BIOL130 Chapter Notes - Chapter 3: Nicotinamide Adenine Dinucleotide Phosphate, Phosphatidylethanolamine, Phosphatidylinositol

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Unit 3: Thermodynamics and Catalysis
Unit 3a: Thermodynamics
1st Law of Thermodynamics: energy can be transferred and transformed, it cannot be
created nor destroyed
energy: the capacity to do work (move against opposing forces, to rearrange matter
etc.)
kinetic energy (EK) : the energy of motion or heat
potential energy (EP) : store energy due to location and structure (arrangement of
atoms within molecule)
 electrons within chemical bonds are a source of potential energy
 breaking chemical bonds releases energy
 bond formation is favourable when atoms are more stable together than apart
2nd Law of Thermodynamics: Energy spontaneously disperses, and spreads out 
disorder (entropy).
 A chemical reaction can produce disorder in two ways:
1) Each time energy is converted from one form to another, some of the energy
becomes unusable
2) the reaction can decrease entropy in reacting molecules - by breaking apart a long
chain of molecules or by disturbing interactions that prevent bond rotations
Exergonic reactions (Downhill reaction): products are less “ordered” (increase in
entropy) and have lower potential energy then the reactants. Spontaneous reactions
that release energy
Endergonic reactions (Uphill reaction): products are more “ordered” (decrease in
entropy) and have higher potential energy than the reactants. Non-spontaneous
reactions that absorb energy
Gibbs free energy: a quantitative measure of energy that can do useful work from a
system at constant temperature and pressure; also called free energy
 predicts spontaneity, but not reaction rates or chemical equilibria
 a negative G value indicates the reaction is spontaneous (exergonic) and entropy
increase. Molecules&Energy PRODUCTS > Molecules&EnergyREACTANTS. The G value is negative
because the products contain less free energy = ENERGETICALLY FAVORABLE REACTION
 A positive G value indicates the reaction is non-spontaneous (endergonic) and entropy
decrease. Molecules&Energy PRODUCTS < Molecules&Energy REACTANTS. Free energy is required
to make this reaction possible = ENERGETICALLY UNFAVORABLE REACTION
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G depends on concentration of molecules in a mixture, it is not useful for comparing the
relative energies of different reactions
Standard free energy: used to compare different reactions, G°. Depends only on
characteristic of molecules under ideal conditions where concentration of all reactants
is 1M and pH is 7.0
 the quantity of G° represents the gain or loss of free energy as one mole of reactant is
converted to one mole of product. This will predict the outcome of a reaction
Energy coupling: the transfer of energy from one reaction to another in order to drive
the second reaction; cells are able to make endergonic reactions possible by fueling
them with the free energy given off from the exergonic reactios. Cells couple exergonic
reactions with endergonic reactions. This is how we can synthesize more complex
molecules that are endergonic.
Rates of spontaneous reactions: even if it is spontaneous, does not mean it is fast
 iron to rust occurs very slowly
Collision: influenced by temperature and concentration
Catalysts: can work under physiological conditions of pH, temperature, concentration
etc.
 enzymes bind to reactants and accelerate their production to products
Enzymes do not: change equilibrium position of reaction or catalyze non-spontaneous
reactions (positive ΔG°)
Hill analogy: even to roll a boulder downhill needs a small push just like exergonic
reactions need catalysts
Catalysts changes the rate of the reaction but is not consumed by the reaction
Enzymes catalyze a reaction by:
 substrates binding very specifically to the enzyme’s active site
 enzyme changes shape when substrate is bound
 energy level of products is different than substrates
 product is released and enzyme returns to its original shape
Cofactors: inorganic molecules  metal ions needed in trace amounts in diet
Coenzymes: organic molecules  shuttling of electrons (NADH), vitamins
 coenzymes are chemically changed during the reaction and must be regenerated
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Regulatory molecule: binds to an enzyme and changes its reactivity depending on the
needs of the cell
 inhibitor: decreases enzyme activity
 activator: increase activity
Two types of regulation: allosteric and competitive
Enzyme inhibitors
competitive inhibition binds to active site instead of substrate, can be overcome by
increasing the substrate
 non-competitive inhibitor: binds to allosteric site, can’t be overcome by excess
substrate. It binds at a site away from active site; however, it changes the enzymes
shape so that the substrate no longer fits
Regulation of enzyme activity can be the result of covalent modification by functional
groups on enzymes
Chapter 4: Energy
Energy obtained from chemical bond energy stored in ‘food’ and stored/transported in high
energy bonds of carrier molecules (ATP and NADH)
 most important source is carbohydrate (sugar)
 sugars oxized to CO2 and H2O
Macromolecule, nucleic acids, synthesis requires ATP
Energy stored in:
 phosphate group in ATP
 electrons and hydrogens in NADH, NADPH, FADH2
 acetyl group in acetyl CoA
Coenzymes that carry electrons from one reaction to another: accepts a hydride atom (H-, 2
electrons and a proton) and donates it
 key players in harvesting energy during oxidation of glucose
NAD+ = nicotinamide adenine dinucleotide (vitamin B3)
FAD = flavin adenine dinucleotide (vitamin B2)
NADP+ = nicotinamide adenine dinucleotide phosphate
Catabolism: breakdown of complex molecules into simpler ones (by enzymes)
Anabolism: build molecules from simpler ones, also called biosynthetic pathway
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