4.1 Energy and Metabolism

The building and breaking down of complex molecule occur through stepwise chemical reactions.

Some of the chemical reactions require energy to proceed, whereas others require no energy at all.

Cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that take place, just as living things must continually consume food to replenish their energy supplies.

Most life forms get their energy from the sun.

Plants capture sunlight and herbivores eat them to get energy.
The decomposition of plant and animal material contributes to the pool of nutrition.

Consider the metabolism of sugar.

This is an example of a cellular process that uses and produces energy.
Sugars are a major source of energy for living things because they have a lot of energy stored within their bonds.
Plants produce most of the sugars.
Plants use energy from the sun to convert CO2 into sugar.
Oxygen is produced as a waste product.

This process requires energy input because it involves synthesizing an energy-storing molecule.

The primary energy currency of all cells is a molecule called adenosine triphosphate.
Cells use the same molecule of energy as the dollar to perform work.
The energy-storage molecule such asglucose is consumed only to be broken down to use their energy.
The reverse reaction to photosynthesis harvests the energy of a sugar molecule in cells requiring oxygen to survive.
Oxygen is consumed and carbon dioxide is released as a waste product.

Many steps are involved in both of these reactions.

Two examples of metabolic pathways are shown in the processes of making and breaking down sugar.

A metabolic pathway is a series of chemical reactions that take a starting molecule and modify it, step-by-step, through a series of metabolic intermediates, eventually yielding a final product.
In the example of sugar metabolism, the first pathway breaks sugar down into smaller molecule sugars.
metabolism is composed of synthesis and degradation

The chemical reactions of the pathways do not happen on their own.

Each step of a reaction iscatalyzed by an enzyme.
Catalyzing all types of biological reactions requires the use of Enzymes.

There arebolic pathways that generate energy.

There arebolic pathways that need energy.
Maintaining the cell's energy balance requires two types of pathways.

The system and surroundings are related to a particular case of energy transfer.

When heating a pot of water on the stove, the system includes the stove, the pot, and the water.
Between the stove, pot, and water, energy is transferred.
There are two types of systems.
Energy can be exchanged in an open system.
The heat can be lost to the air.
A closed system can't exchange energy with its surroundings.

The organisms are open.

Energy is exchanged between them and their surroundings as they use energy from the sun to perform photosynthesis or consume energy-storing molecules and release energy to the environment by doing work and releasing heat.
Energy is subject to the laws of the physical world.
The laws of the universe govern the transfer of energy.

Energy can be defined as the ability to do work or to create change.

There are different types of energy.

Understanding two of the physical laws that govern energy is important to appreciate how energy flows into and out of biological systems.

The first law of thermodynamics states that the total amount of energy in the universe is constant.

There has always been the same amount of energy in the universe.

The first law of thermodynamics states that energy can be transferred from place to place, but it can't be created or destroyed.

The transfers and transformations of energy happen all the time.
Light bulbs convert electrical energy into light and heat.
Natural gas is transformed into heat energy by gas stoves.

The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work.

Living cells are able to meet this challenge.
Through a series of cellular chemical reactions, sugars and fats are transformed into energy within the molecule of the same name.
It is easy to do work with the energy in the ATP molecule.
Examples of the types of work that cells need to do include building complex molecules, transporting materials, and contracting muscle fibers to create movement.

The examples show how energy can be transferred from one system to another and from one form to another.

Light energy and food both provide our cells with the energy they need to carry out our bodily functions.

The primary tasks of a living cell may seem simple.

The second law of thermodynamics explains why these tasks are harder than they appear.
Energy transfers and transformations are not always efficient.
Some amount of energy is lost in a form that is not usable.
This form is usually heat energy.
When a light bulb is turned on, some of the electrical energy being converted into light energy is lost as heat energy.
During cellular reactions, some energy is lost as heat energy.

Order and disorder are important concepts in physical systems.

The less ordered the system is, the more energy it loses to its surroundings.
The measure of randomness or disorder within a system is referred to by scientists.
There is high disorder and low energy.
There are different levels of entropy for Molecules and Chemical reactions.
The second law of thermodynamics says that heat will always be lost in energy transfers.

Living things need constant energy input to be maintained in a state of low entropy.

There is energy associated with an object when it is moving.

Think of a demolition ball.
A slow moving ball can do a lot of damage.
A bullet, a walking person, and a molecule in the air all have the same energy.

The answer is yes.

The force of gravity acting on the wrecking ball has stored the energy that was required to lift it.
Wrecking balls swing like a pendulum, with a constant change of potential energy at the top and bottom of the swing.
Water behind a dam or a person about to skydive out of an airplane are examples of potential energy.

The water in a waterfall has potential energy, while the water in a rapidly flowing river has kinetic energy.

The structure of matter and potential energy are related.

A rubber band that is pulled taut has potential energy if it is compressed.
The bonds that hold the atoms together exist in a structure that has potential energy.
When complex molecules are broken down, catabolic pathways release energy.
The breakdown of certain chemical bonds means that they have potential energy.
There is potential energy within the bonds of food that can be harnessed for use.
When bonds are broken, energy can be released.
Chemical energy is the type of potential energy that is released when bonds are broken.
Living cells get their energy from food.
The release of energy occurs when the bonds within the food are broken.

You can see the potential energy of a pendulum in motion by visiting the site and selecting "Pendulum" from the "Work and Energy" menu.

A measurement of free energy is used.

According to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form.
After the losses are accounted for, free energy is the energy associated with a chemical reaction.
Free energy is usable energy that can be used to do work.

The products of the reaction have less free energy than the reactants because they release some free energy during the reaction.

The products of these reactions have less stored energy than the reactants.

There is a distinction between the term spontaneously and the idea of a chemical reaction immediately.

A spontaneously occurring reaction is not one that happens suddenly or quickly.

The rusting of iron is an example of a gradual reaction that happens slowly over time.

The products have more free energy than the reactants.

The products of these reactions can be thought of as energy-storing molecule.
Without free energy, an endergonic reaction won't take place.

Some examples of endergonic processes and exergonic processes are shown.

Determine if the processes shown are endergonic or exergonic by looking at them.

The concept of endergonic and exergonic reactions must be considered.

Exergonic reactions need a small amount of energy input to get going.

The reactions have a net release of energy, but still need some energy input in the beginning.

An animation shows the move from free energy to transition state.

The activation energies of chemical reactions inside the cell are lowered by most enzymes.

Without the ability to speed up these reactions, life could not continue.

The chemical bond-breaking and -forming processes take place more easily if the reactant molecule is held in such a way as to make the chemical bond-breaking easier.
If a reaction is exergonic or endergonic, it's important to remember that enzymes don't change.
They don't change the free energy of the reactants.
The activation energy required for the reaction to go forward is reduced by them.
Anidase is unchanged by the reaction it creates.
The enzyme can participate in other reactions after one reaction has been catalyzed.

The free energy of the reaction is not changed by the lowering of the activation energy of the reaction.

Depending on the reaction, there may be more than one.

A single reactant is broken down into multiple products.
One larger molecule may be created in some cases.
Two reactants might enter a reaction and become modified, but they leave the reaction as two products.
The action happens on the active site.
There is a unique combination of side chains within the active site.
There are different properties to each side chain.
They can be large or small, weakly acidic or basic, positively or negatively charged, or neutral.
A very specific chemical environment is created by the unique combination of side chains.
The environment is suited to bind to a specific chemical.

The local environment has an influence on active sites.

Increasing the environmental temperature increases reaction rates.
Outside of an optimal range, temperatures reduce the rate at which an enzyme makes a reaction.
The function of the enzyme will be affected by hot temperatures, which will cause a change in the three-dimensional shape of the enzyme.
Extreme pH and salt concentrations can cause enzymes to denature, as with temperature and salt concentrations, and are suited to function best within a certain pH and salt concentration range.

Scientists thought that the binding was done in a "lock and key" fashion.

The model claimed that the two items fit together perfectly.
The lock-and-key model is supported by current research which supports a model called induced fit.
An ideal binding arrangement is formed when the enzyme and substrate come together.

An enzyme-substrate complex is formed when an enzymebinds its substrate.

This complex promotes the rapid progression of the reaction in multiple ways.
Chemical reactions that involve more than one substrate can be promoted by the use of enzymes.
An optimal environment within the active site for the reaction to occur is created by creating an optimal environment within the enzymes.
The perfect environment for an enzyme's specific substrates to react is created by the chemical properties of the specific arrangement of R groups within an active site.

The bond structure can be compromised so that it is easier to break.

The chemical reaction itself can be reduced by taking part in the enzymes.
It is important to remember that the enzyme will always return to its original state once the reaction is complete.
One of the hallmark properties of enzymes is that they remain unchanged by their reactions.
A new reaction can be created by releasing the product of the catalyzed reaction.

An adjustment to the lock-and-key model is explained in the induced-fit model.

It would make sense to have a scenario in which all of the organisms'idases existed in abundant supply and functioned perfectly in all cells at all times.

A variety of mechanisms ensure that this doesn't happen.
The needs and conditions of individual cells change over time.
Fat storage cells, skin cells, blood cells, and nerve cells all have the same required enzymes.
The time that follows a meal is harder for the bicyle to process and break down than the time after a meal.
As the demands and conditions of the cells vary, so must the amounts and functions of different enzymes.

The rates of biochemical reactions are controlled by the amount of activated energy and the amount of functioning of the variety of enzymes within a cell.

In cells, this determination is tightly controlled.
Environmental factors such as temperature, salt concentration, and pH control the activity of enzymes in certain cellular environments.

It is possible to regulate the activity of the enzymes in ways that promote or reduce activity.

There are many different kinds of molecule that affect the function of the enzyme.
In some cases, an inhibitor molecule can bind to the active site and block the substrate from binding.

In a location where their binding causes a change in the structure of the enzyme, some inhibitors bind to it.

When an allosteric inhibitor binding to a region on an enzyme, all active sites on the protein subunits are changed so that they bind their targets with less efficiency.
There are both allosteric and inhibitors.
Allosteric activators bind to locations away from the active site, inducing a conformational change that increases the affinity of the enzyme's active site.

Allosteric inhibition works by inducing a change in the structure of the active site.

The shape of the active site is changed by the molecule in allosteric activation.

Understanding how enzymes work and how they can be regulated are key principles behind the development of many of the pharmaceutical drugs on the market today.

One class of drugs that can reduce cholesterol levels is called statins and is designed by biologists working in this field.
The HMG-CoA reductase is an important part of cholesterol synthesis in the body.
The level of cholesterol in the body can be reduced by blocking this enzyme.
The drug is marketed under the brand name "Tylenol".
It's mechanism of action is still not fully understood, even though it's used to provide relief from inflammation.

Identifying a drug target is one of the biggest challenges in drug discovery.

A molecule is the target of a drug.
HMG-CoA reductase is a drug target in the case of vastatin.
Drug targets are identified through research.
Scientists need to know how the target acts inside the cell in order to prevent disease.
Drug design begins once the target and pathway are identified.
In this stage, biologists and chemists work together to create compounds that can block a reaction.
If a drug prototype is successful in performing its function, then it is subjected to many tests before it can be approved by the FDA.

Unless bound to other specific non-protein helpers, many enzymes don't work well.

The shape and function of the respective enzymes can be improved by binding to these molecules.
Two examples of helpers are cofactors and coenzymes.
Iron and magnesium have cofactors.
The basic atomic structure of coenzymes is made up of carbon and hydrogen.
These molecules participate in reactions without being changed and are recycled and reused.
Coenzymes can be found in vitamins.
Some vitamins act as coenzymes.
The key to the health of the human body is the building of the important connective tissue, collagen.
The abundance of various cofactors and coenzymes, which may be supplied by an organisms diet or produced by it, regulates the function of the enzyme.

There are many ways in which Molecules can regulate the function of the enzyme.

You have learned that some are cofactors and coenzymes.
The products of the cellular metabolism are the most relevant sources of regulatory molecule.