Chapter 6: Pathways that Harvest and Store Energy
Free Energy - a thermodynamic quantity equivalent to the capacity of a system to do work.
Endergonic - (of a metabolic or chemical process) accompanied by or requiring the absorption of
energy, the products being of greater free energy than the reactants.
Exergonic - (of a metabolic or chemical process) accompanied by the release of energy.
1st Law of Thermodynamics - The law of conservation of energy states that the total energy of an
isolated system is constant; energy can be transformed from one form to another, but cannot be
created or destroyed.
2nd Law of Thermodynamics - states that in a natural thermodynamic process, there is an increase
in the sum of the entropies of the participating systems.
Phosphate Level Phosphorylation - a type of metabolic reaction that results in the formation of
adenosine triphosphate (ATP) or guanosine triphosphate (GTP) by the direct transfer and
donation of a phosphoryl (PO3) group to adenosine diphosphate (ADP) or guanosine diphosphate
(GDP) from a phosphorylated reactive.
Oxidative Phosphorylation - a biochemical process in cells. It is the final metabolic pathway of
cellular respiration, after glycolysis and the citric acid cycle. 26 of the total 30 ATP (energy
carrier) molecules generated from a single glucose molecule during cellular respiration.
Chemiosmosis - the movement of ions across a selectively permeable membrane, down their
electrochemical gradient. More specifically, it relates to the generation of ATP by the movement
of hydrogen ions across a membrane during cellular respiration or photosynthesis.
Oxidation - the process or result of oxidizing or being oxidized.
Reduction - the halving of the number of chromosomes per cell that occurs at one of the two
anaphases of meiosis.
Pigment - the natural coloring matter of animal or plant tissue.
Photosystem - a biochemical mechanism in plants by which chlorophyll absorbs light energy for
photosynthesis. There are two such mechanisms ( photosystems I and II ) involving different
chlorophyll-protein complexes.
Questions:
1. (1) A Complex chemical transformation occurs in a series of separate, intermediate
reactions that form a metabolic pathway.
(2) EACH reaction is Catalyzed by a SPECIFIC Enzyme
(3) Most metabolic pathways are similar in ALL organisms, from Bacteria to Plants to
Humans.
(4) In Eukaryotes, many metabolic pathways are compartmentalized, with certain
reactions occurring inside specific organelles.
(5) Each metabolic pathway is controlled by key enzymes that can be Inhibited or
Activated, thereby determining how fast the reactions will go.
2. In order to lose electrons and be oxidized, another element or compound must be there to
gain the electrons and be reduced. In other words, oxidation (loss of electrons) must be
accompanied by reduction (gain of electrons).
3. Glycolysis produces 4 ATP's and 2 NADH, but uses 2 ATP's in the process for a net of
2 ATP and 2 NADH. The Krebs cycle and the conversion of pyruvate to Acetyl CoA
produce 2 ATP's, 8 NADH's, and 2FADH2's per glucose molecule.
4. Lacking α-ketoglutarate dehydrogenase causes the cell to not carry out the complete set
of citric acid cycle reactions. By the action of several important auxiliary enzymes,
certain intermediates of the citric acid cycle, particularly α-ketoglutarate and
oxaloacetate, can be removed from the cycle to serve as precursors of amino acids.
Aspartate and glutamate have the same carbon skeletons as oxaloacetate and αketoglutarate, respectively, and are synthesized from them by simple transamination
(Chapter 21). Through aspartate and glutamate the carbons of oxaloacetate and αketoglutarate are used to build other amino acids as well as purine and pyrimidine
nucleotides.
5.
6.
7. Proton Pump – The mitochondrial proton pump is driven by the electron transport
system. An integral membrane protein facilitates movement of protons across a cell
membrane in an endergonic reaction, creating a concentration gradient along the inner
membrane due to the higher concentration of protons outside the matrix than inside. The
proton pump does not create energy; it sets up a bank of stored potential energy in the
resulting proton (H+ ) gradient.
ATP Synthase - ATP synthase is also an integral membrane protein that couples the
movement of protons back down their concentration gradient to binding ADP and HPO4
- , forming ATP. This enzyme provides energy for the cell by facilitating the synthesis of
ATP by utilizing the proton gradient described above. The proton pump and ATP
synthase form an interdependent energy-coupling complex. This process occurs in the
inner mitochondrial membrane where the energy needed for ATP formation by the
enzyme ATP synthase is transferred from the proton gradient.
8. The first law of thermodynamics states that energy cannot be created nor destroyed, and
therefore the total amount of energy in a closed system remains constant. Even though
less than half of the energy produced during cellular respiration is transferred to ATP
synthesis, the remainder is not destroyed but is given off as heat. Therefore, energy
changes form but is not “lost” by this metabolic process. The second law states that the
amount of available energy in a closed system is continually decreasing, or that entropy is
increasing. While the efficiency of ATP synthesis is greater than 10%, it is not 100%
efficient, nor is any other physical process or chemical reaction. Biological processes all
tend to increase entropy, and the tendency gives direction to these processes. Changes in
entropy are mathematically related to changes in free energy, which explains why some
reactions proceed in one direction rather than another.
9. Substrate-level: production of ATP molecules via transfer of a phosphate group from an
intermediate high-energy substrate directly to ADP.
Oxidative: production of ATP molecules from the redox reactions of an electron transport
chain
Gylcolysis and Krebs cycle use substrate-level phosphorylation. Electron transport chain
uses oxidative phosphorylation.
10. Fermentation is the chemical breakdown of a substance by bacteria, yeasts, or other
microorganisms, typically involving effervescence and the giving off of heat. Lactic acid
fermentation occurs in some organims like Humans while alcohol fermentation occurs in
organism e.g. yeast. Alcoholic fermentation produces CO2 gas , Lactic acid fermentation
doesn't Both Recycle NADH into NAD+. And obviously the main difference is the
product, one is Ethanol the other is Lactic acid.
11. Lipids – Lipids are broken down into their constituents: glycerol and fatty acids. Glycerol
is converted into dihydroxyacetone phosphate, an intermediate in glycolysis. Fatty acids
are highly reduced molecules that are converted to acetyl CoA in a process called βoxidation. The acetyl CoA can then enter the citric acid cycle and be catabolized to CO2.
Amino Acids—Proteins are hydrolyzed to their amino acid building blocks. After
deamination (removal of the amino group, resulting in ammonia formation), the
catabolites feed into glycolysis or the citric acid cycle at different points. An example is
the amino acid glutamate, which, after deamination, is converted into α-ketoglutarate, an
intermediate in the citric acid cycle.
12. Plants use only visible wavelengths of light. Blue light has more energy than red light.
When an object reflects a color, that is the color it appears. For example, a green leaf will
reflect green light and will absorb all other colors. Photosynthetic plant pigments have the
capability to absorb certain wavelengths (colors) of light & change the light energy to
chemical energy.
The plant pigments are found in chloroplasts on the membranes of the thylakoids.
4 Plant Pigments in Green Plants:
1. Chlorophyll a: Light to medium green. Main photosynthetic pigment.
2. Chlorophyll b: Blue-green. Accessory Pigment.
3. Carotene: Orange. Accessory Pigment.
4. Xanthophyll: Yellow. Accessory Pigment.
Accessory pigments: absorb other colors of light (green) that chlorophyll a can't absorb. They
help boost energy absorption.
Think of plant pigments as being like TV antennas. Each type of pigment absorbs and
uses a different wavelength of light (just as antennas pick up different stations). All the pigments
are linked together, to give the energy they pick up to then energize electrons.
13.
14.
Cyclic
~No PS II is involved. (onlyPS I)
~No oxygen is evolved.
~No NADPH is made.
~ATP is still made.
Noncyclic
~PS I & II both involved.
~Water is split. (photolysis)
~Oxygen produced.
~ATP made.
~NADPH made.
15. During photosynthetic electron transport, hydrogen protons (H+) accumulate in the
thylakoid space, due to splitting of water and transport between PQH2 to Cytf. Increase
in the number of hydrogen protons in the thylakoid space results in increase of proton
gradient. Down flow of protons from high to low concentration along H+ conc. gradient
through ATPase complex provides the energy that allows an ATP synthase enzyme to
produce ATP from ADP + Pi.
16. The calvin cycle also known as the "dark" reaction of photosynthesis. However, this is
misleading because the reaction doesn't have to occur in the dark. It just doesn't need
light in order to occur.
The Calvin cycle takes place in the stroma of the chloroplast.
The calvins cycle relies on the energy(ATP and NADPH) from light dependent reaction
to run.
Basically, the calvins cycle takes the ATP and NADPH produced from the light
dependent reaction to produce carbohydrates.
1)start off with a molecule ribulose biphospate made of 5 carbon atoms
2)a molecule of carbon dioxide is added to this to make a 6 carbon atom
3)in a series of reactions, the 6 carbon molecule is broken in half to form two 3 carbon
molecules called glyceraldehyde-3-phosphate(G3P)
4)one of the G3P molecule is used to make glucose and other carbohydrates while the
other G3P molecule is used to regenerate the original ribulose biphosphate.
5)the cycle repeats again
17. C3 plants are your regular everyday plants, they open their stomata during the day to
breathe in CO2 and release O2. They go through the light and dark reactions normally
because they are not exposed to extremely hot conditions. C4 plants and CAM plants
have devised ways to overcome the rough environment.
C4 plants have 2 separate cells, mesophyll cells and bundle sheath cells. C4 plants use
this method to combat photorespiration, which is when the plants break down glucose to
form CO2 instead building glucose from CO2 and releasing O2. the CO2 enters the
mesophyll cell, and PEP (phosphoenolpyruvate) carboxylase binds the CO2 to PEP to
produce a 4 carbon compound. PEP carboxylase has no affinity for O2, unlike rubisco,
which is why it will bind with the CO2 instead of the O2 in the plant. so the 4 carbon
compound (could be oxaloacetate, malate) is then transferred through plasmodesmata to
the bundle sheath cells, where it is broken down to CO2 and pyruvate. and the CO2
enters the calvin cycle to produce glucose. the pyruvate is then sent back to the mesophyll
cells and with the use of ATP is converted to back to PEP so that it can combine with
more CO2.
CAM plants also developed because of photorespiration. the difference between CAM
and C4 is that CAM plants have only one cell, and they they open their stomata at night
and close them during the day. the CO2 they take in at night is incorporated into 4 carbon
compounds (organic acids) and is sent off to the calvin cycle during the day to make
glucose. CAM plants are usually found in dry desert areas.
18. For oxygenic photosynthesis, both photosystems I and II are required. The photosystem I
was named "I" since it was discovered before photosystem II, but this does not represent
the order of the electron flow.
When photosystem II absorbs light, electrons in the reaction-center chlorophyll are
excited to a higher energy level and are trapped by the primary electron acceptors. To
replenish the deficit of electrons, electrons are extracted from water by a cluster of four
Manganese ions in photosystem II and supplied to the chlorophyll via a redox-active
tyrosine.
Photoexcited electrons travel through the cytochrome b6f complex to photosystem I via
an electron transport chain set in the thylakoid membrane. This energy fall is harnessed,
(the whole process termed chemiosmosis), to transport hydrogen (H+) through the
membrane, to the lumen, to provide a proton-motive force to generate ATP. The protons
are transported by the plastoquinone. If electrons only pass through once, the process is
termed noncyclic photophosphorylation.
When the electron reaches photosystem I, it fills the electron deficit of the reaction-center
chlorophyll of photosystem I. The deficit is due to photo-excitation of electrons that are
again trapped in an electron acceptor molecule, this time that of photosystem I.
19. Carotenoids are a group of accessory pigments which occur in all photosynthetic
organisms. They contain about forty carbon atoms, often without oxygen atoms and are
fat soluble. They are chemically unrelated to chlorophyll and consist of rings connected
by long chains of carbon atoms. They absorb light maximally at wavelengths between
460 and 550 nm and are therefore yellow, red or orange in colour as they reflect the
wavelengths in this part of the spectrum. Carotenoids are found in all photosynthetic
organisms. The accessory pigments play an important role in photosynthesis as they
increase the range of wavelengths which the photosynthetic machinery of a plant can
absorb. They thus tap sources of light energy which would otherwise be unused by the
plant, if the plant relied only on chlorophyll a as a light harvesting pigment.
20. Light gets into the upper layers of the ocean and that’s where the process of
photosynthesis traps that light and converts it into energy — into carbohydrates, that the
rest of the food chain relies on. So it’s really the idea is that you have to maintain plant
life, algae has to maintain itself in the upper layers of the ocean because once you get
further down into the depths of the ocean, first of all red light gets absorbed which is why
the oceans look blue and green-y colours. Light does get down there but it has to
maintain itself up in the high levels. Some of the seaweeds are red seaweeds, that’s right
and that’s a kind of branch of the algae. They have different types of pigment that do—
they use up the green and the blue lights and red is reflected back and that’s why they
look red.
21. Fifty percent of the protein in leaves of plants is composed of rubisco, the enzyme
responsible for the first major step in carbon fixation during the initial phase of the
Calvin cycle. Without rubisco, carbon dioxide cannot be converted to energy-rich
molecules in plants. The enzyme rubisco catalyzes the reaction of CO2 and RuBP to form
3PG, which is necessary for the cycle to continue to its next phase, reduction and sugar
production. Since all life on earth depends directly or indirectly on primary producers,
which form the base of the food chain, the claim that “rubisco is the most abundant
protein on the planet” seems convincing.
22. Nathan is correct. Both photosynthesis and respiration are reduction-oxidation reactions.
Respiration is the process by which organisms oxidize organic molecules (sugars) and
obtain energy (APT) from the breaking of chemical bonds, with CO2 and water as the
end products. Photosynthesis is the opposite chemical process, where carbon dioxide and
water combine with the input of light energy to form sugars, with oxygen being released
as an end product of this reaction. The two chemical processes rely upon one another,
with the molecules necessary for one reaction coming from the end products of the
opposite reaction. They are integral parts of one large cycle, and plant life could not exist
without both photosynthesis and respiration.
23. a) The control reaction mixture is “complete, pH 3.8, minus chloroplasts”
b) Luciferase activity (light emission)
Reaction mixture Raw data Corrected data
Complete, pH 3.8 141 134
Complete, pH 7.0 12 5
Complete, pH 3.8 - Pi 12 5
“ “ - ADP 4 -3 “ “ - Mg2+ 60 53 “ “ - chloroplasts 7 0
c) This experiment shows that the greatest production of ATP, as measured by luciferase
activity, occurs when all reaction components (Pi, ADP, Mg2+, and chloroplasts) are
present and under conditions of high acidity (pH 3.8). A more neutral pH (7.0) and the
lack of phosphate ions both reduce ATP production. Removing Mg2+ under conditions
of high acidity improves ATP production, but the elimination of ADP causes negative
ATP production.
d) The formation of ATP from ADP requires a phosphate ion, as suggested by the names
of these two molecules: “adenosine tri-phosphate,” and “adenosine di-phosphate.”
e) The Calvin cycle’s carbon fixation phase of photosynthesis requires ATP in order to
reduce 3PG to G3P, and this ATP is normally derived from the light reactions of
photosynthesis. In the absence of ADP in the reaction mixture, ATP cannot be produced.
ATP is, therefore, consumed rather than produced, hence the negative ATP production in
the absence of ADP.
f) The free energy driving the production of ATP ultimately comes from the sun. The
energy from the sun, in the form of a photon, is absorbed by the molecule which causes
its energy level to jump to an excited state. This is the basis for the hydrogen
concentration gradient that provides the energy for ATP production in cells.
1. B
2. D
3. A
4. B
5. B
6. A
7. A
8. E
9. C
10. D
11. E
12. C
13. E
14. E
15. E
16. E
17. C