chem 4311- chapter17

10/28/2012

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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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Autotrophs use CO2; Heterotrophs use organic carbon; Phototrophs

use light; Chemotrophs use organic and inorganic electron donors

Metabolic diversity

•Classification based on carbon source- e.g. (a) Autotrophs (b)

Heterotrophs

•Classification based on energy source- e.g. (a) Phototrops (b)

Chemotrops

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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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.


•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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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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•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

Organization in Pathways

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 Büchner (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?

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.

Inhibition or mutation of an enzyme accumulates its subtract and may

that may cause (a) Lethality (b) Toxicity to the organism

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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.


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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.

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

phosphorylation.

Metabolic Pathways are Compartmentalized Within

Cells

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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 small-

molecule 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

chem 4311- chapter17

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