Metabolism and Enzymes - AP Biology Unit 3: Energetics

Concept 6.1: An organism's metabolism transforms matter and energy

Metabolism = the totality of an organism's chemical reactions
Emergent property of life: metabolism arises from interactions between molecules within the cell
Metabolic pathways are regulated series of enzymatic activities that maintain acceptable ranges of reactants and products (inhibition helps prevent buildup or depletion)
Examples of cellular locales where pathways occur: lysosomes, matrix of mitochondria, stroma of chloroplasts
Each enzyme typically catalyzes a single type of chemical transformation (one thing) to maintain specificity

Biochemical Pathways: Key ideas

Pathways consist of many small enzymatic steps working to keep cells in a stable state
Pathways can be catabolic (breakdown) or anabolic (build-up); pathways are essential for energy flow and biosynthesis

Catabolic vs Anabolic Pathways

Catabolic pathways release energy by breaking complex molecules into simpler ones
Cellular respiration (glucose breakdown in presence of O₂) is an example of catabolism
Reaction example (aerobic cellular respiration):
ext{C}6 ext{H}{12} ext{O}6 + 6 ext{O}2
ightarrow 6 ext{CO}2 + 6 ext{H}2 ext{O} + ext{ATP (energy)}
Anabolic pathways consume energy to build complex molecules from simpler ones (e.g., protein synthesis from amino acids)

Bioenergetics and Metabolic Pathways

Bioenergetics = study of how organisms manage their energy resources
Anabolic vs Catabolic pathways (summary):
- Anabolic: small molecules assembled into larger ones; require energy;
- Catabolic: large molecules broken down into small ones; release energy
Forms of energy involved in metabolism include kinetic, potential, chemical energy, etc.

Forms of Energy (Overview)

Energy is the capacity to do work or cause change
Major forms listed (examples):
- Kinetic energy: energy of motion
- Potential energy: stored energy due to location or structure
- Thermal energy: kinetic energy of random particle motion (related to temperature)
- Mechanical energy, Electrical energy, Magnetic energy, Sound energy, Light energy
- Chemical energy: energy stored in chemical bonds (e.g., in food, fuels)
- Elastic energy: stored in stretched/compressed objects
- Nuclear energy: stored in atomic nuclei
- Gravitational energy: energy due to position above Earth’s surface
Note: Energy forms can be converted from one to another in biological systems

Kinetic Molecular Theory (KMT) & Enzymes as Matchmakers

Reactions require collisions between molecules with correct orientation and sufficient energy
Enzymes act as biological matchmakers that bring reactants together in the right orientation and environment to lower activation energy
Activation energy (E): the initial energy required to start a chemical reaction
Thermal energy often provides activation energy for reactions without enzymes
Enzymes do not change the overall thermodynamics (ΔG) of a reaction; they accelerate the rate

Chemical Energy in Life

Chemical energy is a form of potential energy available for release in reactions
In cells, energy is captured and stored primarily as ATP; chemical energy from nutrients is ultimately converted to ATP
ATP hydrolysis is a key energy-releasing step used to drive other endergonic processes
Metabolic waste products include CO₂ and H₂O
Energy transformations are part of metabolism and produce usable energy (ATP) for work

The Laws of Energy Transformation (Thermodynamics)

Thermodynamics studies energy transformations; energy cannot be created or destroyed in an isolated system
Organisms are open systems: they exchange energy and matter with their surroundings
Isolated vs open systems: An isolated system approximates a thermos; organisms are not perfectly isolated

The First Law of Thermodynamics

Energy of the universe is constant; energy can be transferred and transformed but not created/destroyed
In biology, energy is conserved as it flows through the system (e.g., chemical energy stored in glucose becomes other forms during metabolism)
Mathematical form (conceptual):
ext{Energy is conserved: } ext{no net creation or destruction}

The Second Law of Thermodynamics

During every energy transfer or transformation, some energy becomes unusable (often as heat)
Entropy of the universe increases with every energy transfer or transformation
Entropy = measure of disorder/randomness
Biological implication: living cells must acquire energy inputs to maintain order, while the universe’s total entropy increases

Biological Order vs Disorder and Energy Flow

Cells build ordered structures from less ordered materials (local decrease in entropy)
However, organisms increase the entropy of the surroundings and of the universe overall
Energy enters ecosystems as light and exits as heat; energy flow is unidirectional (with loss at each trophic transfer)

Energy Flow in Ecosystems and Trophic Levels

Sunlight is captured by producers (plants, algae) and converted to chemical energy
Typical energy transfer efficiency is low; energy decreases at each trophic level
Example energy cascade (illustrative):
- Sun to producers: large amount (e.g., 10,000 kcal)
- Producers to primary consumers: ~1,000 kcal
- Primary to secondary: ~100 kcal
- Secondary to tertiary: ~10 kcal
- Heat loss occurs at each transfer
Food chains usually reach 4–5 levels due to energy loss and inefficiency

The Evolution of Complex Organisms and the Second Law

Evolution does not violate the second law: local decreases in entropy are offset by increases in the universe’s total entropy
Organisms can be seen as islands of low entropy embedded in a higher-entropy universe

Concept 6.2: The Free-Energy Change of a Reaction Tells Us Whether or Not the Reaction Occurs Spontaneously

Biologists seek to predict which reactions occur spontaneously and which require energy input
Determine energy changes for chemical reactions to assess spontaneity

Free-Energy Change (ΔG), Stability, and Equilibrium

Free energy (G) of a living system is the energy that can do work under uniform conditions (temperature and pressure)
ΔG (change in free energy) for a reaction:
oxed{ riangle G = G{ ext{final}} - G{ ext{initial}}}
Spontaneous processes have riangle G < 0
Spontaneous processes can be harnessed to perform work
Free energy is a measure of a system's instability; systems move toward greater stability (lower G)
At equilibrium, forward and reverse reactions occur at the same rate; maximum stability is reached
A process can perform work only when moving toward equilibrium

Free Energy in Metabolism: Energy Landscapes

In a spontaneous change, free energy decreases and system becomes more stable
The magnitude of ΔG indicates the maximum work the reaction can perform
Reactions with higher initial free energy have greater work capacity when they proceed spontaneously

Exergonic and Endergonic Reactions in Metabolism

Exergonic reactions: release free energy; ΔG < 0; spontaneous; energy released can perform work
Endergonic reactions: require input of free energy; ΔG > 0; nonspontaneous; energy must be supplied
Magnitude of ΔG indicates the amount of energy that can be used to drive other processes
Illustrative diagrams (conceptual):
- Exergonic: reactants at higher free energy; energy released to products
- Endergonic: energy absorbed from surroundings to form products at higher free energy

Equilibrium and Metabolism in Cells

In closed systems, reactions reach equilibrium and no work can be done
Cells are open systems with continuous material exchange; metabolism is never at equilibrium
Photosynthesis and cellular respiration illustrate opposite directions of energy flow in metabolism

Concept 6.3: ATP Powers Cellular Work by Coupling Exergonic Reactions to Endergonic Reactions

Cells perform three main kinds of work: chemical, transport, and mechanical
Energy coupling uses energy released by an exergonic process to drive an endergonic one
Most cellular energy coupling is mediated by ATP

ATP: Structure, Hydrolysis, and Role in Work

ATP = adenosine triphosphate
Structure components: adenine base, ribose sugar, three phosphate groups
ATP is also used to synthesize RNA
Hydrolysis of ATP (energetically favorable step):
ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{energy}
The energy released during hydrolysis comes from a transition to a lower free-energy state, not from the phosphate bonds themselves
ATP hydrolysis powers: mechanical work (muscle contraction, etc.), transport work (pumping substances across membranes), and chemical work (driving endergonic reactions)
Overall, coupled reactions are exergonic

How ATP Drives Work

The energy released from ATP hydrolysis is used to drive endergonic reactions in a coupled manner
Example: the energy from ATP hydrolysis can be used to drive synthesis of macromolecules or to move substances against a gradient

Concept 6.4: Enzymes Speed Up Metabolic Reactions by Lowering Energy Barriers

Enzyme = biological catalyst; enzymes are typically proteins
Enzymes speed up reactions without being consumed; they are not reactants or products
Sucrose hydrolysis example: sucrose + H₂O with enzyme sucrase yields glucose and fructose
Enzymes dramatically increase reaction rates by lowering activation energy
Enzymes do not alter ΔG of the reaction

Enzymes: Key Characteristics

Enzymes are proteins; many end with the suffix -ase (e.g., lactase, amylase, catalase, helicase, hydrolase)
Some enzymes are RNA molecules (ribozymes), but most enzymes discussed in biology courses are proteins
Substrates bind to the enzyme at the active site to form an enzyme-substrate complex

Substrate Specificity and the Active Site

Enzymes are highly specific for their substrates
Active site: region of the enzyme where substrate binds
Induced fit: binding induces conformational changes that position catalytic groups to enhance catalysis
Enzymes lower the activation energy barrier through various mechanisms

How Enzymes Speed Reactions

Enzymes lower the activation energy (E) but do not affect the overall ΔG of the reaction
The reaction coordinate with and without an enzyme shows a lower peak (lower Ea) when an enzyme is present
The presence of an enzyme increases the rate at which equilibrium is reached

Catalysis in the Active Site

Substrate binds to the active site forming the enzyme-substrate complex
Catalytic mechanisms include:
- Orientation: aligning substrates properly for reaction
- Straining substrate bonds to promote breakage
- Providing a favorable microenvironment (pH, polarity, etc.)
- Covalent bonding to the substrate (transiently forming a covalent enzyme-substrate intermediate)

Enzyme Structure-Function Relationships

Enzymes are sensitive to their environment; temperature and pH influence activity
Denaturation occurs when the enzyme loses its three-dimensional structure due to extreme conditions
Activation energy and rate are influenced by temperature and pH
Enzyme concentration affects reaction rate; higher concentration generally increases rate up to a maximum (Vmax)
Substrate concentration also affects rate; approaching saturation, the rate levels off at Vmax

Temperature and pH Effects on Enzyme Activity

Each enzyme has an optimal temperature and pH where activity is highest
Example: human enzymes typically have an optimal body temperature around 37°C; thermophilic bacteria have higher optimal temperatures (e.g., 77°C)
pH optima vary by enzyme (e.g., pepsin in the stomach is acidic; trypsin in the intestine is more neutral/basic)

Concentration Effects on Enzyme Activity

Enzyme concentration influences reaction rate: more enzymes mean more catalytic events per unit time (up to saturation)
Substrate concentration also influences rate; at high substrate levels, all active sites are occupied (Vmax)

Cofactors and Coenzymes

Cofactors = nonprotein helpers needed for enzyme activity; can be inorganic (e.g., metal ions) or organic
Organic cofactors are called coenzymes; vitamins are often precursors to coenzymes

Enzyme Inhibitors

Competitive inhibitors bind to the enzyme's active site, competing with the substrate
Noncompetitive inhibitors bind to a different part of the enzyme, causing a change in shape that reduces active-site efficiency
Examples include toxins, poisons, pesticides, and antibiotics

Regulation of Enzyme Activity (Concept 6.5)

Cells regulate metabolism to avoid chemical chaos by turning genes encoding enzymes on/off or by regulating enzyme activity

Allosteric Regulation of Enzymes

Allosteric regulation can inhibit or stimulate enzyme activity
A regulatory molecule binds to a site other than the active site and alters enzyme function at another site
Active and inactive forms exist; activator stabilizes the active form, inhibitor stabilizes the inactive form

Cooperativity and Regulation

Cooperativity is a form of allosteric regulation where one substrate molecule primes the enzyme to act on additional substrate molecules more readily
Binding at one active site affects catalysis at other sites, amplifying enzyme activity

Feedback Inhibition

End product of a metabolic pathway inhibits an enzyme earlier in the pathway
Negative feedback prevents excessive production and conserves resources

Localization of Enzymes Within the Cell

Enzymes are organized within cells to improve efficiency and regulation
Some enzymes are membrane-associated or localized within specific organelles
In eukaryotes, organelles compartmentalize steps of respiration and other metabolic processes
Example: mitochondria house enzymes for different stages of cellular respiration; matrix hosts soluble enzymes, inner membrane hosts others

Practical Examples and Diagrams (conceptual descriptions)

Figure references in the text illustrate energy flow, activation energy, enzyme mechanisms, and cellular localization (descriptions summarized above)
Sucrose hydrolysis example uses sucrase to produce glucose and fructose; shown as enzyme-substrate complex and product release
ATP hydrolysis diagrams illustrate conversion of ATP to ADP and Pi with energy release used for work

Key Formulas and Symbols (Summary)

Free energy change of a reaction:
riangle G = G{ ext{final}} - G{ ext{initial}}
Spontaneity criteria:
- riangle G < 0
  ightarrow ext{spontaneous}
- riangle G > 0
  ightarrow ext{nonspontaneous (requires input)}
ATP hydrolysis (energy release):
ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{energy}
Aerobic cellular respiration (illustrative overall reaction):
ext{C}6 ext{H}{12} ext{O}6 + 6 ext{O}2
ightarrow 6 ext{CO}2 + 6 ext{H}2 ext{O} + ext{ATP}
Activation energy (E) is the initial energy input required to start a reaction

Connections to Foundational Principles and Real-World Relevance

Energy coupling via ATP is fundamental to all cellular activities (growth, transport, movement, biosynthesis)
Enzyme regulation ensures metabolic pathways respond to cellular needs and environmental conditions
Regulation by allosteric effectors, cooperativity, and feedback inhibition maintains homeostasis and resource efficiency
Understanding energy flow and metabolism links biochemistry to physiology, ecology, and evolutionary biology