Thousands of enzyme-catalyzed reactions go on all the time in

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					                            10th GRADE
                   BIOLOGY HANDOUT




Content
 1. Energy conversions in living things
     Cellular respiration, photosynthesis
 2. Cellular division and reproduction
     Mitosis-asexual reproduction, meiosis-sexual reproduction
 3. Ecology of ecosystems
     Ecosystems, energy flow and matter cycles
                               Benan Gülay-2009
 1: ENERGY CONVERSIONS IN LIVING THINGS
       ENERGY AND METABOLISM
       Thousands of enzyme-catalyzed reactions go on all the time in every organism, each of
them catalyzed by a specific protein with a particular three-dimensional structure. Taken together,
these reactions make up metabolism, which is the total chemical activity of a living organism; at
any instant, metabolism consists of thousands of individual chemical reactions.
       Many metabolic reactions can be classified as either the building up of complexity in the
cell, using energy to do so, or the breaking down of complex substances into simpler ones,
releasing energy in the process.
       Physicists define energy as the capacity to do work, which occurs when a force operates on
an object over a distance. In biochemistry, it is more useful to consider energy as the capacity for
change. No cell creates energy—all living things must obtain energy from the environment.
Indeed, one of the fundamental physical laws is that energy can neither be created nor destroyed.
However, energy can be transformed from one type into another, and living cells carry out many
such energy transformations. Energy transformations are linked to the chemical transformations
that occur in cells—the breaking of chemical bonds, the movement of substances across
membranes.
       In all cells of all organisms, two types of metabolic reactions occur:
_ Anabolic reactions (anabolism) link together simple molecules to form more complex
molecules. The synthesis of a protein from amino acids is an anabolic reaction. Anabolic reactions
require an input of energy and capture it in the chemical bonds that are formed.
_ Catabolic reactions (catabolism) break down complex molecules into simpler ones and release
the energy stored in chemical bonds.
The first law of thermodynamics states that in any such conversion of energy, energy is neither
created nor destroyed. The first law tells us that in any conversion of energy from one form to
another, the total energy before and after the conversion is the same.




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       The second law of thermodynamics states that, although energycannot be created or
destroyed, when energy is converted from one form to another, some of that energy becomes
unavailable to do work
       In any system, the total energy includes the usable energy that can do work and the
unusable energy that is lost to disorder:
Total energy = usable energy + unusable energy
Constructing 1 kg of a human body requires that about 10 kg of biological materials be
metabolized and in the process converted to CO2, H2O, and other simple molecules, and these
conversions require a lot of energy. This metabolism creates far more disorder than the order in 1
kg of flesh. Life requires a constant input of energy to maintain order.

       ATP
All living cells rely on adenosine triphosphate, or ATP, for the capture and transfer of the free
energy needed to do chemical work and maintain the cells. ATP is not an unusual molecule. In
fact, it has another important use in the cell: it can be converted into a building block for DNA and
RNA. An ATP molecule consists of the nitrogenous base adenine bonded to ribose (a sugar),
which is attached to a sequence of three phosphate groups
The hydrolysis of ATP yields ADP (adenosine diphosphate) and an inorganic
phosphate ion (abbreviated Pi, short for HPO4 2–), as well as free energy:
ATP + H2O


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The important property of this reaction is that it is exergonic, releasing free energy.




The reverse reaction, the formation of ATP from ADP and Pi, is endergonic and consumes as much
free energy as is released by the breakdown of ATP:
ADP + Pi + free energy                 ATP + H2O
Many different exergonic reactions in the cell can provide the energy to convert ADP to ATP. In
eukaryotes, the most important of these reactions is cellular respiration, in which some of the
energy released from fuel molecules is captured in ATP.
Phosphorylation: Adding P to ADP(occurs in cytoplasm, mitochondria and chloroplasts)
ATP + H2O →ADP + Pi + free energy
Dephosphorylation: breaking P bond from ATP(occurs in cytoplasm and chloroplasts and i
anabolic (dehydration reactions)




The reactions that occur in cells are so slow that they could not contribute to life unless the cells
did something to speed them up. That is the role of catalysts. Most biological catalysts are proteins
called enzymes.




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PHOSPHORYLATION IN CELLS
    Photophosphorylation: ATP production by using light energy(adding P to ADP)
    Oxidative phosphorylation: ATP synthesis by oxidation of organic compounds. (Oxygen is
        used)
    Substrate level phosphorylation: ATP synthesis by the help of enzymes but oxygen is not
        used.
    Chemosynthetic phosphorylation: ATP synthesis by the oxidation of inorganic
        compounds(NH3,NO2)(Oxygen is used)
P addition or é transfer
The addition of phosphate groups to ADP to make ATP as an endergonic reaction that can extract
and store energy from exergonic reactions. Another way of transferring energy is to transfer
electrons. A reaction in which one substance transfers one or more electrons to another substance is
called an oxidation–reduction reaction, or redox reaction.
Reduction is the gain of one or more electrons by an atom, ion, or molecule.
Oxidation is the loss of one or more electrons.




ADP acts as a coenzyme when it picks up energy released in an exergonic reaction and uses it to
make ATP (an endergonic reaction). In a similar fashion, the coenzyme NAD (nicotinamide
adenine dinucleotide) acts as an energy carrier, in this case in redox reactions
NAD exists in two chemically distinct forms, one oxidized (NAD+) and the other reduced (NADH
+ H+)
NAD+ + 2 H → NADH + H+ reduction
NADH + H+ + 1⁄2 O2 → NAD+ + H2O oxidation
FAD (flavin adenine dinucleotide), is also involved in transferring electrons during glucose
metabolism(only in oxidative phosphorylation).
   FAD + H → FADH2


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If NADH2 and FADH stay reduced(loaded by electrons) they can not take in electrons or H again
so reactions at thet level stop.(will not proceed)
Cells trap free energy while metabolizing glucose
       The process of combustion (burning) is very similar to the chemical processes that release
energy in cells. If glucose is burned in a flame, it reacts with O2, rapidly forming carbon dioxide
and water and releasing a lot of energy. The balanced equation for this combustion reaction is
C6H12O6 + 6 O2
       The same equation applies to the metabolism of glucose in cells. The metabolism of
glucose, however, is a multistep, controlled series of reactions.                                  G) for
the complete conversion of glucose and O2 to CO2 and water, whether by combustion or by
metabolism, is –686 kcal/mol (–2,870 kJ/mol).
       Thus the overall reaction is highly exergonic and can drive the endergonic formation of a
great deal of ATP from ADP and phosphate. It is the capture of this energy in ATP that requires
the many steps characteristic of glucose metabolism. Three metabolic processes play roles in the
utilization of glucose for energy: glycolysis, cellular respiration, and fermentation. All three
involve metabolic pathways made up of many distinct chemical reactions.




Glycolysis begins glucose metabolism in all cells and produces two molecules of the three-
carbon product pyruvate. Asmall amount of the energy stored in glucose is captured in usable
forms. Glycolysis does not use O2.
_ Cellular respiration uses O2 from the environment and completely converts each pyruvate
molecule to three molecules of CO2 through a set of metabolic pathways. In the process, a great
deal of the energy stored in the covalent bonds of pyruvate is released and transferred to ADP and
phosphate to form ATP.


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_ Fermentation does not involve O2. Fermentation converts pyruvate into products such as lactic
acid or ethyl alcohol (ethanol), which are still relatively energy-rich molecules. Because the
breakdown of glucose is incomplete, much less energy is released by fermentation than by cellular
respiration, and no ATP is produced.
       Glycolysis and fermentation are anaerobic metabolic processes—that is, they do not
involve O2. Cellular respiration is an aerobic metabolic process, requiring the direct participation
of O2 the addition of phosphate groups to ADP to make ATP as an endergonic reaction that can
extract and store energy from exergonic reactions
An Overview: Releasing Energy from Glucose
       Depending on the presence or absence of O2, the energy-harvesting processes in cells use
different combinations of metabolic pathways When O2 is available as the final electron acceptor,
four pathways operate. Glycolysis takes place first, and is followed by the three pathways of
cellular respiration: pyruvate oxidation, the citric acid cycle, and the respiratory chain (also
known as the electron transport chain).
_ When O2 is unavailable, pyruvate oxidation, the citric acid cycle, and the respiratory chain do
not function, and the pyruvate produced by glycolysis is further metabolized by fermentation.
Glycolysis: From Glucose to Pyruvate
       Glycolysis takes place in the cytoplasm of cells. It converts glucose to pyruvate, produces a
small amount of energy, and generates no CO2. In glycolysis, a reduced fuel molecule, glucose,
gets partially oxidized and in the process releases some of its energy. After ten enzyme-catalyzed
reactions, the end products of glycolysis are two molecules of pyruvate. These reactions are
                                  accompanied by the net formation of two molecules of ATP and
                                  by the reduction of two molecules of NAD+ to two molecules of
                                  NADH + H+       for each molecule of glucose.


                                  Glycolysis
                                       1. energy-investing reactions that use 2 ATP, Unstable 6C-
                                          2P compound forms
                                       2. 6C-2P compound is broken into two 3C-P (PGAL).
                                          electrons are transfered to 2 NAD( reduced)
                                       3. and energy-harvesting reactions that produce 4 ATP and 2
                                          molecules of pyruvate(3C) are formed.



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       Glycolysis is followed by cellular respiration (if O2 is present) or fermentation (if no O2 is
present).
Oxidation of pyruvate
The oxidation of pyruvate to acetate and its subsequent conversion to acetyl CoA is the link
between glycolysis and all the other reactions of cellular respiration
                           Pyruvate diffuses into the mitochondrion, where a series of coupled
                           reactions takes place:
                           1. Pyruvate is oxidized to a two-carbon acetyl group, and CO2 is
                           released.
                           2. Part of the energy from the oxidation is captured by the reduction of
                           NAD+ to NADH + H+.
                                3. Some of the remaining energy is stored temporarily by the
combining of the acetyl group with CoA, forming acetyl CoA:
pyruvate + NAD+ + CoA→Acetyl CoA + NADH + H+ + CO2


Krebs cycle(Citric acid cycle)
Acetyl CoA is the starting point for the citric acid cycle. This pathway of eight reactions
completely oxidizes the two-carbon acetyl group to two molecules of carbon dioxide. The free
energy released from these reactions is captured by ADP and the electron carriers NAD and FAD.
All reactions occur in matrix of mitochondria. (cytoplasm in prokaryotes)
The inputs to the citric acid cycle are acetate (in the form of acetyl CoA), water, and oxidized
electron carriers (NAD+ and FAD).
The outputs are carbon dioxide, reduced electron carriers (NADH + H+ and FADH2), and a small
amount of ATP. Overall, for each acetyl group, the citric acid cycle removes two carbons as CO2
and uses four pairs of hydrogen atoms to reduce electron carriers.




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1. Acetyl coA separates from co-A , the two-carbon acetyl group and four-carbon oxaloacetate
combine, forming six-carbon citrate.
2. CO2 is released from 6C compound. 5C compound occurs. NAD is reduced
3. CO2 is released from 5C compound. 4C compound occurs. NAD is reduced and also ATP is
formed by substrate level phosphorylation
4. FAD is reduced
5. NAD is reduced




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Electron Transport System




Pyruvate oxidation and the operation of the citric acid cycle generate large amounts of reduced
electron carriers containing trapped energy. To liberate this energy and produce ATP, something
must happen to these reduced carriers.


To regenerate NAD+ and FAD, the reduced forms of these carriers must have some way to get rid
of their hydrogens (H+ + e–). The fate of these protons and electrons is the rest of the story of
cellular respiration.
Steps of ETS
These reactions are formed in the cristae of the mitochondria in eukaryotes and mesosomes of
prokaryotes.
1. The electrons(from NADH2 and FADH2) pass through a series of membrane-associated
electron carriers called the respiratory chain or the electron transport chain.
2. The flow of electrons along the chain accomplishes the active transport of protons across the
inner mitochondrial membrane, out of the matrix, creating a proton concentration gradient.
3. The protons diffuse back into the mitochondrial matrix through a proton channel, which couples
this diffusion to the synthesis of ATP.




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The electron carriers contained in the three large protein complexes are arranged such that protons
are taken up on one side of the membrane (the mitochondrial matrix) and transported along with
electrons to the other side (intermembrane space). Electrons from NADH2 pass through a long
ETS chain. Electrons from FADH2 pass through a shorter ETS. So the ATP produced from the e of
NADH2 is more than the e of FADH2. The last e acceptor is the OXYGEN in that way it is
reduced to make water.
1 mol. Of       Substrate level        ETS (oxidative
glucose         Phosphorylation        phosphorylation)
                ATP                    FADH2            NADH+H          Net yield

Glycolysis      2                      -                2x3             8
Pyruvate-       -                      -                2x3             6
Acetyl coA
Krebs cycle     2                      2x2              6x3             24

Total           4ATP                   4ATP             30ATP           38ATP


2NADH+H x 3              6 ATP                   Glycolysis
2NADH+H x 3              6 ATP                   Mitochondria-Pyruvate- Acetyl coA

6NADH+H x 3              18 ATP                  Mitochondria-Krebs

2FADH+H x 2              4 ATP                   Mitochondria-Krebs

                         34 ATP

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Fermentation: ATP from Glucose, without O2
     Fermentation is the breakdown of the pyruvate produced by glycolysis in the absence of
        O2.
     If oxygen is no longer available to pick up electrons at the end of the respiratory chain.
     no NAD+ and no FAD are regenerated from their reduced forms(NADH2,FADH2).
     Under anaerobic conditions, many (but not all) cells can produce a small amount of ATP by
        glycolysis, provided that fermentation metabolizes and regenerates the NAD+ necessary to
        keep glycolysis running.
     Fermentation, like glycolysis, occurs in the cytoplasm.
Because fermentation results in the incomplete oxidation of glucose, it releases much less energy
than cellular respiration.
       Suppose the supply of oxygen to a respiring cell is reduced (an anaerobic condition). As a
consequence, oxygen is no longer available to pick up electrons at the end of the respiratory chain.
so all of that compound is soon in the reduced form. Under these circumstances, no NAD+ and no
FAD are regenerated from their reduced forms. steps in glycolysis, pyruvate oxidation, and the
citric acid cycle also stop. If the cell has no other way to obtain energy from its food, it will die.
Under anaerobic conditions, many (but not all) cells can produce a small amount of ATP by
glycolysis, provided that fermentation metabolizes and regenerates the NAD+ necessary to keep
glycolysis running. Fermentation, like glycolysis, occurs in the cytoplasm. It has two defining
characteristics:

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_ Fermentation uses NADH + H+ formed by glycolysis to reduce pyruvate or one of its
metabolites, and consequently NAD+ is regenerated. NAD+ is required , so once the cell has
replenished its NAD+ supply in this way, it can carry more glucose through glycolysis.
_ Fermentation enables glycolysis to produce a small but sustained amount of ATP. The reactions
of fermentation do not themselves produce any ATP. Only as much ATP is produced as can be
obtained from substrate-level phosphorylation. The total net energy yield from glycolysis using
fermentation is two molecules of ATP per molecule of glucose oxidized.
    Fermentation enables glycolysis to produce a small but sustained amount of ATP. The
       reactions of fermentation do not themselves produce any ATP.
    Different types of fermentation are carried out by different bacteria and eukaryotic body
       cells. These different fermentation processes are distinguished by the final product
       produced.
    For example, in lactic acid fermentation, pyruvate is reduced to lactate(3C compound).
    Certain yeasts and some plant cells carry on a process called alcoholic fermentation under
       anaerobic conditions
    First, carbon dioxide is removed from pyruvate,
leaving the compound acetaldehyde. Second, the acetaldehyde is reduced by NADH + H+,
producing NAD+ and ethyl alcohol(2C) (ethanol). This is how beer and wine are made.




                                                     AIM: Oxidation of NADH2 . In that way
                                                     glycolysis can proceed and ATP can be
                                                     formed.
                                                  Lactic acid fermentation Ethyl alcohol
                                                                           fermentation
                                                  2 ATP                    2 ATP

                                                  2 LActic acid            2 ethyl alcohol

                                                  Animal, bacteria, yeast 2 CO2
                                                                           Yeast, bacteria, plant




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Why is so much more ATP produced by cellular respiration?
Glycolysis is only a partial oxidation of glucose, as is fermentation. Much more energy remains in
the end products of fermentation, such as lactic acid and ethanol, than in the end product of cellular
respiration, CO2.


CATABOLIC INTERCONVERSIONS
Polysaccharides, lipids, and proteins can all be broken down to provide energy:
Polysaccharides are hydrolyzed to glucose. Glucose then passes through glycolysis and the citric
acid cycle, where its energy is captured in NADH and ATP.
_ Lipids are broken down into their substituents, glycerol and fatty acids. Glycerol is converted to
dihydroxyacetone phosphate, an intermediate in glycolysis, and fatty acids are converted to acetate
and then acetyl CoA in the mitochondria. In both cases, further oxidation to CO2 and release of
energy then occur.
_ Proteins are hydrolyzed to their amino acid building blocks. The 20 different amino acids feed
into glycolysis or the citric acid cycle at different points.




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Anaerobic                                                          Aerobic



        Cytoplasm                                         Cytoplasm and mitochondria
        Products are organic (lactic acid, ethyl          Products are inorganic (CO2 and H2O).
         alcohol). Energy is kept in these
         molecules.
                                                           ETS exists. Large amounts of ATP is
                                                            formed there by oxidative
        No ETS                                             phosphorylation
        2 ATP net yield(2 ATP is used) by                 38 ATP net yield(2 ATP is used in
         Substrate level phosphorylation                    glycolysis)
        NAD is reduced and oxidized                      substrate level ph. is in glycolysis and krebs
                                                            cycle
        Last electron acceptor is pyruvate or            Oxidative ph. in ETS
         acetaldehyde
                                                            NAD and FAD are reduced and oxidized
        CO2 is formed only in ethyl alcohol               Last electron acceptor is oxygen and water
         fermentation.                                      is formed.
        Water is not formed
REVIEW QUESTIONS
1. The role of oxygen gas in our cells is to
       a. catalyze reactions in glycolysis.
       b. produce CO2.
       c. form ATP.
       d. accept electrons from the electron transport chain.
       e. react with glucose to split water.
2. Oxidation and reduction
       a. entail the gain or loss of proteins.
       b. are defined as the loss of electrons.
       c. are both endergonic reactions.
       d. always occur together.
       e. proceed only under aerobic conditions.
3. NAD+ is
       a. a type of organelle.
       b. a protein.
       c. present only in mitochondria.
       d. a part of ATP.
       e. formed in the reaction that produces ethanol.




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4. Glycolysis
       a. takes place in the mitochondrion.
       b. produces no ATP.
       c. has no connection with the respiratory chain.
       d. is the same thing as fermentation.
       e. reduces two molecules of NAD+ for every glucose molecule processed.
5. Fermentation
       a. takes place in the mitochondrion.
       b. takes place in all animal cells.
       c. does not require O2.
       d. requires lactic acid.
       e. prevents glycolysis.
6. Which statement about pyruvate is not true?
       a. It is the end product of glycolysis.
       b. It becomes reduced during fermentation.
       c. It is a precursor of acetyl CoA.
       d. It is a protein.
       e. It contains three carbon atoms.
7. The citric acid cycle
       a. takes place in the mitochondrion.
       b. produces no ATP.
       c. has no connection with the respiratory chain.
       d. is the same thing as fermentation.
       e. reduces two NAD+ for every glucose processed.
8. The electron transport chain
       a. operates in the mitochondrial matrix.
       b. uses proteins embedded within a membrane.
       c. always leads to the production of ATP.
       d. regenerates reduced coenzymes.
       e. operates simultaneously with fermentation.




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9. Compared to anaerobic metabolism, aerobic breakdown of glucose produces
       a. more ATP.
       b. pyruvate.
       c. fewer protons for pumping in mitochondria.
       d. less CO2.
       e. more oxidized coenzymes.
10. Which statement about oxidative phosphorylation is not true?
       a. It is the formation of ATP by the respiratory chain.
       b. It is brought about by the chemiosmotic mechanism.
       c. It requires aerobic conditions.
       d. In eukaryotes, it takes place in mitochondria.
       e. Its functions can be served equally well by fermentation.




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PHOTOSYNTHESIS
       Powered by sunlight, green plants convert CO2 and water into carbohydrates by a process
called photosynthesis. The emergence of this metabolic pathway was a key event in the evolution
of life. Photosynthesizing organisms, called autotrophs (“self-feeders”), use solar energy to make
their own food from simple chemicals in the nvironment. In this way, they provide an entry point
to the biosphere for chemical energy.


6CO2+12H2O           C6H12O6+6H2O+6O2


CO2+2H2S            (CH2O)n +2 S+ H2O
CO2+2H2             (CH2O)n + H2O (prokaryotes)


Light energy
Light is a form of electromagnetic radiation. It comes in discrete packets called photons. Light
also behaves as if it were propagated in waves. The amount of energy contained in a single photon
is inversely proportional to its wavelength: the shorter the wavelength, the greater the energy of the
photons.
When a photon meets a molecule, one of three things happens:
   •    The photon may bounce off the molecule—it may be scattered.
   •    The photon may pass through the molecule—it may be transmitted.
   •    The photon may be absorbed by the molecule.
Neither of the first two outcomes causes any change in the molecule. In the third case, the photon
disappears. Its energy, however, cannot disappear, because energy is neither created nor
destroyed.




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                              When a molecule absorbs a photon, that molecule acquires the
                              energy of the photon. It is thereby raised from a ground state (lower
                              energy) to an excited state (higher energy)


                              When a beam of white light (light containing visible light of all
                              wavelengths) falls on a pigment, certain wavelengths of the light are
                              absorbed.




                              if a pigment absorbs both blue and red light—as chlorophyll does—
                              what we see is the remaining light, which is primarily green.


Chloroplast

                                                              Chloroplast contains 3 membrane
                                                              systems.
                                                              Outer membrane
                                                              Inner membrane
                                                              Thylakoid membrane
                                                              Thylakoids together form the grana.
                                                              Thylakoid membrane carries ETS
                                                              enzymes and
                                                              Photosystems(chlorophyll)
                                                              And the fluid which fills the inner
                                                              membrane is called as stroma.
                                                              Stroma carries enzymes, DNA,RNA,
                                                              ribosomes.




Like glycolysis and the other metabolic pathways that yield energy in cells, photosynthesis consists
not of one single reaction but of many reactions. The reactions of photosynthesis can be divided
into two pathways:



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_ The light reactions are driven by light energy. This pathway produces ATP and a reduced
electron carrier (NADPH + H+).
_ The second pathway, called the Calvin–Benson cycle, does not use light directly. It uses ATP,
NADPH + H+ (made by the light reactions), and CO2 to produce sugars.
The two pathways are linked by the exchange of ATP and ADP, and of NADP+ and NADPH.


LIGHT DEPENDENT


          ATP,
AIM: produce
NADPH, ( O2)




LIGHT INDEPENDENT

AIM: UseATP
NADPH to fix CO2
and produce organic
molecules.




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       Molecules that absorb wavelengths in the visible spectrum—that region of the spectrum that
is visible to humans—are called pigments.




       When a beam of white light (light containing visible light of all wavelengths) falls on a
pigment, certain wavelengths of the light are absorbed. The remaining wavelengths, which are
scattered or transmitted, make the pigment appear to us to be colored. For example, if a pigment
absorbs both blue and red light—as chlorophyll does—what we see is the remaining light, which is
primarily green.
       In photosynthetic organisms of all kinds (plants, protists, and bacteria), these pigments
include chlorophylls, carotenoids, and phycobilins. After a pigment molecule absorbs a photon and
enters an excited state , that molecule may return to the ground state. The pigments in
photosynthetic organisms are arranged into energy-absorbing antenna systems. In these systems,
the pigments are packed together and attached to thylakoid membrane proteins in such a way that
the excitation energy from an absorbed photon can be passed along from one pigment molecule in
the system to another. Excitation energy moves from pigments that absorb shorter wavelengths
(higher energy) to pigments that absorb longer wavelengths (lower energy). Thus the excitation
ends up in the one pigment molecule in the antenna system that absorbs the longest wavelengths;
this molecule is in the reaction center of the antenna system. It is the reaction center that converts
the light absorbed into chemical energy.
       The chlorophyll becomes a reducing agent and participates in a redox reaction. The
energized electron that leaves the activated chlorophyll in the reaction center needs somewhere to
go. It immediately participates in a series of oxidation-reduction (redox) reactions. The energy-rich
electron is passed through a chain of electron carriers in the thylakoid membrane in a process
termed electron transport. Two energy-rich products of the light reactions, NADPH + H+ and

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ATP, are the result. The energy-rich NADPH + H+ is a stable, reduced coenzyme. Its oxidized
form is NADP+ (nicotinamide adenine dinucleotide phosphate) NADP+ is identical to NAD+
except that the former has an additional phosphate group attached to each ribose. Whereas NAD+
participates in catabolism, NADP+ is used in anabolic (synthetic) reactions Electron transport in
the thylakoid membrane sets up a charge separation, just as electron transport in the inner
mitochondrial membrane does . This potential energy is captured by the chemiosmotic synthesis of
ATP in a process called photophosphorylation. There are two different systems of electron
transport in photosynthesis:
_ Noncyclic electron transport produces NADPH + H+ and ATP.
_ Cyclic electron transport produces only ATP.


Cyclic electron transport produces ATP but no NADPH
Cyclic electron transport occurs in some organisms when the ratio of NADPH + H+ to NADP+ in
the chloroplast is high. This process, which produces only ATP, is called cyclic because an electron
passed from an excited chlorophyll molecule at the outset cycles back to the same chlorophyll
molecule the end of the chain of reactions.




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Noncyclic electron transport produces ATP and NADPH
In noncyclic electron transport, light energy is used to oxidize water, forming O2, H+, and
electrons.




       Electrons from water replenish the electrons that chlorophyll molecules lose when they are
excited by light. As the electrons are passed from water to chlorophyll, and ultimately to NADP+,
they pass through a chain of electron carriers. These redox reactions are exergonic, and some of the
free energy released is used ultimately to form ATP by a chemiosmotic mechanism. Noncyclic
electron transport requires the participation of two different photosystems. These photosystems are
light-driven molecular units, each of which consists of many chlorophyll molecules and accessory
pigments bound to proteins in separate energy-absorbing antenna systems.
_ Photosystem I uses light energy to reduce NADP+ to NADPH + H+.
_ Photosystem II uses light energy to oxidize water molecules, producing electrons, protons (H+),
and O2.
       The reaction center for photosystem I contains a chlorophyll a molecule called P700
because it can best absorb light of wavelength 700 nm. The reaction center for photosystem II
contains a chlorophyll a molecule called P680 because it absorbs light maximally at 680 nm. Thus
photosystem II requires photons that are somewhat more energetic (i.e., shorter wavelengths) than
those required by photosystem I. To keep noncyclic electron transport going, both photosystems I
and II must constantly be absorbing light,




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DETAILS OF THE REACTIONS.
    Noncyclic electron transport requires the participation of two different photosystems.
    Electrons from Photosystem II pass through the ETS on thylakoid membrane and at last
       excited Photosystem I accepts electrons from II. During these reactions ATP is formed.
    The electrons from Photosystem I pass through the ferredoxin electron accceptor then to
       NADP to make it reduced(NADPH2)
    Photosystem I retakes electron it loses from photosystem II but Photosystem I has to take
       and become reduced again. To get electrons that it needs, photosystem II splits water into
       ions H and O2. From H it takes electrons and oxygen diffuses out.





In summary:
_ Noncyclic electron transport uses a molecule of water, four photons (two each absorbed by
photosystems I and II), one molecule each of NADP+ and ADP, and one Pi.
_ Noncyclic electron transport produces NADPH + H+ and ATP and half a molecule of oxygen
(1/2 O2).




EK 10.04                                                                            REV:00          24
Making Carbohydrate from CO2: The Calvin–Benson Cycle
       Most of the enzymes that catalyze the reactions of the Calvin–Benson cycle are dissolved in
the chloroplast stroma these enzymes use the energy in ATP and NADPH, produced in the
thylakoids by the light reactions, to reduce CO2 to carbohydrates
The Calvin–Benson cycle is made up of three processes
-Fixation of CO2. As we saw, this reaction is catalyzed by rubisco, and its product is 3PG.
_ Reduction of 3PG to form a carbohydrate, glyceraldehyde 3-phosphate (G3P). This series of
reactions involves a phosphorylation (using the ATP made in the light reactions) and a reduction
(using the NADPH made in the light reactions).
-Regeneration of the CO2 acceptor, RuBP. Most of the G3P ends up as RuMP (ribulose
monophosphate), and ATP is used to convert this compound to RuBP. So for every “turn” of the
cycle, with one CO2 fixed, the CO2 acceptor is regenerated.




Calvin–Benson cycle, uses ATP and NADPH + H+          to fix CO2 into carbohydrates. These
reactions occur in the stroma.
To fix 1 molecule of CO2 , 3 ATP and 2 NADPH2 are used. For 1 molecule glucose 6CO2 are
used and : 18 ATP and 12 NADPH2.

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There are three processes that make up the cycle:
     1. Fixation of CO2. As we saw, this reaction is catalyzed by rubisco, and its product is 3PG.
     2. Reduction of 3PG to form a carbohydrate, glyceraldehyde 3-phosphate (G3P). This series
        of reactions involves a phosphorylation (using the ATP made in the
light reactions) and a reduction (using the NADPH made in the light reactions).
3.   Regeneration of the CO2 acceptor, RuBP
The end product of this cycle is glyceraldehyde 3-phosphate (G3P), which is a three-carbon sugar
phosphate, also called triose phosphate:
In a typical leaf, there are two fates for the G3P:
_ One-third of it ends up in the polysaccharide starch, which is stored in the chloroplast.
_ Two-thirds of it is converted in the cytosol to the disaccharide sucrose, which is transported out
of the leaf to other organs in the plant, where it is hydrolyzed to its constituent monosaccharides:
glucose and fructose.
Photosynthesis and respiration are closely linked through the Calvin–Benson cycle . The
partitioning of G3P is particularly important:
_ Some G3P from the Calvin–Benson cycle can be converted to pyruvate, the end product of
glycolysis. This pyruvate can be used in cellular respiration for energy, or its carbon skeletons can
be used anabolically to make lipids, proteins, and other carbohydrates .
_ Some G3P can enter a pathway that is the reverse of glycolysis (the gluconeogenic pathway). In
this case, sucrose is formed and transported to the nonphotosynthetic tissues of the plant, such as
the root.




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Rate of Photosynthesis
    What is a rate?
    It is the activity per unit time.
    What factors can affect the photosynthetic rate?

The Effect of Light Intensity on Photosynthetic Rate




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The Effect of Temperature on Photosynthetic Rate




The Effect of Light Intensity and Temperature on Photosynthetic Rate




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Oxygen Concentration




What would a graph for increasing levels of CO2 look like?




REVIEW QUESTIONS
1. In noncyclic photosynthetic electron transport, water is used to
       a. excite chlorophyll.
       b. hydrolyze ATP.
       c. reduce chlorophyll.
       d. oxidize NADPH.
       e. synthesize chlorophyll.




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2. Which statement about light is true?
       a. An absorption spectrum is a plot of biological effectiveness versus wavelength.
       b. An absorption spectrum may be a good means of identifying a pigment.
       c. Light need not be absorbed to produce a biological effect.
       d. A given kind of molecule can occupy any energy level.
       e. A pigment loses energy as it absorbs a photon.
3. Which statement about chlorophylls is not true?
       a. They absorb light near both ends of the visible spectrum.
       b. They can accept energy from other pigments, such as carotenoids.
       c. Excited chlorophyll can either reduce another substance or fluoresce.
       d. Excited chlorophyll may be an oxidizing agent.
       e. They contain magnesium.
4. In cyclic electron transport,
       a. oxygen gas is released.
       b. ATP is formed.
       c. water donates electrons and protons.
       d. NADPH + H+ forms.
       e. CO2 reacts with RuBP.
5. Which of the following does not happen in noncyclic electron transport?
       a. Oxygen gas is released.
       b. ATP forms.
       c. Water donates electrons and protons.
       d. NADPH + H+ forms.
       e. CO2 reacts with RuBP.
6. In the chloroplasts,
       a. light leads to the pumping of protons out of the thylakoids.
       b. ATP forms when protons are pumped into the thylakoids.
       c. light causes the stroma to become more basic than the thylakoids.
       d. protons return passively to the stroma through protein channels.
       e. proton pumping requires ATP.
7. Which statement about the Calvin–Benson cycle is not true?
       a. CO2 reacts with RuBP to form 3PG.
       b. RuBP forms by the metabolism of 3PG.
       c. ATP and NADPH + H+ form when 3PG is reduced.

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       d. The concentration of 3PG rises if the light is switched off.
       e. Rubisco catalyzes the reaction of CO2 and RuBP.
8. In C4 photosynthesis,
       a. 3PG is the first product of CO2 fixation.
       b. rubisco catalyzes the first step in the pathway.
       c. four-carbon acids are formed by PEP carboxylase in bundle sheath cells.
       d. photosynthesis continues at lower CO2 levels than in C3 plants.
       e. CO2 released from RuBP is transferred to PEP.
9. Photosynthesis in green plants occurs only during the day. Respiration in plants occurs
       a. only at night.
       b. only when there is enough ATP.
       c. only during the day.
       d. all the time.
       e. in the chloroplast after photosynthesis.
10. Photorespiration
       a. takes place only in C4 plants.
       b. includes reactions carried out in peroxisomes.
       c. increases the yield of photosynthesis.
       d. is catalyzed by PEP carboxylase.
       e. is independent of light intensity.




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          READING – C3 AND C4 PLANTS
In plants such as roses, wheat, and rice, the mesophyll cells, which lie just below the surface of the
leaf, are full of chloroplasts that contain abundant rubisco (Figure 8.16a). On a hot day, these
leaves close their stomata to conserve water. The level of CO2 in the air spaces of the leaves falls,
and that of O2 continues to rise, as photosynthesis goes on. seen, rubisco acts as an oxygenase, and
photorespiration occurs, under these conditions. Because the first product of CO2 fixation in these
plants is the three-carbon molecule 3PG, they are called C3 plants. Corn, sugarcane, and other
                                                           tropical grasses (Figure 8.16b) also close
                                                           their stomata on a hot day, but their rate
                                                           of photosynthesis does not fall, nor does
                                                           photorespiration occur. They keep the
                                                           ratio of CO2 to O2 around rubisco high
                                                           so that rubisco continues to act as a
                                                           carboxylase. They do this in part by
                                                           making a four-carbon compound,
                                                           oxaloacetate, as the first product of CO2
                                                           fixation, and so are called C4 plants. C4
                                                           plants perform the normal Calvin–Benson
                                                           cycle, but they have an additional early
                                                           reaction that fixes CO2 without losing
                                                           carbon to photorespiration, greatly
                                                           increasing the overall photosynthetic
                                                           yield. Because this initial CO2 fixation
                                                           step can function even at low levels of
                                                           CO2 and high temperatures, C4 plants
                                                           very effectively optimize photosynthesis
                                                           under conditions that inhibit it in C3
plants.




http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html


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2. CELL DIVISION AND REPRODUCTION
Systems of Cell Reproduction
   How cell division (and thus tissue growth) is controlled is very complex. The following terms
   are some of the features that are important in regulation, and places where errors can lead to
   cancer. Cancer is a disease where regulation of the cell cycle goes awry and normal cell growth
   and behavior is lost. But in order for any cell to divide, four events must occur:
   1. There must be a reproductive signal. This signal, which may come either from inside or
       outside the cell, initiates the cellular reproductive events.
   2. Replication of DNA (the genetic material) and other vital cell components must occur so
       that each of the two new cells will be identical and have complete cell functions.
   3. The cell must distribute the replicated DNA to each of the two new cells. This process is
       called segregation.
   4. New material must be added to the cell membrane (and the cell wall, in organisms that
       have one) in order to separate the two new cells in a process called cytokinesis.


Structure of genetic material- DNA Chromosomes




DNA         DNA with proteins chromatin           DNA replication      Chromosome
                                    Structure
       The nucleus is a membrane bound organelle that contains the genetic information in the
form of chromatin, highly folded ribbon-like complexes of deoxyribonucleic acid (DNA) and a
class of proteins . When a cell divides, chromatin fibers are very highly folded, and become visible



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in the light microscope as chromosomes. During interphase (between divisions), chromatin is more
extended, a form used for expression genetic information.
       The threadlike material is called chromatin. It condenses during cell division and form
chromosomes.
       Sister chromatids are the 2 chromatins after then DNA replication. Same with each other.
The threadlike material is called chromatin. It condenses during cell division and form
chromosomes.
       Each chromosome contains DNA and protein.
       Chromosomes carry genes which code for the characters.
Humans have 46 chromosomes. 23 pairs of chromosomes. 23 of them come from father and 23 of
them come from mother. Each pair codes for same trait (characteristic).They are called
homologous chromosomes.




Karyotype: A pictorial display of metaphase chromosomes from a mitotic cell




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Cell life cycle
   •   Cells should produce new cells by dividing. But during reproduction or formation of new
       cells, The genetic material should be kept untouched.
   •   Cells undergo 2 types of division. Mitosis and meiosis.
                                                                 –   Mitosis is the process of making
                                                                     new body cells.
                                                                 –   Meiosis is the type of cell
                                                                     division that creates egg and
                                                                     sperm cells(gametes).
                                                     The series of events from one cell division to
                                                     the next is called cell cycle.
                                                     In the life cycle of a cell:
                                                         1. Cell grows (G1)
                                                         2. Decide to divide and replicate DNA (S)
                                                         3. Prepare for division(G2)
                                                         4. Divide
                                                     This cycle occurs in every cell but not in nerve
and muscle cells. They stay at G1 phase, never divide.

Mitosis
Mitosis is important in:
   •   Repair and regeneration.
   •   Growth
   •   Reproduction in one celled organisms.
   •   Mitosis is a fundamental process for life. During mitosis, a cell duplicates all of its
       contents, including its chromosomes, and splits to form two identical daughter cells.
As a result of the mitosis:
   •   2 new cells are formed
   •   New cells have same genetic material and chromosome number with mother cell.
   •   The genetic material and chromosome number of the new cells are same.




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   •   Interphase: Resting period of the cell. Cell carries out normal activities. In S phase DNA of
       the cell replicates itself(S phase). 2 sister chromatids are formed.
   •   Prophase: nuclear membrane disappears. Centrioles go to the opposite poles(in animal
                                                                  cells). Chromatin in the nucleus
                                                                  begins to condense and becomes
                                                                  visible.
                                                              •   Metaphase: Chromosomes with
                                                                  sister chromatids stay in the middle
                                                                  of the cell (equator). Spindle fibers
                                                                  are formed. Proteins attach to the
                                                                  centromeres creating the
                                                                  kinetochores. Microtubules attach
                                                                  at the kinetochores and the
                                                                  chromosomes begin moving.
                                                              •   Anaphase: Sister chromatids
                                                                  separate from each other and go to
                                                                  the opposite poles with the help of
                                                                  the spindle fibers. Motion results
                                                                  from a combination of kinetochore
                                                                  movement along the spindle
                                                                  microtubules and through the
                                                                  physical interaction of polar
                                                                  microtubules.
   •   Telophase: Chromatids reach to the poles and nuclear membrane is formed . Spindle fibers
       disappear. In animal cells, cytokinesis results when a fiber ring composed of a protein
       called actin around the center of the cell contracts pinching the cell into two daughter cells,
       each with one nucleus. In plant cells, the rigid wall requires that a cell plate(formed by
       golgi) be synthesized between the two daughter cells.




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Changes in chromosome number, DNA amount and volume of cell




   •




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ASEXUAL REPRODUCTION
   •   Reproduction from one organism.
      The cell division is mitosis. A form of duplication using only mitosis.
   •   The genetic traits are same with the parent organism. Example, a new plant grows out of
       the root or a shoot from an existing plant
      Doesn’t effect evolution or variation. Produces only genetically identical offspring since all
       divisions are by mitosis.
           1. Offspring called clones meaning that each is an exact copy of the original organism
           2. This method of reproduction is rapid and effective allowing the spread of an
              organism
           3. Since the offspring are identical, there is no mechanism for introducing diversity
   •   Seen in primitive organisms
   •   Only mutations can form variations
   •   Monoploid (n) or diploid(2n) organisms can be formed
   •   Reproduce rapidly
Asexual reproduction types
1. Division(binary fission)




2. Budding


                                        Young organism is formed from the body of the existing
                                        organism. Offspring develop as a growth on the body of
                                        the parent. In some, the buds remain attached to the parent
                                        and the process results in colonies of animals.
                                        Yeast cells, hydra




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3. Sporing-sporulation ( fungi, algae, plasmodium,, fern, moss)




    Spores(n)              gametophyte plant(monoploid)          gametes               fertilization
       diploid plant (2n)        (meiosis) SPORES
Moss, ferns, fungi and plasmodium
Spores are different from gametes. They are seen in asexual reproduction. Forms new individual by
germination.
4. Vegetative reproduction
   The parent plant grows runners and forms new plant. They are typically same. Strawberry,
   onion, violet, potato.
   rhizomes , bulbs , corms and tubers are used for asexual reproduction as well as for food
   storage. Commercially-important plants are often deliberately propagated by asexual means in
   order to keep particularly desirable traits. Cuttings may be taken from the parent and rooted.
   Grafting is widely used to propagate a desired variety of shrub or tree. All apple varieties, for
   example, are propagated this way.




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5. REGENERATION
    The parts which are cut off the plant or animal can form a new organism or an organ.
       Starfish, earthworm, lizard. But some animals can not produce new organism just form the
       organ or heal the wound.

Meiosis
Meiosis is important in:
   •   formation of gametes (sperm, egg)
   •   reducing chromosome number
   •   genetic variation
As a result of the meiosis:
   •   4 new cells are formed
   •   New cells can have different genetic makeup from the mother cell
   •   New cells have half of the chromosome number of the mother cell.(n)
   •   The genetic makeup of the new cells can be different from each other.




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Interphase: DNA replicates itself
Prophase I: 2 Homologous chromosomes pair(tetrad-bivalents) and form synapses exchange
    genes (crossing over)
Metaphase I: Homologous chromosomes (tetrad) line up in the middle of the cell(equator). The
orientation is random, with either parental homologue on a side. Spindle fibers attach to the
chromosomes. One kinetochore forms per chromosome rather than one per chromatid, and the
chromosomes attached to spindle fibers begin to move.
Anaphase I: Homologous chromosomes separate from each other and go to the opposite poles.
Each of the daughter cells is now haploid (23 chromosomes), but each chromosome has two
chromatids
Telophase I: Chromosomes reach to the opposite poles. Two cells are formed . The chromosome
number is reduced by meiosis I.
Prophase II: The chromosomes become shorter and thicker.
Metaphase II: Spindle fibers attach to the chromatids of the chromosomes.
Anaphase II: Sister chromatids of the chromosomes are separated and go to the opposite poles of
the cells.
Telophase II: Totally 4 cells are formed. Each cell can have a different genetic make up and half
of chromosome number




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   •   What should we know about meiosis I?
  Crossing over(gene exchange)between homologous chromosomes occurs in Meiosis I
(Prophase). Genetic variation occurs .
 Homologous chromosomes are separated from each other in meiosis I, chromosome number is
reduced by half in Meiosis I.
 Homologous chromosomes line randomly in Metaphase I. Causes variation.
   •   What should we know about meiosis II?
 Sister chromatids are separated from each other in Meiosis II. (similar to mitosis)




                  MITOSIS                                            MEIOSIS
1. takes place in body cells.                  1. takes place in germ cells and forms sex cells.

2. No crossing over (gene Exchange)            2. Crossing over can happen between homologous
                                               chromosomes.(Tetrad forms)
3. It has 1 cycle of the phases (1 division)   3. It has 2 cycle of phases (2 division)

4. Produces 2 cells                            4. Produces 4 cells
5. newly formed cells have the same            5. Newly formed cells have the half of the
chromosome number of the parent cell(2n)       chromosome number of the parent cell (n)

6. The genetic make up of the newly formed 6. The genetic make up of the newly formed cells
cells are same with each other and with the    can be different from each other and from the
parent cell                                    parent cell (recombination)
7. Only sister chromatids separarte.           7. Homologous chromosomes separate at the 1st
                                               division, sister chromatids separarte in the 2nd
                                               division.




EK 10.04                                                                                  REV:00   43
        A    A           If this cell undergoes meiosis, draw the genetic
        B    b           makeup uf the new cells? 2n= 2



•   If there is no crossing over                           •     If there is crossing over,
     at the end of 1 st part of meiosis                         between A-B and A-b
                                                                           A                             A
        A                     A                                            b                             B
        B                     b            n=1
                                                           crossing over doesn’t change the gene
Homologous chromosomes separated and went                     combination
   to opposite 2 cells (chr number is halved)               n=1

At the end of the 2nd part of the meiosis
    A            A                A              A                    A           A                  A              A
    B            B                b              b                    b           b                  B              B


                                                 n=1           Sister chromatids are separated and
                                                               went to the opposite to cells
Sister chromatids are separated and went to the
    opposite to cells




                              If this cell undergoes meiosis, draw
        A        a               the genetic makeup uf the new
        B        b
                                            cells? 2n= 2
                                                       •       If there is crossing over
•   If there is no crossing over                                   at the end of 1 st part of meiosis
     at the end of 1 st part of meiosis

                                                               A                    a
     A                    a
                                                               b                    B
     B                    b                                                                             n=1
                                          n=1
                                                       New genetic makeup is formed as a result of
Homologous chromosomes separated and went                 crossing over
   to opposite 2 cells (chr number is halved)
                                                       At the end of the 2nd part of the meiosis
At the end of the 2nd part of the meiosis
                                           a           A                                         a
         A           A            a                                       A             a
                                           b           b                                         B
         B           B            b                                       b             B
                                                                                                              n=1
                                                n=1
                                                       Sister chromatids are separated and went to the
Sister chromatids are separated and went to the            opposite to cells
    opposite to cells




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Nondisjunction
Normal meiosis




    Failure of separation of homologous chromosomes or separation of sister chromatids




           1. Trisomy 21, exception leading to Downs syndrome
           2. Sex chromosomes
                  1. Turner syndrome: monosomy X
                  2. Klinefelter syndrome: XXY



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                                  SEXUAL REPRODUCTION
      Reproduction from 2 parents. (one forms sperm, the other forms egg) Formation of new
       individual by a combination of two haploid sex cells (gametes). Both gametes are haploid,
       with a single set of chromosomes . The new individual is called a zygote, with two sets of
       chromosomes (diploid).
      Major Division is meiosis (Meiosis is a process to convert a diploid cell to a haploid
       gamete, and cause a change in the genetic information to increase diversity in the offspring)
       and the major process is fertilization. Fertilization- combination of genetic information
       from two separate cells that have one half the original genetic information
    Newly formed organisms have new traits different from the parents and the other new
       organisms.
    Sexual reproduction enhance evolution and variation.
    These variations help organisms to survive better.
    Can be seen in higher organisms like animals and plants.
    The reasons for the genetic variations are: meiosis (crossing over, chromosomal lining in
       the metaphase) , fertilization and mutations.
    Newly formed organisms are diploid(2n)
    It is a long and slow process.

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PARTHENOGENESIS
It is the formation of a new organism from the unfertilized egg.

Male bee (n)                                 Queen bee(2n)

           Mitosis                                                 Meiosis


Sperm(n)                                               Egg(n)

                                                                     parthenogenesis
                      Female bee(2n)
                                                           Male bee(n)
Queen bee(2n)                                  Worker bee(2n)
Fed by Royal jelly                             fed by pollen



In parthenogenesis ("virgin birth"), the females produce eggs, but these develop into young without
ever being fertilized.

Parthenogenesis occurs in some fishes, several kinds of insects, and a few species of frogs and
lizards




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Formation of egg in humans




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   •   Meiosis occurs in ovaries. But the meiosis in humans is unequal division. Ony one oocyte
       is big and can live and be fertilized. Oocyte develops with follicle cells aroud it. Follicle
       cells protects and nourishes the egg. Only one follicle with one egg gets mature in one
       month. Every month one egg is thrown out(ovulated) from the ovary.
   •   The ovulated oocyte enters fallopian tube. The fertilization happens in the fallopian tube.
   •   After fertilization zygote forms and begins mitotic divisions.
   •   The fertilized egg travels down the fallopian tube and reaches uterus where it binds and
       develops.

Formation of Sperms in humans




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   •   Sperm formation occurs in seminiferous tubules of testis.
   •   Spern mother cells(spermatogonia) undergoes meiosis. But these cells have cytoplasmic
       bridges. These cytoplasmic bridges enables simultaneous maturation of sperm cells.
   •   Sperms taht are formed at the end of the meiosis don’t have the mobility, they undergo
       some changes. They lose their excess cytoplasm and produce flagella to move. Most of the
       mobility is gained in epididymis. The entire process takes 100 days.


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Fertilization
   •   Fertilization happens after ovulation in fallopian tubes.
   •   Sperm cells penetrate to the cell membrane of the egg and acrosome vesicle help
       penetration. It has hydrolytic enzymes. Only sperm nucleus enters egg. When it enters
       nuclei of gametes unite and form 2n zygote. Embryo forms from zygote with mitotic
       divisions.
   •   Zygote undergo mitosis during its journey to the uterus. There it binds to the endometrium
       (implantation).




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1-2 . Fertilization begins with the binding of a sperm head to the outer coating of the egg (called
the zona pellucida).
3-4 Exocytosis of the acrosome at the tip of the sperm head releases enzymes that digest a path
through the zona and enable the sperm head to bind to the plasma membrane of the egg.
5. Fusion of their respective membranes allows the entire contents of the sperm to be drawn into
the cytosol of the egg. (Even though the sperm's mitochondria enter the egg, they are almost
always destroyed and do not contribute their genes to the embryo. So human mitochondrial DNA is
almost always inherited from mothers only.
6. Within moments, enzymes released from the egg cytosol act on the zona making it impermeable
to the other sperm that arrive. Sperm and egg pronuclei unite. The fertilized egg or zygote is now
ready for its first mitosis.




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QUESTIONS
Choose the best answer:
   1. The following phase is taken from cell which undergoes mitosis. What phase is that?
          a. Prophase      b. metaphase c. anaphase d. Telophase e. interphase




2. In a dividing cell, sister chromatids are separated and move to the opposite poles. Which figure
shows that action.




      a.                           ,     b.                                 c.

                         d.

    3. In a dividing cell homologous chromosomes line at the middle of the cell. Which phase is that?
           a. Prophase         b. Interphase c. Telophase d. Anaphase e. Metaphase

    4. Define the following terms:

            a. Sister chromatid:


            b. Chromatin structure:


            c. Homologous chromosomes:


            d. Centriole:


5. In a dividing cell sister chromatids are separated from each other. Which phase is that?
             a. Prophase I b. Metaphase I c. Metaphase II d. Anaphase I e. Anaphase II


6. Define the following terms:

            b. diploid


            c. haploid

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7. Compare mitosis with meiosis:




8. What are the reasons of genetic variation?




9. The following graph shows the chromosome number changes of a cell during different cell divisions.
Which one of the choices shows the exact names of the divisions?
  chromosome
    number
            20

           10           I       II           III

                0                                    time
                      I           II            III
            d.      Meiosis      Mitosis        Fertilisation
            e.      Mitosis      Meiosis        Fertilisation
            f.      Fertilisition Mitosis       Mitosis
            g.      Fertilisation Meiosis      Meiosis
            h.      Meiosis       Fertilisation Mitosis


10. If a body cell with 12 chromosome undergoes firstly 1 mitosis and then undergoes 1 meiosis, How many
cells are formed at the end? Howmany chromosomes does each cell have?




11. A gamete cell has a chromosome number of 22. What is the chromosome number in body cells?



12. A skin cell of an organism has a chromosome number of 16, undergoes two mitotic cell divisions. What
        will be the chromosome number of the resulting cells?




13. A sperm cell has 6 chromosomes. How many chromosomes does it have?




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14. Draw the graph of a cell’s(with 18 chromosome number) chromosome number changes, during two
       mitosis and one meiosis.

   Chromosome
     number




                             I     II           III           time

    15. A cell with 8 chromosomes(2n=8) undergoes 4 mitosis. What is the number of new cells and what is
    the number of chromosomes?




    16. i. Cells in brain(nerve tissue)
         ii. Cells in skin
         iii. sperm cells
         iv. cells in mouth
         In which of the above cells a mitotic division can be observed?
a. ii and iv     b. i and ii     c. i, ii and iii     d. i and iv    e. All




3. ECOLOGY OF ECOSYSTEMS

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WHAT IS ECOLOGY
   •   Ecology studies the relationships among organisms and the interactions between organisms
       and their environment.
   •   All organisms and their environment make up the ECOSYSTEM. Within the ecosystem
       each organism has its own life to live and role to play.
   •   Ecosystem is a certain area in which organisms interact with each other and their
       environment.
   •   Within the Ecosystem, there are living and nonliving factors.
   •   Biotic and abiotic factors effect:
           –   Distribution of organisms
           –   Size of the population
           –   Ability to reproduce




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Climate( temperature, water amount, light)
   •    Climate influences natural vegetation. It determines the type of plants and animals which
        can live in that area.
   •    Deserts, rain forests, temperate and arctic regions.
   •    Also some plants effect the climate of some area. In our Back sea region forest make this
        area wetter. The increase in rainfall , increases the humidity of that area.
   •    Man also increases the temperature of the world (global warming.)
Oxygen
   •    Oxygen determines the life in the ecosystem.
   •    Organisms need oxygen for respiration. If the amount is insufficient, the organisms can die.
   •    Depth of the water,
   •    Height of the mountain
   •    Pollution also effects the amount of available oxygen.
   •    Also plants effect the oxygen amount of the system
Carbondioxide
   •    Carbondioxide is important for plants for photosynthesis.
   •    It effects the plants directly and animals indirectly.
   •    Also we change the amount of carbondioxide by using fossil fuels.




Light
   •    Plants directly need light for photosynthesis.
   •    Light effects the rate of photosynthesis and indirectly it effects the animals.
   •    Also plants determine the amount of light within the ecosystem. Huge trees make shadows
        for small plants. They can prevent small plants from taking direct sun light.
   •    The plants that live in shade have large leaf surface than the ones that live in light.
Soil
   •    It effects plants directly. Because plants need soil to take in minerals.
   •    It is important for anchorage, water, minerals and air.
   •    Also plants help formation of soil. Plant roots help rocks to breakdown easily.

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     •   And most of the minerals in the soil come from the decaying of dead organisms.
pH
     •   pH shows the acidity. H ion concentration.
     •   Organisms need to keep their body pH constant.
If the pH increases in the outside, it effects the chemical reactions. For example: Acid rain
Also Man increases the pH of the environment as a result of industry.
Water
     •   Water is the major component of cells.
     •   Animals that live in land try to decrease their water loss. They have furs,scales or protective
         layer (skin). Their respiratory organs are inside their body.
     •   Plants that live in dry lands also try to decrease their water loss.They have small leaves
         with cuticle, the number of stoma is decreased and they are embedded in the deeper layers.
         Most of them have hairs in leaves.




     NUTRITIONAL RELATIONSHIPS
         Each organism need other organisms and the abiotic factors to live. So each organism
interact with each other for their needs. The major need of organisms is the energy. All living
things use energy for their life activities.
The major energy source of all living things is the sun.
Organisms are divided into 3 groups according to how they get energy.




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Autotrophs                                       Heterotrophs
Can produce food or organic                      Can’t produce organic compounds
compounds(glucose, aminoacid, lipids)            from inorganic molecules.
from inorganic molecules                         Take in organic compounds from
I. Photosynthesis: Plants and algae that         autotrophs or heterotrophs.
use sunlight energy to get energy (ATP)          I. Holozoic animals take in solid food.
for using CO2 and H2O to produce                 Extra cellular digestion.
glucose and O2. Have                             II. Symbiotic organisms
chlorophyll(prokaryotes) or                          a. Mutualistic:2 organisms that are
chloroplasts(eukaryotes). Use CO2.               dependent to each other.
Need light.                                           b. Parasitic :2 organisms that live
II. Chemosynthesis: Bacteria that live           together but one harms the other.
in soil, which use oxidation of inorganic             c. Commensal: they live together,
compounds to get energy(ATP) to make             one benefits, but the other doesn’t
glucose from CO2. They don’t have                effected .
chlorophyll. They don’t need light. But they     III. Saprophytes: breakdown dead
use CO2. Nitrification bacteria.                 bodies outside of their bodies.




 II. The permanent relationship between two different organisms for the purpose of feeding, shelter
 or protection is called symbiosis.


 Mutualism: Both of the organisms benefit from each other. Lichens(algae and fungi live together),
            (N fixing bacteria and leguminosae plant)
            number
            of the
            organisms




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 2. Commensalism: One organism benefits, the other one neither benefits nor is harmed. (shark
            and small fishes)
            number
            of the
           organisms




3. Parasitism: One organism benefits, the other is harmed. (tapeworms, lice)


                number
                 of the
                organisms


  PLANT PARASITES
    •   Holoparasites: they are completely dependent on the host plant. rafflesia
    •   Hemiparasites: they are not completely dependent on the host, they can be dependent on
        their host for nutrition(organic matter) or for water needs. mistletoe
ANIMAL PARASITES
    •   Endoparasites: They live inside the body of the host. Most of their organ systems
        degenerate.
    •   Exoparasites: They live on the outer layer(skin, fur, hair) of the host.
3. Both autotroph and heterotroph organisms.
   They live in soil that lack of nitrogen and to get their nitrogen they kill flies and digest them
outside of their body then absorb the necessary materials. Venus fly trap
FOOD CHAINS AND FOOD WEBS
Feeding relationships of organisms form a food chain in which energy is passed from one organism
to the other.


Grass                grasshopper          frog           snake             hawk
Producer             consumer         consumer           consumer       consumer
                       Primary          secondary          tertiary     querternary
The sequence by which energy, in the form of food, passes from a plant to an animal and then to
other animals is called a food chain.



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 But feeding relationships are not as simple as this one. Many organisms can eat different kinds of
organisms. As a result many food chains form a network called food web. In the food web there is
a complex relationship of organisms.
In most of the food webs, organisms have complex relationships. They affect each other.
Predator: kill prey for food.
Prey : is the food of predators.
Their relationship determines the population size.
In these relationships organisms compete with each other.
In Competition, organisms fight for the same thing(food or mate)
If the competition is among the organisms of same species , it is intraspecific competition.( foxes)
If the competition is among the organisms of different species, it is interspecific competition.(foxes
and hawks)




Pyramids
ENERGY PYRAMIDS
   •   Each time an organism feeds on the other, there is a transfer of materials and energy. But
       not all of the energy pass to the other one, Some of the energy is lost as heat.(1/10)
   •   Because of this loss, the energy flow within the system is shown by a pyramid.
As you see that the energy decreases very much in the 3rd or 4 th level, so there is no 5th or 6th
level . The most informative pyramid is the pyramid of energy
This shows the amount of energy (in kiloJoules [kJ]) present at each trophic level.
This pyramid is also always upright (given the same as for the pyramid of biomass)




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Ecological Effeciency
   •   How much of energy is actually available to the next trophic level?
   •   Usually around 10% is available
   •   Why is it that we don’t see 6th order consumers?
   •   There is not enough energy available to support consumers at this level.
   •   Each level in the system depends on the previous one.
   •   If the number of the producers decreases, number of the primary consumers decreases.
   •   If number of the primary consumers increases, number of the secondary consumers
       increases but the number of the producers decreases.
   •   Also some chemicals pass with the food. If a chemical is firstly seen in producers, the
       amount of the chemical increases until the top consumer.
   •   The amount of dangerous chemicals is less in first levels but it increases until the top.




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Biomass pyramid
     •     Biomass shows the total living matter of a trophic(feeding) level at a specific time.
     •      Biomass shows the dried organic mass of an ecosystem. As the trophic level increases, the
           biomass of each trophic level decreases .
The dry weight of an individual is the mass of organic material contained within that individual -
the determine this the organism is dried in an oven to remove the water then weighed. This is done
because the water content of an organism (which has no impact on the amount of energy or
nutrients available to the ecosystem) varies considerably
The pyramid of biomass will always be upright since all organisms have to consume more biomass
than they contain.
The exceptions to this rule occur when measurements are taken at particular times e.g. the biomass
of producers may be relatively low in winter (when there is little sunlight) when compared to the
biomass of consumers which persists all year round.
Showing pyramids of biomass for the whole year (and thus taking into account seasonal variations)
will produce upright pyramids.
The units for pyramids of biomass are: dry weight of organic matter (per square metre)
Pyramid of Number


In this example the number of individuals at each trophic level are shown. The length (or area to
be more accurate) of each bar is proportional to the number of individuals.
This often produces an upright pyramid - but not always
In the diagram below, two pyramids of number are shown.
In example A the pyramid is upright while in example B (which shows a food chain from an
ecosystem present on a single tree) the number of individuals at the producer level is relatively
small (it is in fact one - the tree). This latter pyramid is said to be inverted.


Image from http://www.envf.port.ac.uk/geog/teaching/environ/sect2-3c.htm

The inverted pyramid may give a misleading impression of the ecosystem so the pyramid of
biomass also shown in the diagram is preferred.
With certain constraints the pyramid of biomass will always be an upright pyramid so the pyramid
of biomass shown corresponds to both of the pyramids of number in the diagram


 RECYCLING OF MATTER


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As we know from the energy pyramid, energy is lost through the food chain. But it is always
replaced by the sun. But the matter within the system is limited. We have to gain back this matter.
The amount of Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus is not exhausted, They always
recycle within the system between organisms and environment. Recycling of materials prevents
accumulation wastes and provides an unlimited resource for organisms.
The cycles of materials between organisms and the environment are called biogeochemical cycles.


WATER CYCLE
The water cycle is the only way that Earth can be continually supplied with fresh water. The heat
from the sun is the most important part of renewing our water supply.
This heat soaks up water from the oceans, lakes, rivers, trees and plants in a process called
evaporation.
As the water mixes with the air it forms water vapor. As the air cools, the water vapor forms
clouds. This is called condensation.
Most of the water is immediately returned to the seas by rain (precipitation). The rest of the water
vapor is carried inside clouds by wind over land where it rains or snows.
Rain and melted snow is brought back to the oceans by rivers, streams, and run-off from glaciers
and water underground.


CARBON CYCLE
Carbon is used during photosynthesis as carbondioxide.
CO2+ H2O              C6H12O6 +O2 + H2O
It is converted into an organic compound carbohydrate. Heterotrophs feed on the carbohydrates
and give carbondioxide back to the air. Decomposers also produce carbondioxide by respiration.
This process balances the CO2 content in the air. But Volcanic activities, burning fossil fuels
increases CO2 content.
The concentration of carbon in living matter (18%) is almost 100 times greater than its
concentration in the earth (0.19%). So living things extract carbon from their nonliving
environment. For life to continue, this carbon must be recycled.
Carbon exists in the nonliving environment as:
      carbon dioxide (CO2) in the atmosphere and dissolved in water (forming HCO3−)
      carbonate rocks (limestone and coral = CaCO3)
      deposits of coal, petroleum, and natural gas derived from once-living things
      dead organic matter, e.g., humus in the soil

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Carbon enters the biotic world through the action of autotrophs.
Carbon returns to the atmosphere and water by
      respiration (as CO2)
      burning
      decay (producing CO2 if oxygen is present, methane (CH4) if it is not.




The Greenhouse Effect and Global Warming
Carbon dioxide is transparent to light but rather opaque to heat rays. Therefore, CO2 in the
atmosphere retards the radiation of heat from the earth back into space — the "greenhouse effect".




Increasing CO2 in the atmosphere absorbs the radiated heat from the earth. This results in an
inrease in the temperature of the earth-global warming. This effect is called “Greenhouse effect”.

Other Greenhouse Gases
Although their levels in the atmosphere are much lower than that of CO2,
      methane (CH4) and
      chlorofluorocarbons (CFCs) Chlorofluorocarbons (CFCs) are synthetic gases in which the
       hydrogen atoms of methane are replaced by atoms of fluorine and chlorine (e.g., CHF2Cl,
       CFCl3, CF2Cl2).
are also potent greenhouse gases.
Their chemical inertness, which makes CFCs so desirable for industry, also makes them a threat to
the atmosphere. Once in the atmosphere, it may take 60–100 years for them to decompose and


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disappear. In the meantime, they may contribute to as much as 25% of the greenhouse effect. But
perhaps even more worrisome is the threat they pose to the ozone shield.
OZONE PROBLEM
Ozone shields the earth's surface from much of the ultraviolet radiation reaching the earth from the
sun. Ultraviolet rays can cause skin cancer, cataracts, and may depress the immune system. While
we often have too much ozone around us, the concentration of ozone high in the stratosphere
(which begins about 7 miles up - where airliners cruise) has declined over the past two decades.
Satellite monitoring of the stratosphere, which began in 1978, has revealed a marked decline.
The most serious decline occurs over Antarctica .
       In the atmosphere the amount of the oxygen also remains constant because of the cycling.
Oxygen is formed by photosynthesis but it is consumed by respiration. The oxygen and carbon
cycles work together.
NITROGEN CYCLE
Nitrogen is an important element for organisms, in aminoacids, nucleic acids there are nitrogen
molecules.
 o Air, which is 79% nitrogen gas (N2), is the major reservoir of nitrogen.
 o But most organisms cannot use nitrogen in this form.
 o Plants must secure their nitrogen in "fixed" form, i.e., incorporated in compounds such as:
 o nitrate ions (NO3−)
 o ammonia (NH3)
 o urea (NH2)2CO
Animals secure their nitrogen (and all other) compounds from plants (or animals that have fed on
plants).




Nitrogen Fixation

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The nitrogen molecule (N2) is quite inert. To break it apart so that its atoms can combine with
other atoms requires the input of substantial amounts of energy.
Three processes are responsible for most of the nitrogen fixation in the biosphere:
atmospheric fixation by lightning
biological fixation by certain microbes — alone or in a symbiotic relationship with some plants
and animals. Some live in a symbiotic relationship with plants of the legume family (e.g.,
soybeans, alfalfa).
Industrial fixation- in artificial fertilizers
Decay
The proteins made by plants enter and pass through food webs just as carbohydrates do. At each
trophic level, their metabolism produces organic nitrogen compounds that return to the
environment, chiefly in excretions. Microorganisms of decay, break down the molecules in
excretions and dead organisms into ammonia.
Nitrification
Ammonia can be taken up directly by plants — usually through their roots. However, most of the
ammonia produced by decay is converted into nitrates. This is accomplished in two steps:
Bacteria of the genus Nitrosomonas oxidize NH3 to nitrites (NO2−).
Bacteria of the genus Nitrobacter oxidize the nitrites to nitrates (NO3−).
These two groups of autotrophic bacteria are called nitrifying bacteria. Through their activities
(which supply them with all their energy needs), nitrogen is made available to the roots of plants.
Plants synthesize their own proteins and amino acids by using these nitrogen molecules. Animals
take nitrogen by feeding on plants and other animals.
Denitrification
The three processes above remove nitrogen from the atmosphere and pass it through ecosystems.
Denitrification reduces nitrates to nitrogen gas, thus replenishing the atmosphere.
Once again, bacteria are the agents. They live deep in soil and in aquatic sediments where
conditions are anaerobic.


ACID RAIN
The smoke and fumes from burning fossil fuels rise into the atmosphere and combine with the
moisture in the air to form acid rain. The main chemicals in air pollution that create acid rain are
sulfur dioxide and nitrogen oxides. Acid rain usually forms high in the clouds where sulfur
dioxide and nitrogen oxides react with water, oxygen, and oxidants. This forms a mild solution of
sulfuric acid and nitric acid. Sunlight increases the rate of most of these reactions. Rainwater,

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snow, fog, and other forms of precipitation containing those mild solutions of sulfuric and nitric
acids fall to the earth as acid rain.


PHOSPHORUS CYCLE
Phosphorus is an important element for living organisms. They use it mainly in nucleic acids.
Plants as usual obtain phosphorus as phosphate from soil. Soil becomes rich in phosphate by the
breakdown of rocks. Fertilizers mainly have phosphate. Metabolic wastes and decaying help
formation of phosphate in soil. Man and animals get their phosphate need by feeding.


The main storage for phosphorus is in the earths crust. On land phosphorus is usually found in the
form of phosphates. By the process of weathering and erosion phosphates enter rivers and streams
that transport them to the ocean. Once in the ocean the phosphorus accumulates on continental
shelves in the form of insoluble deposits.


All organisms require phosphorus for synthesizing phospholopids, NADPH, ATP, nucleic acids,
and other compounds. Plants absorb phosphorus very quickly, and then herbivores get phosphorus
by eating plants. Then carnivours get phosphorus by eating herbivores. Eventully both of these
organisms will excrete phosphorus as a waste. This decomposition will release phosphorus into the
soil. Plants absorb the phosphorus from the soil and they recycle it within the ecosystem.




Eutrophication occurs as a result of increase in P and phytoplanktons.
    1.Increase in P in water
    2. Phytoplanktons increase as a result of P.
    Phytoplanktons make photosynthesis (use CO2 and produce O2)
3. In winter Phytoplanktons die. Saprophytes breakdown deadbodies. (they use O2 and produce
CO2).
4. Animals who need O2 die.

QUESTIONS
1. A naturally occurring group of animals living in a certain area is called a(n)
        a) ecosystem        b) trophic level     c) community      d) food chain
2. As you move up the food chain the amount of energy available at the next level
        a) increases      b) decreases         c) stays the same
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       d) increases or decreases depending on the animals involved.
3. In order for plants to use nitrogen it must first be converted to nitrates by
       a) denitrifying bacteria     b) nitrifying bacteria    c) nitrate viruses
       d) ammonification
4. The study of organisms and their interaction with the environment is called
       a) ecosystem     b) biosphere       c) community       d) ecology
5. If two species are competing with each other for a limited resource in a specific location,
    the species able to use the resource most efficiently will eventually eliminate the other
    species in that location. This is the principle of
       a) competitive exclusion        b) community survival      c) energy flow
       d) chemical cycles
6. A symbiotic relationship where one member benefits and the other is harmed is called
       a) mutualism      b) commensalism        c) parasitism      d) cannibalism
7. Herbivores feed on
       a) plants      b) animals     c) both a+b       d) none of the above
8. Omnivores feed on
       a) plants      b) animals     c) both a+b       d) none of the above
9. Humans have microscopic organisms which exist inside the follicles of our eyelashes. These
     microorganisms receive nutrition, protection, and an ideal habitat while humans exhibit no
     positive or adverse effects from this relationship, which is an example of
       a) mutualism      b) commensalism        c) parasitism      d) cannibalism
10. Energy flows through an ecosystem
       a) forward and backward constantly          b) in a cycle pattern   c) in one direction only
       d) from consumer to producer
11. All the ecosystems of the world put together make up the
       a) biosphere      b) league of ecosystems         c) ecological environment    d) organism
12. Barnacles on a whale is an example of
       a) mutualism      b) commensalism        c) parasitism      d) cannibalism
13. In the nitrogen cycle, the organisms which convert nitrates back into nitrogen gas are
     called
       a) denitrifying bacteria     b) nitrifying bacteria    c) nitrate viruses
       d) ammoniums
14. Food webs are composed of interwoven
       a) nutrient sources    b) symbionts      c)food chains     d) energy cycles

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15. Most of the energy in a food chain is lost as
       a) light   b) biomass   c) heat      d) electricity
16. Your body may be currently composed of carbon atoms that were once part of
       a) dinosaurs     b) sugars        c) dodo birds       d) all of the above

REFERENCES
Life- the science of Biology-7th ed. Purves, Sadava, Orians, Heller
2. Biology -6th ed. Star
3. http://upper.usm.k12.wi.us/academics/faculty/rheun/welcome.html
4. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/




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