# Energy, Enzymes, Metabolism

### Energy

Energy refers to the capacity to move or change matter. These forms of energy are important to life:

• chemical
• heat
• mechanical
• electrical
• nuclear

Energy can be transformed from one form to another.

Chemical energy is the energy contained in the chemical bonds of molecules.

Radiant energy travels in waves and is sometimes called electromagnetic energy. An example is visible light.

Photosynthesis converts light energy to chemical energy.

Energy that is stored is called potential energy.

### Laws of Thermodynamics

#### 1st law- Energy cannot be created or destroyed.

Energy cannot be created or destroyed. It can be converted from one form to another. The sum of the energy before the conversion is equal to the sum of the energy after the conversion.

#### 2nd law- Some usable energy dissipates during transformations and is lost.

During changes from one form of energy to another, some usable energy dissipates, usually as heat. The amount of usable energy therefore decreases.

### Catabolic and Anabolic Reactions

The energy-related reactions within cells generally involve the synthesis or the breakdown of complex organic compounds.

Anabolic reactions are those that synthesize compounds. Energy is required for these reactions.

The graph below shows that energy must be supplied to a reaction in which covalent bonds are formed.

Reactions that break down molecules are called catabolic reactions. Energy is released when molecules are broken down.

The graph below shows that catebolic reactions break bonds and release energy.

The energy in one glucose molecule is used to produce 36 ATP.  ATP has approximately the right amount of energy for most cellular reactions. ATP is produced and used continuously. The entire amount of ATP in an organism is recycled once per minute. Most cells maintain only a few seconds supply of ATP.

#### ATP is a Nucleotide

Nucleotides are the building blocks of nucleic acids such as DNA and RNA.  They contain a nitrogen-containing base, a 5-carbon sugar, and a phosphate group. ATP is a nucleotide that contains adenine (base), ribose (sugar), and three phosphate groups.

Hydrolysis of the molecule results in the removal of a phosphate group and the release of energy. ATP is created by reactions that bond Pi to ADP. This reaction consumes energy; energy is stored in the ATP molecule.

Reactions that release energy are called exergonic reactions and those that require an input of energy are called endergonic reactions. Endergonic reactions do not occur spontaneously; energy must be supplied to drive the reaction.

ATP is continually produced and consumed as illustrated below.

ATP produced by catabolic reactions provides the energy for anabolic reactions. Anabolic and catabolic reactions are therefore coupled (they require each other) through the use of ATP.

### Oxidation-reduction Reactions

Oxidation is the loss of electrons from an atom or molecule and reduction is the gain of electrons. In the chemistry chapter, we discussed how electrons are transferred from one atom to another when an ionic bond is formed. In the example below, an electron is transferred from sodium to chlorine. As a result, each atom has a complete outer shell. A sodium ion and a chlorine ion are formed. In this redox reaction, the sodium atom has been oxidized and the chlorine atom has been reduced.

Unequal sharing of electrons may result in an atom having less access to electrons after a covalent bond is formed. For example, the combustion of methane (CH4) results in the hydrogen atoms being removed from methane and the attachment of oxygen to form CO2.

$\mathrm{CH_4 + 2 O_2 → CO_2 + 2H_2O + Energy}$

Before the reaction, the carbon atom shares electrons equally with the hydrogen atoms because their electronegativites are similar. After the reaction, the sharing is unequal because oxygen is more electronegative than carbon. The formation of CO2 results in reduced access to electrons by the carbon atom. It has been oxidized.

Similarly, the two atoms of oxygen in an oxygen molecule (O2) share electrons equally before the reaction. After the reaction, each oxygen atom has bonded with two hydrogen atoms to form water. Oxygen does not share electrons equally with hydrogen, so as a result of the reaction, each oxygen atom has greater access to electrons; they have been reduced.

Organic compounds in cells often contain a large number of carbon atoms. These molecules are oxidized when hydrogen atoms are transferred to other compounds and the carbon atoms have reduced access to electrons.

Energy is released when electrons move to a more electronegative atom. Reactions in which hydrogen atoms are removed from organic molecules often release energy. This can be seen in the combustion of methane discussed above.

### Enzymes

#### What Are Enzymes?

Substances that speed up chemical reactions are called catalystsOrganic catalysts are called enzymes.

Enzymes are specific for one particular reaction or group of related reactions.

Many reactions cannot occur without the correct enzyme present.

They are often named by adding "ase" to the name of the substrate. Example: Dehydrogenases are enzymes that remove hydrogen.

#### Induced-fit Theory

The shape of the enzyme matches the shape of the substrate. Enzymes are therefore very specific; they will only function correctly if the shape of the substrate matches the active site.

An enzyme-substrate complex forms when the enzyme’s active site binds with the substrate like a key fitting a lock.

The product is released from the enzyme. The enzyme can be reused.

The substrate molecule normally does not fit exactly in the active site. This induces a change in the enzymes conformation (shape) to make a closer fit.

In reactions that involve breaking bonds, the inexact fit puts stress on certain bonds of the substrate. This lowers the amount of energy needed to break them.

After the reaction, the products are released and the enzyme returns to its original configuration. Because is unchanged it can be reused. Only a small amount of enzyme is needed because they can be used repeatedly.

#### Activation Energy and Enzymes

In either catebolic or anabolic reactions (described earlier), additional energy must be supplied to start the reaction. This energy is called activation energy.

The amount of activation energy that is required is considerably less when enzyme is present.

### Cofactors

Many enzymes require an additional component called a cofactor. Cofactors are not protein; they are often ions or organic molecules.
Organic cofactors are called coenzymes.

Coenzymes participate in the reaction. They may carry atoms removed from or added to the substrate or they may carry electrons.

The protein portion of the enzyme without a cofactor is inactive. It is called an apoenzyme. The complete enzyme and cofactor is called a holoenzyme.

Some important cofactors that function to carry electrons are:

### Conditions that Affect Enzymatic Reactions

#### Rate of Reaction

Reactions with enzymes are up to 10 billion times faster than those without enzymes. Enzymes typically react with between 1 and 10,000 molecules per second.

Fast enzymes catalyze up to 500,000 molecules per second.

Substrate concentration, enzyme concentration, Temperature, and pH  affect the rate of enzyme reactions.

#### Substrate Concentration

At lower concentrations, the active sites on most of the enzyme molecules are not filled because there is not much substrate.  Higher concentrations cause more collisions between the molecules.  With more molecules and collisions, enzymes are more likely to encounter molecules of reactant.

The maximum velocity of a reaction is reached when the active sites are almost continuously filled. Increased substrate concentration after this point will not increase the rate.  Reaction rate therefore increases as substrate concentration is increased but it levels off.

#### Enzyme Concentration

If there is insufficient enzyme present, the reaction will not proceed as fast as it otherwise would because all of the active sites are occupied with the reaction. Additional active sites could speed up the reaction.

As the amount of enzyme is increased, the rate of reaction increases. If there are more enzyme molecules than are needed, adding additional enzyme will not increase the rate. Reaction rate therefore increases as enzyme concentration increases but then it levels off.

#### Temperature

Higher temperature generally causes more collisions among the molecules and therefore increases the rate of a reaction. More collisions increase the likelihood that substrate will collide with the active site of the enzyme, thus increasing the rate of an enzyme-catalyzed reaction.

Above a certain temperature, activity begins to decline because the enzyme begins to denature.

The rate of chemical reactions therefore increases with temperature but then decreases.

#### pH

Each enzyme has an optimal pH.

A change in pH can alter the ionization of the R groups of the amino acids. When the charges on the amino acids change, hydrogen bonding within the protein molecule change and the molecule changes shape. The new shape may not be effective.

The diagram below shows that pepsin functions best in an acid environment. This makes sense because pepsin is an enzyme that is normally found in the stomach where the pH is low due to the presence of hydrochloric acid. Trypsin is found in the duodenum, and therefore, its optimum pH is in the neutral range to match the pH of the duodenum.

### Metabolic Pathways

Metabolism refers to the chemical reactions that occur within cells. A hypothetical metabolic pathway is shown below.

Reactions occur in a sequence and a specific enzyme catalyzes each step.

Intermediates can be used as starting points for other pathways. For example, "C" in the diagram above can be used to produce "D" but can also be used to produce "F".

#### Cyclic Pathways

Some metabolic pathways are cyclic. The function of the cyclic pathway below is to produce E from A. Several intermediate steps are involved in the production of E.

First, "A" combines with "F" to produce "B". "B" is then converted to "C", which is then converted to "D". "D" is then split to produce "E" (the desired product) and "F". "F" can be reused by combining with more "A".

### Regulation of Enzyme Activity

Cells have built-in control mechanisms to regulate enzyme concentration and activity.

#### Regulation of Protein Synthesis (Genetic Regulation)

Enzymes are proteins. You can regulate them by making more or less of them as needed. The topic of regulating protein synthesis is deferred to a later chapter.

#### Regulation of Enzymes Already Produced

##### Competitive Inhibition

In competitive inhibition, a similar-shaped molecule competes with the substrate for active sites.

##### Noncompetitive Inhibition

Another form of inhibition involves an inhibitor that binds to an allostericsite of an enzyme.  An allosteric site is a different location than the active site.

The binding of an inhibitor to the allosteric site alters the shape of the enzyme, resulting in a distorted active site that does not function properly.

The binding of an inhibitor to an allosteric site is usually temporary.   Poisons are inhibitors that bind irreversibly. For example, penicillin inhibits an enzyme needed by bacteria to build the cell wall.

##### Feedback Inhibition

Negative feedback inhibition is like a thermostat. When it is cold, the thermostat turns on a heater which produces heat. Heat causes the thermostat to turn off the heater. Heat has a negative effect on the thermostat; it feeds back to an earlier stage in the control sequence as diagrammed below.

Many enzymatic pathways are regulated by feedback inhibition. As an enzyme's product accumulates, it turns off the enzyme just as heat causes a thermostat to turn off the production of heat.  The end product of the pathway binds to an allosteric site on the first enzyme in the pathway and shuts down the entire sequence.

Feedback inhibition occurs in most cells.

### Ribozymes

Ribozymes are molecules of RNA that function like enzymes, that is, they have an active site and increase the rate of specific chemical reactions.

### Formation of ATP

Phosphorylation refers to the chemical reactions that make ATP by adding Pi to ADP:

$\mathrm{ADP + P_i + energy \rightarrow ATP + H_2O}$

Phosphorylation occurs by two different kinds of reactions discussed below.

#### Substrate-Level Phosphorylation

The formation of ATP in the cytoplasm is substrate-level phosphorylation.

Energy from a high-energy substrate is used to transfer a phosphate group to ADP to form ATP.

#### Chemiosmotic Phosphorylation

##### Oxidative Phosphorylation

Most ATP is produced in the mitochondrion by a process that involves pumping hydrogen ions (protons) into the intermembrane space.

Energy is required to pump hydrogen ions into the intermembrane space. The enzyme ATP synthase is able to use the energy of this osmotic gradient to produce ATP as the hydrogen ions move by osmosis back into the matrix of the mitochondrion.

##### Photophosphorylation

Photophosphorylation occurs in the chloroplast. The diagram below shows a chloroplast that has been cut lengthwise to reveal the interior.

A hydrogen ion gradient is also used to produce ATP in the chloroplast (diagram below). In this case, sunlight provides energy to pump hydrogen ions into the thylakoid.  The energy of their movement back into the stroma by osmotic pressure is used to produce ATP. The enzyme that uses a hydrogen ion concentration gradient to phosphorylate ADP is ATP synthase.   Photophosphorylation and oxidative phosphorylation (discussed above) both use an osmotic concentration gradient of hydrogen ions to produce ATP, therefore these two processes are often referred to as chemiosmosis.

### Oxidation and Reduction Reactions

Oxidation is the loss of electrons or hydrogen atoms.  Oxidation reactions release energy.

Reduction is gain of electrons or hydrogen atoms and is associated with a gain of energy.

Oxidation and reduction occur together. When a molecule is oxidized, another must be reduced.

The square object in the middle diagram below represents an electron carrier. It is capable of removing electrons or hydrogen atoms (oxidizing) from molecules and giving them to others (reducing them).

### Coenzymes

Many enzymes require a cofactor to assist in the reaction.  These "assistants" are nonprotein and may be metal ions such as magnesium (Mg++), potassium (K+), and calcium (Ca++).  The cofactors bind to the enzyme and participate in the reaction by removing electrons, protons , or chemical groups from the substrate.

Cofactors that are  organic molecules are coenzymes. In oxidation-reduction reactions, coenzymes often remove electrons from the substrate and pass them to other molecules. Often the electron is added to a proton to form a hydrogen atom before it is passed. In this way, coenzymes serve to carry energy in the form of electrons (or hydrogen atoms) from one compound to another.

Vitamins are small organic molecules required in trace amounts. They usually act as coenzymes or precursors to coenzymes.

### Electron Carriers in Cellular Respiration

NAD+ functions in cellular respiration by carrying two electrons from one reaction site to another.

$\mathrm{NAD^+ + 2H \rightarrow NADH + H^+}$

It oxidizes its substrate by removing two hydrogen atoms. One of the hydrogen atoms bonds to the NAD+. The electron from the other hydrogen atom remains with the NADH molecule but the proton (H+) is released.  NAD+ becomes reduced to NADH.

NADH can transfer two electrons (one of them is a hydrogen atom) to another molecule.

FAD is reduced to FADH2. It can transfer two electrons to another molecule.

$\mathrm{FAD + 2H \rightarrow FADH_2}$

NADH and FADH2 bring electrons to the electron transport system in cellular respiration.

#### Electron Carrier in Photosynthesis

$\mathrm{NADP^+ + 2H \rightarrow NADPH + H^+}$