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Chapter 17 Metabolism: An Overview

Dr Khairul Ansari

Metabolism
Metabolism- sum of the chemical changes that convert nutrients What are the anabolic and catabolic processes that satisfy the metabolic needs of the cell? Is metabolism similar in different organisms? Prominent metabolic pathways are virtually ubiquitous among organisms. Living organisms exhibit metabolic diversity

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Metabolic diversity
Classification based on carbon source- e.g. (a) Autotrophs (b) Heterotrophs Classification based on energy source- e.g. (a) Phototrops (b) Chemotrops

Autotrophs use CO2; Heterotrophs use organic carbon; Phototrophs use light; Chemotrophs use organic and inorganic electron donors

Metabolic diversity
Prokaryotes are more diverse than eukaryotes Prokaryotes can be -chemoheterotrophic -Photoautotrophic -Photoheterotrophic -chemoautotrophic No Protists are chemoautotrophic Fungi and animals are exclusively chemoautotrophic Plants are mostly photoautotrophic with heterotrophic exception.

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Oxygen in Metabolism
- Aerobes - Anaerobes Obligate aerobes- Homo sapiens Facultative anaerobes- E coli Obligate anaerobes-Clostridium (associated with food poisoning)

The Sun is Energy for Life

Phototrophs use light to drive synthesis of organic molecules Heterotrophs use these as building blocks CO2, O2, and H2O are recycled

Figure 17.1 The flow of energy in the biosphere is coupled to the carbon and oxygen cycles

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Calcium Carbonate-A biological sink of CO2

Ca2+ + 2HCO3- = CaCO3 + H2CO3 H2CO3= H20 + CO2 H2O + CO2 Carbohydrate + O2 O2 is reduced to Water CO2 is released to atmosphere Solar energy is converted to chimerical energy

What can be learned from metabolic maps?

Portray the principal reactions of the intermediary metabolism of carbohydrates, lipids, amino acids and their derivatives. How do anabolic and catabolic processes form the core of metabolic pathways? What experiments can be used to elucidate metabolic pathways? What can the metabolome tell us about a biological system? What food substances form the basis of human nutrition?

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What can be learned from metabolic maps?

Organisms show remarkable similarity in their major metabolic pathways This is evidence that all life descended from a common ancestral form And yet, living things also exhibit metabolic diversity Oxygen is essential for aerobes, but obligate 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

17.2 What Can Be Learned From Metabolic Maps?

Metabolism consists of catabolism and anabolism Catabolism: degradative pathways Usually energy-yielding Anabolism: biosynthetic pathways Usually energy-requiring Metabolic maps portray the principal reactions of intermediary metabolism When the major metabolic routes are known and their functions are understood, the maps become easy to follow, in spite of their complexity

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17.2 What Can Be Learned From Metabolic Maps?

Figure 17.2 A metabolic map, indicating the reactions of intermediary metabolism and the enzymes that catalyze them. More than 500 different chemical intermediates, or metabolites, and a greater number of enzymes are represented here.

17.2 What Can Be Learned From Metabolic Maps?

One interesting transformation of the metabolic map represents each intermediate as a black dot and each enzyme as a line In this way, more than a thousand enzymes and substrates are represented by just two symbols A dot connected to a single line must be a nutrient, a storage form, an end product, or an excretory product A dot connected to just two lines is probably an intermediate in one pathway and has only one fate in metabolism A dot connected to three represents an intermediate that has two metabolic fates

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17.2 What Can Be Learned From Metabolic Maps?

17.2 What Can Be Learned From Metabolic Maps?

Figure 17.3 The metabolic map as a set of dots and lines. The heavy dots and lines trace the central energy-releasing pathways known as glycolysis and the citric acid cycle.

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Organization in Pathways
Pathways consist of sequential steps The enzymes may be separate Or may form a multienzyme complex Or may be a membrane-bound system New research indicates that multienzyme complexes are more common than once thought

Alternative Models Can Provide New Insights Into Pathways

Figure 17.4 (a) The traditional view of a metabolic pathway is metabolite-centric. (b) Julia Gerrard has proposed that a protein-centric view is more informative for some purposes. (c) A simplified version of the protein-centric view where proteins in the pathway form multifunctional complexes. (see next slide)

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Alternative Models Can Provide New Insights Into Pathways

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

Multienzyme Systems May Take Different Forms

Figure 17.5 Schematic representation of types of multienzyme systems carrying out a metabolic pathway. (a) Physically separate, soluble enzymes with diffusing intermediates. (b) A multienzyme complex. Substrate enters the complex and becomes bound and then modified by E1 to E5. No intermediates are free to diffuse away. (c) A membrane-bound multienzyme system.

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17.3 How Do Anabolic and Catabolic Processes Form the Core of Metabolic Pathways?
Catabolic pathways are characteristically energy-yielding Anabolic pathways are characteristically energy-requiring Catabolism involves the oxidative degradation of complex nutrient molecules- resulting formation of simpler molecules Catabolic reactions are usually exergonic in nature (energy is stored in ATP, NADH, NADPH etc) Anabolism is a synthetic process in which the varied and complex biomolecules are assembled from simpler precursors Generally endergonic in nature (consumed stored energy from ATP, NADH, NADPH etc)

Figure 17.6 Anabolism and Catabolism are Interrelated

Products from one provide substrates for the other.

Many intermediates are shared between anabolism and catabolism.

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Anabolism and Catabolism Are Not Mutually Exclusive

Catabolic pathways converge to a few end products In aerobic catabolism the end products are mostly CO2, H2O and NH4 In 1st stage of aerobic catabolism the macromolecules breakdown to their building blocks In 2nd stage building blocks degraded to limited set of simpler product In 3rd stage the end products mostly CO2, H2O and NH4 are produced Anabolic pathways diverge to synthesize many biomolecules Some pathways serve both in catabolism and anabolism Such pathways are amphibolic Cell tightly regulates both Catabolic and anabolic pathways Catabolic and anabolic pathways often localized within different cellular compartments

Comparing Pathways
Anabolic & catabolic pathways involving the same product are not the same E.g. Acetyl-Co-A is produced by both anabolic & catabolic pathways Several intermediates of TCA cycle and many metabolites serve both in anabolic & catabolic pathways Some steps may be common to both Others must be different - to ensure that each pathway is spontaneous/thermodynamically favorable This also allows regulatory mechanisms to turn one pathway on and the other off

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The Pathways of Catabolism Converge to a Few End Products

Figure 17.7 The three stages of catabolism. Stage 1: Proteins, polysaccharides, and lipids are broken down into their component building blocks. Stage 2: The building blocks are degraded into the common product, the acetyl groups of acetyl-CoA. Stage 3: Catabolism converges to three principal end products: water, carbon dioxide, and ammonia.

Metabolic Regulation Requires Different Pathways for Oppositely Directed Metabolic Sequences

Figure 17.8 Parallel pathways of catabolism and anabolism must differ in at least one metabolic step so that they can be regulated independently. Shown here are two possible arrangements of opposing catabolic and anabolic sequences between A and P. (a) Parallel sequences proceed by independent routes. (b) Only one reaction has two different enzymes.

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ATP Serves in a Cellular Energy Cycle

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

Figure 17.9 The ATP Cycle in Cells

ATP is formed via photosynthesis in phototrophic cells or catabolism in heterotrophic cells.

Energy-requiring cellular activities are powered by ATP hydrolysis, liberating ADP and Pi.

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The Substrates of Catabolism Contain Relatively Reduced Forms of Carbon

Figure 17.10 Comparison of the state of reduction of carbon atoms in biomolecules. Chains of CH2- groups are the most energy-rich form of reduced carbon in the biosphere. Carbon dioxide is the final product of catabolism and the most oxidized form of carbon in the biosphere.

NAD+ Collects Electrons Released in Catabolism

The substrates of catabolism proteins, carbohydrates, and lipids 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+ molecules, reducing them to NADH NADH in turn passes these reducing equivalents to other acceptors The ultimate oxidizing agent, O2, is the final acceptor of electrons, becoming reduced to H2O

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NAD+ Collects Electrons Released in Catabolism

Figure 17.11 Hydrogen and electrons released in the course of oxidative catabolism are transferred as hydride ions (H:-) to the pyridine nucleotide, NAD+, to form NADH + H+ in dehydrogenase reactions.

NADPH Provides the Reducing Power for Anabolic Processes

Whereas catabolism is oxidative, anabolism is reductive Biosynthesis typically relies on reducing equivalents from NADPH NADPH can be viewed as the carrier of electrons from catabolic reactions to anabolic reactions In photosynthesis, light energy is used to pull electrons from water and transfer them to NADP+ O2 is a by-product of this process Oxidation reactions are exergonic in nature and energy released is coupled with ATP formation by oxidative phosphorylation NAD+-NADH acts as shuttle that carries electron released from catabolic substrates to mitochondria where they are transferred to O2

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NADPH Provides the Reducing Power for Anabolic Processes

Whereas catabolism is fundamentally an oxidative process, anabolism is, by its contracting nature reductive Biosynthesis begins with oxidized substances such as CO2. When glucose is synthesized from CO2 during photosynthesis reducing power (NADPH) is required NADPH is generated when NADP+ is reduced with electron from hydride ion. In heterotrophs these electrons are removed from fuel molecule by NADP+ specific dehydrogenases During photosynthesis the light energy is used to pull the electrons from water and transfer them to NADP+ , O2 is by-product

Figure 17.12 Transfer of reducing equivalents from catabolism to anabolism via the NADPH cycle.

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Vitamins and Metabolism

In addition to NADPH and NADP+ several small molecules (nutrients and vitamins) are essential for metabolism Vitamins are not synthesized by cell Supply externally from food Either water or fat soluble Except Ascorbic acid (Vitamin C) , most of the water soluble vitamins are coenzymes Coenzymes acts as carrier of specific functional group (such as methyl or acetyl) Coenzymes modified in those reactions are converted back to its natural forms by enzymes small amount is required

A Summary of Vitamins and Coenzymes Discussed Elsewhere in the Text

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17.4 What Experiments Can Be Used to Elucidate Metabolic Pathways?

Eduard Bchner (late 19th century) showed that fermentation of glucose in yeast cells yielded ethanol and carbon dioxide This led to a search for intermediates of glucose breakdown Metabolic inhibitors were important tools for elucidating the pathway steps. Mutations also were used to create specific metabolic blocks

17.4 What Experiments Can Be Used to Elucidate Metabolic Pathways?

Inhibition or mutation of an enzyme accumulates its subtract and may that may cause (a) Lethality (b) Toxicity to the organism

Figure 17.13 The use of inhibitors to reveal the sequence of reactions in a metabolic pathway. (a) Control. (b) Plus inhibitor. Intermediates upstream of the metabolic block (B, C, and D) accumulate, revealing themselves as intermediates in the pathway. The concentration of intermediates lying downstream (E and F) will fall.

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Isotopic Tracers 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 14C and 32P Stable heavy isotopes, such as 18O and 15N Heavy isotopes endow the compounds in a way that they appear with slightly greater mass and can be separated using mass spectrometry.

Isotopic Tracers Can Be Used as Metabolic Probes

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Isotopic Tracers Can Be Used as Metabolic Probes

Figure 17.14 One of the earliest experiments using a radioactive isotope as a
metabolic tracer. Melvin Calvin found that 3-phosphoglycerate (PGA) is the first metabolite labeled when algae are incubated with radioactive CO2.

NMR Spectroscopy is a Noninvasive Metabolic Probe

The nuclei of certain atomic isotopes have magnetic moments Such nuclei can absorb radio-frequency energy in the presence of a magnetic field at a unique resonant frequency The nuclear magnetic resonance (NMR) absorption is influenced in predictable ways by the chemical nature of its neighboring atoms and by its dynamic behavior (motion) For these reasons, NMR signals can provide a wide range of structural and dynamic information about biomolecules

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NMR Spectroscopy is a Noninvasive Metabolic Probe

Figure 17.15 The metabolism of a living subject can be observed in real time with NMR spectroscopy.

Metabolic Pathways are Compartmentalized Within Cells

Figure 17.16 Fractionation of a cell extract by differential centrifugation.

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Metabolic Pathways are Compartmentalized Within Cells

Figure 17.16 continued. Fractionation of a cell extract by differential centrifugation.

Metabolic Pathways are Compartmentalized Within Cells

Figure 17.17 Compartmentalization of glycolysis, the citric acid cycle, and oxidative phosphorylation.

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17.5 What Can the Metabolome Tell Us About a Biological System?

The metabolome is the complete set of low-molecular weight molecules present in an organism and excreted by it under a given set of circumstances Metabolomics is the systematic identification and quantitation of all these metabolites in a given organism or sample Mass spectrometry (MS) and nuclear magnetic resonance (NMR) are both powerful techniques for metabolomic analysis MS offers unmatched sensitivity for detection of metabolites at low concentrations NMR provides remarkable resolution and discrimination of metabolites in complex mixtures

Figure 17.18 Mass spectrometry offers remarkable sensitivity for metabolomic analyses.

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17.5 What Can the Metabolome Tell Us About a Biological System?

Figure 17.19 NMR provides remarkable resolution and discrimination of metabolites in complex mixtures. (a) One-dimensional NMR of 26 smallmolecule standards. (b) Two-dimensional NMR of the same set of standards overlaid on an aqueous extract of Arabidopsis

Fluxomics
The true phenotype of a cell depends not only on knowledge of all the metabolites in a cell at any given moment, but also on information about the flow of metabolites through its metabolic network The quantitative study of metabolite flow, or flux, is termed fluxomics The fluxome is all of the metabolic fluxes in a metabolic network It thus represents systems-level information on those cellular processes defined by the metabolic network The fluxome is a dynamic view of the metabolic processes in a cell or organism

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17.6 What Food Substances Form the Basis of Human Nutrition?

Protein is a rich source of nitrogen and also provides essential amino acids Carbohydrates provide needed energy and essential components for nucleotides and nucleic acids Lipids provide essential fatty acids that are key components of membranes and also important signal molecules Fiber whether soluble or insoluble can be a beneficial component in the human diet

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