Chemistry of Life Lecture 19 (Thermodynamics is the study of energy…
Chemistry of Life Lecture 19
Thermodynamics is the study of energy transformations.
In an open system, energy and matter can be transferred between a the system and its surroundings.
Organism's and Open Systems
A closed system will exchange energy with its surroundings but not matter.
An isolated system, such as that approximated by a liquid in a thermos is unable to exchange energy or matter with its surroundings.
LIFE IS GOVERNED BY THE LAWS OF THERMODYNAMICS:
The First Law of Thermodynamics, According to the first law of thermodynamics, the energy of the universe is constant. Energy can be transferred and transformed but it cannot be created or destroyed. The first law is also called the principal of conservation of energy.
The second law of thermodynamics;
During every energy transfer or transformation some energy is unusable and is often lost as heat. According to the second law of thermodynamics Every energy transfer or transformation increases the entropy of the universe. Entropy is a measure of molecular disorder or randomness
FREE ENERGY, STABILITY AND EQUILIBRIUM: Free energy is a measure of a system's instability, its tendency to change to a more stable state. During a spontaneous change free energy decreases and the stability of a system increases. Equilibrium is a state of maximum stability. A process is spontaneous and can perform work only when it is moving toward equilibrium.
Reactions in a closed and open system
Reactions in a closed system eventually reach equilibrium and can then do no work. Cells are not in equilibrium. They are open systems experiencing a constant flow of materials.
A defining feature of life is that metabolism is never at equilibrium. Catabolic pathways release energy by breaking down complex molecules into simpler ones. Cellular respiration in the prsence of oxygen, is an example of a pathway of catabolism.
Ananbolic pathways; consume energy to build complex ones. For example the synthesis of protein from amino acids is an anabolic pathway.
Free energy and DELTA G in a reaction
A iiving system's free energy is energy that can do work when temperature and pressure are uniform. As in a living cell. Biologists want to know which reactions occur spontaneously and which require an input of energy. To do so they need to determine the energy and entropy changes that occur in chemical reactions. The free energy change of a reaction tells us whether or not the reaction occurs spontaneously, generates energy(exergonic) or is not spontaneous, requires energy ( endergonic)
The change in free energy is related to the change in enthalpy during a process. Change in total energy (DELTA H) Change in entropy (DELTA S) and temperature in kelvin units (T)
DELTA G is negative for all spontaneous processes. Spontaneous processes can be harnessed to perform work. Processes with zero or positive DELTA G are never spontaneous.
The activation Energy (Ea) is the energy needed to reach the transition state.
Every chemical reaction between molecules involves bond breaking and bond forming. The initial energy needed to start a chemical reaction is called the free energy of activation or activation energy (Ea)
Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings.
A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction. An enzyme is a catalytic protein. Enzymes speed up metabolic reactions by lowering the energy barriers (Ea).
The active site can lower an Ea barrier by 1). orientating substrates correctly 2). straining substrate bonds providing a favorable microenvironment 3). covalently bonding to the substrate.
Animation of an enzyme's catalysed reaction:
Even in an exergonic reaction, energy is needed initially to break the bonds (Ea) that act as a barrier to runaway reactions. In catalysis, enzymes speed up specific reactions by lowering the Ea barrier. Enzymes do not affect the free energy instead they hasten reactions that will occur eventually.
Spontaneous and non spontaneous steps in a metabolic pathway
A metabolic pathway begins with a specific molecule and ends with a product. Each step is catalyzed by a specific enzyme that all have their own specific Gibb's free energy. Spontaneous processes occur without energy input they can happen quickly or slowly For a process to occur spontaneously it must increase the entropy of the universe. Processes that decrease the entropy of the universe are non-spontaneous, they will occur only if energy is provided
Endergonic reactions ATP allows transfer of energy from catabolic reactions to anabolic reactions
ATP is a renewable energy source that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP). The energy to phosphorylate ADP comes from catabolic reactions in the cell. The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways.
ATP is composed of a ribose (a sugar), adenine (a nitrogenous base ) and three phosphate groups. The bonds between the phosphate groups of ATP's tail can be broken by hydrolysis. Energy is released from ATP when the terminal phosphate bond is broken. This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves. Most energy coupling in cells is mediated by ATP.
ATP powers cellular work by coupling exergonic reactions to endergonic reactions. A cell does three main kinds of work: 1). Chemical work pushing endergonic reactions
2). Transport work pumping substances against the direction of spontaneous movement
3). Mechanical work such as the movement of muscles
To do work, cells manage energy resources by coupling, the use of an exergonic process to drive an endergonic one
Example of how ATP can promote non-spontaneous endergonic reaction:
In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction. Overall the coupled reactions are exergonic. ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant. The recipiant molecule is now called a phosphorylated intermediate.
ATP hydrolysis leads to a change in protein shape and binding ability.
Substrate specificity of enzymes
The reactant that an enzyme works on is called is substrate. The enzyme binds to its substrate forming an enzyme substrate complex. While bound the activity of the enzyme converts substrate to product. The reaction catalyzed by each enzyme is very specific. The active site is the region on the enzyme where the substrate binds. Induced fit of a substrate brings chemical groups of the enzyme into positions that enhance their ability to catalyze the reaction.
Cofactors bind to an apoenzyme to facilitate a reaction
Cofactors are nonprotein enzyme helpers. Cofactors may be inorganic (such as a metal in ionic form) or organic. An organic cofactor is call a coenzyme. Coenzymes include vitamins. Small quantities of these vitamins must be consumed in order for our enzymes to function correctly. many of the cofactors will sit in the enzyme active site and assist in the binding of the substrate. An inactive without the cofactor is called an apoenzyme, while the complete enzyme with the cofactor is called a holoenzyme.
Enzyme inhibitors can be used as drug molecules:
Competitive inhibitors bind to the active site of the enzyme competing with the enzyme. Noncompetitve inhibitors bind to another part of the enzyme, causing the enzyme to change shape and making the active site less effective. Some examples of inhibitors are toxins, poisons, pesticides and antibiotics.
Allosteric activation and inhibition of enzymes
Regulation of enzyme activity helps control metabolism. Chemical chaos would result if a cell's metabolic pathways were not tightly regulated. A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes. Allosteric regulation may either inhibit or stimulate an enzyme's activity. Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein's function at another site. Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site. The enzyme complex has active and inactive forms. The binding of an activator stabilizes the active form of the enzyme. The binding of an inhibitor stabilizes the inactive form of the enzyme.
Feedback inhibition controls cellular reactions to produce only what's needed
In feedback inhibition, the end product of a metabolic pathway shuts down the pathway. Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
Co-oparativity is another allosteric activity
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