Download Chapter 8 - Energy and Enzymes

Chapter 6 - Energy and Enzymes
Energy
Energy refers to the capacity to move or change matter.
Forms of Energy
These forms of energy are important to life:
chemical
radiant (examples: heat, light)
mechanical
electrical
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 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.
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 Pi to ADP:
ADP + Pi + energy  ATP + H2O
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.
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 consume energy while synthesizing
compounds. 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. Reactions that release
energy are called catabolic reactions.
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.
In either kind of reaction, additional energy must be supplied to start the
reaction. This energy is the activation energy.
Enzymes
What Are Enzymes?
Substances that speed up chemical reactions are called catalysts. 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.
Induced-Fit Theory
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.
Activation Energy and Enzymes
The amount of activation energy that is required is considerably less
when enzyme is present.
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 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.
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 allosteric
site 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.
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 circle 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 oxidationreduction 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 (Nicotinamide Adenine Dinucleotide)
NAD+ functions in cellular respiration by carrying two electrons from
one reaction site to another.
NAD+ + 2H  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 (Flavin Adenine Dinucleotide)
FAD is reduced to FADH2. It can transfer two electrons to another
molecule.
FAD + 2H  FADH2
NADH and FADH2 bring electrons to the electron transport system in
cellular respiration.
Electron Carrier in Photosynthesis
NADP+ (Nicotinamide Adenine Dinucleotide Phosphate)
NADP+ + 2H  NADPH + H+
NADP+ is similar to NAD+ in that it can carry two electrons. One of the
electrons is contained within a hydrogen atom, the other is removed from
a hydrogen atom and the remaining proton is released..
Electrons carried by NADPH in photosynthesis are ultimately used to
reduce CO2 to carbohydrate.