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Metabolism can be divided into what two types of activities?

1. Anabolic reactions : link simple molecules together to make complex ones. These are energy-storing reactions. They require energy.

2. Catabolic reactions: break down complex molecules into simpler ones. They release energy.

*Cells must constantly acquire energy from their environment!*


Energy Conversions

- chemical reactions are energy conversions
ex. a brick falling (potential energy due to position, then kinetic energy when falling and finally heat energy when brick hits the floor)
ex. chemical bond energy (covalent)(chemical bond energy in bonds of individual molecules, rapid molecular motions in the newly formed molecules, heat energy is dispersed to the surroundings)


What drives energy conversions?

NOT the energy content, because:
• First Law of Thermodynamics: during any conversion of energy, the total initial energy equals the total final energy. Energy is neither created nor destroyed
- energy will come in different forms in the products
- the number of atoms also stays the same

• Second Law of Thermodynamics: Energy spontaneously disperses from being localized to becoming spread out if it is not hindered from doing so (entropy increases).
- Energy conversions, e.g. chemical reactions only occur if energy disperses in the universe. The dispersing energy is the driving force for energy conversions.
- Another way to put it: Energy transformations always result in a state of higher probability (a more disordered state). Examples: cooling coffee


How do you judge biochemical reactions?

- need an equation that gives us the amount of energy released to drive a reaction (change in entropy in the universe, or free energy).


How can a cell release free energy? (drive a chemical reaction)

- By dispersing energy/increasing entropy (in the universe) How?
1) with a chemical reaction creating disorder in the cell (digesting a polymer into its monomers) (creating entropy, ∆S; measure of disorder or randomness)
2) with a chemical reaction releasing heat which generates disorder/disperses energy in the surroundings (ex. binding to different atoms, which releases heat into surroundings which cause molecules around to move faster; creating enthalpy, ∆H; the sum of internal energy of a system)


Total free energy

G = H - TS
• T= absolute temperature
• We don’t want to know (and cannot calculate) the total free energy of a molecule, only the change associated with a specific chemical reaction. This change can be measured in calories or joules
• Free energy change:
• +∆G= energy is required
• -∆G= energy is released/dispersed, disorder is created in the universe (the main cause of chemical reactions)


Four Types of Reactions

1. heat is released and disorder is increased: always spontaneous (exergonic).
- most catabolic reactions
- both terms in equation are negative
2. heat is released, but disorder decreases: only spontaneous below a certain temperature; e.g. denatured/native protein, lipid bilayer vs. individual lipids
- Only occurs if heat released is greater, than the increase in order (ex. protein folding, depends of T- the higher the T the higher the entropy (which is why protein folding only works at low temperatures)
3. heat is used, but disorder increases: spontaneous above a certain temperature; e.g. dissolving NaCl in water.
4. heat is used and disorder decreases: never spontaneous (endergonic). Includes most anabolic reactions.

*Basically, these ΔG calculations are good for finding out which reactions can occur and which cannot.*


How do endergonic (anabolic) reactions occur?

- By coupling endergonic to exergonic reactions

Endergonic reactions: non- spontaneous
Exergonic reactions: spontaneous


Complications of Thermodynamics: Reversible reactions

• In principle, all reactions are reversible (A B)
• Adding more A speeds up the forward reaction, adding more B speeds up the reverse reaction.
• At the point of chemical equilibrium, the relative concentrations of A and B are such that forward and reverse reactions take place at the same rate (∆G = 0).


At equilibrium

The standard free energy (ΔG°) applies to 37° C and 1M
concentration of all reactants and products.
- Therefore the concentrations have to be taken into
account in most cases to calculate the actual ∆G.


Transferring energy in cells

• All living cells use adenosine triphosphate (ATP) for capture, transfer, and storage of energy
• Some of the free energy released by exergonic reactions is captured in ATP, which then can drive endergonic reactions



• can hydrolyze to yield ADP and an inorganic phosphate ion (Pi) when reacted with water
• Why so much ATP in our cells? A: For respiration

• The reaction is exergonic (∆G = -12kcal/mole) for two reasons:
1. the energy of the P-O bond is much higher than the H-O bond that forms after hydrolysis, because the phosphates are negatively charged, so energy is required to get them near each other to bond
2. ADP is constantly removed either by reforming ATP or by hydrolysis to AMP (∆G° = -7.3kcal/mole)


More thermodynamic Complications: Activation energy

• The direction of a reaction can be predicted if ∆G is known, but not the rate of the reaction. Many exergonic reactions occur immeasurably slow, and that’s good
• Exergonic reactions proceed only after the addition of a small amount of added energy, called the activation energy
• In a chemical reaction, activation energy is the energy needed to put molecules into a transition state


Activation energy

- energy barrier to keep molecules stable
- activation energy in chem is heating up the sample, but this cant be done in our bodies because we would die



• A catalyst is any substance that speeds up a chemical reaction without itself being used up
• They lower the activation energy (∆G is not changed)
• Most biological catalysts are proteins called enzymes.


Enzyme substrate Complex

1. Initiation: reactants bind to the active site in a specific orientation, forming the enzyme substrate complex
2. Transitions state facilitation: interactions between enzyme and substrate lower the activation energy required
3. Termination: Products have lower affinity for active site and are released. Enzyme is unchanged after the reaction.


Enzyme and Substrate interactions

1. Proximity and Orientation- green is enzyme, blue and red are reactants; reactants are bound in exactly the goth proximity and orientation
2. Charge Environment: some chemical reactions are facilitated by positive and negative reactions. Enzyme carries charge and brings close to reactant which facilitates chemical reaction. If you were to lower the pH, you would effect the charges.
3. Strain: sometimes reactant changes shape when bound



• Some enzymes require cofactors in order to function:
• These can be metal ions (zinc, copper), small organic molecules temporarily binding, and small organic molecules that are permanently bound to the protein (heme). ANYTHING THAT IS NOT AN AMINO ACID


Enzyme saturation

• Enzymes are saturated when all binding sites are occupied; maximum rate = turnover from 1 molecule/sec for lysozyme to 40 million/sec for catalase

- when it reaches max speed o reaction: gives turnover rate of enzyme