BIS 1A Handout 8 - Biological Energy

An organism's metabolism transforms matter and energy

The totality of an organism's chemical reactions is called metabolism.

The chemistry of life is organized into metabolic pathways.

Metabolic pathways begin with a specific molecule, which is then altered in a series of defined steps to form a specific product.

A specific enzyme catalyzes each step of the pathway.

Catabolic pathways release energy by breaking down complex molecules to simpler compounds.

A major pathway of catabolism is cellular respiration, in which the sugar glucose is broken down in the presence of oxygen to carbon dioxide and water.

Anabolic pathways consume energy to build complicated molecules from simpler compounds. They are also called biosynthetic pathways.

The synthesis of glycogen from glucose is an example of anabolism.

The energy released by catabolic pathways can be stored and then used to drive anabolic pathways.

Bioenergetics is the study of how organisms manage their energy resources.

Organisms transform energy.

Energy is the capacity to do work.

Kinetic energy is the energy associated with the relative motion of objects.

Photons of light can be captured and their energy harnessed to power photosynthesis in green plants.

Heat or thermal energy is kinetic energy associated with the random movement of atoms or molecules.

Potential energy is the energy that matter possesses because of its location or structure.

Chemical energy is a form of potential energy stored in molecules because of the bonding of their atoms.

The energy transformations of life are subject to two laws of thermodynamics.

Thermodynamics is the study of energy transformations.

The first law of thermodynamics states that energy can be transferred and transformed, but it cannot be created or destroyed.

The first law is also known as the principle of conservation of energy.

Plants do not produce energy; they transform light energy to chemical energy.

Entropy is a quantity used as a measure of disorder or randomness.

The more random a collection of matter, the greater its entropy.

The second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe.

Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of random molecular motion.

Living cells unavoidably convert organized forms of energy to heat.

The word spontaneous describes a process that can occur without an input of energy.

Some spontaneous processes are instantaneous, such as an explosion. Some are very slow, such as the rusting of an old car.

Living systems create ordered structures from less ordered starting materials.

For example, amino acids are ordered into polypeptide chains.

However, an organism also takes in organized forms of matter and energy from its surroundings and replaces them with less ordered forms.

For example, an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water.

Organisms are islands of low entropy in an increasingly random universe.

The free-energy change of a reaction tells us whether the reaction occurs spontaneously

The concept of free energy provides a useful function for measuring spontaneity of a system.

Free energy is the portion of a system's energy that is able to perform work when temperature and pressure is uniform throughout the system, as in a living cell.

Free energy can be thought of as a measure of the stability of a system.

Systems that are high in free energy-compressed springs, separated charges, organic polymers-are unstable and tend to move toward a more stable state.

In any spontaneous process, the free energy of a system decreases.

The greater the decrease in free energy, the more work a spontaneous process can perform.

A system at equilibrium is at maximum stability, and the system can do no work.

A process is spontaneous and can perform work only when it is moving toward equilibrium.

Movements away from equilibrium are nonspontaneous and require the addition of energy from an outside energy source (the surroundings).

Chemical reactions can be classified as either exergonic or endergonic based on free energy.

An exergonic reaction proceeds with a net release of free energy.

An endergonic reaction is one that absorbs free energy from its surroundings.

Endergonic reactions are nonspontaneous, and store energy in molecules.

Photosynthesis is strongly endergonic, powered by the absorption of light energy.

A catabolic process in a cell releases free energy in a series of reactions, not in a single step.

Some reversible reactions of respiration are constantly "pulled" in one direction, as the product of one reaction does not accumulate but becomes the reactant in the next step.

Sunlight provides a daily source of free energy for photosynthetic organisms.

Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

ATP powers cellular work by coupling exergonic reactions to endergonic reactions

Cells manage their energy resources to do this work by energy coupling, the use of an exergonic process to drive an endergonic one.

In most cases, the immediate source of energy to power cellular work is ATP.

ATP (adenosine triphosphate) is a type of nucleotide consisting of the nitrogenous base adenine, the sugar ribose, and a chain of three phosphate groups.

The bonds between phosphate groups can be broken by hydrolysis.

Hydrolysis of the end phosphate group forms adenosine diphosphate.

ATP -> ADP + Pi

The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.

Why does the hydrolysis of ATP yield so much energy?

Each of the three phosphate groups has a negative charge.

These three like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule.

In the cell, the energy from the hydrolysis of ATP is directly coupled to endergonic processes by the transfer of the phosphate group to another molecule.

This recipient molecule is now phosphorylated.

This molecule is now more reactive (less stable) than the original unphosphorylated molecules.

ATP is a renewable resource that can be regenerated by the addition of a phosphate group to ADP.

The energy to phosphorylate ADP comes from catabolic reactions in the cell.

The chemical potential energy temporarily stored in ATP drives most cellular work.

Enzymes speed up metabolic reactions by lowering energy barriers

Spontaneous chemical reactions may occur so slowly as to be imperceptible.

A catalyst is a chemical agent that speeds up the rate of a reaction without being consumed by the reaction.

An enzyme is a catalytic protein.

Enzymes regulate metabolic pathways.

Every chemical reaction involves bond breaking and bond forming.

To hydrolyze sucrose, the bond between glucose and fructose must be broken and new bonds must form with hydrogen and hydroxyl ions from water.

To reach a state where bonds can break and reform, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat as the molecules assume stable shapes with lower energy.

The initial investment of energy for starting a reaction is the free energy of activation or activation energy (EA).

Activation energy is the amount of energy necessary to push the reactants over an energy barrier so that the reaction can proceed.

For some processes, EA is not high, and the thermal energy provided by room temperature is sufficient for many reactants to reach the transition state. Green tea becomes brown after one day.

Proteins, DNA, and other complex organic molecules are rich in free energy. Their hydrolysis is spontaneous, with the release of large amounts of energy.

However, there is not enough energy at the temperatures typical of the cell for the vast majority of organic molecules to make it over the hump of activation energy.

Enzymes speed reactions by lowering EA.

The transition state can then be reached even at moderate temperatures.

Enzymes are substrate specific.

The reactant that an enzyme acts on is the substrate.

The enzyme binds to a substrate, or substrates, forming an enzyme-substrate complex.

While the enzyme and substrate are bound, the catalytic action of the enzyme converts the substrate to the product or products.

The reaction catalyzed by each enzyme is very specific.

What accounts for this molecular recognition?

The specificity of an enzyme results from its three-dimensional shape.

Only a portion of the enzyme binds to the substrate.

The active site of an enzyme is typically a pocket or groove on the surface of the protein into which the substrate fits.

The active site is usually formed by only a few amino acids.

The active site is an enzyme's catalytic center.

In most cases, substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds.

A single enzyme molecule can catalyze thousands of reactions a second.

Most metabolic enzymes can catalyze a reaction in both the forward and reverse directions.

The actual direction depends on the relative concentrations of products and reactants.

Enzymes catalyze reactions in the direction of equilibrium.

Enzymes use a variety of mechanisms to lower activation energy and speed up a reaction.

In reactions involving more than one reactant, the active site brings substrates together in the correct orientation for the reaction to proceed.

As the active site binds the substrate, it may put stress on bonds that must be broken, making it easier for the reactants to reach the transition state.

R groups at the active site may create a microenvironment that is conducive to a specific reaction.

An active site may be a pocket of low pH, facilitating H+ transfer to the substrate as a key step in catalyzing the reaction.

A cell's physical and chemical environment affects enzyme activity.

The activity of an enzyme is affected by general environmental conditions, such as temperature and pH.

Each enzyme works best at certain optimal conditions, which favor the most active conformation for the enzyme molecule.

Temperature has a major impact on reaction rate.

As temperature increases, collisions between substrates and active sites occur more frequently as molecules move more rapidly.

As temperature increases further, thermal agitation begins to disrupt the weak bonds that stabilize the protein's active conformation, and the protein denatures.

Each enzyme has an optimal temperature.

Most human enzymes have optimal temperatures of about 35-40°C.

Each enzyme also has an optimal pH.

This falls between pH 6 and 8 for most enzymes.

However, digestive enzymes in the stomach are designed to work best at pH 2, while those in the intestine have an optimum of pH 8.

Many enzymes require nonprotein helpers, called cofactors, for catalytic activity.

Cofactors bind permanently or reversibly to the enzyme.

Some inorganic cofactors include zinc, iron, and copper, members of the microelements

Organic cofactors are called coenzymes.

Many vitamins are coenzymes.

Binding by inhibitors prevents enzymes from catalyzing reactions.

If inhibitors attach to the enzyme by covalent bonds, inhibition may be irreversible.

If inhibitors bind by weak bonds, inhibition may be reversible.

Toxins and poisons are often irreversible enzyme inhibitors.

Regulation of enzyme activity helps control metabolism

Metabolic control often depends on allosteric regulation.

Regulatory molecules often bind weakly to an allosteric site, a specific receptor on the enzyme away from the active site.

Binding by these molecules can either inhibit or stimulate enzyme activity.

Most allosterically regulated enzymes are constructed of two or more polypeptide chains.

Each subunit has its own active site.

Allosteric sites are often located where subunits join.

The binding of an activator stabilizes the conformation that has functional active sites, while the binding of an inhibitor stabilizes the inactive form of the enzyme.

ATP and ADP plays a major role in balancing the rates of anabolic and catabolic pathways.

For example, ATP binds to several catabolic enzymes allosterically, inhibiting their activity by lowering their affinity for substrate.

ADP functions as an activator of the same enzymes.

A common method of metabolic control is feedback inhibition in which an early step in a metabolic pathway is switched off by the pathway's final product.

The product acts as an inhibitor of an enzyme in the pathway.

Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.

The localization of enzymes within a cell helps order metabolism.

Structures within the cell help bring order to metabolic pathways.

A team of enzymes for several steps of a metabolic pathway may be assembled as a multienzyme complex.

The product from the first reaction can then pass quickly to the next enzyme until the final product is released.

Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes.

Others are confined within membrane-enclosed eukaryotic organelles.

Metabolism is a regulated network of chemical pathways characteristic of life.