1. Energy and Enzymes
For BIOS 302

2. Life and Energy
Life is “just” a large set of interlocking chemical reactions: metabolism.
We take in food molecules and break them down into smaller components (catabolism)
Then we build the component molecules into macromolecules that become part of our body (anabolism)
All of this requires energy.

3. Energy
Energy is defined as the ability to do work. In the cell, this can mean synthesizing a new molecule, or transporting something across a membrane, cell movement, …
Energy is measured in Joules (J)
However, until recently energy was measured in calories. A calorie is the amount of energy needed to raise 1 milliliter of water 1oC.
The Calorie (capital C) is equal to 1000 calories. It is the unit used for energy content of food.
1 J = 0.24 cal (or, about 4 joules per calorie)
The Sun is the source of most of the energy used in biological systems
However, a substantial amount of energy comes from various inorganic compounds that have been present in the Earth’s crust since its formation 4.6 billion years ago. Various bacteria use this energy source and don’t have any reliance on sunlight.

4. Kinetic and Potential Energy
Energy is in two basic forms:
Potential energy, which is energy stored up, ready to use, like a coiled spring, the capacity to do work.
Kinetic energy, which is energy of motion, actually doing work.
Some biologically relevant forms of kinetic energy:
Heat: the motions and vibrations of molecules
Electromagnetic radiation: visible light mostly
Electrical: the energy involved in moving charged molecules or electrons
Mechanical: moving objects within the cell, or moving the cell itself, or moving atoms closer to each other to get them to react
Some biologically relevant forms of potential energy:
Energy stored in chemical bonds
Concentration gradients
Electrical potential (voltage) differences.

5. Laws of Thermodynamics
First Law: the total mount of energy in the Universe is constant. Energy is neither created not destroyed, it just changes form.
When energy is expended, part of it goes to do useful work, and the rest ends up as heat. None of it is lost, but it changes forms.
Second Law: disorder (entropy) increases. Energy goes from useful forms to useless heat.
Every energy transformation step is inefficient (as a consequence of the Second Law), meaning that some of the energy is converted to waste heat at every step, and the amount of useful work decreases with every step.
Life is very orderly compared to non-living things. Living things are able to locally reverse the overall direction of entropy by using a lot of energy.
We live by taking in energy, using some of it to do useful work, and releasing the rest as waste heat.

6. Free Energy
Concept from J. Willard Gibbs, so it is also called Gibbs free energy and symbolized as G.
A reaction will occur if the free energy is released: if the free energy of the products is less than the free energy of the reactants:
Gproducts < Greactants
Or, we can define the change in free energy, ΔG:
ΔG = Gproducts - Greactants
a reaction goes in the direction that has a negative free energy change
So, the reaction will occur if ΔG < 0.

7. Free Energy and Thermodynamics
Free energy has 2 components: enthalpy (heat content of the chemical bonds being altered: ΔH) and entropy (measure of disorder: ΔS). T is temperature, which is usually close to constant in biological systems.
ΔG = ΔH - TΔS
ΔS is mostly a matter of how many separate molecules are involved. Going from fewer molecules to more molecules means an increase in entropy. This makes ΔG more likely to be less than 0, so the reaction will proceed.
For example, burning glucose: C6H12O6 ⇌ 6CO2 + 6H20 .
Synthesis of macromolecules is a big decrease in entropy: an assembled macromolecule is much more ordered than the subunits moving freely. Independent of one another.
This means that TΔS is less than 0, so to get the reaction to go it needs to be coupled to a big loss of ΔH.
ΔH is a depends on the compounds involved. For example, methane (CH4) molecules contain much more energy than the CO2 and H20 molecules produced when you burn the methane. The number of molecules stays the same, so ΔS is relatively constant.
CH4 + 2O2 ⇌ CO H2O

8. Standard Free Energy
The ΔG changes with the concentrations of the molecules involved.
If we want to compare different reactions under different conditions, we need to measure ΔG under standard conditions:
All compounds at 1 M concentration
298 K ( = 25oC)
1 atmosphere pressure
In pure water, pH 7.0
The ΔG measured under these conditions is the standard free energy of the reaction, ΔGo’. It is measured in kilocalories per mole (or kilojoules per mole). (4 J is about 1 calorie)

9. Equilibrium Constant

10. Free Energy and Equilibrium

11. Coupled Reactions
Many biological reactions are energetically unfavorable: the cell is often trying to build up complex macromolecules from subunits, which is a reversal of entropy. A macromolecule is much more ordered than its separate components.
The cell gets around this by coupling two reactions together: the energetically unfavorable synthesis reaction with an energetically favorable reaction, such as ATP → ADP + Pi.
The ΔG’s for the two coupled reactions add together, so if the sum is less than 0, the reaction can occur.
Also common in membrane transport: one molecule comes into the cell going down its concentration gradient, and it drags another molecule along that is going up its concentration gradient.

12. ATP
In living cells, energy is carried by molecules of ATP, adenosine triphosphate.
Energy is stored in the phosphoanhydride bonds between the phosphate groups. The free energy (ΔG) from hydrolyzing these bonds under biological conditions is about -57 kJ/mol.
When the energy is used, one of the phosphates attached to ATP is released, giving ADP, adenosine diphosphate.
Some reactions convert ATP directly to adenosine monophosphate:
ATP  AMP + PPi.
PPi stands for pyrophosphate, two phosphate groups linked together. PPi is further hydrolyzed to phosphate.
Formation of ATP is energetically unfavorable, and most of the energy carried in the chemical bonds of food molecules goes to synthesizing ATP from ADP.

13. Biological Energy Comes from the Movement of Electrons
During the process of respiration, cells generate ATP by oxidizing glucose to form carbon dioxide and water.
The cell removes high energy electrons from glucose through a series of steps, converting it to carbon dioxide. The energy stored in the electrons is used to make ATP. In the last step, the electrons are given to oxygen molecules, converting them to water.
During photosynthesis, the energy in photons of light is used to remove low energy electrons from water (converting the water to oxygen), and convert them to high energy electrons stored in the chemical bonds of sugar.

14. Oxidation and Reduction
A chemical reaction that moves electrons from one molecule to another is an oxidation-reduction reaction, or a redox reaction.
Since electrons aren’t gained or lost, when one molecule is oxidized, another molecule is reduced.
The molecule that loses electrons is oxidized (Lose Electrons = Oxidation). The molecule that is oxidized in a reaction is the electron donor.
The molecule that gains electrons is reduced (Gain Electrons = Reduction). The molecule that is reduced in a reaction is the electron acceptor.
For example,
Fe2+  Fe3+
is an oxidation: the iron atom lost 1 electron, moving its charge from +2 to +3.
LEO: Lose Electrons = Oxidation
GER: Gain Electrons = Reduction

15. Other Ways of Viewing Redox Reactions
The original meaning of oxidation was adding an oxygen. The movement of electrons in biological systems is often accompanied by an H atom.
So, in a reaction like:
NAD+ + H+  NADH
NAD+ is reduced to NADH.
NADH and its cousin NADPH are the most common carriers of electrons to be used to reduce other compounds.
There are many enzymes called dehydrogenases. These enzymes all perform redox reactions.
As shown on the right, a reaction that removes a C-H bond is an oxidation, and a reaction that adds a C-H bond is a reduction.
Thus, methane is fully reduced and carbon dioxide is fully oxidized.

16. Reduction Potential
Any redox reaction could run in either direction. To determine which way a reaction will go, the standard reduction potential (E0’) is used.
All reactions are written as reductions, such as
Fe3+ + e-  Fe2+
Note this a half-reaction: the electron must come from another molecule.
All reactions are performed under standard conditions (298 K, 1 atm pressure, 1 M reactants)
Reduction potentials are measured in volts, relative to :
H+ + e-  1/2 H
which is defined as 0 volts.
Electrons move spontaneously toward the molecule with a more positive reduction potential.

17. More Reduction Potential
Electrons move spontaneously toward the molecule with a more positive reduction potential.
Two half-reactions need to be summed, with one of the reactions reversed. Free electrons don’t exist in biological systems.
The reduction potential of the reversed reaction changes sign, and then the two reduction potentials are added.
Reactions proceed in the forward direction if the sum of the reduction potentials is greater than 0.
For example, the reaction below is the final step in respiration, the reduction of oxygen to water. Simulataneously, NADH is oxidized to NAD+.
The half-reaction with NAD+ has been reversed and had the sign of its reduction potential reversed.

18. Biological Electron Carriers
Electrons aren’t soluble in water, so they have to be transferred directly from one molecule to another.
The most common carriers of electrons are NAD+, which is reduced to NADH when it is carrying a pair of electrons, and NADP, which is reduced to NADPH when it is carrying a pair of electrons.
NAD= nicotine adenine dinucleotide
NADP is nicotine adenine dinucleotide phosphate
The half-reaction is:
NAD+ + 2e-  NADH + H+

19. Enzymes
Free energy determines whether a reaction can occur or not, but the rate of the reaction depends on the presence of enzymes.
Enzymes are proteins that cause specific chemical reactions to occur.
Enzymes act as catalysts: they help the reaction occur, but they aren’t used up in the reaction.
All reactions require an input of energy to get them started: the activation energy. Think of touching a match to a piece of paper to start a fire: the match is supplying the activation energy.
Enzymes work by lowering the activation energy for a reaction. The reaction occurs thousands or millions of times faster than without the enzyme. The little bit of activation energy needed is supplied by the collision of the molecules involved.
Enzymes are very specific for their substrates: they work on only a very limited number of similar molecules.

20. Enzyme-Substrate Interactions
Each enzyme has an active site, a special region that holds the substrates together and causes them to react.
The active site promotes the reaction by orienting the substrates properly, straining their bonds so they break more easily, and by providing acidic or basic amino acids to help the reaction along.
The substrates reach the active site by random diffusion. This process is very fast for small molecules.
For example, a relatively common substrate in a cell might have a concentration of 0.5 mM. The active site of a single enzyme molecule will be hit about 500,000 times per second by these substrate molecules.
The substrate binds to the enzyme by numerous hydrogen bonds, electrostatic interactions, and Van der Waals forces. This means that enzymes are usually very specific for which substrate molecules they can work with.

21. Factors Influencing Enzyme Activity
Enzymes often use small accessory molecules called coenzymes to help carry out the reaction. Most vitamins are coenzymes.
Enzymes often have small molecules that act as inhibitors or activators of their activity. These molecules alter the active site so the enzyme reacts differently to the substrate.
Enzyme activity is strongly influenced by temperature. They have an optimum temperature: to hot or too cold slows them down. Most of the enzymes in humans have an optimum temperature near body temperature.
pH and salt level also influence enzyme activity, with optimum values for each.

22. Reaction Rates
There are only a limited number of enzyme molecules available to perform a reaction, and they have a maximum speed at which they can act.
The maximum speed is the turnover number: how many substrate molecules can be processed per second.
The maximum speed occurs when there is so much substrate present that as soon as the enzyme finishes converting a reactant into a product, another reactant molecule is ready to be processed.

23. Rate vs. Substrate Concentration
The speed of enzyme action depends on the substrate concentration as well as the turnover number and the number of enzyme molecules present.
At low substrate concentrations, the enzyme molecules spend part of their time idle, so the reaction rate is low.
When substrate concentration isn’t limiting, all enzyme molecules are operating at their maximum speed. The rate of reaction under these conditions is the Vmax.
In practice, it is easier to measure the substrate concentration that gives the half maximal reaction rate. This substrate concentration is the Michaelis-Menton constant, Km.