Catabolism and anabolism occur by highly integrated network of chemical reactions

collectively known as metabolism or intermediary metabolism

General principles of metabolism :
1. Fuels are degraded and large molecules are constructed step by step in a series of linked
reactions called metabolic pathways .
2. An energy currency common to all life forms, adenosine triphosphate (ATP) , links
energy-releasing pathways with energy-requiring pathways.
3. The oxidation of carbon fuels powers formation of ATP.
4. Although there are many metabolic pathways, a limited number of types of reactions and
particular intermediates are common to many pathways.
5. Metabolic pathways are highly regulated

Metabolism Is Composed of Many Coupled,

Interconnecting Reactions

Living organisms need continuous energy inputs for :

performance of mechanical work in muscle contraction and cellular movements
active transport of molecules and ions
synthesis of macromolecules and other biomolecules from simple precursors
Free energy used in the processes derived from environment
Photosynthetic organisms, or phototrophs obtain energy by trapping sunlight and
chemotrophs (animals) obtain energy by oxidation of foodstuffs generated by phototrophs
Metabolism is essentially a sequence of chemical reactions that begins with a
particular molecule and results in the formation of some other molecule or
molecules in a carefully defined fashion
Metabolism = energy-yielding reaction + energy-requiring reactions
Many defined, interdependent and highly regulated (mainly allosterically by enzymes)
pathways exist
Pathways divided as :
those that convert energy from fuels into biologically useful forms
those that Require inputs of energy to proceed
Reactions transforming fuels into cellular energy are called catabolic reactions or catabolism

Reaction pic

Reactions requiring energy—such as the synthesis of glucose, fats, or DNA—are called

anabolic reactions or anabolism
Useful forms of energy produced in catabolism employed in anabolism to generate complex
structures from simple ones, or energy-rich states from energy-poor ones.

Reaction pic

Pathways that are either anabolic or catabolic, depending on energy conditions in the cell
are called amphibolic pathways
Important general principle of metabolism - biosynthetic and degradative pathways are
almost always distinct for energetic reasons and to control metabolism

A thermodynamically unfavourable reaction can be driven by a favourable reaction

Pathway must fulfill 2 criteria :
the individual reactions must be specific
entire set of reactions that constitute pathway must be thermodynamically favoured
Specific reaction yields only one particular product from reactants
Reaction occurs spontaneously if delta G (change in free energy) is negative
Delta G for formation of products C and D from substrates A and B is given by :
Equation pic

Therefore, delta G depends on nature of reactants and products (delta G o' - standard
free-energy change) and on concentrations (expressed by second term)
Important thermodynamic fact - Overall free-energy change for a chemically coupled series
of reactions is equal to sum of free-energy changes of individual steps

Net reaction pic

Under standard conditions, A cannot be spontaneously converted into B and C - because

delta G o’ is positive
But because free-energy changes are additive, conversion of A into C and D has delta G o’
of -13 kJ mol -1 (-3 kcal mol -1) thus reaction can occur spontaneously under standard
conditions
Thus, conversion of B into D under standard conditions is thermodynamically feasible
Thus, a thermodynamically favourable reaction can be driven by a thermodynamically
favourable reaction to which it is coupled
Metabolic pathways are formed by coupling of
enzyme-catalysed reactions such that overall free energy of the pathway is negative.

Is ATP to be added ?

The Oxidation of Carbon Fuels Is an Important

Source of Cellular Energy

ATP - principal immediate donor of free energy in biological systems

It does not store free energy for long term
Total quantity of ATP in body is 100g, but turnover of this small quantity of ATP is very high :
ATP consumed within a minute of its formation; human consumed 40 kg (88 pounds) of ATP
in 24 hours
During strenuous exertion, ATP utilisation is 0.5 kg/minute and for 2-hour run, 60 kg (132
pounds) of ATP is utilised.
Motion, active transport, signal amplification, and biosynthesis require ATP, making
mechanisms of regeneration of ATP vital
generation of ATP is one of the primary roles of catabolism
Carbon in fuel molecules—such as glucose and fats—is oxidized to CO2 and resulting
electrons are captured and used to regenerate ATP from ADP and Pi
In aerobic organisms ultimate electron acceptor in carbon oxidation is O2 and oxidation
product is CO2
The more reduced a carbon is to begin with, the more free energy is released by its
oxidation

Image

Fuel molecules are more complex, but oxidation of these fuels takes place one carbon at a
time
Carbon-oxidation energy from these fuels used for - creating compound with high
phosphoryl-transfer potential or to create an ion gradient & terminates with formation of ATP

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Compounds with high phosphoryl-transfer potential can couple carbon oxidation to ATP
synthesis

Energy released from oxidation of a carbon compound is converted into ATP

glyceraldehyde 3-phosphate is converted to 3-Phosphoglyceric acid by oxidation
C-1 of glyceraldehyde 3-phosphate is at aldehyde oxidation level and not in its most oxidised
state, but oxidation of aldehyde to acid will release energy

Image

Oxidation does not proceed directly

Carbon oxidation generates 1,3-bisphosphoglycerate (acyl phosphate) and electrons
released are captured by NAD+

Image

1,3-bisphosphoglycerate has high phosphoryl-transfer potential, greater than ATP

Thus, hydrolysis of 1,3-bisphosphoglycerate can be coupled to ATP synthesis

Image

Thus, energy of oxidation initially trapped as high-phosphoryl-transfer-potential compound

and thus used to form ATP
The oxidation energy of a carbon atom is
transformed into phosphoryl-transfer potential, first as 1,3-bisphosphoglycerate and
ultimately as ATP

Ion gradients across membranes provide an important form of cellular energy that can be
coupled to ATP synthesis

Electrochemical potential of ion gradients across membrane due to oxidation of fuel

molecules or by photosynthesis powers ATP synthesis
Thus, Electrochemical potential is an effective means of storing free energy
Ion gradients - versatile means of coupling thermodynamically unfavourable reactions to
favourable ones
Proton gradients generated by oxidation of carbon fuels i.e. oxidative phosphorylation - 90%
of ATP generation
ATP hydrolysis used to form ion gradients of different types and functions
Image
Eg - electrochemical potential of a Na + gradient tapped to pump Ca2+ out of cells or to
transport sugars and amino acids into cells

Phosphates play a prominent role in biochemical processes

Characteristics of phosphate esters making it useful for biochemical systems :

●​ phosphate esters are thermodynamically unstable while being kinetically stable
●​ Enzymes can manipulate the energy release from phosphate esters
●​ Negative charges on phosphate esters make them resistant to hydrolysis in absence
of enzymes and confer them stability (thus, phosphate present in DNA backbone)
●​ phosphate esters are kinetically stable - ideal regulatory molecules, added to proteins
by kinases and removed only by phosphatases.
●​ Phosphate added to trap metabolite that might otherwise diffuse through cell
membrane
●​ Although transporters exist for unphosphorylated forms of metabolite, addition of
phosphate changes geometry and polarity of molecules so that they no longer fit in
binding sites of transporters

No other ions have chemical characteristics of phosphate

Citrate - not sufficiently charged to prevent hydrolysis
Arsenate - forms esters that are unstable and susceptible to spontaneous hydrolysis
Arsenate is poisonous to cells because it replaces phosphate in ATP synthesis reactions,
generates unstable compounds and prevents ATP synthesis.
Silicate - virtually insoluble and used for biomineralization
Only phosphate has chemical properties to meet the needs of living systems

Energy from foodstuffs is extracted in three stages

Hans Krebs described 3 stages in generation of energy from the oxidation of foodstuffs
1.​ Complex molecules digested to simpler molecules
large molecules broken down into smaller units in the process of digestion
Proteins hydrolysed to 20 different amino acids
Polysaccharides hydrolyzed to glucose (simple sugars)
Lipids hydrolyzed to glycerol and fatty acids
Degradation products absorbed by cells of intestine and distributed throughout the body
Preparation stage - no useful energy is captured

2.​ numerous small molecules are degraded to a few simple units that play a central role
in metabolism
sugars, fatty acids, glycerol, and amino acids converted into acetyl unit of acetyl CoA.
Very less amount of ATP generated
 3.​ ATP synthesis
ATP produced from complete oxidation of acetyl unit of acetyl CoA
citric acid cycle and oxidative phosphorylation involved
Acetyl CoA brings acetyl units into citric acid cycle (Tricarboxylic acid cycle or Krebs cycle)
where they are completely oxidised to CO2
4 pairs of electrons are transferred (3 to NAD+ and 1 to FAD) for each acetyl group that is
oxidised
Electrons flow from reduced form of these carriers to final electron acceptor O2 and
generate a proton gradient that is used to synthesise ATP

Image

Metabolic Pathways Contain Many Recurring Motifs

Metabolism although appears complex due to number of reactants and reactions, unifying
themes like common metabolites, reactions, and regulatory schemes stemming from
common evolutionary heritage make the comprehension of complex pathways manageable
Activated carriers exemplify the modular design and economy of metabolism
ATP is phosphoryl transfer for :
Drives endergonic reactions
Alter the energy of conformation of protein
Serve as signal to alter activity of protein
ATP is activated carrier of phosphoryl groups because phosphoryl transfer from ATP is
exergonic process
Use of activated carriers is a recurring motif in biochemistry and function as coenzymes
1.Activated Carriers of Electrons for Fuel Oxidation

In aerobic organisms, electron pairs from fuel oxidation ultimately transferred to final electron
acceptor O2
This transfer is not direct but mediated via special carriers
Fuel molecules transfer electrons to special carriers and their reduced form then transfer
electrons further to O2
Special carriers involve - pyridine nucleotides or flavins
Reduced form of carriers transfer their high-potential electrons to O2

NAD :

Nicotinamide adenine dinucleotide (NAD) is major electron carrier in oxidation of fuel

molecules
Nicotinamide ring (pyridine derivative synthesised from vitamin niacin) is the reactive part of
NAD+
In oxidised form Nitrogen atom carries positive charge, NAD+ is electron acceptor in many
reactions
During oxidation of substrate, nicotinamide ring of NAD+ accepts a Hydrogen ion and 2
electrons - equivalent to hydride ion (H: -)
Reduced form of NAD is called NADH
During dehydrogenation, 1 H atom of substrate transferred to NAD+ and other released in
solvent as proton (H+)
Both electrons of substrate transferred to nicotinamide ring

Image

FAD :

coenzyme flavin adenine dinucleotide

Oxidised form is FAD and reduced form is FADH2
Reactive part of FAD is isoalloxazine ring, derivative of vitamin riboflavin
FAD is electron acceptor, it accepts 2 electrons and along with it also accepts 2 protons
Carriers of high-Potential electrons - flavin mononucleotide (FMN) is electron carrier, similar
to FAD but lacks adenine nucleotide
Image

2. An Activated Carrier of Electrons for Reductive Biosynthesis

Because precursors are more oxidised than products, High-potential electrons by reducing
power is needed in addition to ATP
Example :
In fatty acid biosynthesis, keto group is reduced to methylene group in multiple reactions
requiring total of 4 electrons

Image

Electron donor in most reductive biosyntheses is NADPH

NADPH is reduced form of nicotinamide adenine dinucleotide phosphate (NADP+)
NADPH differs from NADH in that 2’ -hydroxyl group of its adenosine moiety is esterified with
phosphate
NADPH carries electrons in same way as NADH
NADPH - used exclusively for reductive biosyntheses
NADH - generation of ATP
Extra phosphoryl group on NADPH is tag enabling enzymes to distinguish between
high-potential electrons to be used in anabolism and those to be used in catabolism.

Image

3. An Activated Carrier of Two-Carbon Fragments

Coenzyme A :

Coenzyme A is another central molecule in metabolism and carrier of acyl groups derived
from the vitamin pantothenate
Acyl groups important constituent of catabolism (eg fatty acid oxidation) and anabolism
(synthesis of membrane lipids)
Reactive site of CoA isTerminal sulfhydryl group
Acyl groups are linked to CoA by thioester bonds resulting in derivative called acyl CoA
Commonly the acyl group linked to CoA is acetyl unit and unit is called acetyl CoA
Delta G o’ for hydrolysis of acetyl CoA has a large negative value

Reaction

Thioester is thermodynamically more unstable than oxygen ester because C=O bond cannot
form resonance structures with C—S bond that are as stable as those that they can form
with C—O bond
Acetyl CoA has high acetyl-group-transfer
potential because transfer of the acetyl group is exergonic
Acetyl CoA has activated acetyl group, just as ATP carries an activated phosphoryl group

Use of activated carriers illustrates two key aspects of metabolism :

1.​

NADH, NADPH, and FADH2 react slowly with O2 in absence of catalyst

ATP and acetyl CoA hydrolysed slowly (after many hours or days) in absence of catalyst
These molecules are kinetically stable in face of a large thermodynamic driving force for
reaction with O2 (regard to electron carriers) and H2O (for ATP and acetyl CoA)
Kinetic stability of these molecules in absence of catalyst essential for their biological
function - it
enables enzymes to control flow of free energy and reducing power

2.

Interchanges of activated groups in metabolism accomplished by small set of carriers

Existence of recurring set of activated carriers in all organisms is one of the unifying motifs of
biochemistry
Small set of molecules carry wide range of tasks

Table

Many activated carriers are derived from vitamins

Most activated carriers acting as coenzymes are derived from vitamins which are modified
before it can serve its function
Vitamins are organic molecules that are needed in small amounts in the diets of some higher
animals
Due to complex biosynthetic pathways for vitamins, ingesting vitamins is biologically more
efficient than synthesising enzymes for their synthesis from simple molecules (dependency
on other organisms for vitamins)
Not all vitamins function as coenzymes
Vitamins - A, C, D, E, and K
Vitamin A (retinol) - precursor of retinal (light-sensitive group in rhodopsin and other visual
pigments) and retinoic acid (important signaling molecule) and its deficiency causes night
blindness; young animals need Vitamin A for growth
Vitamin C (ascorbate) - antioxidant and its deficiency causes scurvy (disease characterised
by skin lesions and blood-vessel fragility) and formation of unstable collagen molecules
Vitamin D - it's metabolite is a hormone regulating metabolism of calcium and phosphorus
and its deficiency impairs bone formation in growing animals
Vitamin E (alpha tocopherol) - antioxidant (inactivated ROS like -OH radicals) and protects
cellular structures, it's deficiency causes neuromuscular pathologies
Vitamin K - normal blood clotting

Key reactions are reiterated throughout metabolism

Economy of design exists in use of activated carriers and in design in biochemical reactions
Thousands of metabolic reactions subdivided into 6 types and specific reactions of each type
occur repeatedly

1. Oxidation –

Energy derived from oxidation of carbon compounds

2 Reactions images
Above 2 reactions are oxidation–reduction reactions of citric acid cycle which completely
oxidises activated 2 carbon acetyl CoA to 2 CO2 molecules
In first reaction, FADH2 carries electrons and in second reaction, electrons are carried by
NADH

2. Ligation reactions -
Bond formation by using free energy from ATP cleavage.
Reaction pic
ATP-dependent formation of a carbon–carbon
bond, to combine smaller molecules forming larger ones.
Oxaloacetate is formed from pyruvate and CO2 .
Oxaloacetate used in citric acid cycle or converted to glucose or amino acids (like aspartic
acid)

3. Isomerization reactions
Rearrangement of particular atoms within a molecule.
It prepares molecule for subsequent reactions such as oxidation–reduction reactions
Image
This reaction is component of citric acid cycle
This is also isomerisation reaction and prepares molecule for subsequent oxidation and
decarboxylation by moving hydroxyl group of citrate from tertiary to secondary position

4. Group - transfer reactions

Image
Phosphoryl group transferred from activated phosphoryl-group carrier ATP to glucose
This reaction activates glucose molecule and traps it in the cell for further catabolism
It is initial step of glycolysis
Also involved in ATP synthesis
 5. Hydrolytic reactions -
Hydrolysis is cleavage bonds by addition of water
It degrades large molecules to facilitate
further metabolism or to reuse some components for biosynthetic purposes
Proteins are hydrolysed to yield smaller peptides
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6. Carbon bonds can be cleaved by means other than hydrolysis or oxidation

Other means may involve wherein two substrates yield one product or vice versa
After release of CO2 or H2O, double bond is formed
Enzymes catalysing these reactions are called lyases
Image
Conversion of 6-carbon molecule fructose 1,6-bisphosphate into two three-carbon
fragments: dihydroxyacetone phosphate and glyceraldehyde 3-phosphate (critical step in
glycolysis)

Image

Dehydration forms double bonds

Eg - formation of phosphoenolpyruvate from 2-phosphoglycerate
Image
Dehydration sets up next step in pathway - group-transfer reaction using high
phosphoryl-transfer potential of product PEP to
form ATP from ADP

These 6 fundamental reaction types are basis of metabolism.

These reactions can proceed in either direction depending on standard free energy for the
specific reaction and the concentrations of reactants and products inside the cell

Metabolic processes are regulated in three principal ways

Levels of available nutrients must be monitored and activity of metabolic pathways must be
altered and integrated to create homeostasis, a stable biochemical environment
Metabolic control must be flexible - able to adjust metabolic activity to constantly changing
extracellular environments
Metabolism is regulated through control of
Amounts of enzymes,
Catalytic activities of enzyme
Accessibility of substrates

1.​ Controlling the amounts of enzymes :

Amount of a particular enzyme depends its rate of synthesis and its rate of degradation
Enzyme levels adjusted by change in rate of transcription of genes encoding them
In E. coli - presence of lactose induces within minutes, 50-fold increase in rate of synthesis
of beta galactosidase (enzymes degrading lactose)

2.​ Controlling catalytic activity

Catalytic activity of enzyme controlled by - allosteric control and covalent modification
Allosteric control :
Enzyme Allosterically inhibited by the ultimate product of the pathway (feedback inhibition)
The product binds to enzyme at a site other than active site and changes its conformation
such that it is unable to carry out it's activity
Eg - inhibition of aspartate transcarbamoylase by cytidine triphosphate
Allosteric control can be almost instantaneous

Covalent modification :
It is reversible modification
Involves phosphorylation and dephosphorylation
Eg - in low glucose levels, glycogen phosphorylase (enzyme catalysing breakdown of
glycogen) is activated by phosphorylation of a particular serine residue
Hormones coordinate metabolic relations between different tissues often by regulating
reversible modification of key enzymes
Eg - hormone epinephrine triggers signal-transduction cascade in muscle leading to
phosphorylation and activation of key enzymes and leading to rapid degradation of glycogen
to glucose, used to supply ATP for muscle contraction
Many hormones act through intracellular messengers like cyclic AMP and Ca2+ ion -
coordinate activities of many target proteins
Metabolic reactions controlled by energy status of cell
Indexes of energy status - energy charge, phosphorylation potential

Energy charge :

Energy charge is proportional to mole fraction of ATP plus half the mole fraction of ADP,
given
that ATP contains two anhydride bonds, whereas ADP contains one.
Energy charge is defined as
Equation pic
Energy charge has value ranging from 0 (all AMP) to 1 (all ATP)
ATP-generating (catabolic) pathways are inhibited by high energy charge, whereas
ATP-utilising (anabolic) pathways are stimulated by a high energy charge
When reaction rates of pathway plotted against energy charge, curves are steep near an
energy charge of 0.9 where they usually intersect
Control of these pathways evolved to maintain energy charge within narrow limits
Energy charge of cell is buffered - ranges from 0.90 to 0.95; falls to less than 0.7 in muscle
during high-intensity exercise

Phosphorylation potential

phosphorylation potential - alternative index of the energy status

Defined as :
Equation pic
The phosphorylation potential depends on concentration of Pi and is directly related to
free-energy storage available from ATP

3.​ Controlling the accessibility of substrates :

Substrate availability in the cell can be controlled
Eg - glucose breakdown takes place in cells only if insulin is present to promote entry of
glucose into cell
In eukaryotes, metabolic regulation and flexibility enhanced by compartmentalization
Transfer of substrates from one compartment to another serves as a control point
Eg - fatty acid oxidation takes place in mitochondria and fatty acid synthesis takes place in
cytoplasm; Compartmentalization segregates opposed reactions

Aspects of metabolism may have evolved from an RNA world

Current thinking - RNA was early biomolecule that dominated metabolism, serving both as
catalyst and information storage molecule
This hypothetical time called RNA world
Activated carriers such as ATP, NADH, FADH2 , and coenzyme A contain adenosine
diphosphate units
These molecules may have evolved from early RNA catalysts
Non-RNA units like isoalloxazine ring recruited to serve as efficient carriers of activated
electrons and chemical units, RNA cannot function like this readily
Adenine ring of FADH2 binds to uracil unit in niche of an RNA enzyme (ribozyme) by base-
pairing
Isoalloxazine ring protrudes and functions as an electron carrier
Although proteins replaced RNA as the major catalysts, ribonucleotide coenzymes remain
unchanged because they are well suited to metabolic roles
Nicotinamide unit of NADH readily transfers electrons irrespective of whether adenine unit
interacts with base in RNA enzyme or with amino acid residues in protein enzyme