I. Cellular respiration
A. Series
of metabolic pathways that allow cells to generate ATP to be used as an
energy source.
B. Involves
the transfer of energy from one source to another in the form of
electrons.
1. Sometimes the electrons are transfered as a Hydrogen
atom.
2. Sometimes the electrons are transfered directly as
electrons.
3. The removal of electrons ( or H atoms) is called oxidation.
The molecule is
said to be oxidized.
4. The addition of electrons (or H atoms) is called reduction.
The molecule is said to
be reduced.
5. Both things must occur. This is a redox reaction
(oxidation-reduction) reaction.
C. During
cellular respiration, energy is removed from organic molecules by redox
reactions
and transferred to co-enzymes that store it temporarily.
D. Some of the energy goes directly to form ATP by substrate-level phosphorylation.
1. This involves the direct transfer of a Phosphate from
an intermediate molecule to
ADP, making ATP. This is enzyme catalyzed.
E. All respiratory pathways begin with Glycolysis. It takes place in the cytoplasm.
1. Glycolysis is the breakdown of glucose to two pyruvate molecules.
2. The net gain is two molecules of ATP and two molecules
of NADH (reduced
coenzyme, temporarily storing energy.
3. The ATP comes from substrate-level phosphorylation;
the NADH comes from a
redox reaction.
4. The first half of the pathway is endergonic, using
up two ATP. The second half
is very exergonic, creating the NADH and four ATP.
F. Some organisms can only make ATP using the glycolysis pathway.
1. These cell types must undergo a fermentation pathway
to regenerate the NAD+
needed to continue another round of glycolysis.
2. There are two types of fermentation, alcoholic fermentation
and lactic acid
fermentation. Both waste much potential energy in the organic molecules
are
not completely oxidized by this process.
3. alcoholic fermentation
a. Takes pyruvate, removes carbon in the form of carbon
dioxide creating
a molecule that is then reduced to ethanol as NADH is oxidized back to
NAD+.
b. Now glycolysis can continue again
c. This process produces only 2 ATP per glucose molecule
entering glycolysis.
d. Used in baking bread (yeast produce carbon dioxide)
and in making
alcoholic beverages (organisms produce the ethanol).
4. lactic acid fermentation
a. Takes pyruvate, reduces it to lactic acid while oxidizing
NADH to NAD+.
b. Now glycolysis can continue.
c. Produces only 2 ATP per glucose molecule entering
glycolysis.
d. Cause of cramping during excessive use of skeletal
muscles which, in absence
of oxygen, switch to this fermentation process for a little more ATP.
G. Aerobic respiration
1. Involves a complex series of reactions that ultimately require
oxygen. They take place
in the mitochondria.
2. The first part is the Gateway reactions. They take
place in the matrix.
a. Takes the two pyruvate from glycolysis, removes a
carbon as carbon dioxide
from each and oxidizes the product to acetyl. 2 NAD+ reduced to 2NADH.
b. Coenzyme A enters. Creates 2 Acetyl Coenzyme A molecules.
c. The Acetyl groups are transfered to the Krebs Cycle
by addition of these
two carbons to oxaloacetate creating citric acid.
3. The Krebs Cycle (Citric Acid Cycle)
a. This is a series of sequential reactions that forms
a continuous cycle,
receiving the two carbons (acetyl group) from the gateway reaactions and
gradually oxidizing them, forming many reduced coenzymes in the process
and giving off carbon dioxide. It takes place in the matrix.
b. Some ATP is also made directly by substrate-level
phosphorylation.
c. The net gain during one cycle is 2 ATP, 6 NADH, and
2 FADH2.
d. All of these represent energy coming from the one
entering glucose molecule
that started glycolysis.
e. The oxidation of glucose is completed here.
f. Much energy remains in the reduced coenzymes, NADH
and FADH2
that came from glycolysis, the gateway reactions, and the Krebs cycle.
g. This energy will be used to generate much ATP during
the last stages of
aerobic respiration: electron transport, chemiosmosis, and oxidative
phosphorylation.
h. The Krebs Cycle intermediates serve as entry points
for many other cellular
metabolites into the respiratory pathway to contribute to energy production.
Also, some enter at earlier steps during glycolysis or the gateway reactions.
i. Some intermediates also serve as
starting points for the synthesis of other
molecules that the cell needs.
j. At all levels, the enzymes catalyzing the reactions
of glycolysis, Krebs, and the
the gateway reactions can be controlled by products produced during the
the reactions, or by ATP or ADP themselves.
4. Electron transport chain
a. NADH and FADH2 transfer the electrons they gained
when reduced to carrier
molecules in the electron transport chain, located in the inner membrane
of
the mitochondria.
b. The electrons are passed down an electrochemical gradient
from carrier to
carrier, gradually losing energy at each step. The carriers are sequentially
reduced (gain the electrons) and then oxidized (lose the electrons).
- some of these carriers are called cytochromes.
c. The final electron acceptor is oxygen. As it accepts
the electrons from the
last carrier molecule in the chain, the oxygen is reduced to water.
5. Chemiosmosis
a. As the energy is released during electron transport,
it is used by carrier
molecules to actively transport protons (hydrogen ions) from
the matrix across the inner mitochondrial membrane into the outer compartment
(between inner and outer membrane of the mitochondria).
b. This creates a concentration gradient for the hydrogen
ions. Potential energy
is stored in this gradient.
c. Located in the inner mitochondrial membrane are ATP
synthase enzymes
that perform two functions.
- they form a channel that allows the diffusion of the hydrogen ions with
the
favorable concentration gradient across the membrane back into the matrix.
- they couple the energy released by the return of the hydrogen ions to
the
endergonic reaction ADP + P making ATP.
d. This process of using the
energy stored in a concentration gradient to
to fuel and endergonic chemical reaction is called chemiosmosis.
6. Oxidative phosphorylation
a. When ATP is made in the above mechanism, it is said
to be made by
oxidative phosphorylation.
b. This emphasizes the inter-relatedness of the various
parts of the process.
c. Ultimately, the presence of oxygen was necessary to
receive the electrons or
the entire chain would back up and no further ATP production could take
place. There would be no active transport possible, therefore no concentration
gradient, therefore no chemiosmosis, therefore no energy for the endergonic
reaction to make ATP.
d. The total yield of ATP is:
The 2 NADH from glycolysis each give 2 ATP.
The other 8 NADH give 3 ATP each. The two FADH2 each give 2 ATP.
This gives a total of 36 ATP from one glucose entering glycolyis in a
eukaryotic cell (remember we also made 4 total ATP by substrate-level
phosphorylation).
II. Photosynthesis
A. This
is the process by which the energy of sunlight is used to synthesize organic
molecules
from atmospheric carbon dioxide.
B. It takes place in the chloroplast of the plant cell.
1. organisms containing cells that can photosynthesize
are called autotrophs.
2. organisms that cannot photosynthesize are called heterotrophs.
C. The
process of photosynthesis is divided into the light reactions and the light-independent
reactions (dark reactions).
D. The Light Reactions
1. Take place in a special structure within the chloroplast
called the thylakoid.
a. The exterior is bounded by the thylakoid membrane
and there is an interior
section called the thylakoid interior.
b. Stacks of thylakoids are called grana.
c. The chloroplast interior where the grana are found
is called the stroma.
2. Located near the thylakoid membranes are the antenna
complexes.
a. These are networks of pigment molecules that can trap
the energy of
sunlight by absorbing it at specific wavelengths.
b. The accessory pigments in the complex pass the energy
to a central location
called the reaction center which contains a special chlorophyll molecule.
c. This chlorophyll at the reaction center absorbs the
energy from the accessory
pigments and two of its electrons are excited and pass to a higher energy
level and out of the molecule.
3. The light reactions use two photosystems.
a. Photosystem I contains chlorophyll P-700 at its reaction
center.
b. Photosystem II contains chlorophyll P-680 at its reaction
center.
4. The light reactions generate the energy-rich molecules
needed for the light-
independent reactions that make the organic molecules (glucose).
a. ATP is needed and is made by a process called photophosphorylation.
b. A reduced coenzyme, NADPH, is also needed.
5. There are two types of photophosphorylation mechanisms.
a. Non-cyclic photophosphorylation generates both ATP
and NADPH.
b. Cyclic photophosphorylation generates only ATP.
E. Non-cyclic photophosphorylation
1. Uses both photosystems I and II.
2. Splits water.
3. Generates oxygen.
4. How it works:
a. Sunlight is trapped by the antenna complex and the
energy is transfered to
P-680 in photosystem II.
b. The electrons from P-680 move into an electron transport
system located in the
thylakoid membranes.
c. The electrons pass down an electrochemical gradient
releasing energy.
d. The energy is used for the active transport of H+
(protons) from the stroma,
across the thylakoid membrane, into the thylakoid interior, creating a
concentration gradient.
e. ATP synthetases in the thylakoid membranes allow the
return of the H+ which
release energy that is used by the synthetase for chemiosmosis to make
ATP.
f. The electrons lost from P-680 are replaced as follows:
- water in the thylakoid interior is split.
- the hydrogens from the water give their electrons to P-680. Their H+
stay
in the interior and participate in chemiosmosis.
- oxygen is given off as a by-product. It can be used by the cells for
aerobic
cellular respiration, but does not participate in photosynthesis.
g. The electrons that came from P-680 move to P-700 in
photosystem I.
- this will replace electrons lost from P-700 when it absorbs light energy
from
the antenna complex and excited electrons move to the electron transport
chain.
h. The electrons from P-700 move to NADP reductase which
uses them to
to reduce NADP+ to NADPH.
F. Cyclic photophosphorylation
1. Used to provide a little more ATP.
2. Not sufficient for the light-independent reactions
because no NADPH is made.
3. No water is split or oxygen generated.
4. Uses only photosystem I.
5. The mechanism is as follows:
a. Sunlight is absorbed and the energy transfered through
the antenna complex
to P-700.
b. P-700 loses electrons to the electron transport chain.
c. The electrons move down an electrochemical gradient
releasing energy.
d. The energy is used to actively transport H+ across
the thylakoid membrane
to the interior to be used in chemiosmosis.
e. The electrons return to the stroma through ATP synthetase,
releasing
energy which is used to make ATP by chemiosmosis.
f. The electrons return back to P-700 from whence they
came.
G. The Light-Independent Reactions (Dark Reactions)
1. These reactions use the ATP and NADPH made in the
light reactions as the
energy to fuel the Calvin-Benson Cycle.
2. These reactions can occur in either the dark or in
the light.
3. Overall, during the Calvin-Benson Cycle, 6 molecules
of carbon dioxide from the
atmosphere are "fixed" to create one glucose molecule.
4. The mechanism is as follows:
a. 3 molecules of a 5-carbon containing molecule, ribulose
biphosphate, has a carbon added
to it that comes from carbon dioxide. (total of 18 carbons)
b. This reaction is catalyzed by the enzyme ribulose
biphosphate carboxylase,
known as rubisco.
c. The 6-C containing intermediate made from this immediately
breaks down
into two 3-C containing molecules. (still 18 carbons)
d. The 6 3-C containing molecules are altered by endergonic
reactions that
require ATP and NADPH. (still 18 carbons)
e. They eventually form 6 glyceraldehyde-3-phosphate.
(still 18 carbons)
f. One leaves the cycle to become a glucose precursor.
(3 carbons)
g. The cycle must run twice to produce 2 glyceraldehyde-phosphates
in order
to eventually make one glucose (needs 6 carbons)
h. The remaining glyceraldehyde-3-phosphates in the cycle
(15 carbons) are used to make
the 5C containing molecules that will ultimately regenerate
the ribulose biphosphate that is needed for the cycle to continue again.
i. These later reactions also require ATP.
H. Problems with Photorespiration
1. Rubisco has an active site that can also bind to oxygen
if carbon dioxide levels
fall.
2. This can happen in dry or hot conditions when the
plant cell closes its stomata.
3. The oxygen that is "fixed" eventually is converted
into a molecule that moves to
the microbody of the plant and is oxidized to a useless molecule, producing
oxygen and carbon dioxide in the process. This is photorespiration.
4. C3 plants that use only the Calvin-Benson Cycle for
photosynthesis must live
with a certain amount of energy lost to photorespiration.
5. C4 plants have solved this problem by having 2 photosynthetic
cell types. In mesophyll, carbon
dioxide is first fixed into a 4 carbon compound that is shunted into underlying
bundle sheath cells
that release the carbon dioxide and use it in a normal Calvin-Benson cycle.
6. CAM plants have another solution to this problem.
They fix carbon dioxide at night into a 4 carbon
molecule and in the day they release it for use in a normal Calvin Benson
cycle.
III. The Cell Cycle
A. Consists
of the phases G1, S, G2, and M. G1, S, and G2 make up Interphase.
1. During Interphase, the DNA is not visible.
2. DNA in eukaryotic cells is in the form of chromatin,
DNA complexed with histone
proteins.
3. Only during M phase is the DNA visible.
B. During
G1, the cell makes the decision to divide or not. It grows and makes special
proteins to use during S phase.
1. cdks are protein kinases. When complexed with a cyclin they become active,
phosphorylating their
targets, and pushing the cell cycle forward.
2. An important point in G1 (Restriction point (R)), is where the DNA is
examined for any errors. If there are
none, then the cdk/cyclin complex phosphorylates Rb (retinoblastoma), preventing
its binding to proteins
involved in DNA synthesis-related events. They can then move the cell cycle
into S phase
3. If the DNA is damaged, synthesis of an inhibitor to the cdk/cyclin is
made (for example, p21). This binds
to the complex preventing it from phosphorylating Rb. The cell cycle does
not progress.
C. During S phase the cell copies all of the chromosomal DNA identically.
D. During
G2 the cell checks if S phase is finished and then prepares for cell division
by growing some more and making more specialized proteins for mitosis or
meiosis.
E. M stands
for mitosis or meiosis.
1. M is the phase that describes the nuclear division
during cell division.
IV. Mitosis
A. Cells
enter mitosis with 2 chromatids for each chromosome, the result of DNA
replication
during S phase.
1. The two chromatids are held together by centromeres
and are called sister
chromatids.
2. For a diploid organism, before S phase, there are
two homologous chromosomes
for each of the somatic (non-sex) chromosomes and two sex chromosomes,
XX for
females and XY for males.
3. Homologous chromosomes contain the same genes but
can have different forms of
those genes.
4. After S phase, we use the term chromatid to describe
the four copies of the
different chromosomes, the two sets of sister chromatids.
B. The
first phase of mitosis is called Prophase.
1. During prophase the DNA condenses and becomes visible
under light
microscopy.
2. During prophase the centrosomes (which can contain
centrioles) move to opposite
sides of the cell and a spindle apparatus made up of microtubules forms.
3. During later prophase into early metaphase, the spindle
attaches to the
centromeres of the sister chromatids at the kinetochores. There are two
kinetochores per sister chromatid pair, one on either side of the centromere.
4. During later prophase the nuclear envelope degrades.
(Often called prometaphase).
C. The second phase of mitosis is called Metaphase.
1. During metaphase, the spindle fibers pull on the kinetochores,
moving the sister
chromatids to the equator of the cell, called the metaphase plate.
a. The sister chromatids align, one on either side of
the plate.
D. The
third phase of mitosis is called Anaphase.
1. During anaphase the spindle fibers attached to the
kinetochores shorten.
2. As the fibers shorten, the centromeres of each sister
chromatid set divide and
the sister chromatids move to opposite sides of the cell.
E. The
fourth phase of mitosis is called Telophase.
1. During telophase, the separated chromatids have a
new nucleus form around
them, one on either side of the cell.
a. This completes mitosis, the division of the nucleus.
F. Some
cells also divide their cytoplasms now by cytokinesis.
1. This will produce two completely separate cells.
2. Some species or cell types do not undergo cytokinesis
following mitosis.
a. An example is human skeletal muscle
V. Meiosis
A. Sexually reproducing organisms must produce haploid cells called gametes.
B. Female gametes are called eggs (ova); Male gametes are called sperm.
C. During
the process of fertilization, the egg and sperm unite to produce the zygote,
a 2n
cell.
D. The
process of meiosis begins with a diploid germ cell that undergoes an S
phase
thus producing sister chromatids held together by a centromere, similar
to what preceeds
mitosis.
E.
The two sets of sister chromatids representing the original homologous
chromosomes,
one inherited from the father (paternal) and the other from the mother
(maternal) stay
associated with one another, forming a tetrad or bivalent.
F. The
cell now enters the first meiotic division, called Meiosis I.
1. The first phase of Meiosis I is called Prophase I.
a. In early to mid prophase the homologs in the tetrads
undergo synapsis.
- This is the intimate, close alignment of the homologs.
b. This allows the homologs to engage in crossing-over.
- This is the exact exchange of genetic information between the homologs,
known as recombination.
c. In late prophase, the evidence of a crossing-over
event can be seen by the
presence of chiasmata on the chromosomes.
d. Meiosis also involves the formation of a spindle apparatus,
etc. exactly as
described for mitosis.This occurs in prophase I.
2. The second phase of Meiosis I is called Metaphase
I.
a. The tetrads align on the metaphase plate such that
one sister-chromatid pair is
on one side and the other on the opposite side.
b. The alignment is random. Maternal or paternal homolgs
can be on either
side. This is called independent assortment.
3. The third phase of Meiosis I is called Anaphase I.
a. The sister chromatids are pulled to opposite sides
of the cell.
4. The fourth phase of Meiosis I is called Telophase
I.
a. In some species, a nucleus reforms around the sister-chromatids
on either
side of the cell. Some do not do this. Some have a cytokinesis, others
not.
b. The two "cells" produced are actually haploid in that
they contain only one
of the original homologs but they they have two sister
chromatids.
G. Each
cell now enters the second meiotic division called Meiosis II.
1. The events of Meiosis II are very similar to those
of Mitosis.
2. There is no S phase preceeding Meiosis II.
3. The phases of Meiosis II are Prophase II, Metaphase
II, Anaphase II, and
Telophase II.
a. The sister-chromatids moving through these phases
act exactly like those that
move through Mitosis.
b. The centromeres split during Anaphase II and the sister
chromatids move into
separate cells during Telophase II as a result.
4. The final result is the production of 4 gametes that
are haploid.
a. All 4 will differ from each other because of recombination
during Prophase I
and independent assortment of paternal vs. maternal homologs along the
metaphase plate during Metaphase I.