Metabolism

- Atp
- Thermodynamics
Bioenergetics
- Is the study of how organisms manage their energy resources via metabolic pathways
Catabolic pathways
- Release energy by breaking down complex molecules into simpler compounds
Anabolic pathways
- Consume energy to build complex molecules from simpler ones
Energy
- Is the capacity to do work or ability to cause change. Any change in the universe
requires energy. Energy comes in 2 forms:
Potential energy
- Is stored energy. Change is currently taking place. Is stored in the location of matter.
Includes chemical energy stored in molecular strategy.
Kinetic energy
- Is currently causing change. This always involves some type of motion. Is the energy
associated with motion.
Free energy
Free energy (G) is a measure of the amount of energy available to do useful work. It depends
on:
The total amount of energy present; this is called enthalpy (H)
The amount of energy being used for non-useful work (random molecular motion); this is called
entropy (S)

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In general:

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G= H - T S
- Where T represents the temperature in degrees kelvin and represents “the change
in”
- This means the amount of energy available for useful work (G) equals the total energy
present (H) minus the energy that is being wasted on random molecular motion (S).
Temperature; pressure increase, entropy and temperature increase
Exergonic reactions
- Reactants have more free energy than the products
- Involve a net release of energy and/or an increase in entropy
- Occur spontaneously (without a net input of energy)
Endergonic reactions
- Reactants have less free energy than the products
- Involve a net input of energy and/or decrease in entropy
- Do not occur spontaneously
Equilibrium and metabolism
- Reactions in a closed system eventually reach equilibrium and then do no work
- Cells are not in equilibrium; they are open systems experiencing a constant flow of
materials
- A catabolic pathway in a cell releases free energy in series of reactions
 - Closed and open hydroelectric systems can serve as analogies
- Reactions in a closed system eventually reach equilibrium
- Cells in our body experience a constant flow materials in and out, preventing metabolic
pathways from reaching equilibrium
Energy coupling
- Living organism have the ability to couple exergonic and endergonic:
- Energy released by exergonic reactions is captured and used to make ATP from ADP
and Pi
- ATP can be broken down to ADP and Pi, releasing energy to power the cell’s endergonic
reactions.
The structure and hydrolysis of ATP
- ATP (adenosine triphosphate)
● Is the cell’s energy shuttle
● Provides energy for cellular functions
● Energy is released from ATP when the terminal phosphate bond is broken

Laws of energy transfer

Chemical (energy) potential
1. Convert one form to another
2. Always “entropy” (disorder happens)
Cellular work
- A cell does three main kinds of work
● Mechanical
● Transport
 ● Chemical
- Energy coupling is a key feature in the way cells manage their energy resources to do
this work.
Energy coupling atp/adp cycle

How does ATP perform work

- ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to
some other molecule, such as a reactant
- The recipient molecule is now phosphorylated
- The three types of cellular work (mechanical, transport, and chemical) are powered by
the hydrolysis of ATP
- ATP drives endergonic reactions by phosphorylation, transferring a phosphate to other
molecules - hydrolysis of ATP
Activation energy
- All reactions, both endergonic and exergonic, require an input of energy to get started.
This energy is called activation energy.
- The activation energy Ea
● Is the initial amount of energy needed to start a chemical reaction
● Activation energy is needed to bring the reactants close together and weaken
existing bonds to initiate a chemical reaction
● Is often supplied in the form of heat from the surroundings in a system
Reaction rates
- In most cases, molecules do not have enough kinetic energy to reach the transition state
when they collide.
- Therefore, most collisions are non-productive, and the reaction process very slowly if at
all.
- What can be done to speed up this reaction?
Increasing reaction rates
- Add Energy(heat) - molecules move faster so they collide more frequently and with
greater force
- Add a Catalyst - a catalyst reduces the energy needed to reach the activation site,
without being changed itself. Proteins that function as catalysts are called enzymes.
Enzymes are biological catalyst
- Enzymes are proteins that carry out most catalyst in living organisms
- Unlike heat, enzymes are highly specific. Each enzyme typically speeds up only one or
few chemical reactions.
 - Unique three-dimensional shape enables an enzyme to stabilize a temporary association
between substrates
- Because the enzyme itself is not changed or consumed in the reaction, only a small
needed, and can then be reused.
- Therefore, by controlling which enzymes are made, a cell can control which reactions
take place in the cell.
Substrate specificity of enzymes
- Almost all enzymes are globular proteins with one or more active sites on their surface
- The substrates is the reactant an enzyme acts on
- Reactants bind to the active site to form an enzyme-substrate complex
- The 3d shape of the active site and the substrate must match, lock and key.
- Binding to the substrates causes the enzyme to adjust its shape slightly, leading to a
better induced fit.
- Induced fit of a substrate
The catalytic cycle of an enzyme
Factors affecting enzyme activity
- Temperature: rate of an enzyme-catalyzed reactions increases with temperature, but
only up to an optimum temperature
- pH: ionic interactions also holds enzymes together
- Inhibitor: substance that binds to an enzyme and decreases its activity - feedback
● Competitive inhibitors - compete with the substrate for the same active site
● Noncompetitive inhibitors - bind to the enzyme in a location other than the
active site
● Allosteric sites - specific binding sites acting as on/off switches
Enzymes Inhibitors
Regulation of enzymes activity helps control metabolism
- Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated
- To regulate metabolic pathways, the cell switches on or off the genes that encode
specific pathway
- Allosteric regulation is the term used to describe any case in which a protein’s function at
one site affected by binding of a regulatory molecule at another site
Allosteric activation and inhibition
- Most allosterically regulated enzymes are made from polypeptide subunits
- Each enzyme has active and inactive forms
- The binding of an activator stabilizes the active form of the enzyme
- The binding of an inhibitor stabilize the inactive form of the enzyme
Allosteric regulation of enzymes
- Allosteric regulation may either inhibit or stimulate an enzyme’s activity

Cooperativity
- Is a form of allosteric regulation that can amplify enzyme activity
Factors affecting enzyme activity
- Activators: substance that bind to allosteric sites and keep the enzymes in their active
configurations - increase enzyme activity
● Cofactors: chemical components that facilitate enzyme activity
● Coenzymes: organic molecules that function as cofactors

Regulation of biochemical pathways

- Biochemical pathways must be coordinated and regulated to operate efficiently
- Advantageous for cells to temporarily shut down biochemical pathways when their
products are not needed.
- Feedback inhibition