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Introduction
Cells capture and utilize energy through a series of chemical reactions which involve:
o Rearrangement of electrons within the molecules involved in the reaction.
o Redistribution of energy that these molecules contain.
Some molecules end up with more energy than they began while some end up with less.
Metabolism complex network of reactions inside the cell that captures the energy and
raw materials of its environment and allows them to be changed into forms that are used
to sustain cells.
All chemical reactions are accompanied by a net energy change, which depends on how
much energy is taken in by the chemicals when chemical bonds form and how much
energy is released when bonds break.
In chemical reactions, there is a balance between energy taken when chemicals break,
energy released when chemical bonds form and energy exchanged with surroundings.
As a result, there is overall loss of usable energy.
Change in Free Energy
o Change in free energy (G) = change in the usable energy that is available for
doing work
Positive G: Reaction will not proceed spontaneously. It is work-requiring
(endergonic.)
Negative G: Reaction will proceed spontaneously. It is work-producing
(exergonic.)
G=H TS
Some molecules like ATP (adenosine triphosphate) contain bonds that are called high
energy phosphate bonds.
Cells capture energy as chemical energy stored with molecules of ATP. This captured
energy is used to drive energy-requiring reactions.
ATP is considered the central currency of energy in the cell. Why?
- Because it is a high energy molecule that is used in many different reactions
throughout the cell as the energy source. You can make or use ATP, like making or
using Philippine peso in normal currency. Also, some reactions might need more than
other reactions, just like how some items cost more than others. But like what was said
before, ATP is not only used, it can also be produced by energy-producing processes
just like how jobs can produce Philippine peso.
Some pathways require inputs of ATP and use the energy of ATP to drive endergonic
reactions.
Living cells continuously form and consume ATP.
Activation Energy
Input of energy which all chemical reactions begin with whether they eventually take in or
release energy overall.
Chemical reactions begin with collision between reactant molecules. Activation energy is
required in a collision to initiate a chemical reaction.
Enzymes are globular proteins with characteristic 3-dimensional shapes that act as
biological catalysts to speed up the rates at which chemical reactions occur by lowering
the activation energy.
Lock and Key Model
Enzyme and substrate are available.
Substrate attach to the active site of the enzyme in order to produce an enzymesubstrate complex.
Substrate is converted to product.
Product is released and enzyme goes back into its original state. Enzymes are not
consumed or modified in the overall course of the reactions they catalyze.
The active site is the binding site for the enzymes substrate.
Enzymes are specific for substrate molecules. These are all shape-driven, so anything that
alters the shape of the active site will affect enzymatic activity.
Enzymes are efficient, can operate at relatively low temperatures and are subject to
various cellular controls.
Enzyme exhibit very precise substrate specificity, i.e. each enzyme can bind to and
catalyze the reactions of only a very small range of molecules.
The specificity of enzymes for a particular substrate depends on the precise structure of
each enzymes active site.
Fundamental unity at the cellular level exists among all living organisms.
The uniqueness of a certain type of cell or organism is not due to uniqueness of
substances and enzymes found in it, but rather due to the uniqueness of combinations of
substances and enzymes found in them.
At high temperatures, enzymes undergo denaturation and lose their catalytic properties;
at low temperatures, the reaction rate decreases. The rate at which enzymatic reactions
process is sensitive to temperature. Above about 40C, most enzymes become structurally
altered via denaturation.
The pH at which enzymatic activity is maximal is known as the optimum pH. Enzymes are
proteins and their molecular structure is affected by pH. Catalysis by enzymes is highly
dependent on molecular structure thus enzyme activity is sensitive to pH change.
Within limits, enzymatic activity increases as substrate concentration increases. At some
high concentration of the substrate, so that all the enzymes active sites are occupied,
increasing the substrate concentration will not further increase the rate of the reaction. At
this substrate concentration, the maximum rate of enzymatic reaction (V max) has been
reached.
Michaelis-Menten Equation
The dependence of the rate of enzymatic reaction (V) on substrate concentration [S]
is given by
V=
Vmax [S]
[ Km+ S]
Km, the Michaelis constant, is the substrate concentration that results in a reaction
rate one-half times the maximum (Vmax).
Km is a measure of the affinity of the enzyme for a particular substance. The
greater the affinity is, the lower the Km is.
Enzyme Regulation
Cofactors
Many enzymes need a cofactor (inorganic substances such as minerals) to activate
them. Without the cofactor, the enzyme cant lock the substrate into its active site,
so the reaction cant take place.
The cofactor can be a metal ion(e.g. Fe2+) or a complex inorganic molecule known
as coenzyme (e.g. NAD+)
Allosteric effectors
The rate of enzymatic reactions can be altered by molecules that can act as
allosteric effectors which are molecules that bind at the enzyme and deform the
active site which disables substrate to bind with the enzyme.
Competitive inhibitors compete with the normal substrate for the active site of the
enzyme.
Noncompetitive inhibitors act on other parts of the apoenzyme or on the cofactor
and decrease the enzymes ability to combine with the normal substrate.
How do enzyme regulation work? A substrate binds with enzyme 1 and produces
intermediate A which becomes the substrate that will bind at the active site of enzyme 2.
This process will produce intermediate B that will now bind with enzyme 3 to produce the
end product which when attaches to enzyme 1 will stop the production of intermediate A
and eventually, the whole process.
Oxidation-Reduction Reactions
Many metabolic reactions, including those involved in energy capture and utilization are
reactions that involve electron transfer.
Many enzymatic reactions require coenzymes (small non-protein organic substances that
bind loosely to specific enzymes and assist in their catalytic function).
They can accept a chemical group (or an electron) produced by one enzymatic reaction,
hold on to it for a short time and then donate it to the substrate of another reaction.
Oxidation of a substrate is often coupled to the simultaneous reduction of a coenzyme.
Reduction Potential
Molecules vary with regard to how easily they gain or accept electrons. This ability is
reflected in the value of their reduction potential, which is a value indicating how readily a
substance accepts/donates electrons. The substance with the most positive reduction
potential has the greatest potential to accept electron.
Electrical Potential
G=nF rxn
Where
Substrate-level phosphorylation
Free energy released from exergonic reactions supplies the free energy required to
combine inorganic phosphate (Pi) or phosphate from an organic molecule and ADP to form
ATP.
In a substrate level phosphorylation, ATP is made during the conversion of an organic
molecule from one form to another.
Energy released during the conversion is partially conserved during the synthesis of the
high energy bond of ATP.
SLP occurs during fermentations and respiration (the TCA cycle), and even during some
lithotrophic transformations of inorganic substrates.
Example:
Phosphoenolpyruvate -> pyruvate
(exergonic)
ADP -> ATP
(endergoni
Chemiosmosis
(endergonic)
Autotrophic Metabolism
Self-feeding
Uses inorganic CO2 as carbon source
Heterotrophic Metabolism
Requires supply of preformed organic matter for the production of cellular biomass and as
a source of chemical energy used to form ATP
Involves conversion of the organic substrate molecule to end products via a metabolic
pathway that releases sufficient energy for it to be couples to the formation of ATP.
Two basic types:
Respiration
Fermentation
Respiration
Requires an external electron acceptor not derived from the organic substrate.
Reduction of final electron acceptor balances the oxidation of initial substrate (electron
transport system)
Fermentation
Metabolism in which energy is derived from the partial oxidation of an organic compound
using organic intermediates as electron donors and electron acceptors.
No outside electron acceptors are involved; no membrane or electron transport system is
required.
All ATP is produced by substrate-level phosphorylation.
Respiratory Metabolism
Aerobic respiration begins with an organic molecule and combines it with oxygen in an
oxidation-reduction process that ends with the formation of CO 2 and H2O plus a substantial
amount of ATP.
3 Phases of Respiratory Metabolism
A catabolic pathway during which the organic molecule is broken down into smaller
molecules usually with the generation of some ATP and reduced coenzymes.
The tricarboxylic acid cycle (TCA), during which the small organic molecules
produced in the first phase are oxidized to inorganic carbon dioxide and water,
accompanied with more production of more ATP and reduced coenzymes
Oxidative phosphorylation, during which
The reduced enzymes are reoxidized
The electrons they release are transported through a series of membrane-bound
carriers to establish a proton gradient across a membrane (electron transport
system)
A terminal acceptor such as oxygen is reduced and ATP is synthesized
At the end of the TCA cycle, all the carbon has been converted to CO 2.
TCA plays a central role in the flow of carbon through the cell.
It supplies organic precursor molecules to many biosynthetic pathways. Some of the
intermediates in the TCA cycle must be resynthesized to maintain TCA cycle.
Anaerobic Respiration
The final electron acceptors in anaerobic respiration include NO 3-, SO42- and CO32-.
NO3- is reduced to NO2SO42- is reduced to H2S.
CO32- is reduced to CH4.
The total ATP yield is less than in anaerobic respiration because only part of the Krebs
cycle operates under anaerobic conditions.
Fermentation
Fermentation is any process that releases energy from sugars or other organic molecules
by oxidation, does not require O2, the Krebs cycle, or an electron transport chain, and uses
an organic molecule as the final electron acceptor.
Fermentation is metabolism in which energy is derived from the partial oxidation of an
organic compound using organic intermediates as electron donors and electron acceptors.
No outside electron acceptors are involved; no membrane or electron transport system is
required; all ATP is produced by substrate level phosphorylation.
Fermentation can sometimes occur in the presence of O 2.
Fermentation produces 2 ATP molecules by substrate-level phosphorylation.
Electrons removed from the substrate reduce NAD + to NADH.
Uses a terminal electron acceptor derived from organic substrate. Both the electron donor
and electron acceptor are internal to the organic substrate in a fermentation pathway, i.e.
the eventual electron acceptor.
Can occur in the absence of air because there is no requirement for O 2 or an external
electron acceptor to achieve a balance in the oxidation-reduction reaction.
Yields less ATP per substrate molecule than respiration (because the organic substrate
molecule must serve as both the internal electron donor and internal electron acceptor).
ATP generation is only during glycolysis.
Not all C and H are oxidized to CO2 and H2O. C and H are rearranged into a form containing
less chemical energy than that with which they began.
Catabolism of Lipids
Before amino acids can be catabolized, they must be converted to various substances that
enter the Krebs cycle or glycolysis.
Transamination (transfer of NH2), decarboxylation (removal of COOH), and
dehydrogenation (H2) reactions convert the amino acids to be catabolized into substances
that enter the glycolytic pathway or Krebs cycle.
Lithotrophic Metabolism
Methanogens the most prevalent and diverse group of Archaea and able to oxidize
hydrogen as a sole source of energy while transferring the electrons from hydrogen to
carbon dioxide in its reduction to methane.
Metabolism of the methanogens is absolutely unique.
Methanogens use H2 and CO2 to produce cell material and methane. They have
unique coenzymes and electron transport processes.
Their type of energy generating metabolism is never seen in the Bacteria, and their
mechanism of autotrophic CO2 fixation is very rare.
The nitrifying bacteria are represented by two genera, Nitrosomonas and Nitrobacter.
Together these bacteria can accomplish the oxidation of NH3 to NO3, known as the
process of nitrification. No single organism can carry out the whole oxidative process.
Nitrosomonas oxidizes ammonia to NO2 and Nitrobacter oxidizes NO2 to NO3.
Nitrifying bacteria grow in environments rich in ammonia, where extensive protein
decomposition is taking place.
Nitrification in soil and aquatic habitats is an essential part of the nitrogen cycle.
Lithotrophic sulfur oxidizers include both Bacteria (e.g. Thiobacillus) and Archaea (e.g.
Sulfolobus).
Sulfur oxidizers oxidize H2S (sulfide) or S (elemental sulfur) as a source of energy.
The purple and green sulfur bacteria oxidize H 2S or S as an electron donor for
photosynthesis, and use the electrons for CO 2 fixation (the dark reaction of
photosynthesis).
Lithoautotrophic sulfur oxidizers are found in environments rich in H 2S, such as volcanic
hot springs and fumaroles, and deep-sea thermal vents.
Some are found as symbionts and endosymbionts of higher organisms.
Since they can generate energy from an inorganic compound and fix CO 2 as autotrophs,
they may play a fundamental role in primary production in environments that lack
sunlight.
As a result of their lithotrophic oxidations, these organisms produce sulfuric acid (SO 4), and
therefore tend to acidify their own environments.
Some of the sulfur oxidizers are acidophiles that will grow at a pH of 1 or less.
Some are hyperthermophiles that grow at temperatures of 115 degrees C.
Phototrophic Metabolism
Phototrophy is the use of light as a source of energy for growth, more specifically the
conversion of light energy into chemical energy in the form of ATP.
Procaryotes that can convert light energy into chemical energy include
The cyanobacteria conduct plant photosynthesis, called oxygenic photosynthesis;
Additional Notes:
Metabolism is the general term for all chemical reactions that happen in the cells of living
organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their
structures, and respond to their environments.
Metabolism can be divided into two general types of reactions. Catabolism is all of the chemical
reactions that break down molecules, either to extract energy or to produce simple molecules for
constructing others. Anabolism refers to all of the metabolic reactions that build or assemble
more complex molecules from simpler ones. Catabolism and anabolism are intimately connected,
and one really cannot occur without the other.
Catabolism is also known as a "downhill" process during which energy is released, while
anabolism requires the input of energy, and is therefore an energetically "uphill" process. At
certain points in the anabolic pathway, the cell must put more energy into a reaction than is
released during catabolism. Such anabolic steps require a different series of reaction than are
used at this point during catabolism.
The chemical reactions of metabolism do not happen randomly. They are organized into
metabolic pathways, in which one molecule is converted through a series of steps into another
molecule. For example, the metabolic pathway called glycolysis converts glucose into pyruvate,
producing ATP. Glycolysis is a catabolic pathway, and all life depends on it. It is the central
metabolic pathway. Metabolic pathways are interconnected. Cells use molecules produced in one
pathway to make others.
Each step in a metabolic pathway will be catalyzed by an enzyme. These enzymes are crucial to
metabolism for several reasons.
They help all metabolic reactions occur faster and more efficiently.
Without a catalyst, some of the metabolic reactions require conditions that are more
extreme than what we see in cells (higher temperatures, extremes of pH, etc.) Metabolic
enzymes lower the activation energy of reactions so they can occur in more moderate
conditions.
Some of the steps in metabolic pathways require energy, and do not happen
spontaneously. Enzymes can couple these reactions to ATP cleavage, which releases the
energy needed to drive the reaction.
Enzymes also let cells regulate metabolic pathways in response to changes in the environment or
signals from other cells. Every metabolic pathway will have at least one rate-limiting enzyme. If
that enzyme is missing, the entire pathway stops. Cells can control the activity of the entire
pathway by:
The Cell
The cell is a complex chemical system that can be distinguished from non-living entities.
Cells are capable of growth and reproduction. They can self-produce another entity
essentially identical to themselves.
Cells are highly organized and selectively restrict what crosses their boundaries. Cells are
at low entropy compared to their environment.
Cells are composed of major elements (C,N,O,S..) that are chemically reduced.
Cells take up necessary elements, electrons, and energy from their external environment
to create and maintain themselves as reproducing, organized and reduced entities.
Some cells may undergo change in form through the process of differentiation.
Cells within the body act differently depending upon whether they form part of an
eye, a muscle or strand of hair.
As part of differentiation, cells can interact with one another through various chemical
signals.
They can evolve into organisms that are markedly different from the parent. -> slow
process
Important to the formation of new organisms or to the development of new
capabilities that may aid in the survival of the organism.
Process of Growth
Cellular Metabolism
Substrate cell functioning and maintenance + new cells (biomass) + waste (byproducts) + heat
Cell Yield
Efficiency of microbial growth (yield of cell material per mole of substrate consumed)
Related to the amount of ATP produced per mole of substrate
Depends on:
Its thermodynamic properties
Type of ATP generating pathway
Biological Growth
Heterotrophic: organic material as electron donor and source of carbon for cell synthesis
Chemoautotrophic (autotrophs): inorganic material as electron donor and CO 2 as carbon
source.
Heterotrophs predominate in wastewater containing mainly organic matter.
Photosynthetic
Algae
Photosynthetic, produces O2, some motile by means of flagella
Bacteria (cyanobacteria)
Photosynthetic, produces O2, some motile by means of gliding movement on solid
surfaces, many can fix N2, some can use H2S as e- donor
Protozoa
Aerobic water treatment is a method of treating sewage and wastewater by adding oxygen
to the waste. This process encourages naturally occurring bacteria to break down the
waste and produce a higher quality effluent that may then be treated with chlorine to
remove the remaining bacteria.
Organic matter + O2 CO2, H2O, biomass (cell materials)
N, P, S compounds NO3-, PO43-, SO42Systems in which aerobic degradation of organic matter occurs:
Activated sludge process
Activated sludge is a complex ecosystem composed mainly of bacteria and
protozoa
95% of the BOD is reduced during this stage
There should be a good balance between different species for
An efficient removal of pollutant (organic matter)
A good settleability of flocs in the final clarifier
Low level of suspended solids in the effluent
Waste stabilization ponds
Trickling filters
As in
Waste or Wastewater Stabilization Ponds (WSPs) are large, man-made water bodies in
which blackwater, greywater or faecal sludge are treated by natural occurring processes
and the influence of solar light, wind, microorganisms and algae.
The ponds can be used individually, or linked in a series for improved treatment.
There are three types of ponds, (1) anaerobic, (2) facultative and (3) aerobic (maturation),
each with different treatment and design characteristics.
WSPs are low-cost for O&M and BOD and pathogen-removal is high. However, large
surface areas and expert design are required.
The effluent still contains nutrients (e.g. N and P) and is therefore appropriate for the reuse
in agriculture, but not for direct recharge in surface waters.
Nitrification
Denitrification
The necessary conditions for the denitrification process to develop in an activated sludge
process can be summarised as:
Presence of a facultative bacterial mass, capable of using oxygen and nitrate or
nitrite
Presence of nitrate and absence of dissolved oxygen in the mixed liquor (i.e. an
anoxic environment)
Suitable environmental conditions for bacterial growth
Presence of an electron donor (nitrate reductor): i.e. organic material