Matter - anything that has mass and occupies space.
Energy - defined indirectly in terms of the movement of matter through a distance, i.e., work.
Work - defined in terms of the force necesary to move matter across a distance (Work = Force X Distance).
Free energy - the capacity of a system to do work under a given set of conditions.
1st Law of Thermodynamics - Conservation of energy (energy can be transformed but not destroyed).
Entropy - a measure of the degree of disorder in a system.
2nd Law of Thermodynamics - Heat can never pass spontaneously from a colder to a hotter body. It implies that all processes tend to proceed in such a directon that the entropy of the universe must increase until an equilibrium is reached. At this equilibrium, the entropy is the maximum that can be attained under the given conditions of temperature and pressure.
The vast majority of organisms obtain energy to build, maintain and perpetuate their improbable arrangements of matter by carrying out the following reaction:
The number of and kinds of atoms are the same on the right and left sides of this equation. What is the difference? Answer: The spatial arrangement of the atoms and the chemical bond energies.
The different molecules that make up the bodies of organisms are manufactured from a small selection of organic compounds. These basic building block compounds are plugged into chemical avenues where these original structures are modified and made into new and different compounds. These avenues of chemical modification are called chemical pathways.
At each step in the pathway, the conversion of one type of molecule into another is mediated by a large protein molecule called an enzyme. These enzyme molecules are organic catalysts; they speed up the rates of the chemical conversion process. None of the chemical reactions in living things proceed fast enough on their own to support the myriad of life processes.
Catalyst-any substance that speeds up the rate of a chem. reaction without itself being consumed or permanently changed by the reaction.
Enzyme-an organic catalyst (usually a protein).
Enzymes differ from Inorganic Catalysts in a number of important ways:1. More Powerful - 100,000 to a million times.
2. Highly specific - usually a single chem. reaction or a set of closely related reactions.
3. Display evolutionary plasticity - structure and efficiency may change over time.
To understand how enzymes effect the rates of chemical reactions, it is necessary first to understand the basic principles of uncatalyzed chemical reactions.
1. Atoms and molecules are always in a state of motion. (except at absolute zero , -273.15o C)
2. Distribution of motions:
3. For a chemical reaction to occur, particles must come into contact in order to exchange or rearrange electrons. The mutual repulsion of the electron clouds must be overcome.
4. Minimum Kinetic Energy for Reaction (K.E.*):
A + B
C + D
5. Ways to Increase the Rates of Reactions:a.) Increase the concentration-more collisions with adequate K.E.* per unit time.
b.) Heat - promotes more molecule beyond the minimum kinetic energy for reaction.
c.) Catalysts - postpone discussion until later in this section (#11)
6. Exergonic and Endergonic reactions:
Where does the energy come from to run endergonic reactions in the cells of living organisms? Answer: Endergonic reactions are coupled to exergonic ones.
7. Chemical Equilibrium- A reaction is said to have reached chemical equilibrium when the rate of the forward reaction equals the rate of the back reaction. Note: Chemical equilibrium is a statement about equal rates, not equal concentrations.
Early in the reaction:
A + B
C + D
At chemical equilibrium:
A + B
C + D
8. Concentration of reactants and products at chemical equilibrium-The relative concentrations of reactants and products at equil. in a given chemical reaction are related to the difference in free energy between the reactants and products. That is, the greater the difference in free energy between the reactants and products, the greater the difference in concentration between them.
9. Reversibility- All chemical reactions are reversible, at least in theory.Consider the following reaction: A + B ======> C
This reaction would be exergonic, not very reversible, a great difference in concentration between the reactants and products, and a great difference in free energy between the reactants and products.
Consider this reaction: A + B ======> D
This reaction would be exergonic, reversible, possibly very reversible, small difference in concentration between reactants and products, and small difference in free energy between reactants and products.
10. Activation Energy - The reaction A ====> B goes through a transition state that has a higher free energy than either A or B. Activation energy is the excess energy over the ground state that must be acquired by a chemical system in order for the reaction to proceed. In this diagram it is the difference in free energy between the ground state of A and the transition state.
Most biochemical reactions would proceed slowly, if at all, at physiological temperatures and pressures even though they are exergonic. How then can we explain or account for the rapid rate of biochemical reactions? Answer: The organic catalysts called enzymes.
11. Catalysts - catalysts speed up chemical reactions by lowering the amount of activation energy necessary for a particular reaction. They create a new transition state that has a lower energy level than the uncatalyzed reaction.
Catalysts only speed up reactions that are thermodynamically possible.
They do not alter:
- the direction of the reaction
- the reactions' final equilibrium point
- the free energy of reaction
Enzymes as catalysts - For every reaction in a biochemical pathway, there is a specific enzyme.
- Structure is determined by the genetic code of the cell-produces an amino acid sequence that is specific for each type of enzyme.
- Synthesis takes place in the cytoplasm on the surface of structures called ribosomes.
- The resultant polypeptide twists and folds to forma a stable three-dimensional configuration.
- The properties of enzymes are totally dependent upon the correct 3-D shape of the enzyme molecules.
- Some enzymes are composed of single polypeptide chains, while others have 2 or more chains that bind together to form an active enzyme. Enzymes composed of two chains are called dimers and those of four chains tetramers.
1. Lock and Key Analogy - Highly specific because of the geometry and charge of the active site of the enzyme and the substrate.
2. Sequence of Enzyme Events:E + S =======> ES Complex =======> E + P
3. Enzymes lower the activation energy necessary for a reaction by forming an ES Complex which has a transition state energy that is lower than the uncatalyzed reaction.
1. Definitions:Oxidation - loss of electrons
Reduction - gain of electrons
2. In biological systems redox reactions most often mean the loss or gain of hydrogens. Why?Hydrogen - an electron in disguise.H =====> H+ + e-
3. Nonbiological example:
CH4 + 2O2 =====> CO2 + 2H2O + energy
4. Biological examples:Respiration: C6H12O6 + 6O2 =====> 6CO2 + 6H2O + energy
Photosynthesis: 12H2O* + 6CO2 + energy =====> C6H12O6 + 6H2O + 6O2
* Hydrogen from water is used to reduce carbon dioxide
5. Redox Scale of Carbon:
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