Chapter 10: Photosynthesis

• Photosynthesis: the conversion of 1. Photosynthesis converts light energy to the chemical energy of food
light energy to chemical energy by 1. The original chloroplast is believed to have been a photosynthetic prokaryote that lived inside a eukaryotic cell.
plants. 2. Leaves are the major sites of photosynthesis in most plants. The color of the leaf is from chlorophyll, the green pigment
• Autotrophs: “self-feeders” who located within chloroplasts. It is the light energy absorbed by chlorophyll that drives the synthesis of organic molecules
sustain themselves without eating in the chloroplast. Chloroplasts are found mainly in the cells of the mesophyll, the tissue in the interior of the leaf.
anything derived from other living 3. Carbon dioxide enters the leaf, and oxygen exits, by way of microscopic pores called stomata. A typical mesophyll cell
beings. has about 30-40 chloroplasts.
• Heterotrophs: obtain their organic 4. An envelope of two membranes encloses the stroma, the dense fluid within a chloroplast. An elaborate system of
material by consuming other interconnected membranous sacks called thylakoids segregates the stroma from the thylakoid space. In some cells,
organisms. thylakoid sacs are stacked in columns called grana. Chlorophyll resides in the thylakoid membranes.
5. We can summarize the complex series of chemical reactions in photosynthesis with this chemical equation:
6 CO2 + 12 H2O + Light energy → C6H12O2 +O2 + 6 H2O
6. O2 give off by plants is derived from H2O. The chloroplast splits water into hydrogen and oxygen. Because the electrons
increase in potential energy as they move from water to sugar, this process require energy (from light).
7. The two stages of photosynthesis are known as the light reactions, and the Calvin cycle.
1. The light reactions are the steps of photosynthesis that convert solar energy to chemical energy. Water is split,
providing a source of electrons and protons and giving off O2 as a by-product. Light absorbed by chlorophyll
drives a transfer of the electrons and hydrogen ions from water to an acceptor called NADP+, a molecule similar
to NAD+. The light reactions also generate ATP, using chemiosmosis to power photophosphorylation.
2. The Calvin cycle begins by incorporating CO2 from the air into organic molecules already present in the
chloroplast (carbon fixation). The Calvin cycle then reduces the fixed carbon to carbohydrate by the addition of
electrons from NADPH. The cycle requires energy in the form of ATP. Thus, it is the Calvin cycle that makes
sugar, but it can do so only with the help of the NADPH and ATP produced by the light reactions.
3. The thylakoids of the chloroplast are the sites of the light reactions, while the Calvin cycle occurs in the stroma.
• Wavelength: the distance between 2. The light reactions convert solar energy to the chemical energy of ATP and NADPH
crests of electromagnetic waves. 1. Chloroplasts are chemical factories powered by the sun.
• Visible light can be detected as 2. Light is a form of energy known as electromagnetic energy, which exists as both a particle (photons) and a wave.
various colors by the human eye (380 3. The amount of energy a photon carries is inversely related to the wavelength of the light: the shorter the wavelength, the
nm-750 nm in wavelength) greater the energy of each photon of that light.
• The ability of a pigment to absorb 4. Substances that absorb visible light are known as pigments. Different pigments absorb light of different wavelengths.
various wavelengths of light can be The color we see is the color most reflected or transmitted by the pigment. We see green when we look at a leaf because
measured with spectrophotometer. chlorophyll absorbs violet-blue and red light while transmitting and reflecting green light.
• Absorption spectrum: A graph 5. The active spectrum for photosynthesis does not exactly match the absorption spectrum of chlorophyll a, because
plotting a pigment’s light absorption accessory pigments with different absorption spectra are also photosynthetically important in chloroplasts and broaden
verses wavelength. the spectrum of colors that can be used for photosynthesis. The accessory pigments include chlorophyll b and
carotenoids.
• Chlorophyll a participates directly in
6. When a molecule absorbs a photon of light, one of the molecule’s electrons is elevated to an orbital where it has more
the light reactions.
potential energy. When the electron is in its normal orbital, the pigment molecule is said to be in its ground state.
• Active spectrum: plots the relative Absorption of a photon boosts an electron to an orbital of higher energy, and the pigment molecule is then said to be in
effectiveness of different an excited state. The excited state, like all high-energy states, is unstable. As excited electrons fall back to the ground
wavelengths for photosynthesis. state, photons are given off. This afterglow is called fluorescence. If a solution of chlorophyll isolated from chloroplasts
is illuminated, it will fluoresce in the red-orange part of the spectrum and also give off heat.
7. A photosystem is composed of a protein complex called a reaction-center complex surrounded by several light
harvesting complexes. Each light-harvesting complex consists of various pigment molecules bound to proteins. The
reaction-center complex contains a molecule capable of accepting electrons (primary electron acceptor) and a very
special pair of chlorophyll a molecules.
8. The solar-powered transfer of an electron from the reaction-center chlorophyll a pair to the primary electron acceptor is
the first step of the light reactions.
9. The thylakoid membrane is populated by two types of photosystems that cooperate in the light reactions of
photosynthesis. They are called photosystem II (PS II) and photosystem I (PS I). They were named in order of their
discovery, but photosystem II functions first in the light reactions. The reaction-center chlorophyll a of photosystem II is
know as P680 because this pigment is best at absorbing light having a wavelength of 680 nm. The chlorophyll a at the
reaction-center complex of photosystem I is called P700 because it most effectively absorbs light of wavelength 700
nm.
10. Linear electron flow: a flow of electrons through the photosystems and other molecular components built into the
thylakoid membrane.
1. A photon of light strikes a pigment molecule in a light-harvesting complex, boosting one of its electrons to a
higher energy level. As this electron falls back to its ground state, an electron in a nearby pigment molecule is
simultaneously raised to an exited state. This process continues, with the energy being relayed to other pigment
molecules until it reaches the P680 pair of chlorophyll a molecules in the PS II reaction-center complex. It excites
an electron in this pair of chlorophylls to a higher energy state.
2. This electron is transferred from the excited P680 to the primary electron acceptor. We can refer to the resulting
form of P680, missing an electron, as P680+.
3. An enzyme catalyzes the splitting of a water molecule into two electrons, two hydrogen ions, and an oxygen
atom. The electrons as supplied one by one two the P680+ pair, each electron replacing one transferred to the
primary electron acceptor. (P680+ is the strongest biological oxidizing agent known.) The oxygen atom
immediately combines with an oxygen atom generated by the splitting of another water molecule, forming O2.
4. Each photoexcited electron passes from the primary electron acceptor of PS II to PS I via an electron transport
chian, the components of which are similar to those of the electron transport chain that functions in cellular
respiration. The electron transport chain between PS II and PS I is made of the electron carrier plastoquinone
(Pq), a cytochrome complex, and a protein called plastocyanin (Pc).
5. The exergonic “fall” of electrons to a lower energy level provides energy for the synthesis of ATP. As electrons
pass through the cytochrome complex, the pumping of protons builds a proton gradient that is subsequently used
in chemiosmosis.
6. Meanwhile, light energy was transferred via light-harvesting complex pigments to the PS I reaction-center
complex, exciting an electron of the P700 pair of chlorophyll a molecules located there. The photoexcited
electron was then transferred to PS I’s primary electron acceptor, and the P700+ can now accept the electron that
reaches the bottom of the electron transport chain from PS II.

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 Chapter 10: Photosynthesis

7. Photoexcited electrons are passed in a series of redox reactions from the primary electron acceptor of PS I down a
second electron transport chain through the protein ferredoxin (Fd). This chain does not create a proton gradient
and thus does not produce ATP.
8. The enzyme NADP+ reductase catalyzes the transfer of electrons from Fd to NADP+. Two electrons are required
for its reduction to NADPH. This molecule is at a higher energy level than water, and its electrons are more
readily available for the reactions of the Calvin cycle than were those of water.
11. Cyclic electron flow: which uses photosystem I but not photosystem II. There is no production of NADPH and no
release of oxygen. Cyclic flow does, however, generate ATP. Several of the currently existing groups of photosynthetic
bacteria are known to have photosystem I but not photosystem II. Evolutionary biologists believe that these bacterial
groups are in which photosynthesis first evolved, in a form similar to cyclic electron flow. Cyclic electron flow may be
photoprotective, protecting cells from light-induced damage.
12. Chloroplasts and mitochondria generate ATP by the same basic mechanism: chemiosmosis. Although the spatial
organization of chemiosmosis differs slightly between chloroplasts and mitochondria, it is easy to see similarities in the
two.
13. Notice that NADPH, like ATP, is produced on the side of the membrane facing the stroma, where the Calvin cycle
reactions take place.
3. The Calvin cycle uses ATP and NADPH to convert CO2 to sugar.
1. The Calvin cycle is similar to the citric acid cycle in that a starting material is regenerated after molecules enter and
leave the cycle. The cycle spends ATP as an energy source and consumes NADPH as a reducing power for adding high-
energy electrons to make the sugar.
2. The carbohydrate produced directly from the Calvin cycle is actually not glucose, but a three carbon sugar
(glyceraldehyde-3-phosphate). For the net synthesis of one molecule of G3P, the cycle must take place three times,
fixing three molecules of CO2. The Calvin cycle can be divided into three phases.
1. Carbon fixation: The Calvin cycle incorporates each CO2 molecule, one at a time, by attaching it to a five-carbon
sugar named ribulose bisphosphate. The enzyme that catalyzes this first step is RuBP carboxylase, or rubisco.
The product of the reaction then splits into two molecules of 3-phosphorglycerate (for each CO2 fixed).
2. Reduction: Each molecule of 3-phosphorglycerate receives an additional phosphate group from ATP, forming 1,3-
biphosphorglycerate, which is reduced by NADPH and also loses phosphate group, becoming glyceraldehyde-3-
phosphate. One molecule exits the cycle; the other five must be recycled to regenerate the three molecules of
RuBP.
3. Regeneration of CO2 acceptor RuBP. In a complex seiries of reactions, the carbon skeletons of five molecules of
G3P are rearranged by the last steps of the Calvin cycle into three molecules of RuBP.
3. Alternative mechanisms of carbon fixation have evolved in hot, arid climates
1. The problem of dehydration is important to plants. Solutions often involve trade-offs. An important example is
the compromise between photosynthesis and the prevention of excessive water lost from the plast.
2. On a hot, dry day, most plants close their stomata, a response that conserves water. This response also reduces
photosynthetic yield by limiting access to CO2, which favors an apparently wasteful process called
photorespiration.
3. In most plants, initial fixation of carbon occurs via rubisco. Such plants are called C3 plants because the first
organic product of carbon fixation is a three-carbon compound. However, when CO2 becomes scarce, rubisco
adds O2 to the Calvin cycle instead. The product splits, and a two carbon-compound leaves the chloroplast, where
it is further degraded into CO2 by peroxisomes and mitochondria. The process is called photorespiration because
it occurs in the light and consumes O2 while producing CO2.
4. Photorespiration is evolutionary baggage—a metabolic relic from a much earlier time when the atmosphere had
less O2 and more CO2.
5. In some cases, photorespiration plays a protective role in plants, neutralizing the otherwise damaging products of
the light reactions, which build up when a low CO2 concentration limits the progress of the Calvin cycle.
6. C4 plants are so named because they preface the Calvin cycle with an alternative mode of carbon fixation that
forms a four-carbon compound as its first product.. In C4 plants, there are two distinct types of photosynthetic
cells: bundle-sheath cells and mesophyll cells.
1. Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the leaf.
2. Between the bundle sheath and the leaf surface are the more loosely arranged mesophyll cells.
3. The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells. However, the cycle is preceded
by incorporation of CO2 into organic compounds in the mesophyll cells.
1. The first step is carried out by an enzyme present only in mesophyll cells called PEP carboxylase,
which adds CO2 to phosphoenolpyruvate (PEP), forming oxaloacetate. PEP carboxylase has a much
higher affinity to CO2 than rubisco and no affinity for O2.
7. Crassulacean acid metabolism (CAM):
1. The mesophyll cells of CAM plants store the organic acids they make during the night in their vacuoles
until morning, when the stomata close. During the day, when the light reactions can supply ATP and
NADPH for the Calvin cycle, CO2 is released from the organic acids made the night before to become
incorporated into the sugar in the chloroplasts.

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 Chapter 11: Cell Communication

1. External signals are converted to responses within the cell.

1. Signal transduction pathway: the process by which a signal on a cell’s surface is converted to a specific cellular
response. The molecular details of signal transduction between yeast and mammals are similar, suggesting that early
versions of the cell-signaling mechanisms used today evolved well before the first multicellular creatures appeared on
Earth.
2. Cells in a multicellular organism usually communicate via chemical messengers targeted for cells that may or may not
be immediately adjacent.
1. Both animals and plants have cell junctions that directly connect the cytoplasms of adjacent cells.
2. Animal cells may communicate via direct contact between membrane-bound cell-surface molecules (cell-cell
recognition).
3. Messenger molecules are also used. Local regulators only travel short distances. Hormones are used for long-
distance signaling.
3. Earl W. Sutherland (who won the Nobel prize in 1971) investigated how the animal hormone epinephrine stimulates the
breakdown of glycogen. His work suggested that the signal transduction pathway can be broken into three stages:
1. Reception: A signaling molecule binds to a receptor protein located at the cell’s surface or inside the cell.
2. Transduction: The binding of the signaling molecule changes the receptor protein. The transduction stage
converts the signal to a form that can bring about a specific cellular response. Transduction sometimes occurs in a
single step but more often requires a sequence of changes in a series of different molecules (relay molecules.)
3. Response: The transduced signal finally triggers a specific cellular response.
2. Reception: A signaling molecule binds to a receptor protein, causing it to change shape.
• Ligand: a molecule that specifically 1. A signaling molecule behaves as a ligand.
binds to another, usually larger, 2. Most signal receptors are plasm membrane proteins. For many receptors, their shape change directly activates the
molecule. receptor, enabling it to interact with other cellular molecules.
• G-protein: a protein that binds the 3. Most water-soluble signaling molecules bind to specific sites on receptor proteins embedded in the cell’s plasma
energy-rich molecule GTP. membrane. There are three major types of membrane receptors:
1. G protein-coupled receptors: A plasm membrane receptor that works with the help of a G-protein. Many
different signaling molecules use G protein-coupled receptors. G protein-coupled receptor proteins are
remarkably similar in structure; they all have seven α helices spanning the membrane.
1. Loosely attached to the cytoplasmic side of the membrane, the G protein functions as a molecular switch
that is either on or off. When GDP is bound to the G protein, the G protein is inactive.
2. When the appropriate signaling molecule binds to the extracellular side of the receptor, the receptor is
activated and changes shape. Its cytoplasmic side then binds an inactive G protein, causing a GTP to
displace the GDP. This activates the G protein.
3. The activated G protein dissociates from the receptor, diffuses along the membrane, and then binds to an
enzyme, altering the enzyme’s shape and activity. When the enzyme is activated, it can trigger the next step
in a pathway leading to a cellular response.
4. The G-protein then hydrolyses the GTP to GDP and a phosphate ion, causing the G-protein to become
inactive and detach from the enzyme, which returns to its original shape.
2. Receptor tyrosine kinases belong to a major class of plasm membrane receptors characterized by having
enzymatic activity. Receptor tyrosine kinases are membrane receptors that attach phosphates to tyrosines.
1. Many receptor tyrosine kinases have an extracellular, an α helix spanning the membrane, and an
intracellular tail containing multiple tyrosines. Before the signal molecule binds, the receptors exist as
individual polypeptides.
2. The binding of a signaling molecule causes two receptor polypeptides to associate closely with each other,
forming a dimer.
3. Dimerization activates the tyrosine kinase region of each polypeptide.
• Kinase: an enzyme that catalyzes the 3. Ion channel receptors: a ligand-gated ion channel is a type of membrane receptor containing a region that can
transfer of phosphate groups. act as a “gate” when the receptor changes shape. When a signaling molecule binds as a ligand to the receptor
protein, the gate opens or closes, allowing or blocking the flow of specific ions through a channel in the receptor.
1. When the ligand binds to the receptor and the gate opens, specific ions can flow through the channel and
rapidly change the concentration of that particular ion inside the cell. This change may directly affect the
activity of the cell in some way. When the ligand dissociates from this receptor, the gate closes and ions no
longer enter the cell.
2. Some gated ion channels are controlled by electrical signals instead of ligands.
4. Intracellular receptor proteins are found either in the cytoplasm or nucleus of target cells. A chemical messenger must
pass through the target cell’s plasma membrane to reach these receptors. Thus, they must be hydrophobic. Examples
include steroids and the thyroid hormones. The hormone binds to the receptor protein, activating it.
5. Specific proteins called transcription factors control which genes are turned on in particular cell at particular time.
3. Tranduction: Cascades of molecular interactions relay signals from receptors to target
• Protein kinase: the general name for molecules in the cell.
an enzyme that transfers phosphate 1. The transduction stage of cell signaling is usually a multistep pathway, which can greatly amplify a signal and provide
groups from ATP to a protein. more opportunities for coordination and regulation than simpler systems do.
• Protein phosphatases: enzymes that 2. Like falling dominoes, the signal-activated receptor activates another molecule, which activates yet another molecule,
can rapidly remove phosphate groups and so on, until the protein that produces the final cellular response is activated. The relay molecules are often proteins.
from proteins, a process called At each step, the signal is transduced into a different form, commonly a shape change in a protein.
3. The phosphorylation/dephosphorylation system acts a molecular switch in the cell, turning activities on or off as
required.
4. Many signaling pathways also involve small, nonprotein, water-soluble molecules or ions called second messengers.
These readily spread throughout the cell by diffusion. Second messengers participate in pathways initiated by both G
protein-coupled receptors and receptor tyrosine kinases.
5. The two most widely used second messengers are cyclic AMP and calcium ions.
1. The binding of epinephrine to the plasma membrane of a liver cell elevates the cytosolic concentration of cyclic
AMP (cAMP). An enzyme embedded in the plasma membrane, adenylyl cyclase, converts ATP to cAMP in
response to an extracellular signal.
2. Another enzyme, phosphodiesterase, converts cAMP to AMP.
3. The immediate affect of cAMP is usually the activation of a serine/threonine kinase called protein kinase A.
4. Further regulation of cell metabolism is provided by other G-protein systems that inhibit adenylyl cyclase.
5. Many signaling molecules in animals induce responses in their target cells via signal transduction pathways that
increase the cytosolic concentration of calcium ions. Calcium is even more widely used that cAMP as a second

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 Chapter 11: Cell Communication

messenger. The pathways leading to calcium release involve still other second messengers, inositol
trisphosphate (IP3) and diacylglycerol (DAG). These two messengers are produced by cleavage of a certain
kind of phosopholipid in the plasma membrane.
4. Response: Cell signaling leads to the regulation of transcription or cytoplasmic activities.
1. Ultimately, a signal transduction pathway leads to the regulation of one or more cellular activities. The response at the
end of the pathway may occur in the nucleus of the cell or in the cytoplasm.
2. Many signaling pathways ultimately regulate protein synthesis, usually by turning specific genes on or off in the
nucleus. The final activated molecule in a signaling pathway may function as a transcription factor.
3. Sometimes a signaling pathway may regulate the activity of proteins rather than their synthesis, directly affecting
proteins that function outside the nucleus.
4. In addition to the regulation of enzymes, signaling events may also affect other cellular attributes, such as overall cell
shape.
5. Signaling pathways with numerous steps between a signaling event at the cell surface and the cell’s response have two
important benefits: They amplify the signal and they provide different points at which a cell’s response can be regulated.
1. Elaborate enzyme cascades amplify the cell’s response to a signal. At each catalytic step in the cascade, the
number of activated products is much greater than the preceding step.
2. Different kinds of cells have different collections of proteins: The response of a particular cell to a signal depends
on its particular collectrion of signal receptor proteins, relay proteins, and proteins needed to carry out the
response.
6. Recent research suggests the efficiency of signal transduction may in many cases be increased by the presence of
scaffolding proteins, large relay proteins to which several other relay proteins are simultaneously attached.
7. Some proteins may participate in more than one pathway, either in different cell types or in the same cell at different
times or under different conditions.
8. A key to a cell’s continuing receptiveness to regulation by signaling is the reversibility of the changes that signals
produce.
5. Apoptosis (programmed cell death) integrates multiple cell-signaling pathways.
1. Cells that are infected or damaged or that have simply reached the end of their functional life span often enter a program
of controlled cell suicide called apoptosis.
2. During this process, cellular agents chop up the DNA and fragment the organelles and other cytoplasmic components.
The cell shrinks and becomes lobed, and the cell’s parts are packaged up in vesicles that are engulfed and digested by
specialized scavenger cells, leaving no trace.
• Proteases: enzymes that cut up 3. Most proteins involved in apoptosis are continually present in cells, but in inactive form; thus, protein activity is
proteins. The main proteases of regulated rather than protein synthesis.
apoptosis are called caspases. 4. In humans and other mammals, several different pathways, involving about 15 different caspases, can carry out
• Nucleases: enzymes that cut up apoptosis.
DNA. 1. One major pathway involves mitochondrial proteins. Apoptotic proteins can form molecular pores in the
mitochondrial outer membrane, causing it to leak and release proteins that promote apoptosis.
2. At key points in the apoptotic program, proteins integrate signals from several different sources and can send a
cell down an apoptotic pathway.
3. When a death-signaling ligand occupies a cell-surface receptor, this binding leads to activation of caspases are
other enzymes that carry out apoptosis, without involving the mitochondrial pathway.
4. Two other types of alarm signals originate from inside the cell. One comes from the nucleus, generated when the
DNA has suffered irreparable damage, and a second comes from the endoplasmic reticulum when excessive
protein misfolding occurs.
5. A built-in cell suicide mechanism is essential to development and maintenance in all animals.

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