Enzymes are three-dimensional structures, composed
primarily of globular proteins. Each enzyme has an active site which
is shaped specifically to allow the binding of only one kind of substrate.
Many are also associated with ions or other organic molecules. Metal
ions, called cofactors, and organic molecules, called prosthetic groups,
help to complete the conformation (shape) of an enzyme, allowing it to
function properly. The protein by itself is called an apoenzyme,
which is nonfunctional unless bonded to its cofactor or prosthetic group.
When bonded to one or both of these, it becomes a fully functional holoenzyme
which can participate in enzymatic reactions. Additionally, there
may be one or more allosteric sites on the molecule which can alter
its shape when some substrate or product is bound or absent. In allosteric
activation, the presence of a substrate bound to the allosteric site of
an enzyme alters its conformation, allowing it to become chemically active
by opening its active site. Conversely, in allosteric inhibition,
a product of an enzyme-mediated reaction binds itself to the allosteric
site of the enzyme, altering its conformation in such a way as to block
its acive site, rendering it unable to bond to its substrate.
Large, complex molecules can be broken down through an enzymatic reaction called hydrolysis. In hydrolysis, a molecule of water is added between two portions of the larger molecule, which causes it to break into two parts. Conversely, large molecules can be built up from small, simple molecules called monomers through a process called condensation (also called dehydration synthesis). In condensation reactions, OH- and H+ ions are removed from adjacent monomers, allowing them to form a bond between one another. The ions bond to become water, which is released. When many monomers are linked together in this way, they can form long-chain molecules called polymers. Many living organisms utilize polymers as structural components. The cell walls of plants are composed of cellulose, which is a polymer of the carbohydrate glucose. Bacterial cell walls are also composed of layers of a carbohydrate polymer called peptidoglycan, held together by amino acid linkages. Proteins are polymers of amino acids, lipids are polymers of glycerol and fatty acids or hydrocarbons, and nucleic acids are compound polymers of sugars, phosphates, and nitrogen-containing molecules called nitrogenous bases.
Phosphorylation occurs when a phosphate group (-PO4) is added to a molecule. Often, the bond which forms between a molecule and a phosphate group retains a great deal of energy, as is the case with the primary energy storage molecule of the cell, adenosine triphosphate (ATP). ATP is composed of a primary molecule called adenosine, which is the nitrogenous base adenine bonded to the pentose (five-carbon) sugar ribose, and three phosphate groups. When the bond between adenosine and one of the phosphate groups is broken, the molecule ADP (adenosine diphosphate) is formed, and approximately 7300 calories (one calorie = the amount of energy necessary to raise 1 ml of water 1o C) are released. This released energy can be utilized to drive cellular activities. Phosphorylation of ATP from ADP, however, does not occur spontaneously. Therefore, it is necessary to couple ATP formation with exergonic reactions during the process of cellular metabolism. If this activ ity takes place due to the release of energy during the catabolism of organic or inorganic molecules, it is referred to as substrate-level phosphorylation.
ATP can also be generated via diffusion across
a cell membrane through a process called chemiosmosis. In
chemiosmosis, protons released from the oxidation of nutrient
macromolecules and delivered by coenzymes are forced to congregate along
the outer sur face of a membrane which is not permiable to such ions.
This generates a concentration gradient, resulting in the development of
protonmotive force. Special enzyme channels, called ATP
synthase (ATPase) molecules allow the protons to pass from the
outer to the inner portion of the membrane, where they form chemical bonds
with acceptors such as oxygen. The passage of these protons through
ATPase drives the enzymatic activity which bonds inorganic phosphate to
ADP, forming ATP.
Heterotrophs are organisms which must utilize metabolic pathways to oxidize organic compounds for the release of the energy necessary to generate ATP. These organisms cannot produce their own nutrients, so all carbon-containing compounds must be obtained from an outside source, either through absorption or digestion. Eubacteria, heterotrophic protists, fungi, and animals are all heterotrophs.
It is important to note that ATP generation
in both heterotrophic and autotrophic organisms is associated with membrane-bound
molecules, but the placement of such membranes differs. In phototrophic
and chemotrophic prokaryotes such as the cyanobacteria and sulfur-using
bacteria, there are internal membranes associated with chemical agents
or light-activated (photosynthetic) pigments lying directly in the cytoplasm,
while in eukaryotic autotrophs such as the algaes and plants, the membranes
and photosynthetic pigments are housed within organelles called chloroplasts.
Heterotrophic organisms lack such pigment- associated membranes or chloroplasts. Both autotrophic and heterotrophic eukaryote cells contain speciallized organelles called mitochondria in which many of the catabolic pathways associated with nutrient oxidation take place, while in prokaryotic organisms, such reactions occur directly in the cytoplasm, in association with the plasma membrane.
One of the most common forms of nutrients which
can enter into the metabolic process is the monosaccharride glucose, which
has the chemical formula C6H12O6.
This molecule is readily broken down by cells, and its elements utilized
in various cellular activities. By degrading the glucose molecule
via a series of enzyme-mediated reactions, the cell can make the most efficient
use of the energy stored between the chemical bonds of it component parts.
The process cells utilize in the breakdown of glucose is called glycolysis.
Fermentations are chemical processes which occur an aerobically in the cytoplasm of the cell following glycolysis. In fermentation, NADH + H+ is oxidized back to NAD by giving the electrons and hydrogens it acquired during glycolysis to one of the organic intermediate com pounds produced as a result of this process. This does generate ATP, but the amount produced is far less than that which is the result of complete respiration. In homolactic acid fermentation, reduced NAD gives its two electrons and hydrogens to the pyruvate generated by glycolysis, which converts pyruvate to lactic acid (lactate). This form of fermentation occurs in such bacteria as the lactobacilli and streptococci, and can also occur in human cells (such as muscle tissue) if sufficient oxygen is not available for complete respiration to occur. In alcoholic fermentation, the electrons and hydrogens carried by NAD are donated to acetaldehyde, converting it to ethyl alcohol (ethanol). Fungi such as Saccharomyces cerevisiae undergo this form of fermentation, and these organisms are commonly used in the baking of bread and production of various alcoholic compounds. Some bacteria, such as various species of Lactobacillus and Leuconostoc, utilize a set of glycolytic reactions called the Entner- Douderoff pathway, wherein one molecule of pyruvate and one of acetaldehyde are produced. Since both intermediates are formed, each can be reduced by accepting the extra hydrogens and electrons carried by reduced NAD. The results of this dual reduction are one molecule each of ethanol and lactic acid per original glucose molecule, thus the process is referred to as heterolactic fermentation. Sourkraut and some types of sau sages can be produced through this form of fermentation.
Some fermentative pathways are of industrial importance, such as butyric-butylic fermentation. In this pathway, pyruvate is converted to solvent compounds such as butyric acid, butanol, isopropanol, and acetone, as well as CO2. In propionic acid fermentation, bacteria such as Propionibacterium utilize lactate as a substrate to produce propionic acid and CO2, which provide the flavor and holes in swiss cheese.
Still other fermentative pathways provide the
basis for the differentiation of bacterial species. Bacteria such
as Escherichia coli undergo mixed acid fermentation, wherein
pyruvate is converted into lactic acid, acetic acid, formic acid, or combinations
of these, along with molecular hydrogen (H2) and CO2.
Other species, such as Enterobacter and Klebsiella, undergo
butanediol fermentation, which results in an intermediate compound
called acetyl methyl carbinol (acetoin) during the production
of the neutral end product, butanediol. Two common tests used
to differentiate between these species on the basis of fermentative by-products
are called the methyl red (MR) and Voges- Proskauer
(VP) tests. Methyl red is an acid indicator which changes
color from clear to red in the presence of mixed acids, while the two indicators
utilized in the VP test turn red in the presence of acetoin. E.
coli produces a positive MR test, but a negative VP, while Enterobacter
produces a negative MR, but a positive VP. These tests are coupled
with two others, indole production and citrate fermentation, to form a
combined technique called the IMViC (Indole, Methyl
red Voges-proskauer Citrate) series.
Ultimately, the electrons are delivered to
an inorganic molecule in the cytoplasm which serves as a final electron
acceptor, such as elemental oxygen in aerobic organisms, nitrate, nitrite,
or sulfate in chemoautotrophic organisms. Since hydrogen ions cannot
bind to cytochromes, they pass out between the inner and outer membranes
of the mito chondrion or into the external environment surrounding the
bacterial cell, building protonmotive force. When the hydrogen electrons
pass through ATP synthase, they bond to the final inorganic electron acceptor,
and in this form can be removed or reused by the cell. In the most
familiar of these pathways, two hydrogens bond to elemental oxygen, forming
a molecule of water (H2O).
ATP CO2 four enzyme electron transport chain coenzyme A NAD+ NADH+H+ Pi ten outer two water thirty-four pyruvic acid decarboxylation citric acid three FADH2 ATPase one
As a result of glycolysis, glucose splits into __________ molecules of pyruvic acid. __________ molecules of ATP were
originally used for this process to begin, and __________ ATP molecules were produced, therefore the net gain of ATP avail
able to the cell is __________. Hydrogens and electrons released from glucose during this process were used to reduce
__________ to ________. If pyruvic acid is acted upon by __________, it is converted into acetyl coenzyme A, and a
molecule of __________ is released. The two-carbon acetyl group can then be transported to the site of the Krebs cycle,
where it is utilized through a series of __________ mediated steps to produce __________ molecules of reduced NAD,
__________ molecule of reduced FAD as __________, and one additional __________. The electrons bound by the
coenzymes are then passed to cytochromes in the __________, and the hydrogens are released to the __________ surface
of the membrane. The hydrogens then pass through __________, where they bond with oxygen to form __________. The
release of energy by electron transport, coupled with the passage of hydrogens through ATP synthase, drives the formation of
__________ new ATP molecules.
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