01 - Introduction to Metabolism

Introduction

Metabolism is the set of enzyme-catalyzed reactions that occur in the body to produce energy and building blocks for biosynthesis.

Because metabolic reactions occur inside cells, they are compartmentalized across cellular and subcellular membranes.

Understanding metabolism therefore requires knowledge of membrane structure, transport systems, and transmembrane electrical potentials.

Why this matters

Metabolic reactions are tightly regulated according to the needs of the organism. Regulation occurs at both the enzyme and gene level and depends heavily on cell signaling (for example hormones and neurotransmitters).

Most diseases involve altered metabolism and/or altered metabolic regulation.

This includes classic metabolic diseases (for example diabetes), but also cardiovascular disease, neurodegenerative disease, psychiatric disorders, and cancer with major metabolic components.

• Degenerative: Alzheimer’s disease is linked to impaired cerebral glucose metabolism
• Psychiatric: Bipolar disorder is linked to mitochondrial dysfunction
• Cancer: Colorectal cancer is strongly linked to hyperinsulinemia

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Core Topics

• Metabolic pathways
• Catabolism and anabolism
• General bioenergetics
• Coupled reactions
• Metabolic regulation

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Catabolism and Anabolism

Important

Catabolism:

• is oxidative
• and releases energy.
• the number of C–O bonds increases.

Anabolism is:

• reductive
• and requires energy.

Palmitate oxidation ← Catabolism

Palmitate -> 8 acetate

$C{H}_3(C{H}_2{)}_{14}COOH\to 8C{H}_{3}COOH$

It requires 14 oxidation steps and generates 28 ATP.

Palmitate synthesis ← Anabolism

8 acetate -> palmitate

It requires 14 reductions and 7 ATP.

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Catabolism is {1:oxidative} and {1:releases} energy.
Anabolism is {1:reductive} and {1:requires} energy.
Extra: Palmitate -> 8 acetate needs 14 oxidations and yields 28 ATP. Palmitate synthesis needs 14 reductions} and 7 ATP.

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Metabolic Pathways

• Linear (for example glycolysis)
• Branched
  • Converging (for example toward pyruvate)
  • Diverging (for example from isopentenyl pyrophosphate)
• Cyclic (for example TCA cycle, ornithine cycle)

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Metabolic pathways can be {1:linear}, {1:branched} (either {2:converging} or {2:diverging}), or {1:cyclic}.
Examples: {2:glycolysis} is linear, pathways to {2:pyruvate} can be converging, and {2:TCA cycle} is cyclic.

Overview of Catabolic Processes

1. Polymers (macromolecules) are broken down to monomers and small molecules.
2. Redox coenzymes are generated from simple molecules.
3. ATP is produced.

Anabolic pathways proceed in the opposite direction

Stage 2 requires ATP and reducing power. Stage 1 also requires ATP.

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Major Concepts in Metabolism

• Metabolic flux
• Steady state
• Direction (thermodynamics)
• Rate (kinetics)
• Quantitative transformation
• Cell compartmentalization
• Metabolic control

Steady State

For a pathway:

$A\stackrel{v_1}{\to }B\stackrel{v_2}{\to }C\stackrel{v_3}{\to }D\stackrel{v_4}{\to }E$

At steady state, concentrations of intermediates remain constant because formation rate equals consumption rate.
For example, $[C]$ is constant when $v_2=v_3$.

Thermodynamics and Kinetics

Thermodynamics determines reaction direction:

• Net flow proceeds toward equilibrium.
• In living systems, true equilibrium is usually not reached; pathways run at steady state.
• At equilibrium, $\Delta G=0$ — meaning no net energy is released. Equilibrium is therefore incompatible with sustained energy production.

Why steady state ≠ equilibrium

At steady state, the system is stable but not at equilibrium. Reactions continue at a constant rate. Equilibrium would mean no further net transformation — no energy output.

Kinetics determines reaction rate:

• Metabolic rate is the amount of matter transformed per unit time.
• Enzymes establish and regulate this rate.
• Only proteins have the versatility to fine-tune chemical reactions.

On standard conditions and $\Delta G^{\circ }$

Standard $\Delta G^{\circ }$ values assume physiological pH ($\Delta G^{\circ \prime }$). Standard conditions are necessary for comparison between reactions, even though cells never operate under true standard conditions.

Why $C{O}_2$ and $H_{2}O$ are common end products

$C{O}_2$ and $H_{2}O$ are always present as end products because they contain the most stable bonds. More stable = less free energy available to release.

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Energy Flow During Metabolism

Cells obtain most usable energy through oxidation reactions, but not by direct reaction with oxygen in a single step.

Part of oxidation energy is conserved as ATP.

Net direction and equilibrium

For $A+B\leftrightarrow C+D$, equilibrium position is given by:

$K_{eq}=\frac{[C{]}^c[D{]}^d}{[A{]}^a[B{]}^b}$

“Reactant” and “product” labels are based on equation position, not on net direction under specific concentrations.

Gibbs Free Energy

For $R\to P$:

$\Delta G=\Delta G^{\circ }+RT\ln \frac{[P]}{[R]}$

Using base-10 logs at physiological temperature (approximation):

$\Delta G\approx \Delta G^{\circ }+6\log \frac{[P]}{[R]}\text{(kJ/mol)}$

At equilibrium:

$\Delta G=0\Rightarrow \Delta G^{\circ }=-6\log K_{eq}$

Practice Problems (Solved)

1 → ATP hydrolysis under cellular concentrations

$ATP\to ADP+P_i$

Given: $\Delta G^{\circ }=-30\text{kJ/mol}$, $[ATP]=10^{-2}M$, $[ADP]=10^{-3}M$, $[P_i]=10^{-3}M$

$\Delta G=\Delta G^{\circ }+6\log \frac{[ADP][P_i]}{[ATP]}$

$\Delta G=-30+6\log \left(\frac{10^{-3}\cdot 10^{-3}}{10^{-2}}\right)$

$\Delta G=-30+6(-4)=-54\text{kJ/mol}$

2 → FBP cleavage under cellular concentrations

$FBP\to GAP+DHAP$

Given: $\Delta G^{\circ }=+24\text{kJ/mol}$, $[FBP]=10^{-2}M$, $[GAP]=10^{-3}M$, $[DHAP]=10^{-3}M$

$\Delta G=24+6\log \left(\frac{10^{-3}\cdot 10^{-3}}{10^{-2}}\right)$

$\Delta G=24+6(-4)=0\text{kJ/mol}$

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Redox Reactions

Basic half-reaction:

$F{e}^{2+}\leftrightarrow F{e}^{3+}+e^{-}$

Oxidations are often dehydrogenations:

$A{H}_2\leftrightarrow A+2H^{+}+2e^{-}$

Reduction partner:

$2H^{+}+2e^{-}+B\leftrightarrow B{H}_2$

Overall redox reaction:

$A{H}_2+B\leftrightarrow A+B{H}_2$

Redox Potential and Nernst Equation

$E=E^{\circ \prime }+\frac{RT}{nF}\ln \frac{[\text{acceptor}]}{[\text{donor}]}$

Approximation:

$E=E^{\circ \prime }+\frac{0.06}{n}\log \frac{[ox]}{[red]}$

Relations to thermodynamics:

$\Delta E^{\circ \prime }=E_B^{\circ \prime }-E_A^{\circ \prime }=\frac{RT}{nF}\ln K_{eq}$

$\Delta G^{\circ \prime }=-RT\ln K_{eq}=-nF\Delta E^{\circ \prime }$

In non-standard conditions:

$\Delta G=-nF\Delta E$

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Coupled Reactions

An unfavorable reaction ($\Delta G>0$) can proceed if it is coupled to a favorable reaction ($\Delta G<0$), as long as total free energy is negative:

$\Delta G_{total}=\Delta G_1+\Delta G_2$

Coupling often occurs through a common intermediate:

• $A+X\to AX$ ($\Delta G_1>0$)
• $BX\to B+X$ ($\Delta G_2<0$)
• Net: $A+BX\to AX+B$ with $\Delta G_1+\Delta G_2<0$

ATP coupling

Amino acid polymerization is endergonic.
ATP hydrolysis is exergonic.
Coupling the two makes overall protein synthesis thermodynamically favorable.

Glucose phosphorylation

$Glucose+P_i\to G6P+H_{2}O$ has $\Delta G^{\circ \prime }=+13.8\text{kJ/mol}$

$ATP+H_{2}O\to ADP+P_i$ has $\Delta G^{\circ \prime }=-30.5\text{kJ/mol}$

Sum: $-16.7\text{kJ/mol}$

Glutamine synthesis

$Glutamate+N{H}_3\to Glutamine+H_{2}O$ has $\Delta G^{\circ \prime }=+3.4\text{kcal/mol}$

Coupled ATP hydrolysis gives:

$Glutamate+ATP+N{H}_3\to Glutamine+ADP+P_i$

Net $\Delta G^{\circ \prime }=-3.9\text{kcal/mol}$

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ATP Synthesis and ATP Utilization

ATP Synthesis (Phosphorylation of ADP)

$ADP+P_i+energy\to ATP$

Mechanisms:

• Substrate-level phosphorylation
• Oxidative phosphorylation

ATP Utilization

Important

ATP hydrolysis in metabolism is functionally a two-step process through enzyme-bound intermediates.

ATP typically provides energy by group transfer (transfer of a phosphoryl group to a substrate), not by direct hydrolysis. “Hydrolysis” is a simplification — the phosphoryl group is transferred either to a substrate or to water.

Orthophosphoric cleavage:

$X+ATP\to X-P+ADP$

Example: glucose + ATP -> glucose-6-phosphate + ADP

Pyrophosphoric cleavage:

$X+ATP\to X-AMP+P{P}_i$

Example: amino acid activation in protein synthesis

Reaction is strongly driven forward by:

$P{P}_i\to 2P_i$

Chemical basis for ATP's high-energy release

The large $\Delta G^{\circ \prime }$ of ATP hydrolysis arises from:

• Charge separation: the products $P_i$ and ADP carry separated negative charges
• Resonance stabilization of $P_i$: inorganic phosphate forms a resonance hybrid, stabilizing the product
• Greater solvation of products ($P_i$ and ADP) relative to ATP

A compound is considered high-energy if $\Delta G^{\circ \prime }$ of hydrolysis $\le -25\text{kJ/mol}$.

Energy Charge

$\text{Energy charge}=\frac{[ATP]+\frac{1}{2}[ADP]}{[ATP]+[ADP]+[AMP]}$

Sample calculations

If ATP = ADP = AMP = 10 mM, then EC = 0.5.

If ATP = 0, ADP = 10 mM, AMP = 0, then EC = 0.5.

If ATP = 10 mM, ADP = AMP = 0, then EC = 1.0.

Physiological energy charge

Most cells maintain an energy charge between 0.8 and 0.95, close to 1 (fully charged).

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Metabolism and Cellular Structure

Metabolism is inseparable from cell structure and compartmentation. Membranes enable concentration gradients, separation from the environment, and selective permeability.

Proteins function as molecular machines through specific interactions determined by their three-dimensional structure, which depends on amino acid sequence.

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Role of Enzymes in Metabolic Regulation

Metabolic regulation occurs at the enzyme level through:

• Compartmentalization
• Thermodynamic and kinetic constraints
• Allosteric regulation
• Covalent regulation (including reversible phosphorylation)
• Genetic regulation

Metabolic regulation: mechanisms maintaining molecular homeostasis.

Metabolic control: mechanisms changing pathway output over time.

Six Classes of Enzymes

Class	Function	Example
Oxidoreductases	Catalyse redox reactions (electron transfer)	Dehydrogenases
Transferases	Transfer functional groups (e.g. methyl, phosphate)	Kinases
Hydrolases	Catalyse hydrolysis (use water to break bonds)	Proteases
Lyases	Break or form double bonds without ATP or water	Aldolase
Isomerases	Rearrange atoms within a molecule	Phosphoglucose isomerase
Ligases	Join two molecules using ATP	Synthetases

Hormone Signaling and Enzyme Regulation

Hormonal regulation of metabolism

• Hydrophilic hormones bind to receptors on the cell membrane → activate signal transduction pathways → modify enzyme activity (e.g. via phosphorylation) or alter gene expression.
• Hydrophobic messengers diffuse into the cell (and sometimes the nucleus) → bind to intracellular receptors/transcription factors → regulate gene expression directly.

An irreversible reaction often corresponds to regulation at a rate-limiting enzyme step. A strongly negative $\Delta G^{\circ \prime }$ helps but is not strictly required.

Roles of enzymes

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Flashcards

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The three broad stages of catabolism are {1:polymer breakdown}, {1:redox coenzyme generation}, and {1:ATP production}.

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At metabolic {1:steady state}, intermediate concentrations are approximately {2:constant} because input and output fluxes are {2:balanced}.

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{1:Thermodynamics} determines reaction {2:direction}, while {1:kinetics} determines reaction {2:rate}.

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For $R\to P$, free energy is: {1:$\Delta G=\Delta G^{\circ }+RT\ln ([P]/[R])$}.

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At equilibrium: {1:$\Delta G=0$} and therefore {1:$\Delta G^{\circ }=-RT\ln K_{eq}$}.

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In metabolism, a reaction with positive $\Delta G$ can proceed by {1:coupling} to a reaction with sufficiently negative $\Delta G$ so that total $\Delta G$ is {2:negative}.

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Oxidation is loss of {1:electrons}; reduction is gain of {1:electrons}.

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Typical dehydrogenation half-reaction: {1:$A{H}_2\leftrightarrow A+2H^{+}+2e^{-}$}.

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The relationship between free energy and redox potential is {1:$\Delta G=-nF\Delta E$}.

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In substrate-level phosphorylation, ATP is produced by {1:direct phosphate transfer} from a high-energy intermediate to {2:ADP}.

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In orthophosphoric ATP cleavage, products are typically {1:ADP and a phosphorylated substrate}.

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In pyrophosphoric ATP cleavage, ATP forms {1:AMP + PP_i}; hydrolysis of {2:$P{P}_i$} to {2:$2P_i$} helps pull reactions forward.

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Energy charge formula: {1:$EC=([ATP]+0.5[ADP])/([ATP]+[ADP]+[AMP])$}.

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A pathway control point is often an {1:irreversible} step catalyzed by a {2:rate-limiting enzyme}.

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Main levels of metabolic regulation include {1:allosteric}, {1:covalent}, and {1:genetic} control.

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Equilibrium cannot sustain energy production because at equilibrium {1:$\Delta G=0$}, meaning {1:no net free energy} is released.

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A compound is considered high-energy if its standard free energy of hydrolysis is {1:$\le -25\text{kJ/mol}$}.

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ATP provides energy primarily through {1:phosphoryl group transfer} to a substrate, not by {1:direct hydrolysis}.

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The three chemical reasons for ATP’s large $\Delta G^{\circ \prime }$ of hydrolysis are {1:charge separation}, {1:resonance stabilization of $P_i$}, and {1:greater solvation of products}.

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Most cells maintain an energy charge between {1:0.8} and {1:0.95}.

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The six enzyme classes are {1:oxidoreductases}, {1:transferases}, {1:hydrolases}, {1:lyases}, {1:isomerases}, and {1:ligases}.

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{1:Hydrophilic} hormones act at the {2:cell membrane receptor}, while {1:hydrophobic} hormones diffuse into the cell and act on {2:intracellular receptors or transcription factors}.

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Alzheimer’s disease is linked to impaired {1:cerebral glucose metabolism}; bipolar disorder is linked to {1:mitochondrial dysfunction}; colorectal cancer is linked to {1:hyperinsulinemia}.

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TARGET DECK: MED::I::Signaling Pathways in Health and Disease::Metabolic Biochemistry::01 - Introduction to metabolism

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TLDR - 01 - Introduction to Metabolism

What is Metabolism?

Metabolism is the complete set of enzyme-catalyzed reactions that produce energy and biosynthetic building blocks. It is compartmentalized across membranes and tightly regulated at both enzyme and gene levels.

Catabolism vs. Anabolism

	Catabolism	Anabolism
Direction	Oxidative	Reductive
Energy	Releases ATP	Requires ATP
Example	Palmitate → 8 acetate (14 oxidations, +28 ATP)	8 acetate → palmitate (14 reductions, −7 ATP)

Pathway Types

• Linear (e.g., glycolysis)
• Branched — converging (e.g., → pyruvate) or diverging (e.g., from isopentenyl pyrophosphate)
• Cyclic (e.g., TCA cycle, ornithine cycle)

Thermodynamics & Kinetics

• Thermodynamics sets reaction direction: $\Delta G=\Delta G^{\circ }+RT\ln \frac{[P]}{[R]}$
• Kinetics sets reaction rate: controlled by enzymes
• At steady state: intermediate concentrations are constant; input flux = output flux
• At equilibrium: $\Delta G=0$, so $\Delta G^{\circ }=-RT\ln K_{eq}$

Coupled Reactions

Unfavorable reactions ($\Delta G>0$) proceed when coupled to favorable ones so that $\Delta G_{total}<0$. ATP hydrolysis ($\Delta G^{\circ \prime }\approx -30\text{kJ/mol}$) is the most common coupling agent.

Redox Reactions

• Oxidation = loss of electrons; often dehydrogenations ($A{H}_2\to A+2H^{+}+2e^{-}$)
• $\Delta G=-nF\Delta E$; electrons flow from low to high reduction potential

ATP Metabolism

Mechanism	Products	Example
Orthophosphoric cleavage	X-P + ADP	Glucose → G6P
Pyrophosphoric cleavage	X-AMP + PP${}_i$	Amino acid activation
Substrate-level phosphorylation	ATP	Glycolysis steps
Oxidative phosphorylation	ATP	Mitochondrial ETC

Energy charge = $\frac{[ATP]+\frac{1}{2}[ADP]}{[ATP]+[ADP]+[AMP]}$; ranges from 0 (fully depleted) to 1 (fully charged).

Metabolic Regulation

Control occurs at irreversible, rate-limiting steps via:

1. Allosteric regulation — small molecule effectors
2. Covalent modification — e.g., reversible phosphorylation
3. Genetic regulation — enzyme expression levels
4. Compartmentalization — separation by membranes

Regulation = maintaining homeostasis; Control = changing pathway output over time.

Enzyme Classes

Class	Action
Oxidoreductases	Redox / electron transfer
Transferases	Group transfer (methyl, phosphate…)
Hydrolases	Hydrolysis
Lyases	Break/form double bonds (no ATP/water)
Isomerases	Isomer rearrangement
Ligases	Join molecules (requires ATP)