Carbohydrate pathways

Fructose, Galactose and Mannose

these all feed into the glycolysis pathway but all enter at different stages.

What can be learned from metabolic maps?

they portray the principle reactions of intermediary metabolism. When the major metabolic routes are known and functions are understood then maps become easy to follow.

Metabolome:

a complete set of low molecular weight molecules present in an organism or excerted by it under a given set a circumstances.

Metabolic maps

A metabolic map indicates the reactions of intermediary metabolism and the enzymes that catalyze them. More than 500 different intermediates or metabolites and a greater number of enzymes can be represented here.

Alternative Maps: C

A simplified version of the protein centric view where proteins in the pathway form multifunctional complexes

Adenosine 5'-triphosphate or ATP

ATP is the energy currency of cells. Phototrophs transform light energy into the chemical energy ATP. In heterotrophs, catabolism produces ATP, which drives activities of the cells. ATP cycle carries energy from photosynthesis or catabolism to the energy requiring processes of cells.

Gluconeogenesis

Amphibolic pathway

Anabolic pathways are characteristically energy requiring. They diverge to synthesize many biomolecules.

Anabolim is a synthetic process in which the varied and complex biomolecules are assembled from simpler precursors.

Ethanol fermentation

Anaerobic catabolism of glucose to ethanol only occurs in microorganisms. In the first step, a CO2 is removed and acetaldehyde is formed. The cofactor, thiamine pyrophosphate, TPP, is essential for this step. In the second step acetaldehyde is reduced by NADH to ethanol.

Lactic Acid fermentation

Anaerobic catabolism of glucose to lactate occurs during short bursts of extreme muscular activity. When oxygen cannot be carried to the muscles fast enough to oxidize pyruvate, then the glucose stored in the muscles is used to generate ATP by fermentation, lactate being the end product, Then it is slowly converted back to glucose by gluconeogenesis.

Metabolic Diversity: Carbon Sources

Autotrophs use CO2. Heterotrophs use organic carbon.

Rate-Limiting Step

By down regulating enzyme activity the specific catalyzed step can become the slowest step in a pathway. At that point it has become the rate limiting step. The rate limiting step determines how fast the whole pathway can be carried out.

Metabolism Classification: Photoautotrophs

Carbon source is CO2. Energy source is Light. Electron donors include H2O, H2S, S and other inorganic compounds. Examples include green plants, algae, cyanobacteria, photosynthetic bacteria.

Metabolism Classification: Chemoautotrophs

Carbon source is CO2. Energy source is oxidation reduction reactions. Electron donors are inorganic compounds, such as H2, H2S, NH4, NO2, Fe2, Mn2. examples are nitrifying bacteria, hydrogen sulfur, and iron bacteria.

Metabolism Classification: Chemoheterotrophs

Carbon source is Organic Compounds. Energy source is oxidation reduction reactions. Electron donors are organic compounds like glucose. Examples are all animals, most microorganisms, nonphotosynthetic plant tissues such as roots, photosynthetic cells in the dark.

Metabolism Classification: Photoheterotrophs

Carbon source is organic compounds. Energy source is light. Electron donors are organic compounds. Examples include nonsulfur purple bacteria.

Catabolic pathways are characteristically energy yielding. The converge to a few end products.

Catabolism involves the oxidative degradation of complex nutrient molecules.

Flux. In a living cell, molecules flow through each metabolic pathway at some rate, called the flux. For the cell to function efficiently it must be able to change the flux of molecules through each pathway.

Control of flux is achieved by altering enzymatic activity, and usually several different enzymes contribute to control of the overall flux through a pathway. In addition, flux through a pathway can be influenced by the concentrations of metabolites in that pathway, such as the starting material.

Glycogen synthesis

First glucose-6-phosphate is converted into glucose-1-phosphate by phosphoglucomutase. Glucose units are then activated for transfer by formation on sugar nucleotides.

Delta G and Flux. Because they are far from equilibrium, irreversible reactions are optimal points at which to control flux through a metabolic pathway. Doubling the enzyme activity could increase the rate of the forward reaction substantially, with little effect on the rate of reverse reaction.

Frequently, the first reaction in a metabolic pathway or after a branch point is irreversible and the enzyme catalyzes it is a target for metabolic control. Altering enzyme activity occurs by many mechanisms and on time scales ranging from seconds to days.

Glyerol

Glycerol is produced in the decomposition of triacylglycerols. It can be converted to glycerol-3-P by glycerol kinase. Glycerol-3-P is then oxidized to dehydroxyacetone phosphate by the action of glycerol phosphate dehydrogenase.

Metabolic pathways are compartmentalized within cells.

Glycolysis in cytosol and TCA cycle and oxidative phosphorylation in the mitochondria. Fatty acid synthesis in the cytosol. Fatty acid break down in the mitochondria.

Fates of NADH and pyruvate. Limited amounts of NAD+ are present. NADH must be recycled to NAD+, otherwise it limits glycolysis. NADH can be recycled via aerobic or anaerobic pathways either of which results in further metabolism of pyruvate.

If O2 is available, NADH is re-oxidized in the electron transport pathway, making ATP oxidative phosphorylation. In anaerobic conditions, NADH is reoxidized by lactate dehydrogenase, providing additional NAD+ for more glycolysis.

Allosteric Regulators vs. Regular inhibitors

In allosteric regulators, the curve becomes sigmoidal instead of hyperbolic. There are negative regulators, which is a curve underneath, and positive regulators, which is a curve above.

Committed Step

In enzymology, the committed step is an effectively irreversible enzymatic reactions that occurs at a branch point during the biosynthesis of some molecules. After the step the molecules are "committed" to the pathway and will ultimately end up in the pathways final product.

Rate Limiting Steps

In the second model present in cells, the pathways are almost identical and one or more reactions steps are catalyzed by different enzymes in different directions.

Rate limiting steps

In this example the first committed step in each pathway is the one that is regulated. This makes sure that compounds will only accumulate in from of the blocked step, A or P, and not after this step, preventing the accumulation of compounds that are not needed and wasting important resources.

Alternative Maps: B

Julia Gerrard has proposed that a protein centric view is more informative for some purposes.

Metabolism represents the sum of the chemical changes that converts nutrients into energy and the chemically complex finished products of cells

It consists of hundreds of enzymatic reactions. It is organized into discrete pathways. Transformation of substrates into end products through many specific chemical intermediates.

What experiments can be used to Elucidate metabolic pathways?

Metabolic inhibitors, or genetic mutations where cells need to be supplemented to be able to grow.

Isotopic traces can be used as metabolic probes

Metabolic pathways have been elucidated by use of isotopic forms of elements. Metabolic substrates and intermediates can be labeled with a measurable isotope and then traced through a series of reactions. Two types of isotopes have been used in this way. Radioactive isotopes such as C14 and P32. Stable heavy isotopes such as O18 and N15.

Rate limiting steps

Metabolic pathways require tight regulation so that the proper compounds get produced in the proper amounts. Often the first committed step is regulated by processes such as feedback inhibition and activation. This regulation ensures that pathway intermediates do not accumulate a situation that can be a harmful to the cell. this become more important when there are parallel pathways with the same start and end.

Metabolic Diversity

Organisms show remarkable similarity in major metabolic pathways. Glycolysis is common to almost every cell, and almost all organisms are capable of glucose degradation and ATP synthesis via glycolysis

Metabolic Diversity

Oxygen is essential for aerobes. Obigate anaerobes are poisoned by oxygen. The flow of energy in the biosphere and the carbon and oxygen cycles are intimately related. The impetus driving the cycle is light energy.

Organization in pathways

Pathways consiist of sequential steps. The enzymes may be separate or they may form a multienzyme complex, or it may be a membrane bound system. Multienzyme complexes are more common than once thought.

Metabolic Diversity

Photoautotrophs utilize light energy to drive the synthesis of organic molecules from atmospheric CO2 and water. The organic molecules are used by hetertrophic cells as building blocks or precursors. CO2 is the end product of hetertrophic carbon metabolism.

Metabolic Diversity:; Energy Source

Phototrophs use organic carbon. Chemotrophs use organic and inorganic electron donors.

Anabolic and Catabolic Processes

Some pathways serve both in catabolism and anabolism; such pathways are amphibiolic. Anabolic and catabolic pathways involving the same products are not the same, however some steps may be common to both. Others must be different to ensure that each pathway is spontaneous, and also allows regulation mechanisms to turn one pathway on and another off.

Far From Equilibrium Reactions

The delta G for metabolically irreversible reactions is either highly positive or highly negative. This is mainly due to Delta G standard being highly positive or negative. The actual concentrations of reactants and products have very little effect on Delta G itself.

Compartmentalization of gluconeogenesis

The pyruvate carboxylase reaction takes place in the matrix of the mitochondrion. The pyruvate can be converted into acetyl-CoA, for use in the TCA cycle, an anaplerotic reactions and then to citrate for fatty acid synthesis. Alternatively it can be converted into oxaloacetate for use in gluconeogenesis.

Allosteric Regulation

The regulation of an enzyme by binding an effector molecule at a site other than the enzymes active site. The site to which the effector binds is termed the allosteric or regulatory site. Binding often results in conformational change, involving protein dynamics.

Alternative Maps. A

The traditional view of a metabolic parhway is metabolite-centric

Nonlinear Metabolic Pathways

There are three types: A. Converging, catabolic. B. Diverging, anabolic. C. cyclic, in which one of the starting materials, oxaloacetate in this case, is regenerated and reenters the pathway.

NAD+ and NADP+ collect electrons released in catabolism. The substrates of catabolism are good sources of chemical energy because their carbon is reduced. The oxidative reactions of catabolism release reducing equivalents from these substrates, often in the form of hydride ions.

These hydrides are transferred to NAD+ or NADP+ molecules reducing them to NADH or NADPH. NADPH in turn passes these reducing equivalents to other acceptors for anabolic biosynthetic reactions. The reductive equivalent from NADH enter the oxidative phosphorylation pathway with O2 as the ultimate electron acceptor producing ATP in the process.

Delta G and Flux

Typical metabolic pathways contain some reactions with delta G near zero under physiological conditions. These are at or near equilibrium, and are said to be reversible. Reactions with a large negative delta G are said to be irreversible. The delta G of the reverse reaction is so large and positive that normal fluctuations in metabolite concentration do not make the reverse reaction occur to any substantial degree.

Metabolomics

a systematic identification and quantitation of all these metabolites in a given organism or sample

Glycolysis phase 1

amphibolic pathway

Mass Spectrometry, MS nuclear magnetic resonance, NMR

powerful techniques for metabolic analysis. MS offers unmatched sensitivity for detection of metabolites at low concentrations. NMR provides remarkable resolution and discrimination of metabolites in complex mixtures.