ATP (Adenosine Triphosphate)

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.

 

The phosphate bonds are high-energy bonds. Energy is required to form the bonds and energy is released when the bonds are broken.

ATP is continually produced and consumed as illustrated below.

Formation of ATP

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

ADP + P_i + energy «  ATP + H₂O

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

Some reactions consume energy while synthesizing compounds because energy is required to form chemical bonds. Energy consumed by the reaction is stored in the chemical bond.

Energy is released when chemical bonds are broken.

 

In either kind of reaction, additional energy must be supplied to start the reaction. This energy is the activation energy.

Catalysts are substances that speed up chemical reactions.  Organic 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.

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

The shape of the enzyme must match 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.

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.

The enzyme does not form a chemical bond with the substrate. After the reaction, the products are released and the enzyme returns to its normal shape.

Because the enzyme does not form chemical bonds with the substrate, it remains unchanged. As a result, the enzyme molecule can be reused. Only a small amount of enzyme is needed because they can be used repeatedly.

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

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.

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.

If there is insufficient enzyme present, the reaction will not proceed as fast as it otherwise would because there is not enough enzyme for all of the reactant molecules.

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.

Higher temperature causes more collisions and therefore increases the rate of a reaction. More collisions increase the likelihood that substrate will collide with the active site of the enzyme.

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.

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.

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".

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".