Acids and bases
Acid -> proton donor
Base -> proton acceptor
Strong acids-> dissociate completely irrespective of the pH of the environment.
HCL <-> H+ + CL-
Weak acids and bases -> dissociate depending on the pH of the environment (or H+ conc)
CH3C3OOH <-> H+ + CH3OO- >pH 3
NH4 + <-> NH3 + H+ >pH8
-Alters the rate of reaction because proteins are held together by weak forces. One of which is salt bridges (pH dependent).
-> THE NEGATIVE LOGARITHM OF THE MOLAR CONCENTRATION OF ACTIVE HYDROGEN IONS (ACTIVITY).
pH = -log10 [aH+]
(log scale of the [H+] concentration
[H+] = 10'-1M pH = 1
[H+] = 10'-7M pH= 7
[H+] = 10'-10M pH = 10
- Acidic amino acids eg: have carboxylic acid groups. Aspartate and Glutamate
- Basic amino acids eg: have amine groups. Lysine and Asparagine.
- Proteins have groups present on their surfaces that can be ionized or deionized depending on the pH. This make it relatively easy to change the charge of a protein because the functional groups point out into the water environment.
- The surface of a protein is covered in positive and negative charge. This is important for proteins that function as enzymes or membrane channels because the proteins active site must have the right surface charge in order to be able to bind a specific substrate.
Factors which effect an enzymes activity
-Every 10'C rise in temp there will be a doubling in the rate of reaction
-Enzymes held together by weak forces which are easily broken by heat.
-Rate of reaction increases when temperature increases until a certain point where the protein structure is unravelled and the enzyme is denatured.
-Optimum temp for most enzymes = 37'C
Laws of thermodynamics
1) The total energy change of a system is constant
Energy cannot be created or destroyed.
The distribution of energy changes and not the amount
2) The total *entropy (randomness) of an isolated system increases for a favourable reaction not at equilibrium. The increase in entropy approaches a maximum as the system approaches equilibrium.
100% energy transfer from one side of the equilibrium to the other is not possible.
*Molecules as solids have low entropy which increases as they move to liquids, and this randomness in their movement increases again as they move to gas phase.
MOLECULES MOVE TO INCREASE THEIR ENTROPY IN AN ISOLATED SYSTEM.
(refer back to acids and bases for diagram and info on free energy)
The progress of a chemical reaction
1) Thermodynamics (negative free energy is favourable)
2) Kinetics rate of reaction
ATP -> ADP + Pi has negative free energy change of -32Kg
It is thermodynamically favourable
The free energy released can be utilised by the cell for the synthesis of other metabolites.
Very stable at room temperature.
The kinetics is favourable at 37'C
Arhenius Activation energy
- All reactions must overcome the Arrhenius activation energy before the reaction can proceed
- Free energy has to reach a certain point ABOVE (transition state) the free energy of the substrate before it reaches the free energy of the product.
- There has to be a certain amount of energy before the reaction can take place
- CATALYSTS: lower the free energy required to start the reaction my lowering the Arrhenius activation energy.
Do not change the overall free energy of the system
Can be recycled
- The free energy of the product is always LOWER than the free energy of the substrate.
- efficient catalysts because they form an ES complex and then an EP complex before the reaction is complete.
- ACTIVE SITE:
-holds substrate in the correct shape to move them to the products
-Prevent unwanted side reactions
-Distort the molecules by slightly stretching bonds
-Amino acid side chains from the active site contribute towards the catalyctic event
-Substrate can fit directly into a active site
-Sometimes the active site has to change shape to fit with the shape of the substrate.
-Substrates are held at the active site in the correct 3D conformation to successfully move substrates to products.
EG hexotinase on binding to a substrate