acetyl-CoA pathway pathway cycle between different states, the pathway itself is linear relative to carbon flow.

AcetylCoA and acetacetylCoA: amino acids : mnemonic:"A Lighter Lease" (A LyTr LeIs): A=AcetylCoA or Acetoacetyl CoA Ly=Lysine Tr=Tryptophan Le=Leucine Is=Isoleucine

external table - enzymes of Acetyl CoA pathways : Saccharomyces cerevisiae carbon monoxide dehydrogenase pathway : Arabidopsis thaliana carbon monoxide dehydrogenase pathway : MetaCyc reductive acetyl coenzyme A pathway :