UNIT 2 - The cell

Surface-to-volume (S-to-V) ratio

(surface area ÷ volume]

The diffusion of solutes across a synthetic membrane

. Each of the large arrows under the diagrams shows the net diffusion of the dye molecules of that color.

The functions of cell division.

1)Asexual reproduction. An amoeba, a single-celled eukaryote, is dividing into two cells. Each new cell will be an individual organism (LM). 2) Growth and development. This micrograph shows a sand dollar embryo shortly after the fertilized egg divided, forming two cells (LM) 3) Tissue renewal. These dividing bone marrow cells will give rise to new blood cells (LM).

The control of cellular respiration

Allosteric enzymes at certain points in the respiratory pathway respond to inhibitors and activators that help set the pace of glycolysis and the citric acid cycle. Phosphofructokinase, which catalyzes an early step in glycolysis (see Figure 9.9, step 3), is one such enzyme. It is stimulated by AMP (derived from ADP) but is inhibited by ATP and by citrate. This feedback regulation adjusts the rate of respiration as the cell's catabolic and anabolic demands change.

What happens as the cell prepares to divide?

As a cell prepares to divide, however, the chromosomes coil (condense) further, becoming thick enough to be distinguished under a microscope as separate structures.

Structural Network

As with mitochondria, the static and rigid appearance of chloroplasts in micrographs or schematic diagrams cannot accurately depict their dynamic behavior in the living cell. Their shape is changeable, and they grow and occasionally pinch in two, reproducing themselves. They are mobile and, with mitochondria and other organelles, move around the cell along tracks of the cytoskeleton, a structural network we will consider in Concept 6.6.

Small Molecules and Ions as Second Messengers: Not all components of signal transduction pathways are proteins. Many signaling pathways also involve small, nonprotein, water-soluble molecules or ions called second messengers. (The pathway's "first messenger" is considered to be the extracellular signaling molecule—the ligand—that binds to the membrane receptor.)

Because second messengers are small and also water-soluble, they can readily spread throughout the cell by diffusion. For example, as we'll see shortly, a second messenger called cyclic AMP carries the signal initiated by epinephrine from the plasma membrane of a liver or muscle cell into the cell's interior, where the signal eventually brings about glycogen breakdown.

The catabolism of various molecules from food

Carbohydrates, fats, and proteins can all be used as fuel for cellular respiration. Monomers of these molecules enter glycolysis or the citric acid cycle at various points. Glycolysis and the citric acid cycle are catabolic funnels through which electrons from all kinds of organic molecules flow on their exergonic fall to oxygen.

As diagrammed in Figure 9.6, glycolysis and then pyruvate oxidation and the citric acid cycle are the catabolic pathways that break down glucose and other organic fuels.

Glycolysis, which occurs in the cytosol, begins the degradation process by breaking glucose into two molecules of a compound called pyruvate.

isotonic

If a cell without a cell wall, such as an animal cell, is immersed in an environment that is isotonic to the cell (iso means "same"), there will be no net movement of water across the plasma membrane

Phagocytosis

In phagocytosis, a cell engulfs a particle by extending pseudopodia (singular, pseudopodium) around it and packaging it within a membranous sac called a food vacuole. The particle will be digested after the food vacuole fuses with a lysosome containing hydrolytic enzymes (see Figure 6.13).

peripheral proteins

Peripheral proteins are not embedded in the lipid bilayer at all; they are loosely bound to the surface of the membrane, often to exposed parts of integral proteins (see Figure 7.3).

In addition to its role in energy coupling, ATP is also one of the nucleoside triphosphates used to make RNA (see Figure 5.23).

The bonds between the phosphate groups of ATP can be broken by hydrolysis. When the terminal phosphate bond is broken by addition of a water molecule, a molecule of inorganic phosphate (HOPO3 2- , abbreviated ~P i throughout this book) leaves the ATP, which becomes adenosine diphosphate, or ADP (Figure 8.9b). The reaction is exergonic and releases 7.3 kcal of energy per mole of ATP hydrolyzed: ATP + H2O S ADP + ~P i ∆G = -7.3 kcal/mol (-30.5 kJ/mol)

Why leaves are green: interaction of light with chloroplasts:

The chlorophyll molecules of chloroplasts absorb violetblue and red light (the colors most effective in driving photosynthesis) and reflect or transmit green light. This is why leaves appear green.

TEM of a plasma membrane.

The plasma membrane, here in a red blood cell, appears as a pair of dark bands separated by a light band.

A scaffolding protein.

The scaffolding protein shown here simultaneously binds to a specific activated membrane receptor and three different protein kinases. This physical arrangement facilitates signal transduction by these molecules.

magnification

Three important parameters in microscopy are magnification, resolution, and contrast. Magnification is the ratio of an object's image size to its real size. Light microscopes can magnify effectively to about 1,000 times the actual size of the specimen; at greater magnifications, additional details cannot be seen clearly

Since ATP formation from ADP and ~P i is not spontaneous, free energy must be spent to make it occur. Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic process of making ATP. Plants also use light energy to produce ATP.

Thus, the ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways.

Cells from duckweed (Spirodela oligorrhiza), a floating plant (colorized TEM)

Unicellular green alga Chlamydomonas (above, colorized SEM; right, colorized TEM)

isotonic

Water diffuses across the membrane, but at the same rate in both directions. In an isotonic environment, the volume of an animal cell is stable (Figure 7.12a)

After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules. Glycolysis releases less than a quarter of the chemical energy in glucose that can be harvested by cells; most of the energy remains stockpiled in the two molecules of pyruvate.

When O2 is present, the pyruvate in eukaryotic cells enters a mitochondrion, where the oxidation of glucose is completed. In aerobically respiring prokaryotic cells, this process occurs in the cytosol. (Later in the chapter, we'll discuss what happens to pyruvate when O2 is unavailable or in a prokaryote that is unable to use O2.)

Chromosomes

Within the nucleus, the DNA is organized into discrete units called chromosomes, structures that carry the genetic information. Each chromosome contains one long DNA molecule associated with many proteins.

A highly condensed, duplicated human chromosome (SEM).

figure 12.4

What do biologists use to study cells?

microscopes and the tools of biochemistry

(a) Transport work: ATP phosphorylates transport proteins, causing a shape change that allows transport of solutes.

(b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed, causing a shape change that walks the motor protein forward.

Flow of Genetic Information in the Cell: DNA -> RNA -> Protein (Chapters 5-7)

1)In the nucleus, DNA serves as a template for the synthesis of mRNA, which moves to the cytoplasm. (See Figures 5.22 and 6.9.) 2)mRNA attaches to a ribosome, which remains free in the cytosol or binds to the rough ER. Proteins are synthesized. (See Figures 5.22 and 6.10.) 3)Proteins and membrane produced by the rough ER flow in vesicles to the Golgi apparatus, where they are processed. (See Figures 6.15 and 7.9.) 4) Transport vesicles carrying proteins pinch off from the Golgi apparatus. (See Figure 6.15.) 5) Some vesicles merge with the plasma membrane, releasing proteins by exocytosis. (See Figure 7.9.) 6) Proteins synthesized on free ribosomes stay in the cell and perform specific functions; examples include the enzymes that catalyze the reactions of cellular respiration and photosynthesis. (See Figures 9.7, 9.9, and 10.19.)

Steroid hormone interacting with an intracellular receptor:

1)The steroid hormone aldosterone passes through the plasma membrane. 2) Aldosterone binds to a receptor protein in the cytoplasm, activating it. 3) The hormonereceptor complex enters the nucleus and binds to specific genes. 4) The bound protein acts as a transcription factor, stimulating the transcription of the gene into mRNA. 5) The mRNA is translated into a specific protein.

1)Many receptor tyrosine kinases have the structure depicted schematically here. Before the signaling molecule binds, the receptors exist as individual units referred to as monomers. Notice that each monomer has an extracellular ligand-binding site, an α helix spanning the membrane, and an intracellular tail containing multiple tyrosines.

2) The binding of a signaling molecule (such as a growth factor) causes two receptor monomers to associate closely with each other, forming a complex known as a dimer, in a process called dimerization. (In some cases, larger clusters form. The details of monomer association are a focus of current research.)

1) Here we show a ligand-gated ion channel receptor in which the channel remains closed until a ligand binds to the receptor.

2) When the ligand binds to the receptor and the channel 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

1)Attached but able to move along the cytoplasmic side of the membrane, a G protein functions as a molecular switch that is either on or off, depending on whether GDP or GTP is attached —hence the term G protein. (GTP, or guanosine triphosphate, is similar to ATP.) When GDP is bound to the G protein, as shown above, the G protein is inactive. The receptor and G protein work together with another protein, usually an enzyme.

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

3)Dimerization activates the tyrosine kinase region of each monomer; each tyrosine kinase adds a phosphate from an ATP molecule to a tyrosine that is part of the tail of the other monomer.

4) Now that the receptor is fully activated, it is recognized by specific relay proteins inside the cell. Each such protein binds to a specific phosphorylated tyrosine, undergoing a resulting structural change that activates the bound relay protein. Each activated protein triggers a transduction pathway, leading to a cellular response.

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. Once activated, the enzyme can trigger the next step leading to a cellular response. Binding of signaling molecules is reversible: Like other ligands, they bind and dissociate many times. The ligand concentration outside the cell determines how often a ligand is bound and initiates signaling.

4) The changes in the enzyme and G protein are only temporary because the G protein also functions as a GTPase enzyme—in other words, it then hydrolyzes its bound GTP to GDP and . Now inactive again, the G protein leaves the enzyme, which returns to its original state. The G protein is now available for reuse. The GTPase function of the G protein allows the pathway to shut down rapidly when the signaling molecule is no longer present.

GLYCOLYSIS: Energy Payoff Phase: The energy payoff phase occurs after glucose is split into two three-carbon sugars. Thus, the coefficient 2 precedes all molecules in this phase.

6)Two sequential reactions: (1) G3P is oxidized by the transfer of electrons to NAD+, forming NADH. (2) Using energy from this exergonic redox reaction, a phosphate group is attached to the oxidized substrate, making a high-energy product. 7)The phosphate group is transferred to ADP (substrate-level phosphorylation) in an exergonic reaction. The carbonyl group of G3P has been oxidized to the carboxyl group (—COO-) of an organic acid (3-phosphoglycerate). 8) This enzyme relocates the remaining phosphate group. 9)Enolase causes a double bond to form in the substrate by extracting a water molecule, yielding phosphoenolpyruvate (PEP), a compound with a very high potential energy 10)The phosphate group is transferred from PEP to ADP (a second example of substrate-level phosphorylation), forming pyruvate

The Structure and Hydrolysis of ATP

ATP (adenosine triphosphate) was introduced when we discussed the phosphate group as a functional group (see Concept 4.3). ATP contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups (the triphosphate group) bonded to it (Figure 8.9a).

Among these are most of the proteins that, in turn, regulate cell division.

Abnormal activity of such a kinase can cause abnormal cell division and contribute to the development of cancer.

There are checkpoints in addition to those in G1, G2, and M. For instance, a checkpoint in S phase stops cells with DNA damage from proceeding in the cell cycle.

And, in 2014, researchers presented evidence for another checkpoint between anaphase and telophase that ensures anaphase is completed and the chromosomes are well separated before cytokinesis can begin, thus avoiding chromosomal damage.

The hydrophilic passageways provided by these proteins can allow water molecules or small ions to diffuse very quickly from one side of the membrane to the other.

Aquaporins, the water channel proteins, facilitate the massive levels of diffusion of water (osmosis) that occur in plant cells and in animal cells such as red blood cells (see Figure 7.12).

The phosphorylationdephosphorylation system acts as a molecular switch in the cell, turning activities on or off, or up or down, as required.

At any given moment, the activity of a protein regulated by phosphorylation depends on the balance in the cell between active kinase molecules and active phosphatase molecules.

Figure 6.3 - Brightfield (stained specimen)

Brightfield (stained specimen). - Staining with various dyes enhances contrast. Most staining procedures require that cells be fixed (preserved), thereby killing them.

Figure 6.3 - Brightfield (unstained specimen)

Brightfield (unstained specimen). - Light passes directly through the specimen. Unless the cell is naturally pigmented or artificially stained, the image has little contrast. (The first four light micrographs show human cheek epithelial cells; the scale bar pertains to all four micrographs.)

In another kind of allosteric activation, a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites (Figure 8.20b)

Called cooperativity, this mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to act on additional substrate molecules more readily.

This simplified model is generally accepted as the main way in which the multitude of different enzymes arose over the past few billion years of life's history

Data supporting this model have been collected by researchers using a lab procedure that mimics evolution in natural populations (Figure 8.19).

Deconvolution

Deconvolution. - The top of this split image is a compilation of standard fluorescence micrographs through the depth of a white blood cell. Below is an image of the same cell reconstructed from many blurry images at different planes, each of which was processed using deconvolution software. This process digitally removes out-of-focus light and reassigns it to its source, creating a much sharper 3-D image.

A cell is greater than the sum of its parts

From our panoramic view of the cell's compartmental organization to our close-up inspection of each organelle's architecture, this tour of the cell has provided many opportunities to correlate structure with function. (This would be a good time to review cell structure by returning to Figure 6.8.)

Overview of cell signaling.

From the perspective of the cell receiving the message, cell signaling can be divided into three stages: signal reception, signal transduction, and cellular response. When reception occurs at the plasma membrane, as shown here, the transduction stage is usually a pathway of several steps (three are shown as an example), with each specific relay molecule in the pathway bringing about a change in the next molecule. The final molecule in the pathway triggers the cell's response.

Which is the main HIV receptor?

Further work showed that although CD4 is the main HIV receptor, HIV must also bind to CCR5 as a "co-receptor" to infect most cells (Figure 7.8a). An absence of CCR5 on the cells of resistant individuals, due to the gene alteration, prevents the virus from entering the cells. This information has been key to developing a treatment for HIV infection.

CD4

Helper T cells

Amoeba

In the unicellular eukaryote Amoeba and some of our white blood cells, localized contractions brought about by actin and myosin are involved in the amoeboid (crawling) movement of the cells. The cell crawls along a surface by extending cellular extensions called pseudopodia (from the Greek pseudes, false, and pod, foot) and moving toward them

ATP, ADP, and other related molecules also affect key enzymes in anabolic pathways.

In this way, allosteric enzymes control the rates of important reactions in both sorts of metabolic pathways.

Amoeboid movement.

Interaction of actin filaments with myosin causes contraction of the cell, pulling the cell's trailing end (at left) forward (to the right) (LM).

Scanning electron microscopy (SEM)

Micrographs taken with a scanning electron microscope show a 3-D image of the surface of a specimen. This SEM shows the surface of a cell from a trachea (windpipe) covered with cell projections called cilia. Electron micrographs are black and white but are often artificially colorized to highlight particular structures, as has been done with both electron micrographs shown here.

For the net synthesis of one G3P molecule, the Calvin cycle consumes a total of nine molecules of ATP and six molecules of NADPH. The light reactions regenerate the ATP and NADPH. The G3P spun off from the Calvin cycle becomes the starting material for metabolic pathways that synthesize other organic compounds, including glucose (from two molecules of G3P), the disaccharide sucrose, and other carbohydrates.

Neither the light reactions nor the Calvin cycle alone can make sugar from CO2. Photosynthesis is an emergent property of the intact chloroplast, which integrates the two stages of photosynthesis.

What establishes the direction of traffic across a membrane? And what mechanisms drive molecules across membranes?

Next section

The Permeability of the Lipid Bilayer

Nonpolar molecules, such as hydrocarbons, CO2, and O2, are hydrophobic, as are lipids. They can all therefore dissolve in the lipid bilayer of the membrane and cross it easily, without the aid of membrane proteins.

Phase contrast

Phase-contrast. -Variations in density within the specimen are amplified to enhance contrast in unstained cells; this is especially useful for examining living, unpigmented cells.

entropy

Scientists use a quantity called entropy as a measure of molecular disorder, or randomness. The more randomly arranged a collection of matter is, the greater its entropy.

Most cytoplasmic protein kinases, however, act on proteins different from themselves. Another distinction is that most cytoplasmic protein kinases phosphorylate either of two other amino acids, serine or threonine, rather than tyrosine.

Serine/threonine kinases are widely involved in signaling pathways in animals, plants, and fungi.

Substrate-level phosphorylation.

Some ATP is made by direct transfer of a phosphate group from an organic substrate to ADP by an enzyme. (For examples in glycolysis, see Figure 9.9, steps 7 and 10.

Microfilaments (Actin Filaments)

Two intertwined strands of actin 7 nm Actin Maintenance of cell shape (tensionbearing elements); changes in cell shape; muscle contraction; cytoplasmic streaming in plant cells; cell motility (as in amoeboid movement); division of animal cells

We can think of free energy as a measure of a system's instability—its tendency to change to a more stable state

Unstable systems (higher G) tend to change in such a way that they become more stable (lower G). For example, a diver on top of a platform is less stable (more likely to fall) than when floating in the water; a drop of concentrated dye is less stable (more likely to disperse) than when the dye is spread randomly through the liquid; and a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split (Figure 8.5).

electron microscope

Until recently, the resolution barrier prevented cell biologists from using standard light microscopy when studying organelles, the membrane-enclosed structures within eukaryotic cells. To see these structures in any detail required the development of a new instrument. In the 1950s, the electron microscope was introduced to biology. Rather than focusing light, the electron microscope (EM) focuses abeam of electrons through the specimen or onto its surface

Malfunctions of the associated G proteins themselves are involved in many human diseases, including bacterial infections. The bacteria that cause cholera, pertussis (whooping cough), and botulism, among others, make their victims ill by producing toxins that interfere with G protein function.

Up to 60% of all medicines used today exert their effects by influencing G protein pathways.

The effect of an enzyme on activation energy.

Without affecting the free-energy change (∆G) for a reaction, an enzyme speeds the reaction by reducing its activation energy (EA).

Total volume

[height × width × length × number of boxes]

Total surface area

[sum of the surface areas (height × width) of all box sides × number of boxes]

Equilibrium and work in open systems.

a) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucose is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction is used as the reactant for the next, so no reaction reaches equilibrium. b)An open hydroelectric system. Water flowing through a turbine keeps driving the generator because intake and outflow of water keep the system from reaching equilibrium.

Protease

enzyme that digests protein

Eukaryotic cells

have internal membranes that compartmentalize their functions

Microtubules (Tubulin Polymers)

hollow tubes; functions: maintenance of cell shape; cell motility (as in cilia or flagella); chromosome movements in cell division; organelle movements Diameter: 25 nm with 15nm lumen. Tubulin, a dimer consisting of α-tubulin and β-tubulin

Chloroplasts do not need molecules from food to make ATP; their photosystems capture light energy and use it to drive the electrons from water to the top of the transport chain.

in other words, mitochondria use chemiosmosis to transfer chemical energy from food molecules to ATP, whereas chloroplasts use it to transform light energy into chemical energy in ATP

Thus, a cell grows (G1), continues to grow as it copies its chromosomes (S), grows more as.....

it completes preparations for cell division (G2), and divides (M). The daughter cells may then repeat the cycle.

As the bear in Figure 8.3b converts chemical energy to kinetic energy,

it is also increasing the disorder of its surroundings by producing heat and small molecules, such as the CO2 it exhales, that are the breakdown products of food

Metaphase plate Centrosome at one spindle pole Spindle

metaphase: * The centrosomes are now at opposite poles of the cell. • The chromosomes have all arrived at the metaphase plate, a plane that is equidistant between the spindle's two poles. The chromo- somes' centromeres lie at the metaphase plate. • For each chromosome, the kinetochores of the sister chromatids are attached to kinetochore microtubules coming from opposite poles.

The Second Law of Thermodynamics: If energy cannot be destroyed, why can't organisms simply recycle their energy over and over again?It turns out that during every energy transfer or transformation, some energy becomes unavailable to do work. In most energy transformations, the more usable forms of energy are at least partly converted to thermal energy and released as heat. Only a small fraction of the chemical energy from the food in Figure 8.3a is transformed into the motion of the brown bear shown in Figure 8.3b; most is lost as heat, which dissipates rapidly through the surroundings.

n the process of carrying out chemical reactions that perform various kinds of work, living cells unavoidably convert other forms of energy to heat. A system can put this energy to work only when there is a temperature difference that results in thermal energy flowing as heat from a warmer location to a cooler one. If temperature is uniform, as it is in a living cell, then the heat generated during a chemical reaction will simply warm a body of matter, such as the organism. (This can make a room crowded with people uncomfortably warm, as each person is carrying out a multitude of chemical reactions!)

The eukaryotic cell's genetic instructions are housed in the

nucleus and carried out by the ribosomes.

. This mode of ATP synthesis

occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP, rather than adding an inorganic phosphate to ADP as in oxidative phosphorylation. "Substrate molecule" here refers to an organic molecule generated as an intermediate during the catabolism of glucose. You'll see examples of substrate-level phosphorylation later in the chapter, in both glycolysis and the citric acid cycle.

Chromosomes (blue) are attached by specific proteins (green) to cell machinery (red) and are moved during division of a rat kangaroo cell.

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The endomembrane system

regulates protein traffic and performs metabolic functions. Many of the different membrane-bounded organelles of the eukaryotic cell are part of the endomembrane system which includes the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, various kinds of vesicles and vacuoles, and the plasma membrane. This system carries out a variety of tasks in the cell, including synthesis of proteins, transport of proteins into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons.

The Endomembrane System: A Review

reviews the endomembrane system, showing the flow of membrane lipids and proteins through the various organelles. As the membrane moves from the ER to the Golgi and then elsewhere, its molecular composition and metabolic functions are modified, along with those of its contents. The endomembrane system is a complex and dynamic player in the cell's compartmental organization. We'll continue our tour of the cell with some organelles that are not closely related to the endomembrane system but play crucial roles in the energy transformations carried out by cells

chromatin

s. Some of the proteins help coil the DNA molecule of each chromosome, reducing its length and allowing it to fit into the nucleus. The complex of DNA and proteins making up chromosomes is called chromatin. When a cell is not dividing, stained chromatin appears as a diffuse mass in micrographs, and the chromosomes cannot be distinguished from one another, even though discrete chromosomes are present

Although we will use ....

some nonliving examples to study energy, the concepts demonstrated by these examples also apply to bioenergetics, the study of how energy flows through living organisms.

step 2: After the CO2 is fixed in the mesophyll cells, the fourcarbon products (malate in the example shown in Figure 10.20) are exported to bundle-sheath cells through plasmodesmata (see Figure 6.29).

step 3 : Within the bundle-sheath cells, the four-carbon compounds release CO2, which is re-fixed into organic material by rubisco and the Calvin cycle. The same reaction regenerates pyruvate, which is transported to mesophyll cells. There, ATP is used to convert pyruvate to PEP, which can accept addition of another CO2, allowing the reaction cycle to continue. This ATP can be thought of, in a sense, as the "price" of concentrating CO2 in the bundle-sheath cells. To generate this extra ATP, bundle-sheath cells carry out cyclic electron flow, the process described earlier in this chapter (see Figure 10.16). In fact, these cells contain PS I but no PS II, so cyclic electron flow is their only photosynthetic mode of generating ATP.

LIGHT REACTIONS

• Are carried out by molecules in the thylakoid membranes • Convert light energy to the chemical energy of ATP and NADPH • Split H2O and release O2 to the atmosphere

CALVIN CYCLE REACTIONS

• Take place in the stroma • Use ATP and NADPH to convert CO2 to the sugar G3P • Return ADP, inorganic phosphate, and NADP+ to the light reactions

The change in free energy, ∆G, can be calculated for a chemical reaction by applying the following equation:

∆G = ∆H - T∆S This equation uses only properties of the system (the reaction) itself: ∆H symbolizes the change in the system's enthalpy (in biological systems, equivalent to total energy); ∆S is the change in the system's entropy; and T is the absolute temperature in Kelvin (K) units (K = °C + 273; see Appendix C).

The effect of platelet-derived growth factor (PDGF) on cell division:

(1) A sample of human connective tissue is cut up into small pieces. (2) Enzymes are used to digest the extracellular matrix in the tissue pieces, resulting in a suspension of free fibroblasts. (3) Cells are transferred to culture vessels containing a basic growth medium consisting of glucose, amino acids, salts, and antibiotics (to prevent bacterial growth). (4) PDGF is added to half the vessels. The culture vessels are incubated at 37°C for 24 hours. Without PDGF: In the basic growth medium without PDGF (the control), the cells fail to divide. With PDGF: In the basic growth medium plus PDGF, the cells proliferate. The SEM shows cultured fibroblasts.

Calcium and IP3 in signaling pathways: Calcium ions (Ca2+ ) and inositol trisphosphate (IP3) function as second messengers in many signal transduction pathways. In this figure, the process is initiated by the binding of a signaling molecule to a G protein-coupled receptor. A receptor tyrosine kinase could also initiate this pathway by activating phospholipase C.

(1)A signaling molecule binds to a receptor, leading to activation of phospholipase C. (2) Phospholipase C cleaves a plasma membrane phospholipid called PIP2 into DAG and IP3. (3) DAG functions as a second messenger in other pathways. (4)IP3 quickly diffuses through the cytosol and binds to an IP3- gated calcium channel in the ER membrane, causing it to open. (5) Calcium ions flow out of the ER (down their concentration gradient), raising the Ca2+ level in the cytosol. (6) The calcium ions activate the next protein in one or more signaling pathways.

GLYCOLYSIS: Energy Payoff Phase

(6) Two sequential reactions: (1) G3P is oxidized by the transfer of electrons to NAD+, forming NADH. (2) Using energy from this exergonic redox reaction, a phosphate group is attached to the oxidized substrate, making a high-energy product. (7) The phosphate group is transferred to ADP (substrate-level phosphorylation) in an exergonic reaction. The carbonyl group of G3P has been oxidized to the carboxyl group (—COO-) of an organic acid (3-phosphoglycerate) (8) This enzyme relocates the remaining phosphate group. (9) Enolase causes a double bond to form in the substrate by extracting a water molecule, yielding phosphoenolpyruvate (PEP), a compound with a very high potential energy. (10) The phosphate group is transferred from PEP to ADP (a second example of substrate-level phosphorylation), forming pyruvate.

Molecular control of the cell cycle at the G2 checkpoint: The steps of the cell cycle are timed by rhythmic fluctuations in the activity of cyclin-dependent kinases (Cdks). Here we focus on a cyclin-Cdk complex in animal cells called MPF, which acts at the G2 checkpoint as a go-ahead signal, triggering the events of mitosis.

(a) ) Fluctuation of MPF activity and cyclin concentration during the cell cycle: (1) Synthesis of cyclin begins in late S phase and continues through G2. Because cyclin is protected from degradation during this stage, it accumulates. (5) During G1, the degradation of cyclin continues, and the Cdk component of MPF is recycled. b) Molecular mechanisms that help regulate the cell cycle (2) Cyclin combines with Cdk, producing MPF. When enough MPF molecules accumulate, the cell passes the G2 checkpoint and begins mitosis. (3) MPF promotes 2 mitosis by phosphorylating various proteins. MPF's activity peaks during metaphase. (4) During anaphase, the cyclin component of MPF is degraded, terminating the M phase. The cell enters the G1 phase

Excitation of isolated chlorophyll by light.

(a) Absorption of a photon causes a transition of the chlorophyll molecule from its ground state to its excited state. The photon boosts an electron to an orbital where it has more potential energy. If the illuminated molecule exists in isolation, its excited electron immediately drops back down to the ground-state orbital, and its excess energy is given off as heat and fluorescence (light). (b) A chlorophyll solution excited with ultraviolet light fluoresces with a red-orange glow

Communication by direct contact between cells.

(a) Cell-cell recognition. Two cells in an animal may communicate by interaction between molecules protruding from their surfaces. Cell junctions : Both animals and plants have cell junctions that allow molecules, including signaling molecules, to pass readily between adjacent cells without crossing plasma membranes.

Cytokinesis in animal and plant cells- figure 12.10 Contractile ring of microfilaments & Daughter cells (b) Vesicles forming cell plate, Wall of parent cell, Cell plate, New cell wall, Daughter cells.

(a) Cleavage of an animal cell (SEM) (b) Cell plate formation in a plant cell (TEM)

Free energy changes ( delta G) in exergonic and endergonic reactions.

(a) Exergonic reaction: energy released, spontaneous (b) Endergonic reaction: energy required, nonspontaneous

Two important checkpoints: At certain checkpoints in the cell cycle (red gates), cells do different things depending on the signals they receive. Events of the (a) G1 and (b) M checkpoints are shown. In (b), the G2 checkpoint has already been passed by the cell.

(a) G1 checkpoint : In the absence of a go-ahead signal, a cell exits the cell cycle and enters G0, a nondividing state. If a cell receives a go-ahead signal, the cell continues on in the cell cycle. (b) M Checkpoint: A cell in mitosis receives a stop signal when any of its chromosomes are not attached to spindle fibers. When all chromosomes are attached to spindle fibers from both poles, a go-ahead signal allows the cell to proceed into anaphase

The structure and function of a photosystem.

(a) How a photosystem harvests light. When a photon strikes a pigment molecule in a light-harvesting complex, the energy is passed from molecule to molecule until it reaches the reaction-center complex. Here, an excited electron from the special pair of chlorophyll a molecules is transferred to the primary electron acceptor. (b) Structure of a photosystem. This computer model, based on X-ray crystallography, shows two photosystem complexes side by side. Chlorophyll molecules (bright green ball-and-stick models within the membrane; the tails are not shown) are interspersed with protein subunits (purple ribbons; notice the many α helices spanning the membrane). For simplicity, a photosystem will be shown as a single complex in the rest of the chapter.

Inhibition of enzyme activity.

(a) Normal binding: A substrate can bind normally to the active site of an enzyme. (b) Competitive inhibition: A competitive inhibitor mimics the substrate, competing for the active site. (c) Noncompetitive inhibition: A noncompetitive inhibitor binds to the enzyme away from the active site, altering the shape of the enzyme so that even if the substrate can bind, the active site functions less effectively, if at all.

Local signaling:

(a) Paracrine signaling. A signaling cell acts on nearby target cells by secreting molecules of a local regulator (a growth factor, for example). (b) Synaptic signaling. A nerve cell releases neurotransmitter molecules into a synapse, stimulating the target cell, such as a muscle or another nerve cell.

Factors that affect membrane fluidity.

(a) Unsaturated versus saturated hydrocarbon tails. Fluid : Unsaturated hydrocarbon tails (kinked) prevent packing, enhancing membrane fluidity. Viscous: Saturated hydrocarbon tails pack together, increasing membrane viscosity. (b) Cholesterol within the animal cell membrane. Cholesterol: Cholesterol reduces membrane fluidity at moderate temperatures by reducing phospholipid movement, but at low temperatures it hinders solidification by disrupting the regular packing of phospholipids

Allosteric regulation of enzyme activity: (a) Allosteric activators and inhibitors: Allosteric activator stabilizes active form. Allosteric inhibitor stabilizes inactive form At low concentrations, activators and inhibitors dissociate from the enzyme. The enzyme can then oscillate again.

(b) Cooperativity: another type of allosteric activation: Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. The inactive form shown on the left oscillates with the active form when the active form is not stabilized by substrate.

Long-distance signaling:

(c) Endocrine (hormonal) signaling. Specialized endocrine cells secrete hormones into body fluids, often blood. Hormones reach most body cells, but are bound by and affect only some cells.

ATP yield per molecule of glucose at each stage of cellular respiration.

+2 ATP from glycogen by substrate level phosphorylation +2 ATP from citric acid cycle by substrate level phosphorylation + about 26 or 28 ATP from oxidative phosphorylation ( ELectron transport and chemiosmosis) by oxidative phosphorylation, depending on which shuttle transports electrons from NADH in cytosol

Structure of dyneins

. A typical dynein protein has two "feet" that "walk" along the microtubule of the adjacent doublet, using ATP for energy. One foot maintains contact, while the other releases and reattaches one step farther along the microtubule (see Figure 6.21). The outer doublets and two central microtubules are held together by flexible cross-linking proteins (blue in the diagram in Figure 6.24), and the walking movement is coordinated so that it happens on one side of the circle at a time. If the doublets were not held in place, the walking action would make them slide past each other. Instead, the movements of the dynein feet cause the microtubules—and the organelle as a whole—to bend.

Fluctuating concentrations of regulators can cause a sophisticated pattern of response in the activity of cellular enzymes. The products of ATP hydrolysis (ADP and ~P i ), for example, play a complex role in balancing the flow of traffic between anabolic and catabolic pathways by their effects on key enzymes.

. ATP binds to several catabolic enzymes allosterically, lowering their affinity for substrate and thus inhibiting their activity. ADP, however, functions as an activator of the same enzymes. This is logical because catabolism functions in regenerating ATP.

Cyclic electron flow can also occur in photosynthetic species that possess both photosystems; this includes some prokaryotes, such as the cyanobacteria shown in Figure 10.2d, as well as the eukaryotic photosynthetic species that have been tested thus far.

. Although the process is probably in part an "evolutionary leftover," research suggests it plays at least one beneficial role for these organisms. Plants with mutations that render them unable to carry out cyclic electron flow are capable of growing well in low light, but do not grow well where light is intense. This is evidence for the idea that cyclic electron flow may be photoprotective. Later you'll learn more about cyclic electron flow as it relates to a particular adaptation of photosynthesis (C4 plants; see Concept 10.4).

Energy must be added to pull an electron away from an atom, just as energy is required to push a ball uphill. The more electronegative the atom (the stronger its pull on electrons), the more energy is required to take an electron away from it

. An electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one, just as a ball loses potential energy when it rolls downhill

. Recall that each glucose gives rise to two molecules of acetyl CoA that enter the cycle.

. Because the numbers noted earlier are obtained from a single acetyl group entering the pathway, the total yield per glucose from the citric acid cycle turns out to be 6 NADH, 2 FADH2, and the equivalent of 2 ATP.

An endergonic reaction is one that absorbs free energy from its surroundings (Figure 8.6b).

. Because this kind of reaction essentially stores free energy in molecules (G increases), ∆G is positive. Such reactions are nonspontaneous, and the magnitude of ∆G is the quantity of energy required to drive the reaction. If a chemical process is exergonic (downhill), releasing energy in one direction, then the reverse process must be endergonic (uphill), using energy. A reversible process cannot be downhill in both directions. If ∆G = -686 kcal/mol for respiration, which converts glucose and oxygen to carbon dioxide and water, then the reverse process—the conversion of carbon dioxide and water to glucose and oxygen—must be strongly endergonic, with ∆G = +686 kcal/mol. Such a reaction would never happen by itself

Local and Long-Distance Signaling: Like bacteria or yeast cells, cells in a multicellular organism usually communicate via signaling molecules targeted for cells that may or may not be immediately adjacent. . As we saw in Concepts 6.7 and 7.1, eukaryotic cells may communicate by direct contact, which is one type of local signaling (Figure 11.4).

. Both animals and plants have cell junctions that, where present, directly connect the cytoplasms of adjacent cells (Figure 11.4a). In these cases, signaling substances dissolved in the cytosol can pass freely between neighboring cells. Moreover, animal cells may communicate via direct contact between membrane-bound cell-surface molecules,in a process called cell-cell recognition (Figure 11.4b). This sort of local signaling is especially important in embryonic development and the immune response.

How do the intermediate filaments help the cell carry out its specific function?

. By supporting a cell's shape, intermediate filaments help the cell carry out its specific function. For example, the network of intermediate filaments shown in Figure 6.25 anchors the microfilaments supporting the intestinal microvilli. Thus, the various kinds of intermediate filaments may function together as the permanent framework of the entire cell.

Chemical treatments that remove microfilaments and microtubules from the cytoplasm of living cells.

. Chemical treatments that remove microfilaments and microtubules from the cytoplasm of living cells leave a web of intermediate filaments that retains its original shape. Such experiments suggest that intermediate filaments are especially sturdy and that they play an important role in reinforcing the shape of a cell and fixing the position of certain organelles. For instance, the nucleus typically sits within a cage made of intermediate filaments, fixed in location by branches of the filaments that extend into the cytoplasm. Other intermediate filaments make up the nuclear lamina, which lines the interior of the nuclear envelope (see Figure 6.9)

Proteins on a cell's surface are important in the medical field

. For example, a protein called CD4 on the surface of immune cells helps the human immunodeficiency virus (HIV) infect these cells, leading to acquired immune deficiency syndrome (AIDS). Despite multiple exposures to HIV, however, a small number of people do not develop AIDS and show no evidence of HIV-infected cells. Comparing their genes with the genes of infected individuals, researchers learned that resistant people have an unusual form of a gene that codes for an immune cell-surface protein called CCR5.

Signal Amplification: Elaborate enzyme cascades amplify the cell's response to a signal. At each catalytic step in the cascade, the number of activated products can be much greater than in the preceding step.

. For example, in the epinephrine-triggered pathway in Figure 11.16, each adenylyl cyclase molecule catalyzes the formation of 100 or so cAMP molecules, each molecule of protein kinase A phosphorylates about 10 molecules of the next kinase in the pathway, and so on. The amplification effect stems from the fact that these proteins persist in their active form long enough to process multiple molecules of substrate before they become inactive again

The cells of most terrestrial (land-dwelling) animals are bathed in an extracellular fluid that is isotonic to the cells. In hypertonic or hypotonic environments, however, organisms that lack rigid cell walls must have other adaptations for osmoregulation, the control of solute concentrations and water balance.

. For example, the unicellular eukaryote Paramecium lives in pond water, which is hypotonic to the cell. Paramecium has a plasma membrane that is much less permeable to water than the membranes of most other cells, but this only slows the uptake of water, which continually enters the cell.

For many receptors, this shape change directly activates the receptor, enabling it to interact with other cellular molecules

. For other kinds of receptors, the immediate effect of ligand binding is to cause the aggregation of two or more receptor proteins, which leads to further molecular events inside the cell.

Abnormal cell behavior in the body can be catastrophic. The problem begins when a single cell in a tissue undergoes the first of many steps that converts a normal cell to a cancer cell. Such a cell often has altered proteins on its surface, and the body's immune system normally recognizes the cell as "nonself"—an insurgent—and destroys it.

. However, if the cell evades destruction, it may proliferate and form a tumor, a mass of abnormal cells within otherwise normal tissue.

Hypotonic

. However, taking up too much water can be just as hazardous as losing water. If we place the cell in a solution that is hypotonic to the cell (hypo means "less"), water will enter the cell faster than it leaves, and the cell will swell and lyse (burst) like an overfilled water balloon

If ATP production lags behind its use, ADP accumulates and activates the enzymes that speed up catabolism, producing more ATP.

. If the supply of ATP exceeds demand, then catabolism slows down as ATP molecules accumulate and bind to the same enzymes, inhibiting them. (You'll see specific examples of this type of regulation when you learn about cellular respiration in the next chapter; see, for example, Figure 9.20.)

For example, with the help of specific enzymes, the cell is able to use the energy released by ATP hydrolysis directly to drive chemical reactions that, by themselves, are endergonic.

. If the ∆G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic. This usually involves phosphorylation, the transfer of a phosphate group from ATP to some other molecule, such as the reactant. The recipient molecule with the phosphate group covalently bonded to it is then called a phosphorylated intermediate

Photorespiration: An Evolutionary Relic? In most plants, initial fixation of carbon occurs via rubisco, the Calvin cycle enzyme that adds CO2 to ribulose bisphosphate. Such plants are called C3 plants because the first organic product of carbon fixation is a three-carbon compound, 3-phosphoglycerate (see Figure 10.19). Rice, wheat, and soybeans are C3 plants that are important in agriculture. When their stomata partially close on hot, dry days, C3 plants produce less sugar because the declining level of CO2 in the leaf starves the Calvin cycle.

. In addition, rubisco is capable of binding O2 in place of CO2. As CO2 becomes scarce within the air spaces of the leaf and O2 builds up, rubisco adds O2 to the Calvin cycle instead of CO2. The product splits, and a two-carbon compound leaves the chloroplast. Peroxisomes and mitochondria within the plant cell rearrange and split this compound, releasing CO2. The process is called photorespiration because it occurs in the light (photo) and consumes O2 while producing CO2 (respiration).

Two types of transport proteins that carry out facilitated diffusion

. In both cases, the protein can transport the solute in either direction, but the net movement is down the concentration gradient of the solute. a) A channel protein has a channel through which water molecules or a specific solute can pass. b) A carrier protein alternates between two shapes, moving a solute across the membrane during the shape change.

Now let's examine the fate of the reactant O2. The two atoms of the oxygen molecule (O2) share their electrons equally. But when oxygen reacts with the hydrogen from methane, forming water, the electrons of the covalent bonds spend more time near the oxygen (see Figure 9.3)

. In effect, each oxygen atom has partially "gained" electrons, so the oxygen molecule has been reduced. Because oxygen is so electronegative, it is one of the most powerful of all oxidizing agents.

The flight response shown here is triggered by a signaling molecule called epinephrine (also called adrenaline; see the space-filling model included here).

. In studying cell communication, biologists have discovered ample evidence for the evolutionary relatedness of all life. The same set of cell-signaling mechanisms shows up again and again in diverse species, in processes ranging from bacterial signaling to embryonic development to cancer. In this chapter, we focus on the main mechanisms by which cells receive, process, and respond to chemical signals sent from other cells. We will also consider apoptosis, a mechanism of programmed cell death that integrates input from multiple signaling pathways.

An overview of photosynthesis: cooperation of the light reactions and the Calvin cycle.

. In the chloroplast, the thylakoid membranes (green) are the sites of the light reactions, whereas the Calvin cycle occurs in the stroma (gray). The light reactions use solar energy to make ATP and NADPH, which supply chemical energy and reducing power, respectively, to the Calvin cycle. The Calvin cycle incorporates CO2 into organic molecules, which are converted to sugar. (Recall that most simple sugars have formulas that are some multiple of CH2O.) To visualize these processes in their cellular context, see Figure 6.32.

Apoptosis in the Soil Worm Caenorhabditis elegans: The molecular mechanisms of apoptosis were worked out by researchers studying embryonic development of a small soil worm, a nematode called Caenorhabditis elegans. Because the adult worm has only about 1,000 cells, the researchers were able to work out the entire ancestry of each cell. The timely suicide of cells occurs exactly 131 times during normal development of C. elegans, at precisely the same points in the cell lineage of each worm.

. In worms and other species, apoptosis is triggered by signals that activate a cascade of "suicide" proteins in the cells destined to die.

Regulation of enzyme activity helps control metabolism: Chemical chaos would result if all of a cell's metabolic pathways were operating simultaneously. Intrinsic to life's processes is a cell's ability to tightly regulate its metabolic pathways by controlling when and where its various enzymes are active.

. It does this either by switching on and off the genes that encode specific enzymes (as we will discuss in Unit Three) or, as we discuss here, by regulating the activity of enzymes once they are made.

Although cell-surface receptors represent 30% of all human proteins, determining their structures has proved challenging: They make up only 1% of the proteins whose structures have been determined by X-ray crystallography (see Figure 5.21). For one thing, cell-surface receptors tend to be flexible and inherently unstable, thus difficult to crystallize.

. It took years of persistent efforts for researchers to determine the first few of these structures, such as the GPCR shown in Figure 11.7. In that case, the β-adrenergic receptor was stable enough to be crystallized only while it was among membrane molecules and in the presence of a molecule mimicking its ligand.

Microvilli

. Larger organisms do not generally have larger cells than smaller organisms—they simply have more cells (see Figure 6.7). A sufficiently high ratio of surface area to volume is especially important in cells that exchange a lot of material with their surroundings, such as intestinal cells.Such cells may have many long, thin projections from their surface called microvilli, which increase surface area without an appreciable increase in volume.

. For other kinds of receptors, the immediate effect of ligand binding is to cause the aggregation of two or more receptor proteins, which leads to further molecular events inside the cell

. Most signal receptors are plasma membrane proteins, but others are located inside the cell. We discuss both of these types next.

The energy stored in the organic molecules of food ultimately comes from the sun. Energy flows into an ecosystem as sunlight and exits as heat; in contrast, the chemical elements essential to life are recycled (Figure 9.2).

. Photosynthesis generates oxygen, as well as organic molecules used by the mitochondria of eukaryotes as fuel for cellular respiration. Respiration breaks this fuel down, using oxygen and generating ATP. The waste products of this type of respiration, carbon dioxide and water, are the raw materials for photosynthesis.

The H+ uses the transport protein as an avenue to diffuse down its own electrochemical gradient, which is maintained by the proton pump

. Plants use H+ /sucrose cotransport to load sucrose produced by photosynthesis into cells in the veins of leaves. The vascular tissue of the plant can then distribute the sugar to roots and other nonphotosynthetic organs that do not make their own food.

A proton pump

. Proton pumps are electrogenic pumps that store energy by generating voltage (charge separation) across membranes. A proton pump translocates positive charge in the form of hydrogen ions. The voltage and H+ concentration gradient represent a dual energy source that can drive other processes, such as the uptake of nutrients. Most proton pumps are powered by ATP hydrolysis.

Oxidation of pyruvate to acetyl CoA, the step before the citric acid cycle.

. Pyruvate is a charged molecule, so in eukaryotic cells it must enter the mitochondrion via active transport, with the help of a transport protein. Next, a complex of several enzymes (the pyruvate dehydrogenase complex) catalyzes the three numbered steps, which are described in the text. The acetyl group of acetyl CoA will enter the citric acid cycle. The CO2 molecule will diffuse out of the cell. By convention, coenzyme A is abbreviated S-CoA when it is attached to a molecule, emphasizing the sulfur atom (S). (The gene encoding the transport protein was finally identified several years ago, after 40 years of research.

A cell without rigid cell walls can tolerate neither excessive uptake nor excessive loss of water. This problem of water balance is automatically solved if such a cell lives in isotonic surroundings.

. Seawater is isotonic to many marine invertebrates

fibronectin and integrin

. Some cells are attached to the ECM by ECM glycoproteins such as fibronectin. Fibronectin and other ECM proteins bind to cell-surface receptor proteins called integrins that are built into the plasma membrane. Integrins span the membrane and bind on their cytoplasmic side to associated proteins attached to microfilaments of the cytoskeleton. The name integrin is based on the word integrate: Integrins are in a position to transmit signals between the ECM and the cytoskeleton and thus to integrate changes occurring outside and inside the cell

Another example of bacterial behavior coordinated by quorum sensing is one that has serious medical implications: the secretion of toxins by infectious bacteria.

. Sometimes treatment by antibiotics doesn't work with such infections due to antibiotic resistance that has evolved in a particular strain of bacteria. Interfering with the signaling pathways used in quorum sensing represents a promising approach as an alternative treatment. In the Problem-Solving Exercise, you can participate in the process of scientific thinking involved in this novel approach.

Life on Earth is solar powered. Plants and other photosynthetic organisms contain cellular organelles called chloroplasts.

. Specialized molecular complexes in chloroplasts capture light energy that has traveled 150 million km from the sun and convert it to chemical energy that is stored in sugar and other organic molecules. This conversion process is called photosynthesis. Let's begin by placing photosynthesis in its ecological context.

Carrier proteins, such as the glucose transporter mentioned earlier, seem to undergo a subtle change in shape that somehow translocates the solute-binding site across the membrane (Figure 7.14b).

. Such a change in shape may be triggered by the binding and release of the transported molecule. Like ion channels, carrier proteins involved in facilitated diffusion result in the net movement of a substance down its concentration gradient. No energy input is thus required: This is passive transport

Alternative mechanisms of carbon fixation have evolved in hot, arid climates: Ever since plants first moved onto land about 475 million years ago, they have been adapting to the problems of terrestrial life, particularly the problem of dehydration. In Concept 36.4, we will consider anatomical adaptations that help plants conserve water, while in this chapter we are concerned with metabolic adaptations. The solutions often involve trade-offs. An important example is the balance between photosynthesis and the prevention of excessive water loss from the plant.

. The CO2 required for photosynthesis enters a leaf (and the resulting O2 exits) via stomata, the pores on the leaf surface (see Figure 10.4). However, stomata are also the main avenues of transpiration, the evaporative loss of water from leaves. O

The Pathway of Electron Transport: The electron transport chain is a collection of molecules embedded in the inner membrane of the mitochondrion in eukaryotic cells. (In prokaryotes, these molecules reside in the plasma membrane.) The folding of the inner membrane to form cristae increases its surface area, providing space for thousands of copies of each component of the electron transport chain in a mitochondrion.

. The infolded membrane with its concentration of electron carrier molecules is well-suited for the series of sequential redox reactions that take place along the electron transport chain. Most components of the chain are proteins, which exist in multiprotein complexes numbered I through IV. Tightly bound to these proteins are prosthetic groups, nonprotein components such as cofactors and coenzymes essential for the catalytic functions of certain enzymes.

Extracellular matrix (ECM) of an animal cell

. The molecular composition and structure of the ECM vary from one cell type to another. In this example, three different types of ECM molecules are present: collagen, fibronectin, and proteoglycans. Collagen fibers are embedded in a web of proteoglycan complexes Fibronectin attaches the ECM to integrins embedded in the plasma membrane. A proteoglycan complex consists of hundreds of proteoglycan molecules attached noncovalently to a single long polysaccharide molecule. Integrins, membrane proteins with two subunits, bind to the ECM on the outside and to associated proteins attached to microfilaments on the inside. This linkage can transmit signals between the cell's external environment and its interior and can result in changes in cell behavior.

Although the sun radiates the full spectrum of electromagnetic energy, the atmosphere acts like a selective window, allowing visible light to pass through while screening out a substantial fraction of other radiation.

. The part of the spectrum we can see—visible light—is also the radiation that drives photosynthesis.

in a sense, the spent exhaust of a process that tapped the free energy stored in the bonds of the sugar molecules.

. The phrase "energy stored in bonds" is shorthand for the potential energy that can be released when new bonds are formed after the original bonds break, as long as the products are of lower free energy than the reactants.

tonicity

. The tonicity of a solution depends in part on its concentration of solutes that cannot cross the membrane (nonpenetrating solutes) relative to that inside the cell. If there is a higher concentration of nonpenetrating solutes in the surrounding solution, water will tend to leave the cell, and vice versa

The Cell Cycle Clock: Cyclins and Cyclin-Dependent Kinases: Rhythmic fluctuations in the abundance and activity of cell cycle control molecules pace the sequential events of the cell cycle.

. These regulatory molecules are mainly proteins of two types: protein kinases and cyclins. Protein kinases are enzymes that activate or inactivate other proteins by phosphorylating them (see Concept 11.3).

consequently, cholesterol accumulates in the blood, where it contributes to early atherosclerosis, the buildup of lipid deposits within the walls of blood vessels.

. This buildup narrows the space in the vessels and impedes blood flow, potentially resulting in heart damage and stroke.

You can think of the whole process this way: When you withdraw a relatively large sum of money from an ATM, it is not delivered to you in a single bill of larger denomination. Instead, a number of smaller-denomination bills are dispensed that you can spend more easily.

. This is analogous to ATP production during cellular respiration. For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to about 32 molecules of ATP, each with 7.3 kcal/mol of free energy. Respiration cashes in the large denomination of energy banked in a single molecule of glucose (686 kcal/mol under standard conditions) for the small change of many molecules of ATP, which is more practical for the cell to spend on its work. This preview has introduced you to how glycolysis, the citric acid cycle, and oxidative phosphorylation fit into the process of cellular respiration. We are now ready to take a closer look at each of these three stages of respiration.

At key gateways into the apoptotic program, relay proteins integrate signals from several different sources and can send a cell down an apoptotic pathway. Often, the signal originates outside the cell, like the death-signaling molecule depicted in Figure 11.20b, which presumably was released by a neighboring cell. When a death-signaling ligand occupies a cell-surface receptor, this binding leads to activation of caspases and other enzymes that carry out apoptosis, without involving the mitochondrial pathway.

. This process of signal reception, transduction, and response is similar to what we have discussed throughout this chapter. In a twist on the classic scenario, two other types of alarm signals that can lead to apoptosis originate from inside the cell rather than from a cell-surface receptor. One signal 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. Mammalian cells make life-or-death "decisions" by somehow integrating the death signals and life signals they receive from these external and internal sources.

In many other cases of local signaling, signaling molecules are secreted by the signaling cell. Some molecules travel only short distances; such local regulators influence cells in the vicinity.

. This type of local signaling in animals is called paracrine signaling (Figure 11.5a). One class of local regulators in animals, growth factors, are compounds that stimulate nearby target cells to grow and divide. Numerous cells can simultaneously receive and respond to the growth factors produced by a single cell in their vicinity.

. In the case of an enzyme, if the changed amino acids are in the active site or some other crucial region, the altered enzyme might have a novel activity or might bind to a different substrate

. Under environmental conditions where the new function benefits the organism, natural selection would tend to favor the mutated form of the gene, causing it to persist in the population.

Some membrane proteins that actively transport ions contribute to the membrane potential. An example is the sodiumpotassium pump. Notice in Figure 7.15 that the pump does not translocate Na+ and K+ one for one, but pumps three sodium ions out of the cell for every two potassium ions it pumps into the cell.

. With each "crank" of the pump, there is a net transfer of one positive charge from the cytoplasm to the extracellular fluid, a process that stores energy as voltage.

The nucleus and its envelope

. Within the nucleus are the chromosomes, which appear as a mass of chromatin (DNA and associated proteins) and one or more nucleoli (singular, nucleolus), which function in ribosome synthesis. The nuclear envelope, which consists of two membranes separated by a narrow space, is perforated with pores and lined by the nuclear lamina.

Channel proteins that transport ions are called ion channels. Many ion channels function as gated channels, which open or close in response to a stimulus.

.For some gated channels, the stimulus is electrical. In a nerve cell, for example, an ion channel opens in response to an electrical stimulus, allowing a stream of potassium ions to leave the cell. (See the potassium ion channel at the beginning of this chapter.) This restores the cell's ability to fire again.

The sequence of steps shown in the figure is similar to many known pathways, including those triggered in yeast by mating factors and in animal cells by many growth factors.

.The signal is transmitted by a cascade of protein phosphorylations, each causing a shape change in the phosphorylated protein. The shape change results from the interaction of the newly added phosphate groups with charged or polar amino acids on the protein being phosphorylated (see Figure 5.14). The shape change in turn alters the function of the protein, most often activating it. In some cases, though, phosphorylation instead decreases the activity of the protein.

A closer look at the citric acid cycle : In the chemical structures, red type traces the fate of the two carbon atoms that enter the cycle via acetyl CoA (step 1), and blue type indicates the two carbons that exit the cycle as CO2 in steps 3 and 4. (The red type goes only through step 5 because the succinate molecule is symmetrical; the two ends cannot be distinguished from each other.) Notice that the carbon atoms that enter the cycle from acetyl CoA do not leave the cycle in the same turn. They remain in the cycle, occupying a different location in the molecules on their next turn, after another acetyl group is added. Therefore, the oxaloacetate regenerated at step 8 is made up of different carbon atoms each time around. In eukaryotic cells, all the citric acid cycle enzymes are located in the mitochondrial matrix except for the enzyme that catalyzes step 6, which resides in the inner mitochondrial membrane. Carboxylic acids are represented in their ionized forms, as —COO- , because the ionized forms prevail at the pH within the mitochondrion.

1 )Acetyl CoA (from oxidation of pyruvate) adds its two-carbon acetyl group to oxaloacetate, producing citrate. 2) Citrate is converted to its isomer, isocitrate, by removal of one water molecule and addition of another. 3) Isocitrate is oxidized, reducing NAD+ to NADH. Then the resulting compound loses a CO2 molecule 4) Another CO2 is lost, and the resulting compound is oxidized, reducing NAD+ to NADH. The remaining molecule is then attached to coenzyme A by an unstable bond 5) CoA is displaced by a phosphate group, which is transferred to GDP, forming GTP, a molecule with functions similar to ATP. GTP can also be used, as shown, to generate ATP. 6) Two hydrogens are transferred to FAD, forming FADH2 and oxidizing succinate. 7)Addition of a water molecule rearranges bonds in the substrate. (8) The substrate is oxidized, reducing NAD+ to NADH and regenerating oxaloacetate.

Linear Electron Flow: Light drives the synthesis of ATP and NADPH by energizing the two types of photosystems embedded in the thylakoid membranes of chloroplasts. The key to this energy transformation is a flow of electrons through the photosystems and other molecular components built into the thylakoid membrane. This is called linear electron flow, and it occurs during the light reactions of photosynthesis, as shown in Figure 10.14. The numbered steps in the text correspond to the numbered steps in the figure.

1) A photon of light strikes one of the pigment molecules in a light-harvesting complex of PS II, 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 excited state. The 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 the negative charge of an electron, as P680+ . 3) An enzyme catalyzes the splitting of a water molecule into two electrons, two hydrogen ions (H+ ), and an oxygen atom. The electrons are supplied one by one to the P680+ pair, each electron replacing one transferred to the primary electron acceptor. (P680+ is the strongest biological oxidizing agent known; its electron "hole" must be filled. This greatly facilitates the transfer of electrons from the split water molecule.) The H+ are released into the thylakoid space (interior of the thylakoid). The oxygen atom immediately combines with an oxygen atom generated by the splitting of another water molecule, forming O2.

The growth and metastasis of a malignant breast tumor: A series of genetic and m cellular changes contribute to a tumor becoming malignant (cancerous). The cells of malignant tumors grow in an uncontrolled way and can spread to neighboring tissues and, via lymph and blood vessels, to other parts of the body. The spread of cancer cells beyond their original site is called metastasis.

1) A tumor grows from 3 a single cancer cell. 2) Cancer cells invade neighboring tissue. 3) Cancer cells spread through lymph and blood vessels to other parts of the body 4) A small percentage of cancer cells may metastasize to another part of the body

Bacterial cell division by binary fission: The bacterium shown here has a single, circular chromosome.

1) Chromosome replication begins. Soon after, one copy of the origin moves rapidly toward the other end of the cell by a mechanism involving an actin-like protein. 2) Replication continues. One copy of the origin is now at each end of the cell. Meanwhile, the cell elongates. 3) Replication finishes. The plasma membrane is pinched inward by a tubulin-like protein, and a new cell wall is deposited. 4) Two daughter cells result.

Communication between mating yeast cells: Saccharomyces cerevisiae cells use chemical signaling to identify cells of opposite mating type and initiate the mating process. The two mating types and their corresponding chemical signaling molecules, or mating factors, are called a and α

1) Exchange of mating factors. Each mating cell type secretes a mating factor that binds to receptors on the other mating type. 2) Mating. Binding of the factors to receptors induces changes in the cells that lead to their fusion. 3) New a/α cell. The nucleus of the fused cell includes all the genes from the a and α cells.

The Stages of Cellular Respiration: A Preview The harvesting of energy from glucose by cellular respiration is a cumulative function of three metabolic stages. We list them here along with a color-coding scheme we will use throughout the chapter to help you keep track of the big picture:

1) GLYCOLYSIS (color-coded blue throughout the chapter) 2)PYRUVATE OXIDATION and the CITRIC ACID CYCLE (color-coded light orange and dark orange) 3) OXIDATIVE PHOSPHORYLATION: Electron transport and chemiosmosis (color-coded purple)

ATP synthase, a molecular mill. Multiple ATP synthases reside in eukaryotic mitochondrial and chloroplast membranes and in prokaryotic plasma membranes.

1) H+ ions flowing down their gradient enter a channel in a stator, which is anchored in the membrane. 2) H+ ions enter binding sites within a rotor, changing the shape of each subunit so that the rotor spins within the membrane. 3) Each H+ ion makes one complete turn before leaving the rotor and passing through a second channel in the stator into the mitochondrial matrix. 4) Spinning of the rotor causes an internal rod to spin as well. This rod extends like a stalk into the knob below it, which is held stationary by part of the stator. 5) Turning of the rod activates catalytic sites in the knob that produce ATP from ADP and phosphate

Chromosome duplication and distribution during cell division.

1) One of the multiple chromosomes in a eukaryotic cell is represented here, not yet duplicated. Normally it would be a long, thin chromatin fiber containing one DNA molecule and associated proteins; here its condensed form is shown for illustration purposes only. Chromosome duplication (including DNA replication) and condensation 2) Once duplicated, a chromosome consists of two sister chromatids connected along their entire lengths by sister chromatid cohesion. Each chromatid contains a copy of the DNA molecule. Separation of sister chromatids into two chromosomes 3) Molecular and mechanical processes separate the sister chromatids into two chromosomes and distribute them to two daughter cells.

The active site and catalytic cycle of an enzyme: An enzyme can convert one or more reactant molecules to one or more product molecules. The enzyme shown here converts two substrate molecules to two product molecules.

1) Substrates enter the 1 active site; enzyme changes shape such that its active site enfolds the substrates (induced fit). 2) Substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds. 3) The active site lowers EA and speeds up the reaction (see text). 4) Substrates are converted to products. 5) Products are released. 6) Active site is available for two new substrate molecules.

Review: relationships among organelles of the endomembrane system. The red arrows show some of the migration pathways for membranes and the materials they enclose.

1) The nuclear envelope is connected to the rough ER, which is also continuous 2) Membranes and proteins produced by the ER move via transport vesicles to the Golgi. 3) The Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes, other types of specialized vesicles, and vacuoles. 4)The lysosome is available for fusion with another vesicle for digestion. 5)A transport vesicle carries proteins to the plasma membrane for secretion. 6) The plasma membrane expands by fusion of vesicles; proteins are secreted from the cell.

The light reactions and chemiosmosis: Current model of the organization of the thylakoid membrane. The gold arrows track the linear electron flow outlined in Figure 10.14. At least three steps in the light reactions contribute to the H+ gradient across the thylakoid membrane:

1) Water is split by photosystem II on the side of the membrane facing the thylakoid space; (2) as plastoquinone (Pq) transfers electrons to the cytochrome complex, four protons are translocated across the membrane into the thylakoid space; and (3)a hydrogen ion is removed from the stroma when it is taken up by NADP+ . Notice that in step 2, hydrogen ions are being pumped from the stroma into the thylakoid space, as in Figure 10.17. The diffusion of H+ from the thylakoid space back to the stroma (along the H+ concentration gradient) powers the ATP synthase. These light-driven reactions store chemical energy in NADPH and ATP, which shuttle the energy to the carbohydrateproducing Calvin cycle.

Sutherland's work suggested that the process going on at the receiving end of a cellular communication can be dissected into three stages: reception, transduction, and response (Figure 11.6):

1)Reception. Reception is the target cell's detection of a signaling molecule coming from outside the cell. A chemical signal is "detected" when the signaling molecule binds to a receptor protein located at the cell's surface (or inside the cell, to be discussed later). 2) Transduction. The binding of the signaling molecule changes the receptor protein in some way, initiating the process of transduction. The transduction stage converts the signal to a form that can bring about a specific cellular response. In Sutherland's system, the binding of epinephrine to a receptor protein in a liver cell's plasma membrane leads to activation of glycogen phosphorylase in the cytosol. Transduction sometimes occurs in a single step but more often requires a sequence of changes in a series of different molecules—a signal transduction pathway. The molecules in the pathway are often called relay molecules; three are shown as an example. 3) Response. In the third stage of cell signaling, the transduced signal finally triggers a specific cellular response. The response may be almost any imaginable cellular activity— such as catalysis by an enzyme (for example, glycogen phosphorylase), rearrangement of the cytoskeleton, or activation of specific genes in the nucleus. The cell-signaling process helps ensure that crucial activities like these occur in the right cells, at the right time, and in proper coordination with the activities of other cells of the organism. We'll now explore the mechanisms of cell signaling in more detail, including a discussion of regulation and termination of the process.

4) Each photoexcited electron passes from the primary electron acceptor of PS II to PS I via an electron transport chain, 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 up of the electron carrier plastoquinone (Pq), a cytochrome complex, and a protein called plastocyanin (Pc). Each component carries out redox reactions as electrons flow down the electron transport chain, releasing free energy that is used to pump protons (H+ ) into the thylakoid space, contributing to a proton gradient across the thylakoid membrane. 5) The potential energy stored in the proton gradient is used to make ATP in a process called chemiosmosis, to be discussed shortly

6) Meanwhile, light energy has been transferred via lightharvesting 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 is then transferred to PS I's primary electron acceptor, creating an electron "hole" in the P700—which we now can call P700+ . In other words, P700+ can now act as an electron acceptor, accepting an electron that reaches the bottom of the electron transport chain from PS II. 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. Electrons in NADPH are at a higher energy level than they are in water (where they started), so they are more readily available for the reactions of the Calvin cycle. This process also removes an H+ from the stroma.

Energy Transformations in the Cell: Photosynthesis and Cellular Respiration (Chapters 8-10)

7)In chloroplasts, the process of photosynthesis uses the energy of light to convert CO2 and H2O to organic molecules, with O2 as a by-product. (See Figure 10.22.) 8) In mitochondria, organic molecules are broken down by cellular respiration, capturing energy in molecules of ATP, which are used to power the work of the cell, such as protein synthesis and active transport. CO2 and H2O are by-products. (See Figures 8.9-8.11, 9.2, and 9.16.)

Movement Across Cell Membranes (Chapter 7)

9)Water diffuses into and out of the cell directly through the plasma membrane and by facilitated diffusion through aquaporins. (See Figure 7.1.) 10) By passive transport, the CO2 used in photosynthesis diffuses into the cell and the O2 formed as a by-product of photosynthesis diffuses out of the cell. Both solutes move down their concentration gradients. (See Figures 7.10 and 10.22.) 11) In active transport, energy (usually supplied by ATP) is used to transport a solute against its concentration gradient. (See Figure 7.16.) 12) Exocytosis (shown in step 5) and endocytosis move larger materials out of and into the cell. (See Figures 7.9 and 7.19.)

Transcription

: In the nucleus, the information contained in a DNA sequence is transferred to messenger RNA (mRNA) by an enzyme called RNA polymerase. After their synthesis, mRNA molecules leave the nucleus via nuclear pores.

Membrane proteins:

: Proteins embedded in the plasma membrane or other cellular membranes help transport substances across membranes, conduct signals from one side of the membrane to the other, and participate in other crucial cellular functions. Many proteins are able to move within the membrane.

distinct structural directionality of Golgi stack

A Golgi stack has a distinct structural directionality, with the membranes of cisternae on opposite sides of the stack differing in thickness and molecular composition. The two sides of a Golgi stack are referred to as the cis face and the trans face; these act, respectively, as the receiving and shipping departments of the Golgi apparatus. The term cis means "on the same side," and the cis face is usually located near the ER. Transport vesicles move material from the ER to the Golgi apparatus. A vesicle that buds from the ER can add its membrane and the contents of its lumen to the cis face by fusing with a Golgi membrane on that side. The trans face ("on the opposite side") gives rise to vesicles that pinch off and travel to other sites.

Cotransport: active transport driven by a concentration gradient

A carrier protein, such as this H+ /sucrose cotransporter in a plant cell (top), is able to use the diffusion of H+ down its electrochemical gradient into the cell to drive the uptake of sucrose. (The cell wall is not shown.) Although not technically part of the cotransport process, an ATP-driven proton pump is shown here (bottom), which concentrates H+ outside the cell. The resulting H+ gradient represents potential energy that can be used for active transport—of sucrose, in this case. Thus, ATP hydrolysis indirectly provides the energy necessary for cotransport.

The lipid bilayer is only one aspect of the gatekeeper system responsible for a cell's selective permeability.

A charged atom or molecule and its surrounding shell of water (see Figure 3.8) are even less likely to penetrate the hydrophobic interior of the membrane. Furthermore, the lipid bilayer is only one aspect of the gatekeeper system responsible for a cell's selective permeability. Proteins built into the membrane play key roles in regulating transport.

. The cell cycle control system has been compared to the control device of a washing machine. Like the washer's timing device, the cell cycle control system proceeds on its own, according to a built-in clock. However, just as a washer's cycle is subject to both internal control (such as the sensor that detects when the tub is filled with water) and external adjustment (such as starting or stopping the machine), the cell cycle is regulated at certain checkpoints by both internal and external signals

A checkpoint in the cell cycle is a control point where stop and go-ahead signals can regulate the cycle. Three important checkpoints are found in the G1, G2, and M phases (red gates in Figure 12.15), which will be discussed shortly.

cilium

A cilium may also act as a signal-receiving "antenna" for the cell. Cilia that have this function are generally nonmotile, and there is only one per cell. (In fact, in vertebrate animals, it appears that almost all cells have such a cilium, which is called a primary cilium.) Membrane proteins on this kind of cilium transmit molecular signals from the cell's environment to its interior, triggering signaling pathways that may lead to changes in the cell's activities. Cilium-based signaling appears to be crucial to brain function and to embryonic development.

Our understanding of signaling pathways involving cyclic AMP or related messengers has allowed us to develop treatments for certain conditions in humans. In one pathway, a molecule similar to cAMP called cyclic GMP (cGMP) is produced by a muscle cell in response to the gas nitric oxide (NO) after it is released by a neighboring cell. cGMP then acts as a second messenger that causes relaxation of muscles, such as those in the walls of arteries.

A compound that inhibits the hydrolysis of cGMP to GMP, thus prolonging the signal, was originally prescribed for chest pains because it relaxed blood vessels and increased blood flow to the heart muscle. Under the trade name Viagra, this compound is now widely used as a treatment for erectile dysfunction in human males. Because Viagra leads to dilation of blood vessels, it also allows increased blood flow to the penis, optimizing physiological conditions for penile erections.

Transformations between potential and kinetic energy.

A diver has more potential energy on the platform than in the water. Diving converts potential energy to kinetic energy Climbing up converts the kinetic energy of muscle movement to potential energy. A diver has less potential energy in the water than on the platform.

Fats make excellent fuels, in large part due to their chemical structure and the high energy level of their electrons (present in many C—H bonds, equally shared between carbon and hydrogen) compared to those of carbohydrates.

A gram of fat oxidized by respiration produces more than twice as much ATP as a gram of carbohydrate. Unfortunately, this also means that a person trying to lose weight must work hard to use up fat stored in the body because so many calories are stockpiled in each gram of fat.

energy coupling

A key feature in the way cells manage their energy resources to do this work is energy coupling, the use of an exergonic process to drive an endergonic one. ATP is responsible for mediating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work.

Cytoplasmic streaming in plant cells

A layer of cytoplasm cycles around the cell, moving over tracks of actin filaments. Myosin motors attached to some organelles drive the streaming by interacting with the actin (LM).

Ion-channel receptors (ligand-gated ion channels)

A ligand-gated ion channel is a type of membrane channel receptor containing a region that can act as a "gate," opening or closing the channel when the receptor changes shape. When a signaling molecule binds as a ligand to the channel receptor, the channel opens or closes, allowing or blocking the flow of specific ions, such as Na+ or Ca2+. Like the other receptors we have discussed, these proteins bind the ligand at a specific site on their extracellular sides.

Lysosomes: Digestive Compartments

A lysosome is a membranous sac of hydrolytic enzymes that many eukaryotic cells use to digest (hydrolyze) macromolecules. Lysosomal enzymes work best in the acidic environment found in lysosomes. If a lysosome breaks open or leaks its contents, the released enzymes are not very active because the cytosol has a near-neutral pH. However, excessive leakage from a large number of lysosomes can destroy a cell by self-digestion.

All cells contain chromosomes, which carry genes in the form of DNA. And all cells have ribosomes, tiny complexes that make proteins according to instructions from the genes

A major difference between prokaryotic and eukaryotic cells is the location of their DNA. In a eukaryotic cell, most of the DNA is in an organelle called the nucleus, which is bounded by a double membrane (see Figure 6.8). In a prokaryotic cell, the DNA is concentrated in a region that is not membrane-enclosed, called the nucleoid.

. Some metabolic pathways release energy by breaking down complex molecules to simpler compounds. These degradative processes are called catabolic pathways, or breakdown pathways.

A major pathway of catabolism is cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water. (Pathways can have more than one starting molecule and/or product.) Energy that was stored in the organic molecules becomes available to do the work of the cell, such as ciliary beating or membrane transport.

A membrane remains fluid to a lower temperature if

A membrane remains fluid as temperature decreases until the phospholipids settle into a closely packed arrangement and the membrane solidifies, much as bacon grease forms lard when it cools. The temperature at which a membrane solidifies depends on the types of lipids it is made of. As the temperature decreases, the membrane remains fluid to a lower temperature if it is rich in phospholipids with unsaturated hydrocarbon tails (see Figures 5.10 and 5.11).

Endoplasmic reticulum (ER).

A membranous system of interconnected tubules and flattened sacs called cisternae, the ER is also continuous with the nuclear envelope, as shown in the cutaway diagram at the top. The membrane of the ER encloses a continuous compartment called the ER lumen (or cisternal space). Rough ER, which is studded on its outer surface with ribosomes, can be distinguished from smooth ER in the electron micrograph (TEM). Transport vesicles bud off from a region of the rough ER called transitional ER and travel to the Golgi apparatus and other destinations.

Intracellular Receptors: Intracellular receptor proteins are found in either the cytoplasm or nucleus of target cells. To reach such a receptor, a signaling molecule passes through the target cell's plasma membrane.

A number of important signaling molecules can do this because they are either hydrophobic enough or small enough to cross the hydrophobic interior of the membrane (see Concept 7.1). The hydrophobic signaling molecules include both steroid hormones and thyroid hormones of animals.

centrioles

A pair of centrioles is located at the center of the centrosome, but they are not essential for cell division: If the centrioles are destroyed with a laser microbeam, a spindle nevertheless forms during mitosis. In fact, centrioles are not even present in plant cells, which do form mitotic spindles.

Amphiphatic

A phospholipid is an amphipathic molecule, meaning it has both a hydrophilic ("water-loving") region and a hydrophobic ("water-fearing") region (see Figure 5.11). Other types of membrane lipids are also amphipathic. A phospholipid bilayer can exist as a stable boundary between two aqueous compartments because the molecular arrangement shelters the hydrophobic tails of the phospholipids from water while exposing the hydrophilic heads to water

nucleolus

A prominent structure within the nondividing nucleus is the nucleolus (plural, nucleoli), which appears through the electron microscope as a mass of densely stained granules and fibers adjoining part of the chromatin. Here a type of RNA called ribosomal RNA (rRNA) is synthesized from instructions in the DNA. Also in the nucleolus, proteins imported from the cytoplasm are assembled with rRNA into large and small subunits of ribosomes. These subunits then exit the nucleus through the nuclear pores to the cytoplasm, where a large and a small subunit can assemble into a ribosome. Sometimes there are two or more nucleoli; the number depends on the species and the stage in the cell's reproductive cycle.

In the case of the epinephrine circulating throughout the bloodstream of the impala in Figure 11.1, the hormone encounters many types of cells, but only certain target cells detect and react to the epinephrine molecule.

A receptor protein on or in the target cell allows the cell to "hear" the signal and respond to it. The signaling molecule is complementary in shape to a specific site on the receptor and attaches there, like a hand in a glove. The signaling molecule acts as a ligand, the term for a molecule that specifically binds to another (often larger) molecule.

Surprisingly, perhaps, it may be beneficial under certain conditions to reduce the efficiency of cellular respiration.

A remarkable adaptation is shown by hibernating mammals, which overwinter in a state of inactivity and lowered metabolism. Although their internal body temperature is lower than normal, it still must be kept significantly higher than the external air temperature.

Oxidative phosphorylation accounts for almost 90% of the ATP generated by respiration.

A smaller amount of ATP is formed directly in a few reactions of glycolysis and the citric acid cycle by a mechanism called substrate-level phosphorylation (Figure 9.7).

Cotransport: Coupled Transport by a Membrane Protein

A solute that exists in different concentrations across a membrane can do work as it moves across that membrane by diffusion down its concentration gradient. This is analogous to water that has been pumped uphill and performs work as it flows back down.

The remainder of this chapter focuses on one of those properties: the ability to regulate transport across cellular boundaries, a function essential to the cell's existence. We will see once again that form fits function: The fluid mosaic model helps explain how membranes regulate the cell's molecular traffic.

A steady traffic of small molecules and ions moves across the plasma membrane in both directions. Consider the chemical exchanges between a muscle cell and the extracellular fluid that bathes it.

Transmission electron microscopy (TEM).

A transmission electron microscope profiles a thin section of a specimen. This TEM shows a section through a tracheal cell, revealing its internal structure. In preparing the specimen, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections.

electrogenic pump

A transport protein that generates voltage across a membrane is called an electrogenic pump. The sodium-potassium pump appears to be the major electrogenic pump of animal cells

exocytosis: As you saw in Figure 6.15, the cell secretes certain molecules by the fusion of vesicles with the plasma membrane; this process is called exocytosis

A transport vesicle that has budded from the Golgi apparatus moves along microtubules of the cytoskeleton to the plasma membrane. When the vesicle membrane and plasma membrane come into contact, specific proteins rearrange the lipid molecules of the two bilayers so that the two membranes fuse. The contents of the vesicle spill out of the cell, and the vesicle membrane becomes part of the plasma membrane (see Figure 7.9, step 4).

cell fractionation

A useful technique for studying cell structure and function is cell fractionation which takes cells apart and separates major organelles and other subcellular structures from one another.

Reception: A signaling molecule binds to a receptor protein, causing it to change shape

A wireless router may broadcast its network signal indiscriminately, but often it can be joined only by computers with the correct password: Reception of the signal depends on the receiver. Similarly, the signals emitted by an a mating type yeast cell are "heard" only by its prospective mates, 훂 cells

primary cell wall

A young plant cell first secretes a relatively thin and flexible wall called the primary cell wall (see the micrograph in Figure 6.27). Between primary walls of adjacent cells is the middle lamella, a thin layer rich in sticky polysaccharides called pectins. The middle lamella glues adjacent cells together. (Pectin is used in cooking as a thickening agent in ams and jellies.) When the cell matures and stops growing, it strengthens its wall. Some plant cells do this simply by secreting hardening substances into the primary wall

Figure 8.13 graphs the energy changes for a hypothetical exergonic reaction that swaps portions of two reactant molecules:

AB + CD S AC + BD Reactants Products The activation of the reactants is represented by the uphill portion of the graph, in which the free-energy content of the reactant molecules is increasing. At the summit, when energy equivalent to EA has been absorbed, the reactants are in the transition state: They are activated, and their bonds can be broken. As the atoms then settle into their new, more stable bonding arrangements, energy is released to the surroundings. This corresponds to the downhill part of the curve, which shows the loss of free energy by the molecules.

How ATP drives transport and mechanical work?

ATP hydrolysis causes changes in the shapes and binding affinities of proteins. This can occur either (a) directly, by phosphorylation, as shown for a membrane protein carrying out active transport of a solute (see also Figure 7.15), or (b) indirectly, via noncovalent binding of ATP and its hydrolytic products, as is the case for motor proteins that move vesicles (and other organelles) along cytoskeletal "tracks" in the cell (see also Figure 6.21).

Chemiosmosis: The Energy-Coupling Mechanism: Populating the inner membrane of the mitochondrion or the prokaryotic plasma membrane are many copies of a protein complex called ATP synthase, the enzyme that makes ATP from ADP and inorganic phosphate (Figure 9.14).

ATP synthase works like an ion pump running in reverse. Ion pumps usually use ATP as an energy source to transport ions against their gradients. Enzymes can catalyze a reaction in either direction, depending on the ∆G for the reaction, which is affected by the local concentrations of reactants and products (see Concepts 8.2 and 8.3).

As for the fates of photosynthetic products, enzymes in the chloroplast and cytosol convert the G3P made in the Calvin cycle to many other organic compounds. In fact, the sugar made in the chloroplasts supplies the entire plant with chemical energy and carbon skeletons for the synthesis of all the major organic molecules of plant cells.

About 50% of the organic material made by photosynthesis is consumed as fuel for cellular respiration in plant cell mitochondria.

Excitation of Chlorophyll by Light What exactly happens when chlorophyll and other pigments absorb light? The colors corresponding to the absorbed wavelengths disappear from the spectrum of the transmitted and reflected light, but energy cannot disappear. When a molecule absorbs a photon of light, one of the molecule's electrons is elevated to an orbital where it has more potential energy (see Figure 2.6b). When the electron is in its normal orbital, the pigment molecule is said to be in its ground state.

Absorption of a photon boosts an electron to an orbital of higher energy, and the pigment molecule is then said to be in an excited state. The only photons absorbed are those whose energy is exactly equal to the energy difference between the ground state and an excited state, and this energy difference varies from one kind of molecule to another. Thus, a particular compound absorbs only photons corresponding to specific wavelengths, which is why each pigment has a unique absorption spectrum.

The initial investment of energy for starting a reaction— the energy required to contort the reactant molecules so the bonds can break—is known as the free energy of activation, or activation energy, abbreviated EA in this book. We can think of activation energy as the amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the "downhill" part of the reaction can begin.

Activation energy is often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings.

One type of tissue, called brown fat, is made up of cells packed full of mitochondria. The inner mitochondrial membrane contains a channel protein called the uncoupling protein that allows protons to flow back down their concentration gradient without generating ATP.

Activation of these proteins in hibernating mammals results in ongoing oxidation of stored fuel (fats), generating heat without any ATP production. In the absence of such an adaptation, the buildup of ATP would eventually cause cellular respiration to be shut down by regulatory mechanisms that will be discussed later.In the Scientific Skills Exercise, you can work with data in a related but different case where a decrease in metabolic efficiency in cells is used to generate heat.

Technically, green cells are the only autotrophic parts of the plant. The rest of the plant depends on organic molecules exported from leaves via veins (see Figure 10.22, top). In most plants, carbohydrate is transported out of the leaves to the rest of the plant in the form of sucrose, a disaccharide.

After arriving at nonphotosynthetic cells, the sucrose provides raw material for cellular respiration and a multitude of anabolic pathways that synthesize proteins, lipids, and other products. A considerable amount of sugar in the form of glucose is linked together to make the polysaccharide cellulose (see Figure 5.6c), especially in plant cells that are still growing and maturing. Cellulose, the main ingredient of cell walls, is the most abundant organic molecule in the plant—and probably on the surface of the planet.

Golgi apparatus

After leaving the ER, many transport vesicles travel to the Golgi apparatus. We can think of the Golgi as a warehouse for receiving, sorting, shipping, and even some manufacturing. Here, products of the ER, such as proteins, are modified and stored and then sent to other destinations. Not surprisingly, the Golgi apparatus is especially extensive in cells specialized for secretion.

In this chapter, we consider how cells harvest the chemical energy stored in organic molecules and use it to generate ATP, the molecule that drives most cellular work

After presenting some basic information about respiration, we'll focus on three key pathways of respiration: glycolysis, pyruvate oxidation and the citric acid cycle, and oxidative phosphorylation. We'll also consider fermentation, a somewhat simpler pathway coupled to glycolysis that has deep evolutionary roots.

transport vesicles

After secretory proteins are formed, the ER membrane keeps them separate from proteins in the cytosol, which are produced by free ribosomes. Secretory proteins depart from the ER wrapped in the membranes of vesicles that bud like bubbles from a specialized region called transitional ER (see Figure 6.11). Vesicles in transit from one part of the cell to another are called transport vesicles; we will discuss their fate shortly.

The cell also controls its catabolism. If the cell is working hard and its ATP concentration begins to drop, respiration speeds up. When there is plenty of ATP to meet demand, respiration slows down, sparing valuable organic molecules for other functions.

Again, control is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway. As shown in Figure 9.20, one important switch is phosphofructokinase, the enzyme that catalyzes step 3 of glycolysis (see Figure 9.9). That is the first step that commits the substrate irreversibly to the glycolytic pathway. By controlling the rate of this step, the cell can speed up or slow down the entire catabolic process. Phosphofructokinase can thus be considered the pacemaker of respiration.

The behavior of aldosterone is a representative example of how steroid hormones work. This hormone is secreted by cells of the adrenal gland, a gland that lies above the kidney.

Aldosterone then travels through the blood and enters cells all over the body. However, a response occurs only in kidney cells, which contain receptor molecules for aldosterone. In these cells, the hormone binds to and activates the receptor protein. With aldosterone attached, the active form of the receptor protein then enters the nucleus and turns on specific genes that control water and sodium flow in kidney cells, ultimately affecting blood volume (Figure 11.9).

Similarities between prokaryotes and eukaryotes

All cells share certain basic features: They are all bounded by a selective barrier, called the plasma membrane. Inside all cells is a semifluid, jellylike substance called cytosol, in which subcellular components are suspended.

Microtubules

All eukaryotic cells have microtubules, hollow rods constructed from globular proteins called tubulins. Each tubulin protein is a dimer, a molecule made up of two subunits. A tubulin dimer consists of two slightly different polypeptides, α-tubulin and β-tubulin. Microtubules grow in length by adding tubulin dimers; they can also be disassembled and their tubulins used to build microtubules elsewhere in the cell. Because of the orientation of tubulin dimers, the two ends of a microtubule are slightly different. One end can accumulate or release tubulin dimers at a much higher rate than the other, thus growing and shrinking significantly during cellular activities. (This is called the "plus end," not because it can only add tubulin proteins but because it's the end where both "on" and "off" rates are much higher.)

Comparing Fermentation with Anaerobic and Aerobic Respiration: Fermentation, anaerobic respiration, and aerobic respiration are three alternative cellular pathways for producing ATP by harvesting the chemical energy of food.

All three use glycolysis to oxidize glucose and other organic fuels to pyruvate, with a net production of 2 ATP by substrate-level phosphorylation. And in all three pathways, NAD+ is the oxidizing agent that accepts electrons from food during glycolysis

Allosteric Regulation of Enzymes: In many cases, the molecules that naturally regulate enzyme activity in a cell behave something like reversible noncompetitive inhibitors (see Figure 8.18c): These regulatory molecules change an enzyme's shape and the functioning of its active site by binding to a site elsewhere on the molecule, via noncovalent interactions.

Allosteric regulation is the term used to describe any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme's activity.

Sugars, amino acids, and other nutrients enter the cell, and metabolic waste products leave it. The cell takes in O2 for use in cellular respiration and expels CO2.

Also, the cell regulates its concentrations of inorganic ions, such as Na+ , K+ , Ca2+ , and Cl- , by shuttling them one way or the other across the plasma membrane. Although the heavy traffic through them may seem to suggest otherwise, cell membranes are selectively permeable, and substances do not cross the barrier indiscriminately. The cell is able to take up some small molecules and ions and exclude others.

The Extracellular Matrix (ECM) of Animal Cells

Although animal cells lack walls akin to those of plant cells, they do have an elaborate extracellular matrix (ECM). The main ingredients of the ECM are glycoproteins and other carbohydrate-containing molecules secreted by the cells. (Recall that glycoproteins are proteins with covalently bonded carbohydrates, usually short chains of sugars.) The most abundant glycoprotein in the ECM of most animal cells is collagen, which forms strong fibers outside the cells (see Figure 5.18)

The energy changes of electrons during their linear flow through the light reactions are shown in a mechanical analogy in Figure 10.15

Although the scheme shown in Figures 10.14 and 10.15 may seem complicated, do not lose track of the big picture: The light reactions use solar power to generate ATP and NADPH, which provide chemical energy and reducing power, respectively, to the carbohydrate-synthesizing reactions of the Calvin cycle.

Proteins can also be used for fuel, but first they must be digested to their constituent amino acids. Many of the amino acids are used by the organism to build new proteins.

Amino acids present in excess are converted by enzymes to intermediates of glycolysis and the citric acid cycle. Before amino acids can feed into glycolysis or the citric acid cycle, their amino groups must be removed, a process called deamination. The nitrogenous waste is excreted from the animal in the form of ammonia (NH3), urea, or other waste products.

C4 Plants: The C4 plants are so named because they preface the Calvin cycle with an alternate mode of carbon fixation that forms a four-carbon compound as its first product. The C4 pathway is believed to have evolved independently at least 45 separate times and is used by several thousand species in at least 19 plant families.

Among the C4 plants important to agriculture are sugarcane and corn, members of the grass family.

Animal cell

An animal cell fares best in an isotonic environment unless it has special adaptations that offset the osmotic uptake or loss of water.

How does an enzyme catalyze a reaction?

An enzyme catalyzes a reaction by lowering the EA barrier (Figure 8.14), enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures, as we'll discuss shortly

When does an infected person develop diarrhea?

An infected person quickly develops profuse diarrhea and if left untreated can soon die from the loss of water and salts.

The Laws of Energy Transformation: The study of the energy transformations that occur in a collection of matter is called thermodynamics. Scientists use the word system to denote the matter under study; they refer to the rest of the universe—everything outside the system—as the surroundings.

An isolated system, such as that approximated by liquid in a thermos bottle, is unable to exchange either energy or matter with its surroundings outside the thermos. In an open system, energy and matter can be transferred between the system and its surroundings. Organisms are open systems. They absorb energy—for instance, light energy or chemical energy in the form of organic molecules—and release heat and metabolic waste products, such as carbon dioxide, to the surroundings. Two laws of thermodynamics govern energy transformations in organisms and all other collections of matter.

The structure of the spindle correlates well with its function during anaphase.

Anaphase begins suddenly when the cohesins holding together the sister chromatids of each chromosome are cleaved by an enzyme called separase. Once separated, the chromatids become individual chromosomes that move toward opposite ends of the cell.

Biologists are currently working out the pathways that link signals originating inside and outside the cell with the responses by cyclin-dependent kinases and other proteins. An example of an internal signal occurs at the third important checkpoint, the M checkpoint (Figure 12.17b).

Anaphase, the separation of sister chromatids, does not begin until all the chromosomes are properly attached to the spindle at the metaphase plate. Researchers have learned that as long as some kinetochores are unattached to spindle microtubules, the sister chromatids remain together, delaying anaphase.

Daughter chromosomes

Anaphase: • Anaphase is the shortest stage of mitosis, often lasting only a few minutes. • Anaphase begins when the cohesin proteins are cleaved. This allows the two sister chromatids of each pair to part suddenly. Each chromatid thus becomes an independent chromosome. • The two new daughter chromosomes begin moving toward opposite ends of the cell as their kinetochore microtubules shorten. Because these microtubules are attached at the centromere region, the centromeres are pulled ahead of the arms, moving at a rate of about 1 µm/min. • The cell elongates as the nonkinetochore microtubules lengthen. • By the end of anaphase, the two ends of the cell have equivalent—and complete— collections of chromosomes.

ion channel

Another type of transport protein is the ion channel shown here; it allows potassium ions to pass through the membrane. To understand how the plasma membrane and its proteins enable cells to survive and function, we begin by examining membrane structure, then explore how plasma membranes control transport into and out of cells.

How do the kinetochore microtubules function in this poleward movement of chromosomes?

Apparently, two mechanisms are in play, both involving motor proteins. (To review how motor proteins move an object along a microtubule, see Figure 6.21.) Results of a cleverly designed experiment suggested that motor proteins on the kinetochores "walk" the chromosomes along the microtubules, which depolymerize at their kinetochore ends after the motor proteins have passed (Figure 12.9). (This is referred to as the "Pac-man" mechanism because of its resemblance to the arcade game character that moves by eating all the dots in its path.)

Research Method - Cell Fractionation

Application : Cell fractionation is used to separate (fractionate) cell components based on size and density. Technique :Cells are homogenized in a blender to break them up. The resulting mixture (homogenate) is centrifuged. The supernatant (the liquid above the pellet) is poured into another tube and centrifuged at a higher speed for a longer period. This process is repeated several times. This "differential centrifugation" results in a series of pellets, each containing different cell components. Results :In early experiments, researchers used microscopy to identify the organelles in each pellet and biochemical methods to determine their metabolic functions. These identifications established a baseline for this method, enabling today's researchers to know which cell fraction they should collect in order to isolate and study particular organelles.

Research Method: Determining an Absorption Spectrum

Application: An absorption spectrum is a visual representation of how well a particular pigment absorbs different wavelengths of visible light. Absorption spectra of various chloroplast pigments help scientists decipher the role of each pigment in a plant Technique: A spectrophotometer measures the relative amounts of light of different wavelengths absorbed and transmitted by a pigment solution. 1) White light is separated into colors (wavelengths) by a prism. 2) One by one, the different colors of light are passed through the sample (chlorophyll in this example). Green light and blue light are shown here. 3) The transmitted light strikes a photoelectric tube, which converts the light energy to electricity. 4) The electric current is measured by a galvanometer. The meter indicates the fraction of light transmitted through the sample, from which we can determine the amount of light absorbed. Slit moves to pass light of selected wavelength. The high transmittance (low absorption) reading indicates that chlorophyll absorbs very little green light. The low transmittance (high absorption) reading indicates that chlorophyll absorbs most blue light. results: See Figure 10.10a for absorption spectra of three types of chloroplast pigments.

What happens as a cell increases in size?

As a cell (or any other object) increases in size, its surface area grows proportionately less than its volume. (Area is proportional to a linear dimension squared, whereas volume is proportional to the linear dimension cubed.) Thus, a smaller object has a greater ratio of surface area to volume (Figure 6.7). The Scientific Skills Exercise gives you a chance to calculate the volumes and surface areas of two actual cells— a mature yeast cell and a cell budding from it. To see different ways organisms maximize the surface area of cells, see Make Connections Figure 33.9.

What is the result of the signal's amplication?

As a result of the signal's amplification, a small number of epinephrine molecules binding to receptors on the surface of a liver cell or muscle cell can lead to the release of hundreds of millions of glucose molecules from glycogen.

Cell division plays several important roles in life. When a prokaryotic cell divides, it is actually reproducing, since the process gives rise to a new organism (another cell). The same is true of any unicellular eukaryote, such as the amoeba shown in Figure 12.2a.

As for multicellular eukaryotes, cell division enables each of these organisms to develop from a single cell—the fertilized egg. A two-celled embryo, the first stage in this process, is shown in Figure 12.2b. And cell division continues to function in renewal and repair in fully grown multicellular eukaryotes, replacing cells that die from accidents or normal wear and tear. For example, dividing cells in your bone marrow continuously make new blood cells (Figure 12.2c).

. Some cells use this fivestep pathway to synthesize the amino acid isoleucine from threonine, another amino acid

As isoleucine accumulates, it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the pathway. Feedback inhibition thereby prevents the cell from making more isoleucine than is necessary and thus wasting chemical resources.

The fluctuating activities of different cyclin-Cdk complexes are of major importance in controlling all the stages of the cell cycle; they also give the go-ahead signals at some checkpoints.

As mentioned above, MPF controls the cell's passage through the G2 checkpoint. Cell behavior at the G1 checkpoint is also regulated by the activity of cyclin-Cdk protein complexes. Animal cells appear to have at least three Cdk proteins and several different cyclins that operate at this checkpoint. Next, let's consider checkpoints in more detail.

Sutherland found that the binding of epinephrine to the plasma membrane of a liver cell elevates the cytosolic concentration of cyclic AMP (cAMP; cyclic adenosine monophosphate).

As shown in Figure 11.11, an enzyme embedded in the plasma membrane, adenylyl cyclase (also known as adenylate cyclase), converts ATP to cAMP in response to an extracellular signal—in this case, provided by epinephrine.

The cytoskeleton

As shown in this fluorescence micrograph, the cytoskeleton extends throughout the cell. The cytoskeletal elements have been tagged with different fluorescent molecules: green for microtubules and reddish-orange for microfilaments. A third component of the cytoskeleton, intermediate filaments, is not evident here. (The blue color tags the DNA in the nucleus.)

Glycolysis harvests chemical energy by oxidizing glucose to pyruvate. The word glycolysis means "sugar splitting," and that is exactly what happens during this pathway. Glucose, a six-carbon sugar, is split into two three-carbon sugars. These smaller sugars are then oxidized and their remaining atoms rearranged to form two molecules of pyruvate. (Pyruvate is the ionized form of pyruvic acid.)

As summarized in Figure 9.8, glycolysis can be divided into two phases: the energy investment phase and the energy payoff phase. During the energy investment phase, the cell actually spends ATP. This investment is repaid with interest during the energy payoff phase, when ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose. The net energy yield from glycolysis, per glucose molecule, is 2 ATP plus 2 NADH. The ten steps of the glycolytic pathway are shown in Figure 9.9

However, a cell wall is of no advantage if the cell is immersed in a hypertonic environment. In this case, a plant cell, like an animal cell, will lose water to its surroundings and shrink.

As the plant cell shrivels, its plasma membrane pulls away from the cell wall at multiple places. This phenomenon, called plasmolysis, causes the plant to wilt and can lead to plant death. The walled cells of bacteria and fungi also plasmolyze in hypertonic environments.

mRNA

As we saw in Figure 5.22, the nucleus directs protein synthesis by synthesizing messenger RNA (mRNA) according to instructions provided by the DNA. The mRNA is then transported to the cytoplasm via the nuclear pores. Once an mRNA molecule reaches the cytoplasm, ribosomes translate the mRNA's genetic message into the primary structure of a specific polypeptide. (This process of transcribing and translating genetic information is described in detail in Chapter 17.)

Free Energy, Stability, and Equilibrium

As we saw in the previous section, when a process occurs spontaneously in a system, we can be sure that ∆G is negative. Another way to think of ∆G is to realize that it represents the difference between the free energy of the final state and the free energy of the initial state:∆G = Gfinal state - Ginitial state

A tumor that appears to be localized may be treated with high-energy radiation, which damages DNA in cancer cells much more than DNA in normal cells, apparently because the majority of cancer cells have lost the ability to repair such damage. To treat known or suspected metastatic tumors, chemotherapy is used, in which drugs that are toxic to actively dividing cells are administered through the circulatory system.

As you might expect, chemotherapeutic drugs interfere with specific steps in the cell cycle. For example, the drug Taxol freezes the mitotic spindle by preventing microtubule depolymerization, which stops actively dividing cells from proceeding past metaphase and leads to their destruction. The side effects of chemotherapy are due to the effects of the drugs on normal cells that divide frequently, due to the function of that cell type in the organism. For example, nausea results from chemotherapy's effects on intestinal cells, hair loss from effects on hair follicle cells, and susceptibility to infection from effects on immune system cells. You'll work with data from an experiment involving a potential chemotherapeutic agent in the Scientific Skills Exercise.

Cellular functions arise from cellular order: The cell is a living unit greater than the sum of its parts. The cell in Figure 6.31 is a good example of integration of cellular processes, seen from the outside. But what about the internal organization of a cell?

As you proceed in your study of biology to consider different cellular processes, it will be helpful to try to visualize the architecture and furnishings inside a cell. Figure 6.32 is designed to help you get a sense of the relative sizes and organization of important biological molecules and macromolecules, along with cellular structures and organelles. As you study this figure, see if you can shrink yourself down to the size of a protein and contemplate your surroundings.

In Chapters 5 through 10, you have learned about many activities of cells. Figure 10.23 integrates these cellular processes into the context of a working plant cell.

As you study the figure, reflect on how each process fits into the big picture: As the most basic unit of living organisms, a cell performs all functions characteristic of life.

At this point, you may be wondering how the electron transport chain pumps hydrogen ions. Researchers have found that certain members of the electron transport chain accept and release protons (H+ ) along with electrons. (The aqueous solutions inside and surrounding the cell are a ready source of H+ .)

At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution.

Keep in mind that the original signaling molecule is not physically passed along a signaling pathway; in most cases, it never even enters the cell. When we say that the signal is relayed along a pathway, we mean that certain information is passed on.

At each step, the signal is transduced into a different form, commonly a shape change in the next protein. Very often, the shape change is brought about by phosphorylation.

. Cellular respiration does not oxidize glucose (or any other organic fuel) in a single explosive step either. Rather, glucose is broken down in a series of steps, each one catalyzed by an enzyme.

At key steps, electrons are stripped from the glucose. As is often the case in oxidation reactions, each electron travels with a proton—thus, as a hydrogen atom.

The rate at which a particular amount of enzyme converts substrate to product is partly a function of the initial concentration of the substrate: The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules. However, there is a limit to how fast the reaction can be pushed by adding more substrate to a fixed concentration of enzyme.

At some point, the concentration of substrate will be high enough that all enzyme molecules will have their active sites engaged. As soon as the product exits an active site, another substrate molecule enters. . At this substrate concentration, the enzyme is said to be saturated, and the rate of the reaction is determined by the speed at which the active site converts substrate to product

pore complex

At the lip of each pore, the inner and outer membranes of the nuclear envelope are continuous. An intricate protein structure called a pore complex lines each pore and plays an important role in the cell by regulating the entry and exit of proteins and RNAs, as well as large complexes of macromolecules.

During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis: Our main objective in this chapter is to learn how cells harvest the energy of glucose and other nutrients in food to make ATP. But the metabolic components of respiration we have examined so far, glycolysis and the citric acid cycle, produce only 4 ATP molecules per glucose molecule, all by substrate-level phosphorylation: 2 net ATP from glycolysis and 2 ATP from the citric acid cycle.

At this point, molecules of NADH (and FADH2) account for most of the energy extracted from each glucose molecule. These electron escorts link glycolysis and the citric acid cycle to the machinery of oxidative phosphorylation, which uses energy released by the electron transport chain to power ATP synthesis. In this section, you will learn first how the electron transport chain works and then how electron flow down the chain is coupled to ATP synthesis.

However, the relatively inelastic cell wall will expand only so much before it exerts a back pressure on the cell, called turgor pressure, that opposes further water uptake

At this point, the cell is turgid (very firm), the healthy state for most plant cells. Plants that are not woody, such as most houseplants, depend for mechanical support on cells kept turgid by a surrounding hypotonic solution. If a plant's cells and surroundings are isotonic, there is no net tendency for water to enter and the cells become flaccid (limp); the plant wilts.

Tight Junctions

At tight junctions, the plasma membranes of neighboring cells are very tightly pressed against each other, bound together by specific proteins. Forming continuous seals around the cells, tight junctions establish a barrier that prevents leakage of extracellular fluid across a layer of epithelial cells (see red dashed arrow). For example, tight junctions between skin cells make us watertight. Tight junctions prevent fluid from moving across a layer of cells.

Photosynthesis nourishes almost the entire living world directly or indirectly. An organism acquires the organic compounds it uses for energy and carbon skeletons by one of two major modes: autotrophic nutrition or heterotrophic nutrition.

Autotrophs are "self-feeders" (auto- means "self," and trophos means "feeder"); they sustain themselves without eating anything derived from other living beings. Autotrophs produce their organic molecules from CO2 and other inorganic raw materials obtained from the environment. They are the ultimate sources of organic compounds for all nonautotrophic organisms, and for this reason, biologists refer to autotrophs as the producers of the biosphere.

For example, the cells of roughly 20% of breast cancer tumors show abnormally high amounts of a cell-surface receptor tyrosine kinase called HER2, and many show an increase in the number of estrogen receptor (ER) molecules, intracellular receptors that can trigger cell division.

Based on lab findings, a physician can prescribe chemotherapy with a molecule that blocks the function of the specific protein (Herceptin for HER2 and tamoxifen for ERs). Treatment using these agents, when appropriate, has led to increased survival rates and fewer cancer recurrences.

Exergonic and Endergonic Reactions in Metabolism:

Based on their free-energy changes, chemical reactions can be classified as either exergonic ("energy outward") or endergonic ("energy inward")

That turnover represents 10 million molecules of ATP consumed and regenerated per second per cell. If ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP each day.

Because both directions of a reversible process cannot be downhill, the regeneration of ATP is necessarily endergonic: ADP + ~P i S ATP + H2O ∆G = +7.3 kcal/mol (+30.5 kJ/mol) (standard conditions)

In this chapter, we will focus on mechanisms common to metabolic pathways.

Because energy is fundamental to all metabolic processes, a basic knowledge of energy is necessary to understand how the living cell works.

Thus, ∆G can be negative only when the process involves a loss of free energy during the change from initial state to final state.

Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously.

Prokaryotes, as already mentioned, generate H+ gradients across their plasma membranes. They then tap the proton-motive force not only to make ATP inside the cell but also to rotate their flagella and to pump nutrients and waste products across the membrane.

Because of its central importance to energy conversions in prokaryotes and eukaryotes, chemiosmosis has helped unify the study of bioenergetics. Peter Mitchell was awarded the Nobel Prize in 1978 for originally proposing the chemiosmotic model.

Why can't unsaturated hydrocarbon tails pack together as closely as saturated hydrocarbon tails?

Because of kinks in the tails where double bonds are located, unsaturated hydrocarbon tails cannot pack together as closely as saturated hydrocarbon tails, making the membrane more fluid (Figure 7.5a).

Many of the kinases that drive the cell cycle are actually present at a constant concentration in the growing cell, but much of the time they are in an inactive form. To be active, such a kinase must be attached to a cyclin, a protein that gets its name from its cyclically fluctuating concentration in the cell

Because of this requirement, these kinases are called cyclin-dependent kinases, or Cdks. The activity of a Cdk rises and falls with changes in the concentration of its cyclin partner. Figure 12.16a shows the fluctuating activity of MPF, the cyclin-Cdk complex that was discovered first (in frog eggs).

. However, evidence shows that within an hour, blood carries the excess lactate from the muscles to the liver, where it is converted back to pyruvate by liver cells.

Because oxygen is available, this pyruvate can then enter the mitochondria in liver cells and complete cellular respiration. (Next-day muscle soreness is more likely caused by trauma to small muscle fibers, which leads to inflammation and pain.)

The membrane potential acts like a battery, an energy source that affects the traffic of all charged substances across the membrane. (Electrochemical gradient)

Because the inside of the cell is negative compared with the outside, the membrane potential favors the passive transport of cations into the cell and anions out of the cell. Thus, two forces drive the diffusion of ions across a membrane: a chemical force (the ion's concentration gradient, which has been our sole consideration thus far in the chapter) and an electrical force (the effect of the membrane potential on the ion's movement). This combination of forces acting on an ion is called the electrochemical gradient.

What happens before a Golgi Stack dispatches its products by budding vesicles from the trans face?

Before a Golgi stack dispatches its products by budding vesicles from the trans face, it sorts these products and targets them for various parts of the cell. Molecular identification tags, such as phosphate groups added to the Golgi products, aid in sorting by acting like zip codes on mailing labels. Finally, transport vesicles budded from the Golgi may have external molecules on their membranes that recognize "docking sites" on the surface of specific organelles or on the plasma membrane, thus targeting the vesicles appropriately

Whether ATP synthesis is driven by linear or cyclic electron flow, the actual mechanism is the same.

Before we move on to consider the Calvin cycle, let's review chemiosmosis, the process that uses membranes to couple redox reactions to ATP production.

The anatomy of a C4 leaf is correlated with the mechanism of C4 photosynthesis. In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells.

Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the leaf (Figure 10.20). Between the bundle sheath and the leaf surface are the more loosely arranged mesophyll cells, which, in C4 leaves, are closely associated and never more than two to three cells away from the bundle-sheath cells.

In mitochondria, the energy for gradient formation comes from exergonic redox reactions along the electron transport chain, and ATP synthesis is the work performed.

But chemiosmosis also occurs elsewhere and in other variations. Chloroplasts use chemiosmosis to generate ATP during photosynthesis; in these organelles, light (rather than chemical energy) drives both electron flow down an electron transport chain and the resulting H+ gradient formation

Oxidation of Organic Fuel Molecules During Cellular Respiration: The oxidation of methane by oxygen is the main combustion reaction that occurs at the burner of a gas stove. The combustion of gasoline in an automobile engine is also a redox reaction; the energy released pushes the pistons

But the energy-yielding redox process of greatest interest to biologists is respiration: the oxidation of glucose and other molecules in food. Examine again the summary equation for cellular respiration, but this time think of it as a redox process: Check page 166 for the equation.

Some of the electron carriers, including the iron-containing proteins called cytochromes, are very similar in chloroplasts and mitochondria. The ATP synthase complexes of the two organelles are also quite similar.

But there are noteworthy differences between photophosphorylation in chloroplasts and oxidative phosphorylation in mitochondria. Both work by way of chemiosmosis, but in chloroplasts, the high-energy electrons dropped down the transport chain come from water, while in mitochondria, they are extracted from organic molecules (which are thus oxidized).

Equally important in the phosphorylation cascade are the protein phosphatases, enzymes that can rapidly remove phosphate groups from proteins, a process called dephosphorylation.

By dephosphorylating and thus inactivating protein kinases, phosphatases provide the mechanism for turning off the signal transduction pathway when the initial signal is no longer present. Phosphatases also make the protein kinases available for reuse, enabling the cell to respond again to an extracellular signal

During interphase in animal cells, the single centrosome duplicates, forming two centrosomes, which remain near the nucleus. The two centrosomes move apart during prophase and prometaphase of mitosis as spindle microtubules grow out from them.

By the end of prometaphase, the two centrosomes, one at each pole of the spindle, are at opposite ends of the cell. An aster, a radial array of short microtubules, extends from each centrosome. The spindle includes the centrosomes, the spindle microtubules, and the asters.

Although cells always contain some Ca2+ , this ion can function as a second messenger because its concentration in the cytosol is normally much lower than the concentration outside the cell (Figure 11.13). In fact, the level of Ca2+ in the blood and extracellular fluid of an animal is often more than 10,000 times higher than that in the cytosol.

Calcium ions are actively transported out of the cell and are actively imported from the cytosol into the endoplasmic reticulum (and, under some conditions, into mitochondria and chloroplasts) by various protein pumps. As a result, the calcium concentration in the ER is usually much higher than that in the cytosol. Because the cytosolic calcium level is low, a small change in absolute numbers of ions represents a relatively large percentage change in calcium concentration.

Calcium Ions and Inositol Trisphosphate (IP3): Many of the signaling molecules that function in animals— including neurotransmitters, growth factors, and some hormones—induce responses in their target cells via signal transduction pathways that increase the cytosolic concentration of calcium ions (Ca2+ ).

Calcium is even more widely used than cAMP as a second messenger. Increasing the cytosolic concentration of Ca2+ causes many responses in animal cells, including muscle cell contraction, exocytosis of molecules (secretion), and cell division. In plant cells, a wide range of hormonal and environmental stimuli can cause brief increases in cytosolic Ca2+ concentration, triggering various signaling pathways, such as the pathway for greening in response to light (see Figure 39.4). Cells use Ca2+ as a second messenger in pathways triggered by both G protein-coupled receptors and receptor tyrosine kinases.

The changes that have occurred in cells of malignant tumors show up in many ways besides excessive proliferation. These cells may have unusual numbers of chromosomes, though whether this is a cause or an effect of tumor-related changes is a topic of debate. Their metabolism may be altered, and they may cease to function in any constructive way. Abnormal changes on the cell surface cause cancer cells to lose attachments to neighboring cells and the extracellular matrix, allowing them to spread into nearby tissues.

Cancer cells may also secrete signaling molecules that cause blood vessels to grow toward the tumor. A few tumor cells may separate from the original tumor, enter blood vessels and lymph vessels, and travel to other parts of the body. There, they may proliferate and form a new tumor. This spread of cancer cells to locations distant from their original site is called metastasis (see Figure 12.20).

Density-dependent inhibition and anchorage dependence appear to function not only in cell culture but also in the body's tissues, checking the growth of cells at some optimal density and location during embryonic development and throughout an organism's life.

Cancer cells, which we discuss next, exhibit neither density-dependent inhibition nor anchorage dependence (Figure 12.19b).

Other accessory pigments include carotenoids, hydrocarbons that are various shades of yellow and orange because they absorb violet and blue-green light (see Figure 10.10a).

Carotenoids may broaden the spectrum of colors that can drive photosynthesis. However, a more important function of at least some carotenoids seems to be photoprotection: These compounds absorb and dissipate excessive light energy that would otherwise damage chlorophyll or interact with oxygen, forming reactive oxidative molecules that are dangerous to the cell.

Recall that a negative ∆G (∆G 6 0) indicates that the products of the chemical process store less energy than the reactants and that the reaction can happen spontaneously—in other words, without an input of energy.

Catabolic pathways do not directly move flagella, pump solutes across membranes, polymerize monomers, or perform other cellular work. Catabolism is linked to work by a chemical drive shaft—ATP (see Concept 8.3).

Direct connections between cells also function in this coordination, as we discuss next.

Cell Junctions Cells in an animal or plant are organized into tissues, organs, and organ systems. Neighboring cells often adhere, interact, and communicate via sites of direct physical contact.

Scientists think that signaling mechanisms first evolved in ancient prokaryotes and single-celled eukaryotes like yeasts and then were adopted for new uses by their multicellular descendants.

Cell signaling is also critical among prokaryotes. For example, bacterial cells secrete molecules that can be detected by other bacterial cells (Figure 11.3).

Cytokinesis in plant cells, which have cell walls, is markedly different. There is no cleavage furrow. Instead, during telophase, vesicles derived from the Golgi apparatus move along microtubules to the middle of the cell, where they coalesce, producing a cell plate.

Cell wall materials carried in the vesicles collect inside the cell plate as it grows (Figure 12.10b) The cell plate enlarges until its surrounding membrane fuses with the plasma membrane along the perimeter of the cell. Two daughter cells result, each with its own plasma membrane. Meanwhile, a new cell wall arising from the contents of the cell plate forms between the daughter cells. Figure 12.11 is a series of micrographs of a dividing plant cell. Examining this figure will help you review mitosis and cytokinesis.

Density-dependent inhibition and anchorage dependence of cell division: 12.19 Individual cells are shown disproportionately large in the drawings.

Cells anchor to dish surface and divide (anchorage dependence). When cells have formed a complete single layer, they stop dividing (density-dependent inhibition). If some cells are scraped away, the remaining cells divide to fill the gap and then stop once they contact each other (densitydependent inhibition). (a) Normal mammalian cells. Cell density is limited to a single layer by contact with neighboring cells and the availability of nutrients, growth factors, and a substratum for attachment. (b) Cancer cells: Cancer cells usually continue to divide well beyond a single layer, forming a clump of overlapping cells. They do not exhibit anchorage dependence or density-dependent inhibition.

What systems allow the trillions of cells in the impala to "talk" to each other, coordinating their activities?

Cells can signal to each other and interpret the signals they receive from other cells and the environment. The signals may include light and touch, but are most often chemicals.

When an enzyme population is saturated, the only way to increase the rate of product formation is to add more enzyme.

Cells often increase the rate of a reaction by producing more enzyme molecules.

Prokaryotic and eukaryotic

Cells—the basic structural and functional units of every organism—are of two distinct types: prokaryotic and eukaryotic. Organisms of the domains Bacteria and Archaea consist of prokaryotic cells. Protists, fungi, animals, and plants all consist of eukaryotic cells. ("Protist" is an informal term referring to a diverse group of mostly unicellular eukaryotes.)

Cellular respiration

Cellular respiration includes many steps, some carried out by individual proteins or protein complexes in the cytoplasm and the mitochondrial matrix. Other proteins and protein complexes, involved in generating ATP from food molecules, form a "chain" in the inner mitochondrial membrane.

Organelles only in plant cells

Central vacuole: prominent organelle in older plant cells; functions include storage, breakdown of waste products, and hydrolysis of macromolecules; enlargement of the vacuole is a major mechanism of plant growth Chloroplast: photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules Plasmodesmata: cytoplasmic channels through cell walls that connect the cytoplasms of adjacent cells Cell wall: outer layer that maintains cell's shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein

Flagellum: motility structure present in some animal cells, composed of a cluster of microtubules within an extension of the plasma membrane

Centrosome: region where the cell's microtubules are initiated; contains a pair of centrioles CYTOSKELETON: reinforces cell's shape; functions in cell movement; components are made of protein. Includes: Ribosomes (small brown dots): complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope Microfilaments Intermediate filaments Microtubules

Aquaporin in kidney cells

Certain kidney cells also have a high number of aquaporins, allowing them to reclaim water from urine before it is excreted. If the kidneys did not perform this function, you would excrete about 180 L of urine per day—and have to drink an equal volume of water!

ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work:

Chemical work, the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers (chemical work will be discussed further here; examples are shown in Chapters 9 and 10) Transport work, the pumping of substances across membranes against the direction of spontaneous movement (see Concept 7.4) Mechanical work, such as the beating of cilia (see Concept 6.6), the contraction of muscle cells, and the movement of chromosomes during cellular reproduction

Structure of chlorophyll molecules in chloroplasts of plants

Chlorophyll a and chlorophyll b differ in only one of the functional groups bonded to the porphyrin ring. (Also see the space-filling model of chlorophyll in Figure 1.3.) Porphyrin ring: light-absorbing "head" of molecule; note magnesium atom at center Hydrocarbon tail: interacts with hydrophobic regions of proteins inside thylakoid membranes of chloroplasts; H atoms not shown

The light reactions convert solar energy to the chemical energy of ATP and NADPH

Chloroplasts are chemical factories powered by the sun. Their thylakoids transform light energy into the chemical energy of ATP and NADPH, which will be used to synthesize glucose and other molecules that can be used as energy sources. To better understand the conversion of light to chemical energy, we need to know about some important properties of light.

Chloroplasts: The Sites of Photosynthesis in Plants- All green parts of a plant, including green stems and unripened fruit, have chloroplasts, but the leaves are the major sites of photosynthesis in most plants (Figure 10.4). There are about half a million chloroplasts in a chunk of leaf with a top surface area of 1 mm2 .

Chloroplasts are found mainly in the cells of the mesophyll, the tissue in the interior of the leaf. Carbon dioxide enters the leaf, and oxygen exits, by way of microscopic pores called stomata (singular, stoma; from the Greek, meaning "mouth"). Water absorbed by the roots is delivered to the leaves in veins. Leaves also use veins to export sugar to roots and other nonphotosynthetic parts of the plant. A typical mesophyll cell has about 30-40 chloroplasts, each measuring about 2-4 µm by 4-7 µm. A chloroplast has two membranes surrounding a dense fluid called the stroma. Suspended within the stroma is a third membrane system, made up of sacs called thylakoids, which segregates the stroma from the thylakoid space inside these sacs. In some places, thylakoid sacs are stacked in columns called grana (singular, granum).

Chloroplasts: Capture of Light Energy

Chloroplasts contain the green pigment chlorophyll, along with enzymes and other molecules that function in the photosynthetic production of sugar. These lens-shaped organelles, about 3-6 µm in length, are found in leaves and other green organs of plants and in algae (Figure 6.18; see also Figure 6.26c).

Chromatin.

Chromatin. This segment of a chromosome from a nondividing cell shows two states of coiling of the DNA (blue) and protein (purple) complex. The thicker form is sometimes also organized into long loops.

Eukaryotic chromosomes:

Chromosomes (stained purple) are visible within the nucleus of this cell from an African blood lily. The thinner red threads in the surrounding cytoplasm are the cytoskeleton. The cell is preparing to divide (LM).

Free-energy change during electron transport.: The overall energy drop (∆G) for electrons traveling from NADH to oxygen is 53 kcal/mol, but this "fall" is broken up into a series of smaller steps by the electron transport chain. (An oxygen atom is represented here as 1 ⁄ 2 O2 to emphasize that the electron transport chain reduces molecular oxygen, O2, not individual oxygen atoms.)

Complexes I-IV each consist of multiple proteins with electron carriers. Electron transport chain Electrons (from NADH or FADH2) move from a less electronegative electron carrier (one with a lower affinity for electrons) to a more electronegative electron carrier down the chain, releasing free energy. The last electron carrier (Cyt a3) passes its electrons to oxygen, which is very electronegative.

Confocal

Confocal. - The top image is a standard fluorescence micrograph of fluorescently labeled nervous tissue (nerve cells are green, support cells are orange, and regions of overlap are yellow); below it is a confocal image of the same tissue. Using a laser, this "optical sectioning" technique eliminates out-of-focus light from a thick sample, creating a single plane of fluorescence in the image. By capturing sharp images at many different planes, a 3-D reconstruction can be created. The standard image is blurry because out-of-focus light is not excluded.

How is energy converted from one form to another?

Consider Figure 8.2. The woman climbing the ladder to the diving platform is releasing chemical energy from the food she ate for lunch and using some of that energy to perform the work of climbing. The kinetic energy of muscle movement is thus being transformed into potential energy due to her increasing height above the water. The man diving is converting his potential energy to kinetic energy, which is then transferred to the water as he enters it, resulting in splashing, noise, and increased movement of water molecules. A small amount of energy is lost as heat due to friction

Now that we know about the role of cAMP in G protein signaling pathways, we can explain in molecular detail how certain microbes cause disease.

Consider cholera, a disease that is frequently epidemic in places where the water supply is contaminated with human feces.

As mentioned in Concept 11.1, a growth factor is a protein released by certain cells that stimulates other cells to divide. Different cell types respond specifically to different growth factors or combinations of growth factors.

Consider, for example, platelet-derived growth factor (PDGF), which is made by blood cell fragments called platelets. The experiment illustrated in Figure 12.18 demonstrates that PDGF is required for the division of cultured fibroblasts, a type of connective tissue cell. Fibroblasts have PDGF receptors on their plasma membranes. The binding of PDGF molecules to these receptors (which are receptor tyrosine kinases; see Figure 11.8) triggers a signal transduction pathway that allows the cells to pass the G1 checkpoint and divide. PDGF stimulates fibroblast division not only in the artificial conditions of cell culture but also in an animal's body. When an injury occurs, platelets release PDGF in the vicinity. The resulting proliferation of fibroblasts helps heal the wound.

cooperativity

Cooperativity is considered allosteric regulation because, even though substrate is binding to an active site, its binding affects catalysis in another active site.

In oxygen-deprived tissues, however, the release of each oxygen molecule decreases the oxygen affinity of the other binding sites, resulting in the release of oxygen where it is most needed.

Cooperativity works similarly in multisubunit enzymes that have been studied.

Over the past several decades, researchers have produced a flood of valuable information about cell-signaling pathways and how their malfunction contributes to the development of cancer through effects on the cell cycle.

Coupled with new molecular techniques, such as the ability to rapidly sequence the DNA of cells in a particular tumor, medical treatments for cancer are beginning to become more "personalized" to a particular patient's tumor (see Make Connections Figure 18.27).

Fibronectin

Current research on fibronectin, other ECM molecules, and integrins reveals the influential role of the ECM in the lives of cells. By communicating with a cell through integrins, the ECM can regulate a cell's behavior. For example, some cells in a developing embryo migrate along specific pathways by matching the orientation of their microfilaments to the "grain" of fibers in the extracellular matrix. Researchers have also learned that the extracellular matrix around a cell can influence the activity of genes in the nucleus.

The Evolutionary Significance of Glycolysis: The role of glycolysis in both fermentation and respiration has an evolutionary basis. Ancient prokaryotes are thought to have used glycolysis to make ATP long before oxygen was present in Earth's atmosphere. . The oldest known fossils of bacteria date back 3.5 billion years, but appreciable quantities of oxygen probably did not begin to accumulate in the atmosphere until about 2.7 billion years ago.

Cyanobacteria produced this O2 as a by-product of photosynthesis. Therefore, early prokaryotes may have generated ATP exclusively from glycolysis . The fact that glycolysis is today the most widespread metabolic pathway among Earth's organisms suggests that it evolved very early in the history of life. The cytosolic location of glycolysis also implies great antiquity; the pathway does not require any of the membrane-enclosed organelles of the eukaryotic cell, which evolved approximately 1 billion years after the first prokaryotic cell. Glycolysis is a metabolic heirloom from early cells that continues to function in fermentation and as the first stage in the breakdown of organic molecules by respiration

Cytoskeleton

Cytoskeletal structures are polymers of protein subunits. Microtubules are hollow structural rods made of tubulin protein subunits, while microfilaments are cables that have two chains of actin proteins wound around each other.

Desmosomes

Desmosomes (one type of anchoring junction) function like rivets, fastening cells together into strong sheets. Intermediate filaments made of sturdy keratin proteins anchor desmosomes in the cytoplasm. Desmosomes attach muscle cells to each other in a muscle. Some "muscle tears" involve the rupture of desmosomes.

Various membranes are not identical.

Despite these relationships, the various membranes are not identical in structure and function. Moreover, the thickness, molecular composition, and types of chemical reactions carried out in a given membrane are not fixed, but may be modified several times during the membrane's life.

differential interference contrast

Differential interference contrast (Nomarski). As in phase-contrast microscopy, optical modifications are used to exaggerate differences in density; the image appears almost 3-D.

Where do the digestion products pass into?

Digestion products, including simple sugars, amino acids, and other monomers, pass into the cytosol and become nutrients for the cell. Some human cells also carry out phagocytosis. Among them are macrophages, a type of white blood cell that helps defend the body by engulfing and destroying bacteria and other invaders (see Figure 6.13a, top, and Figure 6.31).

The G phases were misnamed as "gaps" when they were first observed because the cells appeared inactive, but we now know that intense metabolic activity and growth occur throughout interphase.

During all three phases of interphase, in fact, a cell grows by producing proteins and cytoplasmic organelles such as mitochondria and endoplasmic reticulum. Duplication of the chromosomes, crucial for eventual division of the cell, occurs entirely during the S phase. (We will discuss synthesis, or replication, of DNA in Concept 16.2.)

In a dividing animal cell, the nonkinetochore microtubules are responsible for elongating the whole cell during anaphase.Nonkinetochore microtubules from opposite poles overlap each other extensively during metaphase (see Figure 12.8).

During anaphase, the region of overlap is reduced as motor proteins attached to the microtubules walk them away from one another, using energy from ATP. As the microtubules push apart from each other, their spindle poles are pushed apart, elongating the cell. At the same time, the microtubules lengthen somewhat by the addition of tubulin subunits to their overlapping ends. As a result, the microtubules continue to overlap.

An overview of cellular respiration: During glycolysis, each glucose molecule is broken down into two molecules of pyruvate. In eukaryotic cells, as shown here, the pyruvate enters the mitochondrion. There it is oxidized to acetyl CoA, which will be further oxidized to CO2 in the citric acid cycle. The electron carriers NADH and FADH2 transfer electrons derived from glucose to electron transport chains

During oxidative phosphorylation, electron transport chains convert the chemical energy to a form used for ATP synthesis in the process called chemiosmosis. (During earlier steps of cellular respiration, a few molecules of ATP are synthesized in a process called substrate-level phosphorylation.) To visualize these processes in their cellular context, see Figure 6.32.

Each of the two sister chromatids of a duplicated chromosome has a kinetochore, a structure made up of proteins that have assembled on specific sections of DNA at each centromere. The chromosome's two kinetochores face in opposite directions.

During prometaphase, some of the spindle microtubules attach to the kinetochores; these are called kinetochore microtubules. (The number of microtubules attached to a kinetochore varies among species, from one microtubule in yeast cells to 40 or so in some mammalian cells.)

An Accounting of ATP Production by Cellular Respiration: In the last few sections, we have looked rather closely at the key processes of cellular respiration. Now let's take a step back and remind ourselves of its overall function: harvesting the energy of glucose for ATP synthesis.

During respiration, most energy flows in this sequence: glucose --> NADH --> electron transport chain --> protonmotive force --> ATP. We can do some bookkeeping to calculate the ATP profit when cellular respiration oxidizes a molecule of glucose to six molecules of carbon dioxide.

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 sugar in the chloroplasts.

The tally adds the 4 ATP produced directly by substrate-level phosphorylation during glycolysis and the citric acid cycle to the many more molecules of ATP generated by oxidative phosphorylation

Each NADH that transfers a pair of electrons from glucose to the electron transport chain contributes enough to the proton-motive force to generate a maximum of about 3 ATP.

Distribution of Chromosomes During Eukaryotic Cell Division: When a cell is not dividing, and even as it replicates its DNA in preparation for cell division, each chromosome is in the form of a long, thin chromatin fiber. After DNA replication, however, the chromosomes condense as a part of cell division:

Each chromatin fiber becomes densely coiled and folded, making the chromosomes much shorter and so thick that we can see them with a light microscope.

Figure 9.13 shows the sequence of electron carriers in the electron transport chain and the drop in free energy as electrons travel down the chain. During this electron transport, electron carriers alternate between reduced and oxidized states as they accept and then donate electrons.

Each component of the chain becomes reduced when it accepts electrons from its "uphill" neighbor, which has a lower affinity for electrons (in other words, is less electronegative). It then returns to its oxidized form as it passes electrons to its "downhill," more electronegative neighbor.

sister chromatids

Each duplicated chromosome consists of two sister chromatids, which are joined copies of the original chromosome (Figure 12.4)

Environmental factors affecting enzyme activity

Each enzyme has an optimal (a) temperature and (b) pH that favor the most active shape of the protein molecule. a) The photo shows thermophilic cyanobacteria (green) thriving in the hot water of a Nevada geyser. The graph compares the optimal temperatures for an enzyme from the thermophilic bacterium Thermus oshimai (75°C) and human enzymes (body temperature, 37°C). b) This graph shows the rate of reaction for two digestive enzymes over a range of pH values.

No. of chromosomes

Each eukaryotic species has a characteristic number of chromosomes. For example, a typical human cell has 46 chromosomes in its nucleus; the exceptions are the sex cells (eggs and sperm), which have only 23 chromosomes in humans. A fruit fly cell has 8 chromosomes in most cells and 4 in the sex cells.

The thylakoid membrane is populated by two types of photosystems that cooperate in the light reactions of photosynthesis: 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.)

Each has a characteristic reaction-center complex—a particular kind of primary electron acceptor next to a special pair of chlorophyll a molecules associated with specific proteins. The reaction-center chlorophyll a of photosystem II is known as P680 because this pigment is best at absorbing light having a wavelength of 680 nm (in the red part of the spectrum).

Passive transport is diffusion of a substance across a membrane with no energy investment: Molecules have a type of energy called thermal energy, due to their constant motion (see Concept 3.2). One result of this motion is diffusion, the movement of particles of any substance so that they spread out into the available space.

Each molecule moves randomly, yet diffusion of a population of molecules may be directional. To understand this process, let's imagine a synthetic membrane separating pure water from a solution of a dye in water.

Cristae

Each of the two membranes enclosing the mitochondrion is a phospholipid bilayer with a unique collection of embedded proteins (Figure 6.17). The outer membrane is smooth, but the inner membrane is convoluted, with infoldings called cristae. The inner membrane divides the mitochondrion into two internal compartments. The first is the intermembrane space, the narrow region between the inner and outer membranes

The Nature of Sunlight: Light is a form of energy known as electromagnetic energy, also called electromagnetic radiation. Electromagnetic energy travels in rhythmic waves analogous to those created by dropping a pebble into a pond.

Electromagnetic waves, however, are disturbances of electric and magnetic fields rather than disturbances of a material medium such as water.

benefits and disadvantages of electron microscopes

Electron microscopes have revealed many subcellular structures that were impossible to resolve with the light microscope. But the light microscope offers advantages, especially in studying living cells. A disadvantage of electron microscopy is that the methods used to prepare the specimen kill the cells. Specimen preparation for any type of microscopy can introduce artifacts, structural features seen in micrographs that do not exist in the living cell.

Although the spatial organization of chemiosmosis differs slightly between chloroplasts and mitochondria, it is easy to see similarities in the two (Figure 10.17).

Electron transport chain proteins in the inner membrane of the mitochondrion pump protons from the mitochondrial matrix out to the intermembrane space, which then serves as a reservoir of hydrogen ions.

An electron transport chain consists of a number of molecules, mostly proteins, built into the inner membrane of the mitochondria of eukaryotic cells (and the plasma membrane of respiring prokaryotes).

Electrons removed from glucose are shuttled by NADH to the "top," higher-energy end of the chain. At the "bottom," lower-energy end, O2 captures these electrons along with hydrogen nuclei (H+ ), forming water. (Anaerobically respiring prokaryotes have an electron acceptor at the end of the chain that is different from O2.)

Forms of Energy: Energy is the capacity to cause change. In everyday life, energy is important because some forms of energy can be used to do work—that is, to move matter against opposing forces, such as gravity and friction. Put another way, energy is the ability to rearrange a collection of matter. For example, you expend energy to turn the pages of this book, and your cells expend energy in transporting certain substances across membranes. Energy exists in various forms, and the work of life depends on the ability

Energy can be associated with the relative motion of objects; this energy is called kinetic energy. Moving objects can perform work by imparting motion to other matter: A pool player uses the motion of the cue stick to push the cue ball, which in turn moves the other balls; water gushing through a dam turns turbines; and the contraction of leg muscles pushes bicycle pedals. Thermal energy is kinetic energy associated with the random movement of atoms or molecules; thermal energy in transfer from one object to another is called heat. Light is also a type of energy that can be harnessed to perform work, such as powering photosynthesis in green plants. An object not presently moving may still possess energy. Energy that is not kinetic is called potential energy; it is energy that matter possesses because of its location or structure. Water behind a dam, for instance, possesses energy because of its altitude above sea level. Molecules possess energy because of the arrangement of electrons in the bonds between their atoms. Chemical energy is a term used by biologists to refer to the potential energy available for release in a chemical reaction. Recall that catabolic pathways release energy by breaking down complex molecules. Biologists say that these complex molecules, such as glucose, are high in chemical energy. During a catabolic reaction, some bonds are broken and others are formed, releasing energy and resulting in lower-energy breakdown products. This transformation also occurs in the engine of a car when the hydrocarbons of gasoline react explosively with oxygen, releasing the energy that pushes the pistons and producing exhaust. Although less explosive, a similar reaction of food molecules with oxygen provides chemical energy in biological systems, producing carbon dioxide and water as waste products. Biochemical pathways, carried out in the context of cellular structures, enable cells to release chemical energy from food molecules and use the energy to power life processes.

First law of thermodynamics

Energy can be transferred or transformed but neither created nor destroyed. For example, chemical reactions in this brown bear will convert the chemical (potential) energy in the fish into the kinetic energy of running.

2 Energy flow and chemical recycling in ecosystems.

Energy flows into an ecosystem as sunlight and ultimately leaves as heat, while the chemical elements essential to life are recycled.

The ATP cycle

Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Energy from catabolism (exergonic, energy-releasing processes) Energy for cellular work (endergonic, energy-consuming processes) Figure 8.12

Induced fit between an enzyme and its substrate

Enzyme: In this space-filling model of the enzyme hexokinase (blue), the active site forms a groove on the surface. The enzyme's substrate is glucose (red). Enzyme-substrate complex: When the substrate enters the active site, it forms weak bonds with the enzyme, inducing a change in the shape of the protein. This change allows additional weak bonds to form, causing the active site to enfold the substrate and hold it in place.

How does NAD+ trap electrons from glucose and the other organic molecules in food?

Enzymes called dehydrogenases remove a pair of hydrogen atoms (2 electrons and 2 protons) from the substrate (glucose, in the preceding example), thereby oxidizing it. The enzyme delivers the 2 electrons along with 1 proton to its coenzyme, NAD+ , forming NADH (Figure 9.4). The other proton is released as a hydrogen ion (H+ ) into the surrounding solution: page 167. By receiving 2 negatively charged electrons but only 1 positively charged proton, the nicotinamide portion of NAD+ has its charge neutralized when NAD+ is reduced to NADH. The name NADH shows the hydrogen that has been received in the reaction. NAD+ is the most versatile electron acceptor in cellular respiration and functions in several of the redox steps during the breakdown of glucose.

It is crucial to note that an enzyme cannot change the ∆G for a reaction; it cannot make an endergonic reaction exergonic

Enzymes can only hasten reactions that would eventually occur anyway, but this enables the cell to have a dynamic metabolism, routing chemicals smoothly through metabolic pathways. Also, enzymes are very specific for the reactions they catalyze, so they determine which chemical processes will be going on in the cell at any given time.

Why are enzymes of the smooth ER important?

Enzymes of the smooth ER are important in the synthesis of lipids, including oils, steroids, and new membrane phospholipids. Among the steroids produced by the smooth ER in animal cells are the sex hormones of vertebrates and the various steroid hormones secreted by the adrenal glands. The cells that synthesize and secrete these hormones—in the testes and ovaries, for example—are rich in smooth ER, a structural feature that fits the function of these cells.

Most metabolic reactions are reversible, and an enzyme can catalyze either the forward or the reverse reaction, depending on which direction has a negative ∆G. This in turn depends mainly on the relative concentrations of reactants and products. The net effect is always in the direction of equilibrium.

Enzymes use a variety of mechanisms that lower activation energy and speed up a reaction (see Figure 8.16, step 3 ): When there are two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. As the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending critical chemical bonds to be broken during the reaction. Because EA is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state and reduces the amount of free energy that must be absorbed to achieve that state. The active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme. For example, if the active site has amino acids with acidic R groups, the active site may be a pocket of low pH in an otherwise neutral cell. In such cases, an acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction. Amino acids in the active site directly participate in the chemical reaction. Sometimes this process even involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme. Subsequent steps of the reaction restore the side chains to their original states so that the active site is the same after the reaction as it was before.

How does the inner mitochondrial membrane or the prokaryotic plasma membrane generate and maintain the H+ gradient that drives ATP synthesis by the ATP synthase protein complex?

Establishing the H+ gradient is a major function of the electron transport chain, which is shown in its mitochondrial location in Figure 9.15. The chain is an energy converter that uses the exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane, from the mitochondrial matrix into the intermembrane space.

Meaning of Eukaryotic and prokaryotic

Eukaryotic means "true nucleus" (from the Greek eu, true, and karyon, kernel, referring to the nucleus), and prokaryotic means "before nucleus" (from the Greek pro, before), reflecting the earlier evolution of prokaryotic cells

When we dissect the cell, do the components work alons?

Even as we dissect the cell, remember that none of its components works alone. As an example of cellular integration, consider the microscopic scene in Figure 6.31. The large cell is a macrophage (see Figure 6.13a). It helps defend the mammalian body against infections by ingesting bacteria (the smaller cells) into phagocytic vesicles. The macrophage crawls along a surface and reaches out to the bacteria with thin pseudopodia (specifically, filopodia). . Actin filaments interact with other elements of the cytoskeleton in these movements. After the macrophage engulfs the bacteria, they are destroyed by lysosomes produced by the elaborate endomembrane system. The digestive enzymes of the lysosomes and the proteins of the cytoskeleton are all made by ribosomes. And the synthesis of these proteins is programmed by genetic messages dispatched from the DNA in the nucleus. All these processes require energy, which mitochondria supply in the form of ATP.

The Activation Energy Barrier

Every chemical reaction between molecules involves both bond breaking and bond forming. For example, the hydrolysis of sucrose involves breaking the bond between glucose and fructose and one of the bonds of a water molecule and then forming two new bonds, as shown above.

Second law of thermodynamics:

Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, as the bear runs, disorder is increased around its body by the release of heat and small molecules that are the by-products of metabolism. A brown bear can run at speeds up to 35 miles per hour (56 km/hr) —as fast as a racehorse.

somatic cells

Every eukaryotic species has a characteristic number of chromosomes in each cell's nucleus. For example, the nuclei of human somatic cells (all body cells except the reproductive cells) each contain 46 chromosomes, made up of two set of 23, one set inherited from each parent.

Rather than having both PS II and PS I, several of the currently existing groups of photosynthetic bacteria are known to have a single photosystem related to either PS II or PS I. For these species, which include the purple sulfur bacteria (see Figure 10.2e) and the green sulfur bacteria, cyclic electron flow is the one and only means of generating ATP during the process of photosynthesis.

Evolutionary biologists hypothesize that these bacterial groups are descendants of ancestral bacteria in which photosynthesis first evolved, in a form similar to cyclic electron flow

Anabolic pathways, in contrast, consume energy to build complicated molecules from simpler ones; they are sometimes called biosynthetic pathways.

Examples of anabolism are the synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids. Catabolic and anabolic pathways are the "downhill" and "uphill" avenues of the metabolic landscape. Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways.

nuclear lamina

Except at the pores, the nuclear side of the envelope is lined by the nuclear lamina, a netlike array of protein filaments (in animal cells, called intermediate filaments) that maintains the shape of the nucleus by mechanically supporting the nuclear envelope

Inquiry: Do molecular signals in the cytoplasm regulate the cell cycle? Experiment: Researchers at the University of Colorado wondered whether a cell's progression through the cell cycle is controlled by cytoplasmic molecules. They induced cultured mammalian cells at different phases of the cell cycle to fuse. Two experiments are shown.

Experiment 1 : When a cell in the S phase was fused with a cell in G1, the G1 nucleus immediately entered the S phase—DNA was synthesized. Experiment 2: When a cell in the M phase was fused with a cell in G1, the G1 nucleus immediately began mitosis—a spindle formed and the chromosomes condensed, even though the chromosomes had not been duplicated. Conclusion: The results of fusing a G1 cell with a cell in the S or M phase of the cell cycle suggest that molecules present in the cytoplasm during the S or M phase control the progression to those phases.

Inquiry Do membrane proteins move?

Experiment Larry Frye and Michael Edidin, at Johns Hopkins University, labeled the plasma membrane proteins of a mouse cell and a human cell with two different markers and fused the cells. Using a microscope, they observed the markers on the hybrid cell. Results : Membrane proteins Mouse cell Human cell Hybrid cell Mixed proteins after 1 hour Conclusion: The mixing of the mouse and human membrane proteins indicates that at least some membrane proteins move sideways within the plane of the plasma membrane

Most animal cells also exhibit anchorage dependence (see Figure 12.19a). To divide, they must be attached to a substratum, such as the inside of a culture flask or the extracellular matrix of a tissue.

Experiments suggest that like cell density, anchorage is signaled to the cell cycle control system via pathways involving plasma membrane proteins and elements of the cytoskeleton linked to them.

Active transport uses energy to move solutes against their gradients: Despite the help of transport proteins, facilitated diffusion is considered passive transport because the solute is moving down its concentration gradient, a process that requires no energy

Facilitated diffusion speeds transport of a solute by providing efficient passage through the membrane, but it does not alter the direction of transport. Some other transport proteins, however, can move solutes against their concentration gradients, across the plasma membrane from the side where they are less concentrated (whether inside or outside) to the side where they are more concentrated.

Fluorescence micrographs of fibroblasts

Fibroblasts are a favorite cell type for cell biology studies because they spread out flat and their internal structures are easy to see. In each, the structure of interest has been tagged with fluorescent molecules. The DNA in the nucleus has also been tagged in the first micrograph (blue) and third micrograph (orange).

Intermediate Filaments

Fibrous proteins coiled into cables 8-12 nm One of several different proteins (such as keratins) Maintenance of cell shape (tensionbearing elements); anchorage of nucleus and certain other organelles; formation of nuclear lamina

The absorption spectra of chloroplast pigments provide clues to the relative effectiveness of different wavelengths for driving photosynthesis, since light can perform work in chloroplasts only if it is absorbed.

Figure 10.10a shows the absorption spectra of three types of pigments in chloroplasts: chlorophyll a, the key light-capturing pigment that participates directly in the light reactions; the accessory pigment chlorophyll b; and a separate group of accessory pigments called carotenoids. The spectrum of chlorophyll a suggests that violet-blue and red light work best for photosynthesis, since they are absorbed, while green is the least effective color. This is confirmed by an action spectrum for photosynthesis (Figure 10.10b), which profiles the relative effectiveness of different wavelengths of radiation in driving the process.

Notice by comparing Figures 10.10a and 10.10b that the action spectrum for photosynthesis is much broader than the absorption spectrum of chlorophyll a. The absorption spectrum of chlorophyll a alone underestimates the effectiveness of certain wavelengths in driving photosynthesis. This is partly because accessory pigments with different absorption spectra also present in chloroplasts—including chlorophyll b and carotenoids—broaden the spectrum of colors that can be used for photosynthesis.

Figure 10.11 shows the structure of chlorophyll a compared with that of chlorophyll b. A slight structural difference between them is enough to cause the two pigments to absorb at slightly different wavelengths in the red and blue parts of the spectrum (see Figure 10.10a). As a result, chlorophyll a appears blue green and chlorophyll b olive green under visible light.

Many of the relay molecules in signal transduction pathways are protein kinases, and they often act on other protein kinases in the pathway.

Figure 11.10 depicts a hypothetical pathway containing two different protein kinases that create a phosphorylation cascade.

Light Microscopy (LM)

Figure 6.3

fluid mosaic model

Figure 7.3 shows the currently accepted model of the arrangement of molecules in the plasma membrane. In this fluid mosaic model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids.

Feedback Inhibition: Earlier, we discussed the allosteric inhibition of an enzyme in an ATP-generating pathway by ATP itself. This is a common mode of metabolic control, called feedback inhibition, in which a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway

Figure 8.21 shows an example of feedback inhibition operating on an anabolic pathway.

The three main departments of this metabolic enterprise are glycolysis, pyruvate oxidation and the citric acid cycle, and the electron transport chain, which drives oxidative phosphorylation.

Figure 9.16 gives a detailed accounting of the ATP yield for each glucose molecule that is oxidized

The energy input and output of glycolysis

Figure 9.8

Cells in culture that acquire the ability to divide indefinitely are said to have undergone transformation, the process that causes them to behave like cancer cells. By contrast, nearly all normal, nontransformed mammalian cells growing in culture divide only about 20 to 50 times before they stop dividing, age, and die.

Finally, cancer cells evade the normal controls that trigger a cell to undergo apoptosis when something is wrong—for example, when an irreparable mistake has occurred during DNA replication preceding mitosis.

Endocytosis: In endocytosis, the cell takes in molecules and particulate matter by forming new vesicles from the plasma membrane. Although the proteins involved in the processes are different, the events of endocytosis look like the reverse of exocytosis

First, a small area of the plasma membrane sinks inward to form a pocket. Then, as the pocket deepens, it pinches in, forming a vesicle containing material that had been outside the cell

Regulation of the Response: Whether the response occurs in the nucleus or in the cytoplasm, it is not simply turned "on" or "off." Rather, the extent and specificity of the response are regulated in multiple ways. Here we'll consider four aspects of this regulation.

First, as mentioned earlier, signaling pathways generally amplify the cell's response to a single signaling event. The degree of amplification depends on the function of the specific molecules in the pathway. Second, the many steps in a multistep pathway provide control points at which the cell's response can be further regulated, contributing to the specificity of the response and allowing coordination with other signaling pathways. Third, the overall efficiency of the response is enhanced by the presence of proteins known as scaffolding proteins. Finally, a crucial point in regulating the response is the termination of the signal.

Catalysts

First, high temperature denatures proteins and kills cells. Second, heat would speed up all reactions, not just those that are needed. Instead of heat, organisms carry out catalysis, a process by which a catalyst (for example, an enzyme) selectively speeds up a reaction without itself being consumed. (You learned about catalysts in Concept 5.4.)

Cellular respiration also brings hydrogen and oxygen together to form water, but there are two important differences

First, in cellular respiration, the hydrogen that reacts with oxygen is derived from organic molecules rather than H2. Second, instead of occurring in one explosive reaction, respiration uses an electron transport chain to break the fall of electrons to oxygen into several energy-releasing steps (Figure 9.5b).

Why are the numbers in Figure 9.16 inexact? There are three reasons we cannot state an exact number of ATP molecules generated by the breakdown of one molecule of glucose.

First, phosphorylation and the redox reactions are not directly coupled to each other, so the ratio of the number of NADH molecules to the number of ATP molecules is not a whole number. We know that 1 NADH results in 10 H+ being transported out across the inner mitochondrial membrane, but the exact number of H+ that must reenter the mitochondrial matrix via ATP synthase to generate 1 ATP has long been debated

Fluorescence

Fluorescence. The locations of specific molecules in the cell can be revealed by labeling the molecules with fluorescent dyes or antibodies; some cells have molecules that fluoresce on their own. Fluorescent substances absorb ultraviolet radiation and emit visible light. In this fluorescently labeled uterine cell, nuclear material is blue, organelles called mitochondria are orange, and the cell's "skeleton" is green.

Although very different in mechanism, aerobic respiration is in principle similar to the combustion of gasoline in an automobile engine after oxygen is mixed with the fuel (hydrocarbons).

Food provides the fuel for respiration, and the exhaust is carbon dioxide and water. The overall process can be summarized as follows: Organic compounds + Oxygen S Carbon dioxide + Water + Energy

Termination of the Signal: In the interest of keeping Figure 11.17 simple, we did not show the inactivation mechanisms that are an essential aspect of any cell-signaling pathway.

For a cell of a multicellular organism to remain capable of responding to incoming signals, each molecular change in its signaling pathways must last only a short time. As we saw in the cholera example, if a signaling pathway component becomes locked into one state, whether active or inactive, consequences for the organism can be serious.

Apoptosis integrates multiple cell-signaling pathways: When signaling pathways were first discovered, they were thought to be linear, independent pathways. Our understanding of cellular communication has benefited from the realization that signaling pathway components interact with each other in various ways.

For a cell to carry out the appropriate response, cellular proteins often must integrate multiple signals. Let's consider an important cellular process—cellular suicide—as an example

MPF acts both directly as a kinase and indirectly by activating other kinases.

For example, MPF causes phosphorylation of various proteins of the nuclear lamina (see Figure 6.9), which promotes fragmentation of the nuclear envelope during prometaphase of mitosis. There is also evidence that MPF contributes to molecular events required for chromosome condensation and spindle formation during prophase.

Sometimes a signaling pathway may regulate the activity of proteins rather than causing their synthesis by activating gene expression. This directly affects proteins that function outside the nucleus.

For example, a signal may cause the opening or closing of an ion channel in the plasma membrane or a change in the activity of a metabolic enzyme

A transport protein is specific for the substance it translocates (moves), allowing only a certain substance (or a small group of related substances) to cross the membrane.

For example, a specific carrier protein in the plasma membrane of red blood cells transports glucose across the membrane 50,000 times faster than glucose can pass through on its own. This "glucose transporter" is so selective that it even rejects fructose, a structural isomer of glucose. Thus, the selective permeability of a membrane depends on both the discriminating barrier of the lipid bilayer and the specific transport proteins built into the membrane.

However, an organism also takes in organized forms of matter and energy from the surroundings and replaces them with less ordered forms.

For example, an animal obtains starch, proteins, and other complex molecules from the food it eats. As catabolic pathways break these molecules down, the animal releases carbon dioxide and water—small molecules that possess less chemical energy than the food did (see Figure 8.3b). The depletion of chemical energy is accounted for by heat generated during metabolism. On a larger scale, energy flows into most ecosystems in the form of light and exits in the form of heat (see Figure 1.11).

Biosynthesis (Anabolic Pathways): Cells need substance as well as energy. Not all the organic molecules of food are destined to be oxidized as fuel to make ATP. . In addition to calories, food must also provide the carbon skeletons that cells require to make their own molecules. Some organic monomers obtained from digestion can be used directly.

For example, as previously mentioned, amino acids from the hydrolysis of proteins in food can be incorporated into the organism's own proteins. Often, however, the body needs specific molecules that are not present as such in food.

Thus, two cells that respond differently to the same signal differ in one or more proteins that respond to the signal. Notice in Figure 11.17 that different pathways may have some molecules in common.

For example, cells A, B, and C all use the same receptor protein for the red signaling molecule; differences in other proteins account for their differing responses. In cell D, a different receptor protein is used for the same signaling molecule, leading to yet another response. In cell B, a pathway triggered by one signal diverges to produce two responses; such branched pathways often involve receptor tyrosine kinases (which can activate multiple relay proteins) or second messengers (which can regulate numerous proteins). In cell C, two pathways triggered by separate signals converge to modulate a single response. Branching of pathways and "cross-talk" (interaction) between pathways are important in regulating and coordinating a cell's responses to information coming in from different sources in the body. (You'll learn more about this coordination in Concept 11.5.) Moreover, the use of some of the same proteins in more than one pathway allows the cell to economize on the number of different proteins it must make.

What about the stop and go-ahead signals themselves— what are the signaling molecules? Studies using animal cells in culture have led to the identification of many external factors, both chemical and physical, that can influence cell division

For example, cells fail to divide if an essential nutrient is lacking in the culture medium. (This is analogous to trying to run a washing machine without the water supply hooked up; an internal sensor won't allow the machine to continue past the point where water is needed.) And even if all other conditions are favorable, most types of mammalian cells divide in culture only if the growth medium includes specific growth factors.

Active transport enables a cell to maintain internal concentrations of small solutes that differ from concentrations in its environment.

For example, compared with its surroundings, an animal cell has a much higher concentration of potassium ions (K+ ) and a much lower concentration of sodium ions (Na+ ). The plasma membrane helps maintain these steep gradients by pumping Na+ out of the cell and K+ into the cell.

Enzymes speed up metabolic reactions by lowering energy barriers: The laws of thermodynamics tell us what will and will not happen under given conditions but say nothing about the rate of these processes. A spontaneous chemical reaction occurs without any requirement for outside energy, but it may occur so slowly that it is imperceptible

For example, even though the hydrolysis of sucrose (table sugar) to glucose and fructose is exergonic, occurring spontaneously with a release of free energy (∆G = -7 kcal/mol), a solution of sucrose dissolved in sterile water will sit for years at room temperature with no appreciable hydrolysis. However, if we add a small amount of the enzyme sucrase to the solution, then all the sucrose may be hydrolyzed within seconds, as shown here: 153 pg

Compounds formed as intermediates of glycolysis and the citric acid cycle can be diverted into anabolic pathways as precursors from which the cell can synthesize the molecules it requires.

For example, humans can make about half of the 20 amino acids in proteins by modifying compounds siphoned away from the citric acid cycle; the rest are "essential amino acids" that must be obtained in the diet. Also, glucose can be made from pyruvate, and fatty acids can be synthesized from acetyl CoA. Of course, these anabolic, or biosynthetic, pathways do not generate ATP, but instead consume it.

Cell fractionation enables researchers to prepare specific cell components in bulk and identify their functions, a task not usually possible with intact cells.

For example, on one of the cell fractions, biochemical tests showed the presence of enzymes involved in cellular respiration, while electron microscopy revealed large numbers of the organelles called mitochondria. Together, these data helped biologists determine that mitochondria are the sites of cellular respiration. Biochemistry and cytology thus complement each other in correlating cell function with structure.

Just as each enzyme has an optimal temperature, it also has a pH at which it is most active. The optimal pH values for most enzymes fall in the range of pH 6-8, but there are exceptions

For example, pepsin, a digestive enzyme in the human stomach, works best at a very low pH. Such an acidic environment denatures most enzymes, but pepsin is adapted to maintain its functional three-dimensional structure in the acidic environment of the stomach. In contrast, trypsin, a digestive enzyme residing in the more alkaline environment of the human intestine would be denatured in the stomach (Figure 8.17b).

Eukaryotic cells are generally much larger than prokaryotic cells (see Figure 6.2). Size is a general feature of cell structure that relates to function. The logistics of carrying out cellular metabolism sets limits on cell size. At the lower limit, the smallest cells known are bacteria called mycoplasmas, which have diameters between 0.1 and 1.0 µm. . These are perhaps the smallest packages with enough DNA to program metabolism and enough enzymes and other cellular equipment to carry out the activities necessary for a cell to sustain itself and reproduce. Typical bacteria are 1-5 µm in diameter, about ten times the size of mycoplasmas. Eukaryotic cells are typically 10-100 µm in diameter.

For example, some prokaryotes contain regions surrounded by proteins (not membranes), within which specific reactions take place.

In the case of ions, then, we must refine our concept of passive transport: An ion diffuses not simply down its concentration gradient but, more exactly, down its electrochemical gradient.

For example, the concentration of Na+ inside a resting nerve cell is much lower than outside it. When the cell is stimulated, gated channels open that facilitate Na+ diffusion. Sodium ions then "fall" down their electrochemical gradient, driven by the concentration gradient of Na+ and by the attraction of these cations to the negative side (inside) of the membrane. In this example, both electrical and chemical contributions to the electrochemical gradient act in the same direction across the membrane, but this is not always so. In cases where electrical forces due to the membrane potential oppose the simple diffusion of an ion down its concentration gradient, active transport may be necessary. In Concepts 48.2 and 48.3, you'll learn about the importance of electrochemical gradients and membrane potentials in the transmission of nerve impulses.

The carbohydrates on the extracellular side of the plasma membrane vary from species to species, among individuals of the same species, and even from one cell type to another in a single individual. The diversity of the molecules and their location on the cell's surface enable membrane carbohydrates to function as markers that distinguish one cell from another.

For example, the four human blood types designated A, B, AB, and O reflect variation in the carbohydrate part of glycoproteins on the surface of red blood cells.

aquaporin

For example, the image in Figure 7.1 shows a computer model of a short section of the phospholipid bilayer of a membrane (hydrophilic heads are yellow, and hydrophobic tails are green). The blue ribbons within the lipid bilayer represent helical regions of a membrane transport channel protein called an aquaporin. One molecule of this protein enables billions of water molecules (red and gray) to pass through the membrane every second, many more than could cross on their own.

aquaporins

For example, the passage of water molecules through the membrane in certain cells is greatly facilitated by channel proteins known as aquaporins (see Figure 7.1). Each aquaporin allows entry of up to 3 billion (3 * 109 ) water molecules per second, passing single file through its central channel, which fits ten at a time. Without aquaporins, only a tiny fraction of these water molecules would pass through the same area of the cell membrane in a second, so the channel protein brings about a tremendous increase in rate.

A third variable that reduces the yield of ATP is the use of the proton-motive force generated by the redox reactions of respiration to drive other kinds of work.

For example, the proton-motive force powers the mitochondrion's uptake of pyruvate from the cytosol. However, if all the proton-motive force generated by the electron transport chain were used to drive ATP synthesis, one glucose molecule could generate a maximum of 28 ATP produced by oxidative phosphorylation plus 4 ATP (net) from substrate-level phosphorylation to give a total yield of about 32 ATP (or only about 30 ATP if the less efficient shuttle were functioning).

This is the free-energy change measured under standard conditions. In the cell, conditions do not conform to standard conditions, primarily because reactant and product concentrations differ from 1 M.

For example, when ATP hydrolysis occurs under cellular conditions, the actual ∆G is about -13 kcal/mol, 78% greater than the energy released by ATP hydrolysis under standard conditions.

The reaction catalyzed by each enzyme is very specific; an enzyme can recognize its specific substrate even among closely related compounds.

For instance, sucrase will act only on sucrose and will not bind to other disaccharides, such as maltose. What accounts for this molecular recognition? Recall that most enzymes are proteins, and proteins are macromolecules with unique three-dimensional configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence.

A process that, on its own, leads to a decrease in entropy is said to be nonspontaneous: It will happen only if energy is supplied. We know from experience that certain events occur spontaneously and others do not.

For instance, we know that water flows downhill spontaneously but moves uphill only with an input of energy, such as when a machine pumps the water against gravity. Some energy is inevitably lost as heat, increasing entropy in the surroundings, so usage of energy means that a nonspontaneous process also leads to an increase in the entropy of the universe as a whole.

As we mentioned in Concept 10.1, the carbohydrate produced directly from the Calvin cycle is not glucose. It is actually a three-carbon sugar called glyceraldehyde 3-phosphate (G3P).

For the net synthesis of one molecule of G3P, the cycle must take place three times, fixing three molecules of CO2—one per turn of the cycle. (Recall that the term carbon fixation refers to the initial incorporation of CO2 into organic material.) As we trace the steps of the Calvin cycle, keep in mind that we are following three molecules of CO2 through the reactions. Figure 10.19 divides the Calvin cycle into three phases: carbon fixation, reduction, and regeneration of the CO2 acceptor.

. For a system at equilibrium, G is at its lowest possible value in that system. We can think of the equilibrium state as a free-energy valley. Any change from the equilibrium position will have a positive ∆G and will not be spontaneous

For this reason, systems never spontaneously move away from equilibrium. Because a system at equilibrium cannot spontaneously change, it can do no work. A process is spontaneous and can perform work only when it is moving toward equilibrium.

More than a century of experiments has shown that only processes with a negative ∆G are spontaneous

For ∆G to be negative, ∆H must be negative (the system gives up enthalpy and H decreases) or T∆S must be positive (the system gives up order and S increases), or both: When ∆H and T∆S are tallied, ∆G has a negative value (∆G 6 0) for all spontaneous processes. In other words, every spontaneous process decreases the system's free energy, and processes that have a positive or zero ∆G are never spontaneous

As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases.

Free energy increases when a reaction is somehow pushed away from equilibrium, perhaps by removing some of the products (and thus changing their concentration relative to that of the reactants)

Free energy

Free energy is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. Let's consider how we determine the free-energy change that occurs when a system changes—for example, during a chemical reaction

mitosis and cytokinesis

From a fertilized egg, mitosis and cytokinesis produced the 200 trillion somatic cells that now make up your body, and the same processes continue to generate new cells to replace dead and damaged ones.

Significant evidence points to the involvement of apoptosis in certain degenerative diseases of the nervous system, such as Parkinson's disease and Alzheimer's disease. In Alzheimer's disease, an accumulation of aggregated proteins in neuronal cells activates an enzyme that triggers apoptosis, resulting in the loss of brain function seen in these patients.

Furthermore, cancer can result from a failure of cell suicide; some cases of human melanoma, for example, have been linked to faulty forms of the human version of the C. elegans Ced-4 protein. It is not surprising, therefore, that the signaling pathways feeding into apoptosis are quite elaborate. After all, the life-or-death question is the most fundamental one imaginable for a cell.

Exploring Mitosis in an Animal Cell:

G2 of Interphase: • A nuclear envelope encloses the nucleus. • The nucleus contains one or more nucleoli (singular, nucleolus). • Two centrosomes have formed by duplication of a single centrosome. Centrosomes are regions in animal cells that organize the microtubules of the spindle. Each centrosome contains two centrioles. • Chromosomes, duplicated during S phase, cannot be seen individually because they have not yet condensed.

Referring to Figure 9.12, we can tally the energy-rich molecules produced by the citric acid cycle. For each acetyl group entering the cycle, 3 NAD+ are reduced to NADH (steps 3 , 4 , and 8 ). In step 6 , electrons are transferred not to NAD+ , but to FAD, which accepts 2 electrons and 2 protons to become FADH2. In many animal tissue cells, the reaction in step 5 produces a guanosine triphosphate (GTP) molecule by substrate-level phosphorylation.

GTP is a molecule similar to ATP in its structure and cellular function. This GTP may be used to make an ATP molecule (as shown) or directly power work in the cell. In the cells of plants, bacteria, and some animal tissues, step 5 forms an ATP molecule directly by substrate-level phosphorylation. The output from step 5 represents the only ATP generated during the citric acid cycle.

Gap Junctions

Gap junctions (also called communicating junctions) provide cytoplasmic channels from one cell to an adjacent cell and in this way are similar in their function to the plasmodesmata in plants. Gap junctions consist of membrane proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass. Gap junctions are necessary for communication between cells in many types of tissues, such as heart muscle, and in animal embryos.

The Three Stages of Cell Signaling: A Preview: Our current understanding of how signaling molecules act via signal transduction pathways had its origins in the pioneering work of Earl W. Sutherland, whose research led to a Nobel Prize in 1971. Sutherland and his colleagues at Vanderbilt University were investigating how the animal hormone epinephrine (also called adrenaline) triggers the "fight-or-flight" response in animals by stimulating the breakdown of the storage polysaccharide glycogen within liver cells and skeletal muscle cells.

Glycogen breakdown releases the sugar glucose 1-phosphate, which the cell converts to glucose 6-phosphate. The liver or muscle cell can then use this compound, an early intermediate in glycolysis, for energy production (see Figure 9.9). Alternatively, the compound can be stripped of phosphate and released from the cell into the blood as glucose, which can fuel cells throughout the body. Thus, one effect of epinephrine is the mobilization of fuel reserves, which can be used by the animal to either defend itself (fight) or escape whatever elicited a scare (flight), as the impala in Figure 11.1 is clearly doing.

Sutherland's research team discovered that epinephrine stimulates glycogen breakdown by somehow activating a cytosolic enzyme, glycogen phosphorylase. However, when epinephrine was added to a cell-free mixture containing the enzyme and its substrate, glycogen, no breakdown occurred.

Glycogen phosphorylase could be activated by epinephrine only when the hormone was added to intact cells. This result told Sutherland two things. First, epinephrine does not interact directly with the enzyme responsible for glycogen breakdown; an intermediate step or series of steps must be occurring in the cell. Second, an intact, membrane-bound cell must be present for transmission of the signal to take place

Pyruvate as a key juncture in catabolism.

Glycolysis is common to fermentation and cellular respiration. The end product of glycolysis, pyruvate, represents a fork in the catabolic pathways of glucose oxidation. In a facultative anaerobe or a muscle cell, which are capable of both aerobic cellular respiration and fermentation, pyruvate is committed to one of those two pathways, usually depending on whether or not oxygen is present.

Extracellular components and connections between cells help coordinate cellular activities

Having crisscrossed the cell to explore its interior components, we complete our tour of the cell by returning to the surface of this microscopic world, where there are additional structures with important functions. The plasma membrane is usually regarded as the boundary of the living cell, but most cells synthesize and secrete materials extracellularly (to the outside of the cell). Although these materials and the structures they form are outside the cell, their study is important to cell biology because they are involved in a great many essential cellular functions.

Although hemoglobin is not an enzyme (it carries O2 rather than catalyzing a reaction), classic studies of hemoglobin have elucidated the principle of cooperativity.

Hemoglobin is made up of four subunits, each with an oxygen-binding site (see Figure 5.18). The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining binding sites. Thus, where oxygen is at high levels, such as in the lungs or gills, hemoglobin's affinity for oxygen increases as more binding sites are filled.

Now let's divide the photosynthetic equation by 6 to put it in its simplest possible form: CO2 + H2O --> [CH2O] + O2

Here, the brackets indicate that CH2O is not an actual sugar but represents the general formula for a carbohydrate (see Concept 5.2). In other words, we are imagining the synthesis of a sugar molecule one carbon at a time (with six repetitions theoretically adding up to a glucose molecule—C6H12O6). Let's now see how researchers tracked the elements C, H, and O from the reactants of photosynthesis to the products

A closer look at glycolysis. Note that glycolysis is a source of ATP and NADH. GLYCOLYSIS: Energy Investment Phase

Hexokinase transfers a phosphate group from ATP to glucose, making it more chemically reactive. The charge on the phosphate also traps the sugar in the cell. Glucose 6- phosphate is converted to fructose 6-phosphate. Phosphofructokinase transfers a phosphate group from ATP to the opposite end of the sugar, investing a second molecule of ATP. This is a key step for regulation of glycolysis. Aldolase cleaves the sugar molecule into two different three-carbon sugars. Conversion between DHAP and G3P: This reaction never reaches equilibrium; G3P is used in the next step as fast as it forms.

Redox Reactions: Oxidation and Reduction

How do the catabolic pathways that decompose glucose and other organic fuels yield energy? The answer is based on the transfer of electrons during the chemical reactions. The relocation of electrons releases energy stored in organic molecules, and this energy ultimately is used to synthesize ATP.

Dynein

How does the microtubule assembly produce the bending movements of flagella and motile cilia? Bending involves large motor proteins called dyneins (red in the diagram in Figure 6.24) that are attached along each outer microtubule doublet.

The water balance of living cells.

How living cells react to changes in the solute concentration of their environment depends on whether or not they have cell walls. (a) Animal cells, such as this red blood cell, do not have cell walls. (b) Plant cells do have cell walls. (Arrows indicate net water movement after the cells were first placed in these solutions.)

fluidity buffer

However, because cholesterol also hinders the close packing of phospholipids, it lowers the temperature required for the membrane to solidify. Thus, cholesterol can be thought of as a "fluidity buffer" for the membrane, resisting changes in membrane fluidity that can be caused by changes in temperature. Compared to animals, plants have very low levels of cholesterol; rather, related steroid lipids buffer membrane fluidity in plant cells.

Each type of membrane has a unique composition of

However, each type of membrane has a unique composition of lipids and proteins suited to that membrane's specific functions. For example, enzymes embedded in the membranes of the organelles called mitochondria function in cellular respiration. Because membranes are so fundamental to the organization of the cell, Chapter 7 will discuss them in detail.

All of the carbon originally present in glucose is accounted for in the two molecules of pyruvate; no carbon is released as CO2 during glycolysis. Glycolysis occurs whether or not O2 is present.

However, if O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation.

extreme environmental conditions

However, membranes that are too fluid cannot support protein function either. Therefore, extreme environments pose a challenge for life, resulting in evolutionary adaptations that include differences in membrane lipid composition.

Glycoproteins

However, most are covalently bonded to proteins, which are thereby glycoproteins (see Figure 7.3)

The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar: The Calvin cycle is similar to the citric acid cycle in that a starting material is regenerated after some molecules enter and others exit the cycle.

However, the citric acid cycle is catabolic, oxidizing acetyl CoA and using the energy to synthesize ATP, while the Calvin cycle is anabolic, building carbohydrates from smaller molecules and consuming energy. Carbon enters the Calvin cycle in the form of CO2 and leaves in the form of sugar. The cycle spends ATP as an energy source and consumes NADPH as reducing power for adding high-energy electrons to make the sugar.

Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen : Because most of the ATP generated by cellular respiration is due to the work of oxidative phosphorylation, our estimate of ATP yield from aerobic respiration depends on an adequate supply of oxygen to the cell. Without the electronegative oxygen to pull electrons down the transport chain, oxidative phosphorylation eventually ceases.

However, there are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP without the use of oxygen: anaerobic respiration and fermentation.

During the early history of life, complex organisms evolved from simpler ancestors. For instance, we can trace the ancestry of the plant kingdom from much simpler organisms called green algae to more complex flowering plants.

However, this increase in organization over time in no way violates the second law. The entropy of a particular system, such as an organism, may actually decrease as long as the total entropy of the universe—the system plus its surroundings—increases. Thus, organisms are islands of low entropy in an increasingly random universe. The evolution of biological order is perfectly consistent with the laws of thermodynamics.

When one of a chromosome's kinetochores is "captured" by microtubules, the chromosome begins to move toward the pole from which those microtubules extend.

However, this movement comes to a halt as soon as microtubules from the opposite pole attach to the kinetochore on the other chromatid. What happens next is like a tug-of-war that ends in a draw. The chromosome moves first in one direction and then in the other, back and forth, finally settling midway between the two ends of the cell.

Study Figure 7.19 carefully to understand the three types of endocytosis: phagocytosis ("cellular eating"), pinocytosis ("cellular drinking"), and receptor-mediated endocytosis

Human cells use receptor-mediated endocytosis to take in cholesterol for membrane synthesis and the synthesis of other steroids Cholesterol travels in the blood in particles called low-density lipoproteins (LDLs), each a complex of lipids and a protein. LDLs bind to LDL receptors on plasma membranes and then enter the cells by endocytosis. . In the inherited disease familial hypercholesterolemia, characterized by a very high level of cholesterol in the blood, LDLs cannot enter cells because the LDL receptor proteins are defective or missing:

What are hydrolytic enzymes and lysosomal made up of?

Hydrolytic enzymes and lysosomal membrane are made by rough ER and then transferred to the Golgi apparatus for further processing. At least some lysosomes probably arise by budding from the trans face of the Golgi apparatus (see Figure 6.12). How are the proteins of the inner surface of the lysosomal membrane and the digestive enzymes themselves spared from destruction? Apparently, the three-dimensional shapes of these proteins protect vulnerable bonds from enzymatic attack

Stepwise Energy Harvest via NAD+ and the Electron Transport Chain

If energy is released from a fuel all at once, it cannot be harnessed efficiently for constructive work. For example, if a gasoline tank explodes, it cannot drive a car very far

Three important checkpoints are those in the G1, G2, and M phases (see Figure 12.15). For many cells, the G1 checkpoint seems to be the most important. If a cell receives a goahead signal at the G1 checkpoint, it will usually complete the G1, S, G2, and M phases and divide.

If it does not receive a go-ahead signal at that point, it may exit the cycle, switching into a nondividing state called the G0 phase (Figure 12.17a). Most cells of the human body are actually in the G0 phase. As mentioned earlier, mature nerve cells and muscle cells never divide. Other cells, such as liver cells, can be "called back" from the G0 phase to the cell cycle by external cues, such as growth factors released during injury.

The Cell Cycle Control System: What controls the cell cycle? In the early 1970s, a variety of experiments led to the hypothesis that the cell cycle is driven by specific signaling molecules present in the cytoplasm. Some of the first strong evidence for this hypothesis came from experiments with mammalian cells grown in culture. In these experiments, two cells in different phases of the cell cycle were fused to form a single cell with two nuclei (Figure 12.14).

If one of the original cells was in the S phase and the other was in G1, the G1 nucleus immediately entered the S phase, as though stimulated by signaling molecules present in the cytoplasm of the first cell. Similarly, if a cell undergoing mitosis (M phase) was fused with another cell in any stage of its cell cycle, even G1, the second nucleus immediately entered mitosis, with condensation of the chromatin and formation of a mitotic spindle.

The effect of an external physical factor on cell division is clearly seen in density-dependent inhibition, a phenomenon in which crowded cells stop dividing (Figure 12.19a). As first observed many years ago, cultured cells normally divide until they form a single layer of cells on the inner surface of a culture flask, at which point the cells stop dividing.

If some cells are removed, those bordering the open space begin dividing again and continue until the vacancy is filled. Follow-up studies revealed that the binding of a cell-surface protein to its counterpart on an adjoining cell sends a signal to both cells that inhibits cell division, preventing them from moving forward in the cell cycle, even in the presence of growth factors.

Thus, van Niel hypothesized that plants split H2O as a source of electrons from hydrogen atoms, releasing O2 as a by-product. Nearly 20 years later, scientists confirmed van Niel's hypothesis by using oxygen-18 (18O), a heavy isotope, as a tracer to follow the path of oxygen atoms during photosynthesis. The experiments showed that the O2 from plants was labeled with 18O only if water was the source of the tracer (experiment 1).

If the 18O was introduced to the plant in the form of CO2, the label did not turn up in the released O2 (experiment 2). In the following summary, magenta denotes labeled atoms of oxygen (18O): Experiment 1: CO2 + 2 H2O --> [CH2O] + H2O + O2 Experiment 2: CO2 + 2 H2O --> [CH2O] + H2O + O2 A significant result of the shuffling of atoms during photosynthesis is the extraction of hydrogen from water and its incorporation into sugar. The waste product of photosynthesis, O2, is released to the atmosphere. Figure 10.5 shows the fates of all atoms in photosynthesis.

Depending on the kind of shuttle in a particular cell type, the electrons are passed either to NAD+ or to FAD in the mitochondrial matrix (see Figures 9.15 and 9.16).

If the electrons are passed to FAD, as in brain cells, only about 1.5 ATP can result from each NADH that was originally generated in the cytosol. If the electrons are passed to mitochondrial NAD+ , as in liver cells and heart cells, the yield is about 2.5 ATP per NADH.

The proton (H+ ) gradient, or pH gradient, across the thylakoid membrane is substantial. When chloroplasts in an experimental setting are illuminated, the pH in the thylakoid space drops to about 5 (the H+ concentration increases), and the pH in the stroma increases to about 8 (the H+ concentration decreases). This gradient of three pH units corresponds to a thousandfold difference in H+ concentration.

If the lights are then turned off, the pH gradient is abolished, but it can quickly be restored by turning the lights back on. Experiments such as this provided strong evidence in support of the chemiosmotic model.

In addition, glycolysis and the citric acid cycle function as metabolic interchanges that enable our cells to convert some kinds of molecules to others as we need them. For example, an intermediate compound generated during glycolysis, dihydroxyacetone phosphate (see Figure 9.9, step 5), can be converted to one of the major precursors of fats.

If we eat more food than we need, we store fat even if our diet is fatfree. Metabolism is remarkably versatile and adaptable.

ATP is useful to the cell because the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver. But why does this hydrolysis release so much energy?

If we reexamine the ATP molecule in Figure 8.9a, we can see that all three phosphate groups are negatively charged. These like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule. The triphosphate tail of ATP is the chemical equivalent of a compressed spring.

Similarly, electron transport chain proteins in the thylakoid membrane of the chloroplast pump protons from the stroma into the thylakoid space (interior of the thylakoid), which functions as the H+ reservoir.

If you imagine the cristae of mitochondria pinching off from the inner membrane, this may help you see how the thylakoid space and the intermembrane space are comparable spaces in the two organelles, while the mitochondrial matrix is analogous to the stroma of the chloroplast.

The mitotic phase alternates with interphase in the cell cycle:

In 1882, a German anatomist named Walther Flemming developed dyes that allowed him to observe, for the first time, the behavior of chromosomes during mitosis and cytokinesis. (In fact, Flemming coined the terms mitosis and chromatin.) During the period between one cell division and the next, it appeared to Flemming that the cell was simply growing larger. But we now know that many critical events occur during this stage in the life of a cell.

Phase 3: Regeneration of the CO2 acceptor (RuBP)

In a complex series 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. To accomplish this, the cycle spends three more molecules of ATP. The RuBP is now prepared to recieve CO2 again and the cycle continues.

The cell cycle

In a dividing cell, the mitotic (M) phase alternates with interphase, a growth period. The first part of interphase (G1) is followed by the S phase, when the chromosomes duplicate; G2 is the last part of interphase. In the M phase, mitosis distributes the daughter chromosomes to daughter nuclei, and cytokinesis divides the cytoplasm, producing two daughter cells.

oxidation & reduction

In a redox reaction, the loss of electrons from one substance is called oxidation, and the addition of electrons to another substance is known as reduction. (Note that adding electrons is called reduction; adding negatively charged electrons to an atom reduces the amount of positive charge of that atom.)

Most plants and other photosynthesizers make more organic material each day than they need to use as respiratory fuel and precursors for biosynthesis. They stockpile the extra sugar by synthesizing starch, storing some in the chloroplasts themselves and some in storage cells of roots, tubers, seeds, and fruits.

In accounting for the consumption of the food molecules produced by photosynthesis, let's not forget that most plants lose leaves, roots, stems, fruits, and sometimes their entire bodies to heterotrophs, including humans.

Similar evolutionary history of chloroplasts & mitochondria

In addition to having related functions, mitochondria and chloroplasts share similar evolutionary origins, which we'll discuss briefly before describing their structures. In this section, we will also consider the peroxisome, an oxidative organelle. The evolutionary origin of the peroxisome, as well as its relation to other organelles, is still a matter of some debate. Mitochondria and chloroplasts display similarities with bacteria that led to the endosymbiont theory, illustrated in Figure 6.16. This theory states that an early ancestor of eukaryotic cells engulfed an oxygen-using nonphotosynthetic prokaryotic cell. Eventually, the engulfed cell formed a relationship with the host cell in which it was enclosed, becoming an endosymbiont (a cell living within another cell). Indeed, over the course of evolution, the host cell and its endosymbiont merged into a single organism, a eukaryotic cell with a mitochondrion. At least one of these cells may have then taken up a photosynthetic prokaryote, becoming the ancestor of eukaryotic cells that contain chloroplasts.

Golgi apparatus also manufactures some macromolecules.

In addition to its finishing work, the Golgi apparatus also manufactures some macromolecules. Many polysaccharides secreted by cells are Golgi products. For example, pectins and certain other noncellulose polysaccharides are made in the Golgi of plant cells and then incorporated along with cellulose into their cell walls. Like secretory proteins, nonprotein Golgi products that will be secreted depart from the trans face of the Golgi inside transport vesicles that eventually fuse with the plasma membrane.

How is the rough ER a membrane factory?

In addition to making secretory proteins, rough ER is a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane. As polypeptides destined to be membrane proteins grow from the ribosomes, they are inserted into the ER membrane itself and anchored there by their hydrophobic portions. Like the smooth ER, the rough ER also makes membrane phospholipids; enzymes built into the ER membrane assemble phospholipids from precursors in the cytosol. The ER membrane expands, and portions of it are transferred in the form of transport vesicles to other components of the endomembrane system.

Cytokinesis: A Closer Look

In animal cells, cytokinesis occurs by a process known as cleavage. The first sign of cleavage is the appearance of a cleavage furrow, a shallow groove in the cell surface near the old metaphase plate (Figure 12.10a).

Centrosomes and Centrioles

In animal cells, microtubules grow out from a centrosome, a region that is often located near the nucleus. These microtubules function as compression-resisting girders of the cytoskeleton. Within the centrosome is a pair of centrioles, each composed of nine sets of triplet microtubules arranged in a ring (Figure 6.22). Although centrosomes with centrioles may help organize microtubule assembly in animal cells, many other eukaryotic cells lack centrosomes with centrioles and instead organize microtubules by other means

centrosomes

In animal cells, the assembly of spindle microtubules starts at the centrosome, a subcellular region containing material that functions throughout the cell cycle to organize the cell's microtubules. (It is also a type of microtubule-organizing center.)

Carbohydrates, fats, and protein molecules from food can all be processed and consumed as fuel, as we will discuss later in the chapter.

In animal diets, a major source of carbohydrates is starch, a storage polysaccharide that can be broken down into glucose (C6H12O6) subunits. Here, we will learn the steps of cellular respiration by tracking the degradation of the sugar glucose: C6H12O6 + 6 O2 --> 6 CO2 + 6 H2O + Energy (ATP + heat) This breakdown of glucose is exergonic, having a free-energy change of -686 kcal (2,870 kJ) per mole of glucose decomposed (∆G = -686 kcal/mol).

Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells

In animals, there are three main types of cell junctions: tight junctions, desmosomes, and gap junctions. (Gap junctions are most like the plasmodesmata of plants, although gap junction pores are not lined with membrane.) All three types of cell junctions are especially common in epithelial tissue, which lines the external and internal surfaces of the body. Figure 6.30 uses epithelial cells of the intestinal lining to illustrate these junctions.

Many secretory cells use exocytosis to export products. For example, cells in the pancreas that make insulin secrete it into the extracellular fluid by exocytosis.

In another example, nerve cells use exocytosis to release neurotransmitters that signal other neurons or muscle cells. When plant cells are making cell walls, exocytosis delivers some of the necessary proteins and carbohydrates from Golgi vesicles to the outside of the cell.

Autophagy

In autophagy, lysosomes recycle intracellular materials. Top: In the cytoplasm of this rat liver cell is a vesicle containing two disabled organelles (TEM). The vesicle will fuse with a lysosome in the process of autophagy, which recycles intracellular materials. Bottom: This diagram shows fusion of such a vesicle with a lysosome. This type of vesicle has a double membrane of unknown origin. The outer membrane fuses with the lysosome, and the inner membrane is degraded along with the damaged organelles. Lysosome fuses with vesicle containing damaged organelles Hydrolytic enzymes digest organelle components.

Binary Fission in Bacteria: Prokaryotes (bacteria and archaea) can undergo a type of reproduction in which the cell grows to roughly double its size and then divides to form two cells. The term binary fission, meaning "division in half," refers to this process and to the asexual reproduction of single-celled eukaryotes, such as the amoeba in Figure 12.2a. However, the process in eukaryotes involves mitosis, while that in prokaryotes does not.

In bacteria, most genes are carried on a single bacterial chromosome that consists of a circular DNA molecule and associated proteins. Although bacteria are smaller and simpler than eukaryotic cells, the challenge of replicating their genomes in an orderly fashion and distributing the copies equally to two daughter cells is still formidable. For example, when it is fully stretched out, the chromosome of the bacterium Escherichia coli is about 500 times as long as the cell. For such a long chromosome to fit within the cell, it must be highly coiled and folded.

Comparison of chemiosmosis in mitochondria and chloroplasts

In both kinds of organelles, electron transport chains pump protons (H+ ) across a membrane from a region of low H+ concentration (light gray in this diagram) to one of high H+ concentration (dark gray). The protons then diffuse back across the membrane through ATP synthase, driving the synthesis of ATP.

Local and long-distance cell signaling by secreted molecules in animals.

In both local and long-distance signaling, only specific target cells that can recognize a given signaling molecule will respond to it.

A key difference is the contrasting mechanisms for oxidizing NADH back to NAD+ , which is required to sustain glycolysis. In fermentation, the final electron acceptor is an organic molecule such as pyruvate (lactic acid fermentation) or acetaldehyde (alcohol fermentation).

In cellular respiration, by contrast, electrons carried by NADH are transferred to an electron transport chain, which regenerates the NAD+ required for glycolysis.

cortex

In contrast to the compression-resisting role of microtubules, the structural role of microfilaments in the cytoskeleton is to bear tension (pulling forces). A three-dimensional network formed by microfilaments just inside the plasma membrane (cortical microfilaments) helps support the cell's shape (see Figure 6.8). This network gives the outer cytoplasmic layer of a cell, called the cortex, the semisolid consistency of a gel, in contrast with the more fluid state of the interior cytoplasm.

Rising CO2 levels should benefit C3 plants by lowering the amount of photorespiration that occurs. At the same time, rising temperatures have the opposite effect, increasing photorespiration. (Other factors such as water availability may also come into play.)

In contrast, many C4 plants could be largely unaffected by increasing CO2 levels or temperature. Researchers have investigated aspects of this question in several studies; you can work with data from one such experiment in the Scientific Skills Exercise. In different regions, the particular combination of CO2 concentration and temperature is likely to alter the balance of C3 and C4 plants in varying ways. The effects of such a widespread and variable change in community structure are unpredictable and thus a cause of legitimate concern.

noncompetitive inhibitor

In contrast, noncompetitive inhibitors do not directly compete with the substrate to bind to the enzyme at the active site (Figure 8.18c). Instead, they impede enzymatic reactions by binding to another part of the enzyme. This interaction causes the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product.

The Paramecium cell doesn't burst because it is also equipped with a contractile vacuole, an organelle that functions as a bilge pump to force water out of the cell as fast as it enters by osmosis (Figure 7.13).

In contrast, the bacteria and archaea that live in hypersaline (excessively salty) environments (see Figure 27.1) have cellular mechanisms that balance the internal and external solute concentrations to ensure that water does not move out of the cell. We will examine other evolutionary adaptations for osmoregulation by animals in Concept 44.1.

Like local regulators, hormones vary widely in size and type. For instance, the plant hormone ethylene, a gas that promotes fruit ripening and helps regulate growth, is a hydrocarbon of only six atoms (C2H4), small enough to pass through cell walls.

In contrast, the mammalian hormone insulin, which regulates sugar levels in the blood, is a protein with thousands of atoms.

But when methane reacts with oxygen, forming carbon dioxide, electrons end up shared less equally between the carbon atom and its new covalent partners, the oxygen atoms, which are very electronegative.

In effect, the carbon atom has partially "lost" its shared electrons; thus, methane has been oxidized.

The metabolic steps of the Calvin cycle are sometimes referred to as the dark reactions, or lightindependent reactions, because none of the steps requires light directly. Nevertheless, the Calvin cycle in most plants occurs during daylight, for only then can the light reactions provide the NADPH and ATP that the Calvin cycle requires.

In essence, the chloroplast uses light energy to make sugar by coordinating the two stages of photosynthesis.

Cilia and Flagella

In eukaryotes, a specialized arrangement of microtubules is responsible for the beating of flagella (singular, flagellum) and cilia (singular, cilium), microtubule-containing extensions that project from some cells. (The bacterial flagellum, shown in Figure 6.5, has a completely different structure.) Many unicellular eukaryotes are propelled through water by cilia or flagella that act as locomotor appendages, and the sperm of animals, algae, and some plants have flagella. When cilia or flagella extend from cells that are held in place as part of a tissue layer, they can move fluid over the surface of the tissue. For example, the ciliated lining of the trachea (windpipe) sweeps mucus containing trapped debris out of the lungs (see the EMs in Figure 6.3). In a woman's reproductive tract, the cilia lining the oviducts help move an egg toward the uterus.

Chemiosmosis

In eukaryotic cells, the inner membrane of the mitochondrion is the site of electron transport and another process called chemiosmosis, together making up oxidative phosphorylation. (In prokaryotes, these processes take place in the plasma membrane.)

Stepwise electron transport drives oxidative phosphorylation, yielding ATP. Thus, cellular respiration harvests much more energy from each sugar molecule than fermentation can.

In fact, aerobic respiration yields up to 32 molecules of ATP per glucose molecule—up to 16 times as much as does fermentation.

Proteoglycans

In fact, collagen accounts for about 40% of the total protein in the human body. The collagen fibers are embedded in a network woven out of proteoglycans secreted by cells (Figure 6.28)A proteoglycan molecule consists of a small core protein with many carbohydrate chains covalently attached, so that it may be up to 95% carbohydrate. Large proteoglycan complexes can form when hundreds of proteoglycan molecules become noncovalently attached to a single long polysaccharide molecule, as shown in Figure 6.28.

Citing enzyme inhibitors that are metabolic poisons may give the impression that enzyme inhibition is generally abnormal and harmful.

In fact, molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors. Such regulation—selective inhibition—is essential to the control of cellular metabolism, as we will discuss in Concept 8.5.

Protein Phosphorylation and Dephosphorylation: Dephosphorylation Previous chapters introduced the concept of activating a protein by adding one or more phosphate groups to it (see Figure 8.11a). In Figure 11.8, you have already seen how phosphorylation is involved in the activation of receptor tyrosine kinases

In fact, the phosphorylation and dephosphorylation of proteins is a widespread cellular mechanism for regulating protein activity.

Some organisms, called obligate anaerobes, carry out only fermentation or anaerobic respiration.

In fact, these organisms cannot survive in the presence of oxygen, some forms of which can actually be toxic if protective systems are not present in the cell. A few cell types, such as cells of the vertebrate brain, can carry out only aerobic oxidation of pyruvate, not fermentation.

G protein-coupled receptors vary in the binding sites for their ligands and also for different types of G proteins inside the cell. Nevertheless, GPCR proteins are all remarkably similar in structure.

In fact, they make up a large family of eukaryotic receptor proteins with a secondary structure in which the single polypeptide, represented here in a ribbon model, has seven transmembrane α helices (outlined with cylinders and depicted in a row for clarity). Specific loops between the helices (here, the loops on the right) form binding sites for signaling molecules (outside the cell) and G proteins (on the cytoplasmic side).

Chemiosmosis

In general terms, chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work

GPCR-based signaling systems are extremely widespread and diverse in their functions, including roles in embryonic development and sensory reception.

In humans, for example, vision, smell, and taste depend on GPCRs (see Concept 50.4). Similarities in structure in G proteins and GPCRs in diverse organisms suggest that G proteins and their associated receptors evolved very early among eukaryotes.

Signaling Efficiency: Scaffolding Proteins and Signaling Complexes The illustrations of signaling pathways in Figure 11.17 (as well as diagrams of other pathways in this chapter) are greatly simplified. The diagrams show only a few relay molecules and, for clarity's sake, display these molecules spread out in the cytosol. If this were true in the cell, signaling pathways would operate very inefficiently because most relay molecules are proteins, and proteins are too large to diffuse quickly through the viscous cytosol. How does a given protein kinase, for instance, find its protein substrate?

In many cases, the efficiency of signal transduction is apparently increased by the presence of scaffolding proteins, large relay proteins to which several other relay proteins are simultaneously attached (Figure 11.18). Researchers have found scaffolding proteins in brain cells that permanently hold together networks of signaling pathway proteins at synapses. This hardwiring enhances the speed and accuracy of signal transfer between cells because the rate of protein-protein interaction is not limited by diffusion. Furthermore, in some cases the scaffolding proteins themselves may directly activate relay proteins

Effect of apoptosis during paw development in the mouse.

In mice, humans, other mammals, and land birds, the embryonic region that develops into feet or hands initially has a solid, platelike structure. Apoptosis eliminates the cells in the interdigital regions, thus forming the digits. The embryonic mouse paws shown in these fluorescence light micrographs are stained so that cells undergoing apoptosis appear a bright yellowish green. Apoptosis of cells begins at the margin of each interdigital region (left), peaks as the tissue in these regions is reduced (middle), and is no longer visible when the interdigital tissue has been eliminated (right).

How the Hydrolysis of ATP Performs Work : When ATP is hydrolyzed in a test tube, the release of free energy merely heats the surrounding water. In an organism, this same generation of heat can sometimes be beneficial. For instance, the process of shivering uses ATP hydrolysis during muscle contraction to warm the body.

In most cases in the cell, however, the generation of heat alone would be an inefficient (and potentially dangerous) use of a valuable energy resource. Instead, the cell's proteins harness the energy released during ATP hydrolysis in several ways to perform the three types of cellular work—chemical, transport, and mechanical.

Catalysis in the Enzyme's Active Site

In most enzymatic reactions, the substrate is held in the active site by so-called weak interactions, such as hydrogen bonds and ionic bonds. The R groups of a few of the amino acids that make up the active site catalyze the conversion of substrate to product, and the product departs from the active site. The enzyme is then free to take another substrate molecule into its active site. The entire cycle happens so fast that a single enzyme molecule typically acts on about 1,000 substrate molecules per second, and some enzymes are even faster. Enzymes, like other catalysts, emerge from the reaction in their original form. Therefore, very small amounts of enzyme can have a huge metabolic impact by functioning over and over again in catalytic cycles. Figure 8.16 shows a catalytic cycle involving two substrates and two products.

Phagocytosis

In phagocytosis, lysosomes digest (hydrolyze) materials taken into the cell. Top: In this macrophage (a type of white blood cell) from a rat, the lysosomes are very dark because of a stain that reacts with one of the products of digestion inside the lysosome (TEM). Macrophages ingest bacteria and viruses and destroy them using lysosomes. Bottom: This diagram shows a lysosome fusing with a food vacuole during the process of phagocytosis by a unicellular eukaryote. 1) Lysosome contains active hydrolytic enzymes. 2)Lysosome fuses with food vacuole. 3)Hydrolytic enzymes digest food particles.

Pinocytosis

In pinocytosis, a cell continually "gulps" droplets of extracellular fluid into tiny vesicles, formed by infoldings of the plasma membrane. In this way, the cell obtains molecules dissolved in the droplets. Because any and all solutes are taken into the cell, pinocytosis as shown here is nonspecific for the substances it transports. In many cases, as above, the parts of the plasma membrane that form vesicles are lined on their cytoplasmic side by a fuzzy layer of coat protein; the "pits" and resulting vesicles are said to be "coated.

cytoplasmic streaming

In plant cells, actin-protein interactions contribute to cytoplasmic streaming, a circular flow of cytoplasm within cells (Figure 6.26c). This movement, which is especially common in large plant cells, speeds the movement of organelles and the distribution of materials within the cell.

Bundles of microfilaments

In some kinds of animal cells, such as nutrient-absorbing intestinal cells, bundles of microfilaments make up the core of microvilli, delicate projections that increase the cell's surface area (Figure 6.25). Microfilaments are well known for their role in cell motility. Thousands of actin filaments and thicker filaments made of a protein called myosin interact to cause contraction of muscle cells (Figure 6.26a); muscle contraction is described in detail in Concept 50.5.

Put another way, oxygen pulls electrons down the chain in an energy-yielding tumble analogous to gravity pulling objects downhill

In summary, during cellular respiration, most electrons travel the following "downhill" route: glucose --> NADH --> electron transport chain S oxygen. Later in this chapter, you will learn more about how the cell uses the energy released from this exergonic electron fall to regenerate its supply of ATP. For now, having covered the basic redox mechanisms of cellular respiration, let's look at the entire process by which energy is harvested from organic fuels.

Fermentation.

In the absence of oxygen, many cells use fermentation to produce ATP by substrate-level phosphorylation. NAD+ is regenerated for use in glycolysis when pyruvate, the end product of glycolysis, serves as an electron acceptor for oxidizing NADH. Two of the common end products formed from fermentation are (a) - alcohol fermentation : ethanol and (b)lactic acid fermentation: lactate, the ionized form of lactic acid.

How can we explain the existence of a metabolic process that seems to be counterproductive for the plant? According to one hypothesis, photorespiration is evolutionary baggage— a metabolic relic from a much earlier time when the atmosphere had less O2 and more CO2 than it does today.

In the ancient atmosphere that prevailed when rubisco first evolved, the ability of the enzyme's active site to bind O2 would have made little difference. The hypothesis suggests that modern rubisco retains some of its chance affinity for O2, which is now so concentrated in the atmosphere that a certain amount of photorespiration is inevitable. There is also some evidence that photorespiration may provide protection against the damaging products of the light reactions, which build up when the Calvin cycle slows due to low CO2.

The level of apoptosis between the developing digits is lower in the webbed feet of ducks and other water birds than in the nonwebbed feet of land birds, such as chickens.

In the case of humans, the failure of appropriate apoptosis can result in webbed fingers and toes.

In the mitochondrion, protons diffuse down their concentration gradient from the intermembrane space through ATP synthase to the matrix, driving ATP synthesis.

In the chloroplast, ATP is synthesized as the hydrogen ions diffuse from the thylakoid space back to the stroma through ATP synthase complexes (Figure 10.18), whose catalytic knobs are on the stroma side of the membrane. Thus, ATP forms in the stroma, where it is used to help drive sugar synthesis during the Calvin cycle.

Translation

In the cytoplasm, the information in mRNA is used to assemble a polypeptide with a specific sequence of amino acids. Both transfer RNA (tRNA) molecules and a ribosome play a role. The eukaryotic ribosome, which includes a large subunit and a small subunit, is a colossal complex composed of four large ribosomal RNA (rRNA) molecules and more than 80 proteins. Through transcription and translation, the nucleotide sequence of DNA determines the amino acid sequence of a polypeptide, via the intermediary mRNA

The cytoskeleton is a network of fibers that organizes structures and activities in the cell

In the early days of electron microscopy, biologists thought that the organelles of a eukaryotic cell floated freely in the cytosol. But improvements in both light microscopy and electron microscopy have revealed the cytoskeleton, a network of fibers extending throughout the cytoplasm (Figure 6.20). Bacterial cells also have fibers that form a type of cytoskeleton, constructed of proteins similar to eukaryotic ones, but here we will concentrate on eukaryotes. The eukaryotic cytoskeleton, which plays a major role in organizing the structures and activities of the cell, is composed of three types of molecular structures: microtubules, microfilaments, and intermediate filaments.

. In a mechanism called cotransport, a transport protein (a cotransporter) can couple the "downhill" diffusion of the solute to the "uphill" transport of a second substance against its own concentration gradient. For instance, a plant cell uses the gradient of H+ generated by its ATP-powered proton pumps to drive the active transport of amino acids, sugars, and several other nutrients into the cell.

In the example shown in Figure 7.18, a cotransporter couples the return of H+ to the transport of sucrose into the cell. This protein can translocate sucrose into the cell against its concentration gradient, but only if the sucrose molecule travels in the company of an H+ .

To take a simple, nonbiological example, consider the reaction between the elements sodium (Na) and chlorine (Cl) that forms table salt:

In the generalized reaction, substance Xe- , the electron donor, is called the reducing agent; it reduces Y, which accepts the donated electron. Substance Y, the electron acceptor, is the oxidizing agent; it oxidizes Xe- by removing its electron. Because an electron transfer requires both an electron donor and an acceptor, oxidation and reduction always go hand in hand.

In this section, we explored the complexity of signaling initiation and termination in a single pathway, and we saw the potential for pathways to intersect with each other.

In the next section, we'll consider one especially important network of interacting pathways in the cell.

resolution barrier

In the past several decades, light microscopy has been revitalized by major technical advances (see Figure 6.3). Labeling individual cellular molecules or structures with fluorescent markers has made it possible to see such structures with increasing detail. In addition, both confocal and deconvolution microscopy have produced sharper images of three-dimensional tissues and cells. Finally, a group of new techniques and labeling molecules developed in recent years has allowed researchers to "break" the resolution barrier and distinguish subcellular structures even as small as 10-20 nm across. As this super-resolution microscopy becomes more widespread, the images we see of living cells are proving as exciting for us as van Leeuwenhoek's were for Robert Hooke 350 years ago.

plasma membrane of red blood cells

In the plasma membrane of red blood cells alone, for example, more than 50 kinds of proteins have been found so far.

Most of the ATP produced by respiration results later, from oxidative phosphorylation, when the NADH and FADH2 produced by the citric acid cycle and earlier steps relay the electrons extracted from food to the electron transport chain.

In the process, they supply the necessary energy for the phosphorylation of ADP to ATP. We will explore this process in the next section.

The solar-powered transfer of an electron from the reactioncenter chlorophyll a pair to the primary electron acceptor is the first step of the light reactions. As soon as the chlorophyll electron is excited to a higher energy level, the primary electron acceptor captures it; this is a redox reaction. In the flask shown in Figure 10.12b, isolated chlorophyll fluoresces because there is no electron acceptor, so electrons of photoexcited chlorophyll drop right back to the ground state.

In the structured environment of a chloroplast, however, an electron acceptor is readily available, and the potential energy represented by the excited electron is not dissipated as light and heat. Thus, each photosystem—a reaction-center complex surrounded by light-harvesting complexes—functions in the chloroplast as a unit. It converts light energy to chemical energy, which will ultimately be used for the synthesis of sugar

Some of the steps of glycolysis and the citric acid cycle are redox reactions in which dehydrogenases transfer electrons from substrates to NAD+ or the related electron carrier FAD, forming NADH or FADH2. (You'll learn more about FAD and FADH2 later.)

In the third stage of respiration, the electron transport chain accepts electrons from NADH or FADH2 generated during the first two stages and passes these electrons down the chain.At the end of the chain, the electrons are combined with molecular oxygen and hydrogen ions (H+ ), forming water (see Figure 9.5b)

A Photosystem: A Reaction-Center Complex Associated with Light-Harvesting Complexes Chlorophyll molecules excited by the absorption of light energy produce very different results in an intact chloroplast than they do in isolation (see Figure 10.12).

In their native environment of the thylakoid membrane, chlorophyll molecules are organized along with other small organic molecules and proteins into complexes called photosystems.

Further regulation of cell metabolism is provided by other G protein systems that inhibit adenylyl cyclase.

In these systems, a different signaling molecule activates a different receptor, which in turn activates an inhibitory G protein that blocks activation of adenylyl cyclase.

Microfilaments and motility

In these three examples, interactions between actin filaments and motor proteins bring about cell movement.

How does the enzyme do this?An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction

In this chapter, we are focusing on enzymes that are proteins. (Some RNA molecules, called ribozymes, can function as enzymes; these will be discussed in Concepts 17.3 and 25.1.) Without regulation by enzymes, chemical traffic through the pathways of metabolism would become terribly congested because many chemical reactions would take such a long time. In the next two sections, we will see why spontaneous reactions can be slow and how an enzyme changes the situation.

For example, in eukaryotic cells, the enzymes for the second and third stages of cellular respiration reside in specific locations within mitochondria (Figure 8.22).

In this chapter, you have learned about the laws of thermodynamics that govern metabolism, the intersecting set of chemical pathways characteristic of life. We have explored the bioenergetics of breaking down and building up biological molecules. To continue the theme of bioenergetics, we will next examine cellular respiration, the major catabolic pathway that breaks down organic molecules and releases energy that can be used for the crucial processes of life.

The Earth's supply of fossil fuels was formed from remains of organisms that died hundreds of millions of years ago. In a sense, then, fossil fuels represent stores of the sun's energy from the distant past. Because these resources are being used at a much higher rate than they are replenished, researchers are exploring methods of capitalizing on the photosynthetic process to provide alternative fuels (Figure 10.3).

In this chapter, you'll learn how photosynthesis works. After discussing general principles of photosynthesis, we'll consider the two stages of photosynthesis: the light reactions, which capture solar energy and transform it into chemical energy; and the Calvin cycle, which uses that chemical energy to make the organic molecules of food. Finally, we will consider some aspects of photosynthesis from an evolutionary perspective.

Geometric relationships between surface area and volume

In this diagram, cells are represented as boxes. Using arbitrary units of length, we can calculate the cell's surface area (in square units, or units2 ), volume (in cubic units, or units3 ), and ratio of surface area to volume. A high surface-to-volume ratio facilitates the exchange of materials between a cell and its environment.

Mechanical analogy for the cell cycle control system

In this diagram, the flat "stepping stones" around the perimeter represent sequential events. Like the control device of a washing machine, the cell cycle control system proceeds on its own, driven by a built-in clock. However, the system is subject to internal and external regulation at various checkpoints; three important checkpoints are shown (red).

Mechanical analogy for the cell cycle control system:

In this diagram, the flat "stepping stones" around the perimeter represent sequential events. Like the control device of a washing machine, the cell cycle control system proceeds on its own, driven by a built-in clock. However, the system is subject to internal and external regulation at various checkpoints; three important checkpoints are shown (red).

How ATP drives chemical work: Energy coupling using ATP hydrolysis.

In this example, the exergonic process of ATP hydrolysis is used to drive an endergonic process—the cellular synthesis of the amino acid glutamine from glutamic acid and ammonia. (a) Glutamic acid conversion to glutamine. Glutamine synthesis from glutamic acid (Glu) by itself is endergonic (ΔG is positive), so it is not spontaneous. b) Conversion reaction coupled with ATP hydrolysis. In the cell, glutamine synthesis occurs in two steps, coupled by a phosphorylated intermediate. ATP phosphorylates glutamic acid, making it less stable, with more free energy. Ammonia displaces the phosphate group, forming glutamine. c)Free-energy change for coupled reaction. ΔG for the glutamic acid conversion to glutamine (+3.4 kcal/mol) plus ΔG for ATP hydrolysis (-7.3 kcal/mol) gives the free-energy change for the overall reaction (-3.9 kcal/mol). Because the overall process is exergonic (net ΔG is negative), it occurs spontaneously.

Cytoplasmic response to a signal: the stimulation of glycogen breakdown by epinephrine (adrenaline)

In this signaling system, the hormone epinephrine acts through a G protein-coupled receptor to activate a succession of relay molecules, including cAMP and two protein kinases (see also Figure 11.12). The final protein activated is the enzyme glycogen phosphorylase, which uses inorganic phosphate to release glucose monomers from glycogen in the form of glucose 1-phosphate molecules. This pathway amplifies the hormonal signal: One receptor protein can activate approximately 100 molecules of G protein, and each enzyme in the pathway, once activated, can act on many molecules of its substrate, the next molecule in the cascade. The number of activated molecules given for each step is approximate.

Biochemists usually reserve the term cellular respiration for stages 2 and 3 together.

In this text, however, we include glycolysis as a part of cellular respiration because most respiring cells deriving energy from glucose use glycolysis to produce the starting material for the citric acid cycle.

But epinephrine doesn't stimulate adenylyl cyclase directly. When epinephrine outside the cell binds to a G protein-coupled receptor, the protein activates adenylyl cyclase, which in turn can catalyze the synthesis of many molecules of cAMP.

In this way, the normal cellular concentration of cAMP can be boosted 20-fold in a matter of seconds. . The cAMP broadcasts the signal to the cytoplasm.It does not persist for long in the absence of the hormone because a different enzyme, called phosphodiesterase, converts cAMP to AMP.

A built-in cell suicide mechanism is essential to development and maintenance in all animals. The similarities between apoptosis genes in nematodes and those in mammals, as well as the observation that apoptosis occurs in multicellular fungi and even in single-celled yeasts, indicate that the basic mechanism evolved early in the evolution of eukaryotes.

In vertebrates, apoptosis is essential for normal development of the nervous system, for normal operation of the immune system, and for normal morphogenesis of hands and feet in humans and paws in other mammals (Figure 11.21).

In many types of plants—including a significant number of crop plants—photorespiration drains away as much as 50% of the carbon fixed by the Calvin cycle

Indeed, if photorespiration could be reduced in certain plant species without otherwise affecting photosynthetic productivity, crop yields and food supplies might increase.

How doues information of the ECM probably reach the nucleus?

Information about the ECM probably reaches the nucleus by a combination of mechanical and chemical signaling pathways. Mechanical signaling involves fibronectin, integrins, and microfilaments of the cytoskeleton. Changes in the cytoskeleton may in turn trigger signaling pathways inside the cell, leading to changes in the set of proteins being made by the cell and therefore changes in the cell's function. In this way, the extracellular matrix of a particular tissue may help coordinate the behavior of all the cells of that tissue.

Electron transfer from NADH to oxygen is an exergonic reaction with a free-energy change of -53 kcal/mol (-222 kJ/mol)

Instead of this energy being released and wasted in a single explosive step, electrons cascade down the chain from one carrier molecule to the next in a series of redox reactions, losing a small amount of energy with each step until they finally reach oxygen, the terminal electron acceptor, which has a very great affinity for electrons.

Body temperature is not high enough to initiate burning, of course

Instead, if you swallow some glucose, enzymes in your cells will lower the barrier of activation energy, allowing the sugar to be oxidized in a series of steps.

Interfering with CD4

Interfering with CD4 causes dangerous side effects because of its many important functions in cells. Discovery of the CCR5 co-receptor provided a safer target for development of drugs that mask this protein and block HIV entry. One such drug, maraviroc (brand name Selzentry), was approved for treatment of HIV in 2007 and is now being tested to determine whether this drug might also work to prevent HIV infection in uninfected, at-risk patients.

Intermediate filaments are more of

Intermediate filaments are more permanent fixtures of cells than are microfilaments and microtubules, which are often disassembled and reassembled in various parts of a cell. Even after cells die, intermediate filament networks often persist; for example, the outer layer of our skin consists of dead skin cells full of keratin filaments.

intermediate filaments

Intermediate filaments are named for their diameter, which is larger than the diameter of microfilaments but smaller than that of microtubules (see Table 6.1). While microtubules and microfilaments are found in all eukaryotic cells, intermediate filaments are only found in the cells of some animals, including vertebrates. Specialized for bearing tension (like microfilaments), intermediate filaments are a diverse class of cytoskeletal elements. Each type is constructed from a particular molecular subunit belonging to a family of proteins whose members include the keratins. Microtubules and microfilaments, in contrast, are consistent in diameter and composition in all eukaryotic cells.

3) When the ligand dissociates from this receptor, the channel closes and ions no longer enter the cell. Ligand-gated ion channels are very important in the nervous system. For example, the neurotransmitter molecules released at a synapse between two nerve cells (see Figure 11.5b) bind as ligands to ion channels on the receiving cell, causing the channels to open.

Ions flow in (or, in some cases, out), triggering an electrical signal that propagates down the length of the receiving cell. Some gated ion channels are controlled by electrical signals instead of ligands; these voltage-gated ion channels are also crucial to the functioning of the nervous system, as we will discuss in Chapter 48. Some ion channels are present on membranes of organelles, such as the ER.

The absorption of thermal energy accelerates the reactant molecules, so they collide more often and more forcefully.

It also agitates the atoms within the molecules, making the breakage of bonds more likely. When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state.

The role of membrane carbohydrates in cell to cell recognition: Cell-cell recognition, a cell's ability to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism

It is important, for example, in the sorting of cells into tissues and organs in an animal embryo. It is also the basis for the rejection of foreign cells by the immune system, an important line of defense in vertebrate animals (see Concept 43.1) Cells recognize other cells by binding to molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane (see Figure 7.7d)

Chlorophyll, the green pigment that gives leaves their color, resides in the thylakoid membranes of the chloroplast. (The internal photosynthetic membranes of some prokaryotes are also called thylakoid membranes; see Figure 27.8b.)

It is the light energy absorbed by chlorophyll that drives the synthesis of organic molecules in the chloroplast. Now that we have looked at the sites of photosynthesis in plants, we are ready to look more closely at the process of photosynthesis.

Plasmodesmata in Plant Cells

It might seem that the nonliving cell walls of plants would isolate plant cells from one another. But in fact, as shown in Figure 6.29, cell walls are perforated with plasmodesmata (singular, plasmodesma; from the Greek desma, bond), channels that connect cells. Cytosol passing through the plasmodesmata joins the internal chemical environments of adjacent cells. These connections unify most of the plant into one living continuum. The plasma membranes of adjacent cells line the channel of each plasmodesma and thus are continuous. Water and small solutes can pass freely from cell to cell, and several experiments have shown that in some circumstances, certain proteins and RNA molecules can do this as well (see Concept 36.6). The macromolecules transported to neighboring cells appear to reach the plasmodesmata by moving along fibers of the cytoskeleton

How do electrons that are extracted from glucose and stored as potential energy in NADH finally reach oxygen?

It will help to compare the redox chemistry of cellular respiration to a much simpler reaction: the reaction between hydrogen and oxygen to form water (Figure 9.5a). Mix H2 and O2, provide a spark for activation energy, and the gases combine explosively. In fact, combustion of liquid H2 and O2 is harnessed to help power the rocket engines that boost satellites into orbit and launch spacecraft. The explosion represents a release of energy as the electrons of hydrogen "fall" closer to the electronegative oxygen atoms

Photosynthesis:

Large complexes of proteins with associated nonprotein molecules are embedded in chloroplast membranes. Together, they can trap light energy in molecules that are later used by other proteins inside the chloroplast to make sugars. This is the basis for all life on the planet.

Facilitated Diffusion: Passive Transport Aided by Proteins

Let's look more closely at how water and certain hydrophilic solutes cross a membrane. As mentioned earlier, many polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane. This phenomenon is called facilitated diffusion.

Signal Transduction Pathways: The binding of a specific signaling molecule to a receptor in the plasma membrane triggers the first step in the signal transduction pathway—the chain of molecular interactions that leads to a particular response within the cell.

Like falling dominoes, the signal-activated receptor activates another molecule, which activates yet another molecule, and so on, until the protein that produces the final cellular response is activated. The molecules that relay a signal from receptor to response, which we call relay molecules in this book, are often proteins. Protein-protein interactions are a major theme of cell signaling—indeed, a unifying theme of all cellular activities.

membrane proteins

Like membrane lipids, most membrane proteins are amphipathic. Such proteins can reside in the phospholipid bilayer with their hydrophilic regions protruding. This molecular orientation maximizes contact of hydrophilic regions of proteins with water in the cytosol and extracellular fluid, while providing their hydrophobic parts with a nonaqueous environment

Cellular membranes are fluid mosaics of lipids and proteins

Lipids and proteins are the staple ingredients of membranes, although carbohydrates are also important. The most abundant lipids in most membranes are phospholipids. The ability of phospholipids to form membranes is inherent in their molecular structure.

Biological Order and Disorder

Living systems increase the entropy of their surroundings, as predicted by thermodynamic law. It is true that cells create ordered structures from less organized starting materials. For example, simpler molecules are ordered into the more complex structure of an amino acid, and amino acids are ordered into polypeptide chains. At the organismal level as well, complex and beautifully ordered structures result from biological processes that use simpler starting materials (Figure 8.4).

What do lysosomes use their hydrolytic enzymes for?

Lysosomes also use their hydrolytic enzymes to recycle the cell's own organic material, a process called autophagy. During autophagy, a damaged organelle or small amount of cytosol becomes surrounded by a double membrane (of unknown origin), and a lysosome fuses with the outer membrane of this vesicle (Figure 6.13b). The lysosomal enzymes dismantle the inner membrane with the enclosed material, and the resulting small organic compounds are released to the cytosol for reuse. With the help of lysosomes, the cell continually renews itself. A human liver cell, for example, recycles half of its macromolecules each week.

Phagocytosis

Lysosomes carry out intracellular digestion in a variety of circumstances. Amoebas and many other unicellular eukaryotes eat by engulfing smaller organisms or food particles, a process called phagocytosis (from the Greek phagein, to eat, and kytos, vessel, referring here to the cell). The food vacuole formed in this way then fuses with a lysosome, whose enzymes digest the food

Signal receptors, relay molecules, and second messengers participate in a variety of pathways, leading to both nuclear and cytoplasmic responses, including cell division.

Malfunctioning of growth factor pathways like the one in Figure 11.15 can contribute to abnormal cell division and the development of cancer, as we'll see in Concept 18.5.

Functions of Rough ER

Many cells secrete proteins that are produced by ribosomes attached to rough ER. For example, certain pancreatic cells synthesize the protein insulin in the ER and secrete this hormone into the bloodstream. As a polypeptide chain grows from a bound ribosome, the chain is threaded into the ER lumen through a pore formed by a protein complex in the ER membrane. The new polypeptide folds into its functional shape as it enters the ER lumen.

Exploring Cell-Surface Transmembrane Receptors G Protein-Coupled Receptors: A G protein-coupled receptor (GPCR) is a cell-surface transmembrane receptor that works with the help of a G protein, a protein that binds the energy-rich molecule GTP.

Many different signaling molecules—including yeast mating factors, neurotransmitters, and epinephrine (adrenaline) and many other hormones—use GPCRs.

The Mitotic Spindle: A Closer Look:

Many of the events of mitosis depend on the mitotic spindle, which begins to form in the cytoplasm during prophase. This structure consists of fibers made of microtubules and associated proteins. While the mitotic spindle assembles, the other microtubules of the cytoskeleton partially disassemble, providing the material used to construct the spindle. The spindle microtubules elongate (polymerize) by incorporating more subunits of the protein tubulin (see Table 6.1) and shorten (depolymerize) by losing subunits.

Nuclear and Cytoplasmic Responses: 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.

Many signaling pathways ultimately regulate protein synthesis, usually by turning specific genes on or off in the nucleus. Like an activated steroid receptor (see Figure 11.9), the final activated molecule in a signaling pathway may function as a transcription factor. Figure 11.15 shows an example in which a signaling pathway activates a transcription factor that turns a gene on: The response to this growth factor signal is transcription, the synthesis of one or more specific mRNAs, which will be translated in the cytoplasm into specific proteins. In other cases, the transcription factor might regulate a gene by turning it off. Often a transcription factor regulates several different genes.

central vacuole

Mature plant cells generally contain a large central vacuole (Figure 6.14), which develops by the coalescence of smaller vacuoles. The solution inside the central vacuole, called cell sap, is the plant cell's main repository of inorganic ions, including potassium and chloride. The central vacuole plays a major role in the growth of plant cells, which enlarge as the vacuole absorbs water, enabling the cell to become larger with a minimal investment in new cytoplasm. The cytosol often occupies only a thin layer between the central vacuole and the plasma membrane, so the ratio of plasma membrane surface to cytosolic volume is sufficient, even for a large plant cell.

At metaphase, the centromeres of all the duplicated chromosomes are on a plane midway between the spindle's two poles. This plane is called the metaphase plate, which is an imaginary plate rather than an actual cellular structure (Figure 12.8).

Meanwhile, microtubules that do not attach to kinetochores have been elongating, and by metaphase they overlap and interact with other nonkinetochore microtubules from the opposite pole of the spindle. By metaphase, the microtubules of the asters have also grown and are in contact with the plasma membrane. The spindle is now complete.

In contrast, you produce gametes—eggs or sperm—by a variation of cell division called meiosis, which yields daughter cells with only one set of chromosomes, half as many chromosomes as the parent cell.

Meiosis in humans occurs only in special cells in the ovaries or testes (the gonads). Generating gametes, meiosis reduces the chromosome number from 46 (two sets) to 23 (one set). Fertilization fuses two gametes together and returns the chromosome number to 46 (two sets). Mitosis then conserves that number in every somatic cell nucleus of the new human individual. In Chapter 13, we will examine the role of meiosis in reproduction and inheritance in more detail. In the remainder of this chapter, we focus on mitosis and the rest of the cell cycle in eukaryotes.

Glycolipids

Membrane carbohydrates are usually short, branched chains of fewer than 15 sugar units. Some are covalently bonded to lipids, forming molecules called glycolipids. (Recall that glyco refers to carbohydrate.)

The Fluidity of Membranes

Membranes are not static sheets of molecules locked rigidly in place. A membrane is held together mainly by hydrophobic interactions, which are much weaker than covalent bonds (see Figure 5.18). Most of the lipids and some proteins can shift about sideways—that is, in the plane of the membrane, like partygoers elbowing their way through a crowded room. Very rarely, also, a lipid may flip-flop across the membrane, switching from one phospholipid layer to the other.

Synthesis and Sidedness of Membranes

Membranes have distinct inside and outside faces. The two lipid layers may differ in lipid composition, and each protein has directional orientation in the membrane (see Figure 7.6). Figure 7.9 shows how membrane sidedness arises: The asymmetrical arrangement of proteins, lipids, and their associated carbohydrates in the plasma membrane is determined as the membrane is being built by the endoplasmic reticulum (ER) and Golgi apparatus, components of the endomembrane system (see Figure 6.15).

How does the fluidity of a memrane affect?

Membranes must be fluid to work properly; the fluidity of a membrane affects both its permeability and the ability of membrane proteins to move to where their function is needed. Usually, membranes are about as fluid as salad oil. When a membrane solidifies, its permeability changes, and enzymatic proteins in the membrane may become inactive if their activity requires movement within the membrane.

Catabolic pathways yield energy by oxidizing organic fuels

Metabolic pathways that release stored energy by breaking down complex molecules are called catabolic pathways (see Concept 8.1). Transfer of electrons from fuel molecules (like glucose) to other molecules plays a major role in these pathways. In this section, we consider these processes, which are central to cellular respiration.

plasma membrane (cell membrane)

Metabolic requirements also impose theoretical upper limits on the size that is practical for a single cell. At the boundary of every cell, the plasma membrane functions as a selective barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell (Figure 6.6). For each square micrometer of membrane, only a limited amount of a particular substance can cross per second, so the ratio of surface area to volume is critical.

There are mechanisms that regulate these enzymes, thus balancing metabolic supply and demand, analogous to the red, yellow, and green stoplights that control the flow of automobile traffic

Metabolism as a whole manages the material and energy resources of the cell

A redox reaction that moves electrons closer to oxygen,such as the burning (oxidation) of methane, therefore releases chemical energy that can be put to work.

Methane combustion as an energy-yielding redox reaction: The reaction releases energy to the surroundings because the electrons lose potential energy when they end up being shared unequally, spending more time near electronegative atoms such as oxygen.

Not all redox reactions involve the complete transfer of electrons from one substance to another; some change the degree of electron sharing in covalent bonds.

Methane combustion, shown in Figure 9.3, is an example. The covalent electrons in methane are shared nearly equally between the bonded atoms because carbon and hydrogen have about the same affinity for valence electrons; they are about equally electronegative (see Concept 2.3).

Microfilaments (Actin Filaments)

Microfilaments are thin solid rods. They are also called actin filaments because they are built from molecules of actin, a globular protein. A microfilament is a twisted double chain of actin subunits (see Table 6.1). Besides occurring as linear filaments, microfilaments can form structural networks when certain proteins bind along the side of such a filament and allow a new filament to extend as a branch. Like microtubules, microfilaments seem to be present in all eukaryotic cells.

Cytology

Microscopes are the most important tools of cytology, the study of cell structure. Understanding the function of each structure, however, required the integration of cytology and biochemistry, the study of the chemical processes (metabolism) of cells.

Microtubu function

Microtubules shape and support the cell and also serve as tracks along which organelles equipped with motor proteins can move. In addition to the example in Figure 6.21, microtubules guide vesicles from the ER to the Golgi apparatus and from the Golgi to the plasma membrane. Microtubules are also involved in the separation of chromosomes during cell division, as shown in Figure 12.7.

Mitochondria: Chemical Energy Conversion

Mitochondria are found in nearly all eukaryotic cells, including those of plants, animals, fungi, and most unicellular eukaryotes. Some cells have a single large mitochondrion, but more often a cell has hundreds or even thousands of mitochondria; the number correlates with the cell's level of metabolic activity. For example, cells that move or contract have proportionally more mitochondria per volume than less active cells.

Length of mitochondria

Mitochondria are generally in the range of 1-10 µm long. Time-lapse films of living cells reveal mitochondria moving around, changing their shapes, and fusing or dividing in two, unlike the static structures seen in electron micrographs of dead cells. These studies helped cell biologists understand that mitochondria in a living cell form a branched tubular network, seen in a whole cell in Figure 6.17b, that is in a dynamic state of flux.

Microvilli: projections that increase the cell's surface area Peroxisome: organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product and then converts it to water

Mitochondrion: organelle where cellular respiration occurs and most ATP is generated Plasma membrane: membrane enclosing the cell Ribosomes (small brown dots): complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope Golgi apparatus: organelle active in synthesis, modification, sorting, and secretion of cell products Lysosome: digestive organelle where macromolecules are hydrolyzed

Phases of the Cell Cycle: mitotic phase

Mitosis is just one part of the cell cycle (Figure 12.6). In fact, the mitotic (M) phase, which includes both mitosis and cytokinesis, is usually the shortest part of the cell cycle.

Mitosis

Mitosis, the division of the genetic material in the nucleus, is usually followed immediately by cytokinesis, the division of the cytoplasm. One cell has become two, each the genetic equivalent of the parent cell.

There are other important differences between normal cells and cancer cells that reflect derangements of the cell cycle. If and when they stop dividing, cancer cells do so at random points in the cycle, rather than at the normal checkpoints.

Moreover, cancer cells can go on dividing indefinitely in culture if they are given a continual supply of nutrients; in essence, they are "immortal." A striking example is a cell line that has been reproducing in culture since 1951. Cells of this line are called HeLa cells because their original source was a tumor removed from a woman named Henrietta Lacks.

Centrosome containing a pair of centrioles.

Most animal cells have a centrosome, a region near the nucleus where the cell's microtubules are initiated. Within the centrosome is a pair of centrioles, each about 250 nm (0.25 µm) in diameter. The two centrioles are at right angles to each other, and each is made up of nine sets of three microtubules. The blue portions of the drawing represent nontubulin proteins that connect the microtubule triplets.

The abnormal cells may remain at the original site if they have too few genetic and cellular changes to survive at another site. In that case, the tumor is called a benign tumor.

Most benign tumors do not cause serious problems (depending on their location) and can be removed by surgery. In contrast, a malignant tumor includes cells whose genetic and cellular changes enable them to spread to new tissues and impair the functions of one or more organs; these cells are also sometimes called transformed cells (although usage of this term is generally restricted to cells in culture). An individual with a malignant tumor is said to have cancer (Figure 12.20).

In a more exotic example, the ocean waves shown in Figure 8.1 are brightly illuminated from within by free-floating, single-celled marine organisms called dinoflagellates. These dinoflagellates convert the energy stored in certain organic molecules to light, a process called bioluminescence

Most bioluminescent organisms are found in the oceans, but some exist on land, such as the bioluminescent firefly shown in the small photo. Bioluminescence and other metabolic activities carried out by a cell are precisely coordinated and controlled.

Allosteric Activation and Inhibition:

Most enzymes known to be allosterically regulated are constructed from two or more subunits, each composed of a polypeptide chain with its own active site. The entire complex oscillates between two different shapes, one catalytically active and the other inactive (Figure 8.20a).

Another major difference is the amount of ATP produced. Fermentation yields two molecules of ATP, produced by substrate-level phosphorylation. In the absence of an electron transport chain, the energy stored in pyruvate is unavailable. In cellular respiration, however, pyruvate is completely oxidized in the mitochondrion.

Most of the chemical energy from this process is shuttled by NADH and FADH2 in the form of electrons to the electron transport chain. There, the electrons move stepwise down a series of redox reactions to a final electron acceptor. (In aerobic respiration, the final electron acceptor is oxygen; in anaerobic respiration, the final acceptor is another molecule that is electronegative, although less so than oxygen.)

Catabolism can also harvest energy stored in fats obtained either from food or from fat cells in the body. After fats are digested to glycerol and fatty acids, the glycerol is converted to glyceraldehyde 3-phosphate, an intermediate of glycolysis.

Most of the energy of a fat is stored in the fatty acids. A metabolic sequence called beta oxidation breaks the fatty acids down to two-carbon fragments, which enter the citric acid cycle as acetyl CoA. NADH and FADH2 are also generated during beta oxidation; they can enter the electron transport chain, leading to further ATP production.

cell secretion

Most of the proteins made on free ribosomes function within the cytosol; examples are enzymes that catalyze the first steps of sugar breakdown. Bound ribosomes generally make proteins that are destined for insertion into membranes, for packaging within certain organelles such as lysosomes (see Figure 6.8), or for export from the cell (secretion). Cells that specialize in protein secretion—for instance, the cells of the pancreas that secrete digestive enzymes—frequently have a high proportion of bound ribosomes. (You will learn more about ribosome structure and function in Concept 17.4.)

By acting as a transcription factor, the aldosterone receptor itself carries out the transduction part of the signaling pathway.

Most other intracellular receptors function in the same way, although many of them, such as the thyroid hormone receptor, are already in the nucleus before the signaling molecule reaches them. Interestingly, many of these intracellular receptor proteins are structurally similar, suggesting an evolutionary kinship.

Glycoproteins

Most secretory proteins are glycoproteins, proteins with carbohydrates covalently bonded to them. The carbohydrates are attached to the proteins in the ER lumen by enzymes built into the ER membrane.

Cell biologists are still trying to learn exactly how various transport proteins facilitate diffusion.

Most transport proteins are very specific: They transport some substances but not others. As mentioned earlier, the two types of transport proteins are channel proteins and carrier proteins. Channel proteins simply provide corridors that allow specific molecules or ions to cross the membrane (Figure 7.14a)

Motile cilia

Motile cilia usually occur in large numbers on the cell surface. Flagella are usually limited to just one or a few per cell, and they are longer than cilia. Flagella and cilia differ in their beating patterns. A flagellum has an undulating motion like the tail of a fish. In contrast, cilia have alternating power and recovery strokes, much like the oars of a racing crew boat (Figure 6.23).

A comparison of the beating of flagella and motile cilia.

Motion of flagella: . A flagellum usually undulates, its snakelike motion driving a cell in the same direction as the axis of the flagellum. Propulsion of a human sperm cell is an example of flagellate locomotion (LM). Motion of cilia: Cilia have a back-and-forth motion. The rapid power stroke moves the cell in a direction perpendicular to the axis of the cilium. Then, during the slower recovery stroke,the cilium bends and sweeps sideways, closer to the cell surface. A dense nap of cilia, beating at a rate of about 40 to 60 strokes a second, covers this Colpidium, a freshwater protist (colorized SEM).

Motor proteins and the cytoskeleton.

Motor proteins that attach to receptors on vesicles can "walk" the vesicles along microtubules or, in some cases, along microfilaments. Two vesicles containing neurotransmitters move along a microtubule toward the tip of a nerve cell extension called an axon (SEM).

The physical disintegration of a system's organized structure is a good analogy for an increase in entropy. For example, you can observe the gradual decay of an unmaintained building over time

Much of the increasing entropy of the universe is more abstract, however, because it takes the form of increasing amounts of heat and less ordered forms of matter.

Chemiosmosis couples the electron transport chain to ATP synthesis.

NADH and FADH2 shuttle highenergy electrons extracted from food during glycolysis and the citric acid cycle into an electron transport chain built into the inner mitochondrial membrane. The gold arrows trace the transport of electrons, which are finally passed to a terminal acceptor (O2, in the case of aerobic respiration) at the "downhill" end of the chain, forming water. Most of the electron carriers of the chain are grouped into four complexes (I-IV). Two mobile carriers, ubiquinone (Q) and cytochrome c (Cyt c), move rapidly, ferrying electrons between the large complexes. As the complexes shuttle electrons, they pump protons from the mitochondrial matrix into the intermembrane space. FADH2 deposits its electrons via complex II and so results in fewer protons being pumped into the intermembrane space than occurs with NADH. Chemical energy originally harvested from food is transformed into a proton-motive force, a gradient of H+ across the membrane. 2 During chemiosmosis, the protons flow back down their gradient via ATP synthase, which is built into the membrane nearby. The ATP synthase harnesses the protonmotive force to phosphorylate ADP, forming ATP. Together, electron transport and chemiosmosis make up oxidative phosphorylation.

In most instances of mechanical work involving motor proteins "walking" along cytoskeletal elements (Figure 8.11b), a cycle occurs in which ATP is first bound noncovalently to the motor protein.

Next, ATP is hydrolyzed, releasing ADP and ~P i . Another ATP molecule can then bind. At each stage, the motor protein changes its shape and ability to bind the cytoskeleton, resulting in movement of the protein along the cytoskeletal track. Phosphorylation and dephosphorylation promote crucial protein shape changes during many other important cellular processes as well.

What we know about cotransport proteins in animal cells has helped us find more effective treatments for diarrhea, a serious problem in developing countries.

Normally, sodium in waste is reabsorbed in the colon, maintaining constant levels in the body, but diarrhea expels waste so rapidly that reabsorption is not possible, and sodium levels fall precipitously.

No work must be done to make this happen; diffusion is a spontaneous process, needing no input of energy.

Note that each substance diffuses down its own concentration gradient, unaffected by the concentration gradients of other substances (Figure 7.10b).

Phase 2: Reduction: Each molecule of 3-phosphoglycerate receives an additional phosphate group from ATP, becoming 1,3-bisphosphoglycerate. Next, a pair of electrons donated from NADPH reduces 1,3-bisphosphoglycerate, which also loses a phosphate group in the process, becoming glyceraldehyde 3-phosphate (G3P). Specifically, the electrons from NADPH reduce a carboyxl group on 1,3-bisphosphoglycerate to the aldehyde group of G3P, which stores more potential energy. G3P is a sugar—the same three-carbon sugar formed in glycolysis by the splitting of glucose (see Figure 9.9).

Notice in Figure 10.19 that for every three molecules of CO2 that enter the cycle, there are six molecules of G3P formed. But only one molecule of this three-carbon sugar can be counted as a net gain of carbohydrate because the rest are required to complete the cycle. The cycle began with 15 carbons' worth of carbohydrate in the form of three molecules of the five-carbon sugar RuBP. Now there are 18 carbons' worth of carbohydrate in the form of six molecules of G3P. One molecule exits the cycle to be used by the plant cell, but the other five molecules must be recycled to regenerate the three molecules of RuBP.

integral proteins

Notice in Figure 7.3 that there are two major populations of membrane proteins: integral proteins and peripheral proteins. Integral proteins penetrate the hydrophobic interior of the lipid bilayer. The majority are transmembrane proteins, which span the membrane; other integral proteins extend only partway into the hydrophobic interior. The hydrophobic regions of an integral protein consist of one or more stretches of nonpolar amino acids (see Figure 5.14), typically 20-30 amino acids in length, usually coiled into α helices (Figure 7.6).The hydrophilic parts of the molecule are exposed to the aqueous solutions on either side of the membrane. Some proteins also have one or more hydrophilic channels that allow passage through the membrane of hydrophilic substances (even of water itself; see Figure 7.1)

The currently accepted model for the organization of the light-reaction "machinery" within the thylakoid membrane is based on several research studies. Each of the molecules and molecular complexes in the figure is present in numerous copies in each thylakoid.

Notice that NADPH, like ATP, is produced on the side of the membrane facing the stroma, where the Calvin cycle reactions take place.

Thus, light energy is initially converted to chemical energy in the form of two compounds: NADPH and ATP. NADPH, a source of electrons, acts as "reducing power" that can be passed along to an electron acceptor, reducing it, while ATP is the versatile energy currency of cells.

Notice that the light reactions produce no sugar; that happens in the second stage of photosynthesis, the Calvin cycle.

Components of the Cytoskeleton

Now let's look more closely at the three main types of fibers that make up the cytoskeleton: Microtubules are the thickest of the three types; microfilaments (also called actin filaments) are the thinnest; and intermediate filaments are fibers with diameters in a middle range (Table 6.1).

The chlorophyll a at the reaction-center complex of photosystem I is called P700 because it most effectively absorbs light of wavelength 700 nm (in the far-red part of the spectrum). These two pigments P680 and P700, are nearly identical chlorophyll a molecules. However, their association with different proteins in the thylakoid membrane affects the electron distribution in the two pigments and accounts for the slight differences in their light-absorbing properties

Now let's see how the two types of photosystems work together in using light energy to generate ATP and NADPH, the two main products of the light reactions.

Animals and other nonphotosynthetic organisms in an ecosystem must have a source of free energy in the form of the organic products of photosynthesis

Now that we have applied the free-energy concept to metabolism, we are ready to see how a cell actually performs the work of life.

Membrane Proteins and Their Functions

Now we come to the mosaic aspect of the fluid mosaic model. Somewhat like a tile mosaic (shown here), a membrane is a collage of different proteins, often clustered together in groups, embedded in the fluid matrix of the lipid bilayer (see Figure 7.3).

At the end of anaphase, duplicate groups of chromosomes have arrived at opposite ends of the elongated parent cell.

Nuclei re-form during telophase. Cytokinesis generally begins during anaphase or telophase, and the spindle eventually disassembles by depolymerization of microtubules.

C4 photosynthesis is considered more efficient than C3 photosynthesis because it uses less water and resources.

On our planet today, the world population and demand for food are rapidly increasing. At the same time, the amount of land suitable for growing crops is decreasing due to the effects of global climate change, which include an increase in sea level as well as a hotter, drier climate in many regions.

actin microfilaments

On the cytoplasmic side of the furrow is a contractile ring of actin microfilaments associated with molecules of the protein myosin. The actin microfilaments interact with the myosin molecules, causing the ring to contract. The contraction of the dividing cell's ring of microfilaments is like the pulling of a drawstring. The cleavage furrow deepens until the parent cell is pinched in two, producing two completely separated cells, each with its own nucleus and its own share of cytosol, organelles, and other subcellular structures.

On the cytoplasmic side of the plasme membrane

On the cytoplasmic side of the plasma membrane, some membrane proteins are held in place by attachment to the cytoskeleton. And on the extracellular side, certain membrane proteins may attach to materials outside the cell. For example, in animal cells, membrane proteins may be attached to fibers of the extracellular matrix (see Figure 6.28; integrins are one type of integral, transmembrane protein).

Apoptosis of a human white blood cell.

On the left is a normal white blood cell, while on the right is a white blood cell undergoing apoptosis. The apoptotic cell is shrinking and forming lobes ("blebs"), which eventually are shed as membrane-bounded cell fragments (colorized SEMs).

Another chemical signaling molecule that possesses an intracellular receptor is nitric oxide (NO), a gas; this very small molecule readily passes between the membrane phospholipids.

Once a hormone has entered a cell, its binding to an intracellular receptor changes the receptor into a hormone-receptor complex that is able to cause a response—in many cases, the turning on or off of particular genes.

Only when the kinetochores of all the chromosomes are properly attached to the spindle does the appropriate regulatory protein complex become activated. (In this case, the regulatory molecule is not a cyclin-Cdk complex but, instead, a different complex made up of several proteins.)

Once activated, the complex sets off a chain of molecular events that activates the enzyme separase, which cleaves the cohesins, allowing the sister chromatids to separate. This mechanism ensures that daughter cells do not end up with missing or extra chromosomes.

Study Figure 7.10a carefully to appreciate how diffusion would result in both solutions having equal concentrations of the dye molecules.

Once that point is reached, there will be a dynamic equilibrium, with roughly as many dye molecules crossing the membrane each second in one direction as in the other.

Later in the cell division process, the two sister chromatids of each duplicated chromosome separate and move into two new nuclei, one forming at each end of the cell.

Once the sister chromatids separate, they are no longer called sister chromatids but are considered individual chromosomes; this is the step that essentially doubles the number of chromosomes during cell division. Thus, each new nucleus receives a collection of chromosomes identical to that of the parent cell (Figure 12.5).

Using chemical methods, we can measure ∆G for any reaction. (The value will depend on conditions such as pH, temperature, and concentrations of reactants and products.)

Once we know the value of ∆G for a process, we can use it to predict whether the process will be spontaneous (that is, whether it is energetically favorable and will occur without an input of energy)

Transduction: Cascades of molecular interactions relay signals from receptors to target molecules in the cell When receptors for signaling molecules are plasma membrane proteins, like most of those we have discussed, the transduction stage of cell signaling is usually a multistep pathway involving many molecules. Steps often include activation of proteins by addition or removal of phosphate groups or release of other small molecules or ions that act as signaling molecules.

One benefit of multiple steps is the possibility of greatly amplifying a signal. If each molecule transmits the signal to numerous molecules at the next step in the series, the result is a geometric increase in the number of activated molecules by the end (see Figure 11.16). Moreover, multistep pathways provide more opportunities for coordination and control than do simpler systems. This allows regulation of the response, as we'll discuss later in the chapter.

However, the most efficient catabolic pathway is aerobic respiration, in which oxygen is consumed as a reactant along with the organic fuel (aerobic is from the Greek aer, air, and bios, life).

One catabolic process, fermentation, is a partial degradation of sugars or other organic fuel that occurs without the use of oxygen.

Much of the traffic across cell membranes occurs by diffusion. When a substance is more concentrated on one side of a membrane than on the other, there is a tendency for the substance to diffuse across the membrane down its concentration gradient (assuming that the membrane is permeable to that substance).

One important example is the uptake of oxygen by a cell performing cellular respiration. Dissolved oxygen diffuses into the cell across the plasma membrane. As long as cellular respiration consumes the O2 as it enters, diffusion into the cell will continue because the concentration gradient favors movement in that direction.

By generating voltage across membranes, electrogenic pumps help store energy that can be tapped for cellular work.

One important use of proton gradients in the cell is for ATP synthesis during cellular respiration, as you will see in Concept 9.4. Another is a type of membrane traffic called cotransport.

sodium-potassium pump

One transport system that works this way is the sodium-potassium pump, which exchanges Na+ for K+ across the plasma membrane of animal cells (Figure 7.15). The distinction between passive transport and active transport is reviewed in Figure 7.16.

The main energy-yielding foods—carbohydrates and fats— are reservoirs of electrons associated with hydrogen, often in the form of C—H bonds

Only the barrier of activation energy holds back the flood of electrons to a lower energy state (see Figure 8.13). Without this barrier, a food substance like glucose would combine almost instantaneously with O2. If we supply the activation energy by igniting glucose, it burns in air, releasing 686 kcal (2,870 kJ) of heat per mole of glucose (about 180 g).

In most cases, however, EA is so high and the transition state is reached so rarely that the reaction will hardly proceed at all. In these cases, the reaction will occur at a noticeable rate only if energy is provided, usually by heat. For example, the reaction of gasoline and oxygen is exergonic and will occur spontaneously, but energy is required for the molecules to reach the transition state and react.

Only when the spark plugs fire in an automobile engine can there be the explosive release of energy that pushes the pistons. Without a spark, a mixture of gasoline hydrocarbons and oxygen will not react because the EA barrier is too high.

Order as a characteristic of life.

Order is evident in the detailed structures of the biscuit star and the agave plant shown here. As open systems, organisms can increase their order as long as the order of their surroundings decreases, with an overall increase in entropy in the universe.

Organelles and structural order in metabolism.

Organelles such as the mitochondrion (TEM) contain enzymes that carry out specific functions, in this case the second and third stages of cellular respiration. The matrix contains enzymes in solution that are involved in the second stage of cellular respiration. Enzymes for the third stage of cellular respiration are embedded in the inner membrane.

Catabolic Pathways and Production of ATP

Organic compounds possess potential energy as a result of the arrangement of electrons in the bonds between their atoms. Compounds that can participate in exergonic reactions can act as fuels. Through the activity of enzymes, a cell systematically degrades complex organic molecules that are rich in potential energy to simpler waste products that have less energy. Some of the energy taken out of chemical storage can be used to do work; the rest is dissipated as heat.

Mitochondria and chloroplasts change energy from one form to another

Organisms transform the energy they acquire from their surroundings. In eukaryotic cells, mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work. Mitochondria (singular, mitochondrion) are the sites of cellular respiration, the metabolic process that uses oxygen to drive the generation of ATP by extracting energy from sugars, fats, and other fuels. Chloroplasts, found in plants and algae, are the sites of photosynthesis. This process in chloroplasts converts solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from carbon dioxide and water.

secondary cell wall

Other cells add a secondary cell wall between the plasma membrane and the primary wall. The secondary wall, often deposited in several laminated layers, has a strong and durable matrix that affords the cell protection and support. Wood, for example, consists mainly of secondary walls. Plant cell walls are usually perforated by channels between adjacent cells called plasmodesmata, which will be discussed shortly.

carrier proteins

Other transport proteins, called carrier proteins, hold onto their passengers and change shape in a way that shuttles them across the membrane (see Figure 7.7a, right).

Mitosis is conventionally broken down into five stages: prophase, prometaphase, metaphase, anaphase, and telophase

Overlapping with the latter stages of mitosis, cytokinesis completes the mitotic phase. Figure 12.7 describes these stages in an animal cell. Study this figure thoroughly before progressing to the next two sections, which examine mitosis and cytokinesis more closely.

Let's summarize the light reactions. Electron flow pushes electrons from water, where they are at a state of low potential energy, ultimately to NADPH, where they are stored at a state of high potential energy. The light-driven electron flow also generates ATP. Thus, the equipment of the thylakoid membrane converts light energy to chemical energy stored in ATP and NADPH.

Oxygen is produced as a by-product. Let's now see how the Calvin cycle uses the products of the light reactions to synthesize sugar from CO2.

The cell division process is an integral part of the cell cycle, the life of a cell from the time it is first formed during division of a parent cell until its own division into two daughter cells. (Biologists use the words daughter or sister in relation to cells, but this is not meant to imply gender.)

Passing identical genetic material to cellular offspring is a crucial function of cell division. In this chapter, you will learn how this process occurs in the context of the cell cycle. After studying the cellular mechanics of cell division in eukaryotes and bacteria, you will learn about the molecular control system that regulates progress through the eukaryotic cell cycle and what happens when the control system malfunctions. Because a breakdown in cell cycle control plays a major role in the development of cancer, this aspect of cell biology is an active area of research.

Review: passive and active transport.

Passive transport: Substances diffuse spontaneously down their concentration gradients, crossing a membrane with no expenditure of energy by the cell. The rate of diffusion can be greatly increased by transport proteins in the membrane. Active transport :Some transport proteins act as pumps, moving substances across a membrane against their concentration (or electrochemical) gradients. Energy is usually supplied by ATP hydrolysis. Diffusion : Hydrophobic molecules and (at a slow rate) very small uncharged polar molecules can diffuse through the lipid bilayer. Facilitated diffusion : Many hydrophilic substances diffuse through membranes with the assistance of transport proteins, either channel proteins (left) or carrier proteins (right).

How do people acquire the vibrio cholerae?

People acquire the cholera bacterium, Vibrio cholerae, by drinking contaminated water. The bacteria form a biofilm on the lining of the small intestine and produce a toxin. The cholera toxin is an enzyme that chemically modifies a G protein involved in regulating salt and water secretion. Because the modified G protein is unable to hydrolyze GTP to GDP, it remains stuck in its active form, continuously stimulating adenylyl cyclase to make cAMP (see the question with Figure 11.12). The resulting high concentration of cAMP causes the intestinal cells to secrete large amounts of salts into the intestines, with water following by osmosis

Apoptotic Pathways and the Signals That Trigger Them: In humans and other mammals, several different pathways, involving about 15 different caspases, can carry out apoptosis. The pathway that is used depends on the type of cell and on the particular signal that initiates apoptosis. One major pathway involves certain mitochondrial proteins that are triggered to form molecular pores in the mitochondrial outer membrane, causing it to leak and release other proteins that promote apoptosis.

Perhaps surprisingly, these latter include cytochrome c, which functions in mitochondrial electron transport in healthy cells (see Figure 9.15) but acts as a cell death factor when released from mitochondria. The process of mitochondrial apoptosis in mammals uses proteins similar to the nematode proteins Ced-3, Ced-4, and Ced-9. These can be thought of as relay proteins capable of transducing the apoptotic signal.

phospholipids form the main fabric of the membrane

Phospholipids form the main fabric of the membrane, but proteins determine most of the membrane's functions. Different types of cells contain different sets of membrane proteins, and the various membranes within a cell each have a unique collection of proteins

Cyclic electron flow.

Photoexcited electrons from PS I are occasionally shunted back from ferredoxin (Fd) to chlorophyll via the cytochrome complex and plastocyanin (Pc). This electron shunt supplements the supply of ATP (via chemiosmosis) but produces no NADPH. The "shadow" of linear electron flow is included in the diagram for comparison with the cyclic route. The two Fd molecules in this diagram are actually one and the same—the final electron carrier in the electron transport chain of PS I— although it is depicted twice to clearly show its role in two parts of the process.

The model of light as waves explains many of light's properties, but in certain respects light behaves as though it consists of discrete particles, called photons.

Photons are not tangible objects, but they act like objects in that each of them has a fixed quantity of energy. The amount of energy is inversely related to the wavelength of the light: The shorter the wavelength, the greater the energy of each photon of that light. Thus, a photon of violet light packs nearly twice as much energy as a photon of red light (see Figure 10.7).

On a global scale, photosynthesis is the process responsible for the presence of oxygen in our atmosphere. Furthermore, although each chloroplast is minuscule, their collective productivity in terms of food production is prodigious:

Photosynthesis makes an estimated 150 billion metric tons of carbohydrate per year (a metric ton is 1,000 kg, about 1.1 tons). That's organic matter equivalent in mass to a stack of about 60 trillion biology textbooks—and the stack would reach 17 times the distance from Earth to the sun! No chemical process is more important than photosynthesis to the welfare of life on Earth.

Photosynthesis as a Redox Process: Let's briefly compare photosynthesis with cellular respiration. Both processes involve redox reactions. During cellular respiration, energy is released from sugar when electrons associated with hydrogen are transported by carriers to oxygen, forming water as a by-product (see Concept 9.1). The electrons lose potential energy as they "fall" down the electron transport chain toward electronegative oxygen, and the mitochondrion harnesses that energy to synthesize ATP (see Figure 9.15).

Photosynthesis reverses the direction of electron flow. Water is split, and its electrons are transferred along with hydrogen ions (H+ ) from the water to carbon dioxide, reducing it to sugar. Because the electrons increase in potential energy as they move from water to sugar, this process requires energy—in other words, it is endergonic. This energy boost that occurs during photosynthesis is provided by light.

plant cell wall composition

Plant cell walls are much thicker than the plasma membrane, ranging from 0.1 µm to several micrometers. The exact chemical composition of the wall varies from species to species and even from one cell type to another in the same plant, but the basic design of the wall is consistent. Microfibrils made of the polysaccharide cellulose (see Figure 5.6) are synthesized by an enzyme called cellulose synthase and secreted to the extracellular space, where they become embedded in a matrix of other polysaccharides and proteins. This combination of materials, strong fibers in a "ground substance" (matrix), is the same basic architectural design found in steel-reinforced concrete and in fiberglass.

plant cell

Plant cells are turgid (firm) and generally healthiest in a hypotonic environment, where the uptake of water is eventually balanced by the wall pushing back on the cel

Both animals and plants use molecules called hormones for long-distance signaling. In hormonal signaling in animals, also known as endocrine signaling, specialized cells release hormones, which travel via the circulatory system to other parts of the body, where they reach target cells that can recognize and respond to them (Figure 11.5c).

Plant hormones (often called plant growth regulators) sometimes travel in plant vessels (tubes) but more often reach their targets by moving through cells or by diffusing through the air as a gas (see Concept 39.2)

How, then, do plants make the sugar that organisms use for energy?

Plants get the required energy—686 kcal to make a mole of glucose—from the environment by capturing light and converting its energy to chemical energy. Next, in a long series of exergonic steps, they gradually spend that chemical energy to assemble glucose molecules.

However, the hydrophobic interior of the membrane impedes direct passage through the membrane of ions and polar molecules, which are hydrophilic.

Polar molecules such as glucose and other sugars pass only slowly through a lipid bilayer, and even water, a very small polar molecule, does not cross rapidly relative to nonpolar molecules.

How bacterial chromosomes move and how their specific location is established and maintained are active areas of research. Several proteins that play important roles have been identified.

Polymerization of one protein resembling eukaryotic actin apparently functions in bacterial chromosome movement during cell division, and another protein that is related to tubulin helps pinch the plasma membrane inward, separating the two bacterial daughter cells.

nuclear lamina

Pore complexes (TEM). Each pore is ringed by protein particles. Nuclear lamina (TEM). The netlike lamina lines the inner surface of the nuclear envelope. (The light circular spots are nuclear pores.)

Effects of Osmosis on Water Balance: To see how two solutions with different solute concentrations interact, picture a U-shaped glass tube with a selectively permeable artificial membrane separating two sugar solutions (Figure 7.11)

Pores in this synthetic membrane are too small for sugar molecules to pass through but large enough for water molecules. However, tight clustering of water molecules around the hydrophilic solute molecules makes some of the water unavailable to cross the membrane. As a result, the solution with a higher solute concentration has a lower free water concentration. Water diffuses across the membrane from the region of higher free water concentration (lower solute concentration) to that of lower free water concentration (higher solute concentration) until the solute concentrations on both sides of the membrane are more nearly equal

As eukaryotes with nuclear envelopes and larger genomes evolved, the ancestral process of binary fission, seen today in bacteria, somehow gave rise to mitosis. Variations on cell division exist in different groups of organisms. These variant processes may be similar to mechanisms used by ancestral species and thus may resemble steps in the evolution of mitosis from a binary fission-like process presumably carried out by very early bacteria.

Possible intermediate stages are suggested by two unusual types of nuclear division found today in certain unicellular eukaryotes—dinoflagellates, diatoms, and some yeasts (Figure 12.13). These two modes of nuclear division are thought to be cases where ancestral mechanisms have remained relatively unchanged over evolutionary time. In both types, the nuclear envelope remains intact, in contrast to what happens in most eukaryotic cells. Keep in mind, however, that we can't observe cell division in cells of extinct species. This hypothesis uses only currently existing species as examples and must ignore any potential intermediate mechanisms used by species that disappeared long ago.

Products of the endoplasmic reticulum are usually modified during

Products of the endoplasmic reticulum are usually modified during their transit from the cis region to the trans region of the Golgi apparatus. For example, glycoproteins formed in the ER have their carbohydrates modified, first in the ER itself, and then as they pass through the Golgi. The Golgi removes some sugar monomers and substitutes others, producing a large variety of carbohydrates. Membrane phospholipids may also be altered in the Golgi.

Fragments of nuclear envelope Nonkinetochore microtubules Kinetochore Kinetochore microtubules

Prometaphase: The nuclear envelope fragments. • The microtubules extending from each centrosome can now invade the nuclear area. • The chromosomes have become even more condensed. • A kinetochore, a specialized protein structure, has now formed at the centromere of each chromatid (thus, two per chromosome). • Some of the microtubules attach to the kinetochores, becoming "kinetochore microtubules," which jerk the chromosomes back and forth. • Nonkinetochore microtubules interact with those from the opposite pole of the spindle, lengthening the cell.

Aster

Prophase: • The chromatin fibers become more tightly coiled, condensing into discrete chromosomes observable with a light microscope. • The nucleoli disappear. • Each duplicated chromosome appears as two identical sister chromatids joined at their cen- tromeres and, in some species, all along their arms by cohesins (sister chromatid cohesion). • The mitotic spindle (named for its shape) begins to form. It is composed of the centro- somes and the microtubules that extend from them. The radial arrays of shorter microtubules that extend from the centrosomes are called asters ("stars"). • The centrosomes move away from each other, propelled partly by the lengthening micro- tubules between them.

Mitosis in a plant cell: These light micrographs show mitosis in cells of an onion root

Prophase: The chromosomes are condensing and the nucleolus is beginning to disappear. Although not yet visible in the micrograph, the mitotic spindle is starting to form. Prometaphase: Discrete chromosomes are now visible; each consists of two aligned, identical sister chromatids. Later in prometaphase, the nuclear envelope will fragment Metaphase: The spindle is complete, and the chromosomes, attached to microtubules at their kinetochores, are all at the metaphase plate. Anaphase: The chromatids of each chromosome have separated, and the daughter chromosomes are moving to the ends of the cell as their kinetochore microtubules shorten. Telophase: Daughter nuclei are forming. Meanwhile, cytokinesis has started: The cell plate, which will divide the cytoplasm in two, is growing toward the perimeter of the parent cell

How Enzymes Speed Up Reactions

Proteins, DNA, and other complex cellular molecules are rich in free energy and have the potential to decompose spontaneously; that is, the laws of thermodynamics favor their breakdown. These molecules only persist because at temperatures typical for cells, few molecules can make it over the hump of activation energy. The barriers for selected reactions must occasionally be surmounted, however, for cells to carry out the processes needed for life. Heat can increase the rate of a reaction by allowing reactants to attain the transition state more often, but this would not work well in biological systems

From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation. ATP synthase is a multisubunit complex with four main parts, each made up of multiple polypeptides (see Figure 9.14).

Protons move one by one into binding sites on one of the parts (the rotor), causing it to spin in a way that catalyzes ATP production from ADP and inorganic phosphate. The flow of protons thus behaves somewhat like a rushing stream that turns a waterwheel.

each second in one direction as in the other. We can now state a simple rule of diffusion: In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated.

Put another way, any substance will diffuse down its concentration gradient, the region along which the density of a chemical substance increases or decreases (in this case, decreases).

Oxidation of pyruvate to acetyl CoA, the step before the citric acid cycle.

Pyruvate is a charged molecule, so in eukaryotic cells it must enter the mitochondrion via active transport, with the help of a transport protein. Next, a complex of several enzymes (the pyruvate dehydrogenase complex) catalyzes the three numbered steps, which are described in the text. The acetyl group of acetyl CoA will enter the citric acid cycle. The CO2 molecule will diffuse out of the cell. By convention, coenzyme A is abbreviated S-CoA when it is attached to a molecule, emphasizing the sulfur atom (S). (The gene encoding the transport protein was finally identified several years ago, after 40 years of research.)

Effects of Temperature and pH

Recall from Figure 5.20 that the three-dimensional structures of proteins are sensitive to their environment. As a consequence, each enzyme works better under some conditions than under other conditions, because these optimal conditions favor the most active shape for the enzyme.

An enzyme that transfers phosphate groups from ATP to a protein is generally known as a protein kinase.

Recall that a receptor tyrosine kinase is a specific kind of protein kinase that phosphorylates tyrosines on the other receptor tyrosine kinase in a dimer.

Which type of plant would stand to gain more from increasing CO2 levels?

Recall that in C3 plants, the binding of O2 rather than CO2 by rubisco leads to photorespiration, lowering the efficiency of photosynthesis. C4 plants overcome this problem by concentrating CO2 in the bundle-sheath cells at the cost of ATP.

The Evolution of Enzymes: Thus far, biochemists have identified more than 4,000 different enzymes in various species, most likely a very small fraction of all enzymes. How did this grand profusion of enzymes arise?

Recall that most enzymes are proteins, and proteins are encoded by genes. A permanent change in a gene, known as a mutation, can result in a protein with one or more changed amino acids.

We can now roughly estimate the efficiency of respiration— that is, the percentage of chemical energy in glucose that has been transferred to ATP.

Recall that the complete oxidation of a mole of glucose releases 686 kcal of energy under standard conditions (∆G = -686 kcal/mol). Phosphorylation of ADP to form ATP stores at least 7.3 kcal per mole of ATP. Therefore, the efficiency of respiration is 7.3 kcal per mole of ATP times 32 moles of ATP per mole of glucose divided by 686 kcal per mole of glucose, which equals 0.34. Thus, about 34% of the potential chemical energy in glucose has been transferred to ATP; the actual percentage is bound to vary as ∆G varies under different cellular conditions.

Free-Energy Change, ∆G

Recall that the universe is really equivalent to "the system" plus "the surroundings." In 1878, J. Willard Gibbs, a professor at Yale, defined a very useful function called the Gibbs free energy of a system (without considering its surroundings), symbolized by the letter G. We'll refer to the Gibbs free energy simply as free energy.

The unique match between mating factor and receptor is key to ensuring mating only among cells of the same species of yeast.

Recently, researchers were able to genetically engineer yeast cells with both receptors and mating factors altered so that the altered proteins would bind to each other but not to the original proteins of the parent cells.

receptor-mediated endocytosis

Receptor-mediated endocytosis is a specialized type of pinocytosis that enables the cell to acquire bulk quantities of specific substances, even though those substances may not be very concentrated in the extracellular fluid. Embedded in the plasma membrane are proteins with receptor sites exposed to the extracellular fluid. Specific solutes bind to the receptors. The receptor proteins then cluster in coated pits, and each coated pit forms a vesicle containing the bound molecules. The diagram shows only bound molecules (purple triangles) inside the vesicle, but other molecules from the extracellular fluid are also present. After the ingested material is liberated from the vesicle, the emptied receptors are recycled to the plasma membrane by the same vesicle (not shown).

Membranes are selectively permeable

Remember, however, that membranes are selectively permeable and therefore have different effects on the rates of diffusion of various molecules. In the case of water, the presence of aquaporin proteins allows water to diffuse very rapidly across the membranes of certain cells compared with diffusion in the absence of aquaporins. As we'll see next, the movement of water across the plasma membrane has important consequences for cells.

Fermentation is a way of harvesting chemical energy without using either oxygen or any electron transport chain—in other words, without cellular respiration. How can food be oxidized without cellular respiration?

Remember, oxidation simply refers to the loss of electrons to an electron acceptor, so it does not need to involve oxygen. Glycolysis oxidizes glucose to two molecules of pyruvate. The oxidizing agent of glycolysis is NAD+ , and neither oxygen nor any electron transfer chain is involved. Overall, glycolysis is exergonic, and some of the energy made available is used to produce 2 ATP (net) by substrate-level phosphorylation. If oxygen is present, then additional ATP is made by oxidative phosphorylation when NADH passes electrons removed from glucose to the electron transport chain. But glycolysis generates 2 ATP whether oxygen is present or not—that is, whether conditions are aerobic or anaerobic.

Gametes

Reproductive cells, or gametes—such as sperm and eggs—have half as many chromosomes as somatic cells; in our example, human gametes have one set of 23 chromosomes. The number of chromosomes in somatic cells varies widely among species: 18 in cabbage plants, 48 in chimpanzees, 56 in elephants, 90 in hedgehogs, and 148 in one species of alga. We'll now consider how these chromosomes behave during cell division.

Mimicking evolution of an enzyme with a new function.

Researchers tested whether the function of an enzyme called β-galactosidase, which breaks down the sugar lactose, could change over time in populations of the bacterium Escherichia coli. After seven rounds of mutation and selection in the lab, β-galactosidase evolved into an enzyme specialized for breaking down a sugar other than lactose. This ribbon model shows one subunit of the altered enzyme; six amino acids were different. Two changed amino acids were found near the active site. Two changed amino acids were found in the active site. Two changed amino acids were found on the surface.

Resolution

Resolution is a measure of the clarity of the image; it is the minimum distance two points can be separated and still be distinguished as separate points. For example, what appears to the unaided eye as one star in the sky may be resolved as twin stars with a telescope, which has a higher resolving ability than the eye. Similarly, using standard techniques, the light microscope cannot resolve detail finer than about 0.2 micrometer (µm), or 200 nanometers (nm), regardless of the magnification

Resolution in EM

Resolution is inversely related to the wavelength of the light (or electrons) a microscope uses for imaging, and electron beams have much shorter wavelengths than visible light. Modern electron microscopes can theoretically achieve a resolution of about 0.002 nm, though in practice they usually cannot resolve structures smaller than about 2 nm across. Still, this is a 100-fold improvement over the standard light microscope

Motor proteins

Responsible for transport of vesicles and movement of organelles within the cell. This requires energy, often provided by ATP hydrolysis.

To address issues of food supply, scientists in the Philippines have been working on genetically modifying rice—an important food staple that is a C3 crop—so that it can instead carry out C4 photosynthesis.

Results so far seem promising, and these researchers estimate that the yield of C4 rice might be 30-50% higher than C3 rice with the same input of water and resources.

inquiry: Which wavelengths of light are most effective in driving photosynthesis? Experiment: Absorption and action spectra, along with a classic experiment by Theodor W. Engelmann, reveal which wavelengths of light are photosynthetically important.

Results: (a) Absorption spectra. The three curves show the wavelengths of light best absorbed by three types of chloroplast pigments. (b)Action spectrum. This graph plots the rate of photosynthesis versus wavelength. The resulting action spectrum resembles the absorption spectrum for chlorophyll a but does not match exactly (see part a). This is partly due to the absorption of light by accessory pigments such as chlorophyll b and carotenoids. (c) Engelmann's experiment. In 1883, Theodor W. Engelmann illuminated a filamentous alga with light that had been passed through a prism, exposing different segments of the alga to different wavelengths. He used aerobic bacteria, which congregate near an oxygen source, to determine which segments of the alga were releasing the most O2 and thus photosynthesizing most. Bacteria congregated in greatest numbers around the parts of the alga illuminated with violet-blue or red light. Conclusion: The action spectra, confirmed by Engelmann's experiment, show which portions of the spectrum are most effective in driving photosynthesis.

Inquiry: At which end do kinetochore microtubules shorten during anaphase? Experiment: Gary Borisy and colleagues at the University of Wisconsin wanted to determine whether kinetochore microtubules depolymerize at the kinetochore end or the pole end as chromosomes move toward the poles during mitosis. First they labeled the microtubules of a pig kidney cell in early anaphase with a yellow fluorescent dye. (Nonkinetochore microtubules are not shown.)Then they marked a region of the kinetochore microtubules between one spindle pole and the chromosomes by using a laser to eliminate the fluorescence from that region, while leaving the microtubules intact (see below). As anaphase proceeded, they monitored the changes in microtubule length on either side of the mark.

Results: As the chromosomes moved poleward, the microtubule segments on the kinetochore side of the mark shortened, while those on the spindle pole side stayed the same length. Conclusion: During anaphase in this cell type, chromosome movement is correlated with kinetochore microtubules shortening at their kinetochore ends and not at their spindle pole ends. This experiment supports the hypothesis that during anaphase, a chromosome is walked along a microtubule as the microtubule depolymerizes at its kinetochore end, releasing tubulin subunits.

free ribosomes and bound ribosomes

Ribosomes build proteins in two cytoplasmic locales. At any given time, free ribosomes are suspended in the cytosol, while bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope (see Figure 6.10). Bound and free ribosomes are structurally identical, and ribosomes can play either role at different times.

Ribosomes

Ribosomes, which are complexes made of ribosomal RNAs and proteins, are the cellular components that carry out protein synthesis (Figure 6.10). (Note that ribosomes are not membrane bounded and thus are not considered organelles.) Cells that have high rates of protein synthesis have particularly large numbers of ribosomes as well as prominent nucleoli, which makes sense, given the role of nucleoli in ribosome assembly. For example, a human pancreas cell, which makes many digestive enzymes, has a few million ribosomes. This electron micrograph of a pancreas cell shows both free and bound ribosomes. The simplified diagram and computer model show the two subunits of a ribosome.

The concentration of CO2 in the atmosphere has drastically increased since the Industrial Revolution began in the 1800s, and it continues to rise today due to human activities such as the burning of fossil fuels. The resulting global climate change, including an increase in average temperatures around the planet, may have far-reaching effects on plant species.

Scientists are concerned that increasing CO2 concentration and temperature may affect C3 and C4 plants differently, thus changing the relative abundance of these species in a given plant community.

Similarity

Second, like prokaryotes, mitochondria and chloroplasts contain ribosomes, as well as circular DNA molecules—like bacterial chromosomes—associated with their inner membranes. The DNA in these organelles programs the synthesis of some organelle proteins on ribosomes that have been synthesized and assembled there as well. Third, also consistent with their probable evolutionary origins as cells, mitochondria and chloroplasts are autonomous (somewhat independent) organelles that grow and reproduce within the cell

quorum sensing & biofilm

Sensing the concentration of such signaling molecules allows bacteria to monitor their own local cell density, a phenomenon called quorum sensing. Quorum sensing allows bacterial populations to coordinate their behaviors in activities that require a given number of cells acting synchronously. One example is formation of a biofilm, an aggregation of bacterial cells adhered to a surface. The cells in the biofilm often derive nutrition from the surface they are on. You have probably encountered biofilms many times, perhaps without realizing it. The slimy coating on a fallen log or on leaves lying on a forest path, and even the film on your teeth each morning, are examples of bacterial biofilms. In fact, toothbrushing and flossing disrupt biofilms that would otherwise cause cavities and gum disease.

The Golgi Apparatus:

Shipping and Receiving Center

The structure of a G protein-coupled receptor (GPCR)

Shown here is a model of the human β2-adrenergic receptor, which binds adrenaline (epinephrine) and was able to be crystallized in the presence of both a molecule that mimics adrenaline (green in the model) and cholesterol in the membrane (orange). Two receptor molecules (blue) are shown as ribbon models in a side view. Caffeine can also bind to this receptor; see question 10 at the end of the chapter.

Glycolysis can accept a wide range of carbohydrates for catabolism. In the digestive tract, starch is hydrolyzed to glucose, which can then be broken down in the cells by glycolysis and the citric acid cycle.

Similarly, glycogen, the polysaccharide that humans and many other animals store in their liver and muscle cells, can be hydrolyzed to glucose between meals as fuel for respiration. The digestion of disaccharides, including sucrose, provides glucose and other monosaccharides as fuel for respiration.

Glycolysis and the citric acid cycle connect to many other metabolic pathways

So far, we have treated the oxidative breakdown of glucose in isolation from the cell's overall metabolic economy. In this section, you will learn that glycolysis and the citric acid cycle are major intersections of the cell's catabolic (breakdown) and anabolic (biosynthetic) pathways.

In respiration, the oxidation of glucose transfers electrons to a lower energy state, liberating energy that becomes available for ATP synthesis.

So, in general, we see fuels with multiple C—H bonds oxidized into products with multiple C—O bonds.

Communication among bacteria:

Soil-dwelling bacteria called myxobacteria ("slime bacteria") use chemical signals to share information about nutrient availability. When food is scarce, starving cells secrete a signaling molecule that stimulates neighboring cells to aggregate. The cells form a structure called a fruiting body that produces spores, thick-walled cells capable of surviving until the environment improves. The myxobacteria shown here are the species Myxococcus xanthus (steps 1-3, SEMs; lower photo, LM).

Diffusion of two solutes

Solutions of two different dyes are separated by a membrane that is permeable to both. Each dye diffuses down its own concentration gradient. There will be a net diffusion of the purple dye toward the left, even though the total solute concentration was initially greater on the left side.

We have already mentioned anaerobic respiration, which takes place in certain prokaryotic organisms that live in environments without oxygen. These organisms have an electron transport chain but do not use oxygen as a final electron acceptor at the end of the chain. Oxygen performs this function very well because it is extremely electronegative, but other, less electronegative substances can also serve as final electron acceptors

Some "sulfate-reducing" marine bacteria, for instance, use the sulfate ion (SO4 2- ) at the end of their respiratory chain. Operation of the chain builds up a protonmotive force used to produce ATP, but H2S (hydrogen sulfide) is made as a by-product rather than water.The rotten-egg odor you may have smelled while walking through a salt marsh or a mudflat signals the presence of sulfate-reducing bacteria.

Heterotrophs obtain organic material by the second major mode of nutrition. Unable to make their own food, they live on compounds produced by other organisms (heteromeans "other"). Heterotrophs are the biosphere's consumers. The most obvious "other-feeding" occurs when an animal eats plants or other organisms. But heterotrophic nutrition may be more subtle.

Some heterotrophs consume the remains of other organisms by decomposing and feeding on organic litter such as dead organisms, feces, and fallen leaves; these types of heterotrophs are known as decomposers. Most fungi and many types of prokaryotes get their nourishment this way. Almost all heterotrophs, including humans, are completely dependent, either directly or indirectly, on photoautotrophs for food—and also for oxygen, a by-product of photosynthesis.

motor proteins

Some membrane proteins seem to move in a highly directed manner, perhaps driven along cytoskeletal fibers in the cell by motor proteins connected to the membrane proteins' cytoplasmic regions. However, many other membrane proteins seem to be held immobile by their attachment to the cytoskeleton or to the extracellular matrix (see Figure 7.3).

The eukaryotic cell cycle is regulated by a molecular control system: The timing and rate of cell division in different parts of a plant or animal are crucial to normal growth, development, and maintenance. The frequency of cell division varies with the type of cell. For example, human skin cells divide frequently throughout life, whereas liver cells maintain the ability to divide but keep it in reserve until an appropriate need arises— say, to repair a wound.

Some of the most specialized cells, such as fully formed nerve cells and muscle cells, do not divide at all in a mature human. These cell cycle differences result from regulation at the molecular level. The mechanisms of this regulation are of great interest, not only to understand the life cycles of normal cells but also to learn how cancer cells manage to escape the usual controls.

. The cells of most eukaryotic and many prokaryotic organisms can carry out aerobic respiration.

Some prokaryotes use substances other than oxygen as reactants in a similar process that harvests chemical energy without oxygen; this process is called anaerobic respiration (the prefix an- means "without").

Enzyme Inhibitors: Certain chemicals selectively inhibit the action of specific enzymes. Sometimes the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually irreversible. Many enzyme inhibitors, however, bind to the enzyme by weak interactions, and when this occurs the inhibition is reversible.

Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site (Figure 8.18a and b). These mimics, called competitive inhibitors, reduce the productivity of enzymes by blocking substrates from entering active sites. This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites

cell motility

Some types of cell motility (movement) also involve the cytoskeleton. The term cell motility includes both changes in cell location and movements of cell parts. Cell motility generally requires interaction of the cytoskeleton with motor proteins. There are many such examples: Cytoskeletal elements and motor proteins work together with plasma membrane molecules to allow whole cells to move along fibers outside the cell. Inside the cell, vesicles and other organelles often use motor protein "feet" to "walk" to their destinations along a track provided by the cytoskeleton. For example, this is how vesicles containing neurotransmitter molecules migrate to the tips of axons, the long extensions of nerve cells that release these molecules as chemical signals to adjacent nerve cells (Figure 6.21). The cytoskeleton also manipulates the plasma membrane, bending it inward to form food vacuoles or other phagocytic vesicles.

Mechanisms of cell division in several groups of organisms.

Some unicellular eukaryotes existing today have mechanisms of cell division that may resemble intermediate steps in the evolution of mitosis. Except for (a), cell walls are not shown. (a) Bacteria: During binary fission in bacteria, the origins of the daughter chromosomes move to opposite ends of the cell. The mechanism involves polymerization of actin-like molecules, and possibly proteins that may anchor the daughter chromosomes to specific sites on the plasma membrane. (b)Dinoflagellates: In unicellular protists called dinoflagellates, the chromosomes attach to the nuclear envelope, which remains intact during cell division. Microtubules pass through the nucleus inside cytoplasmic tunnels, reinforcing the spatial orientation of the nucleus, which then divides in a process reminiscent of bacterial binary fission. (c)Diatoms and some yeasts: In these two other groups of unicellular eukaryotes, the nuclear envelope also remains intact during cell division. In these organisms, the microtubules form a spindle within the nucleus. Microtubules separate the chromosomes, and the nucleus splits into two daughter nuclei. (d) Most eukaryotes: In most other eukaryotes, including plants and animals, the spindle forms outside the nucleus, and the nuclear envelope breaks down during mitosis. Microtubules separate the chromosomes, and two nuclear envelopes then form.

How does the activated hormone-receptor complex turn on genes? Recall that the genes in a cell's DNA function by being transcribed and processed into messenger RNA (mRNA), which leaves the nucleus and is translated into a specific protein by ribosomes in the cytoplasm (see Figure 5.22).

Special proteins called transcription factors control which genes are turned on—that is, which genes are transcribed into mRNA— in a particular cell at a particular time. When the aldosterone receptor is activated, it acts as a transcription factor that turns on specific genes. (You'll learn more about transcription factors in Chapters 17 and 18.)

specialized peroxisomes

Specialized peroxisomes called glyoxysomes are found in the fat-storing tissues of plant seeds. These organelles contain enzymes that initiate the conversion of fatty acids to sugar, which the emerging seedling uses as a source of energy and carbon until it can produce its own sugar by photosynthesis.

Transport Proteins

Specific ions and a variety of polar molecules can't move through cell membranes on their own. However, these hydrophilic substances can avoid contact with the lipid bilayer by passing through transport proteins that span the membrane. Some transport proteins, called channel proteins, function by having a hydrophilic channel that certain molecules or atomic ions use as a tunnel through the membrane (see Figure 7.7a, left)

Almost all plants are autotrophs; the only nutrients they require are water and minerals from the soil and carbon dioxide from the air.

Specifically, plants are photoautotrophs, organisms that use light as a source of energy to synthesize organic substances (Figure 10.1). Photosynthesis also occurs in algae, certain unicellular eukaryotes, and some prokaryotes (Figure 10.2). In this chapter, we will touch on these other groups in passing, but our emphasis will be on plants. Variations in autotrophic nutrition that occur in prokaryotes and algae will be described in Concept 27.3.

cAMP as a second messenger in a G protein signaling pathway: G protein-coupled receptor (GPCR) First messenger (signaling molecule such as epinephrine) Adenylyl cyclase Second messenger G protein - GTP ATP cAMP Protein kinase A Cellular responses

Step 1: First messenger binds to GPCR, activating it. Step 2: Activated GPCR binds to G protein, which is then bound by GTP, activating the G protein. Step 3: Activated G protein/ GTP binds to adenylyl cyclase. GTP is hydrolyzed, activating adenylyl cyclase. Step 4: Activated adenylyl cyclase converts ATP to cAMP. Step 5: cAMP, a second messenger, activates another protein, leading to cellular responses.

As long as our cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life.

Stepping back to look at the big picture, we can see once again how important it is to think of organisms as open systems. Sunlight provides a daily source of free energy for an ecosystem's plants and other photosynthetic organisms.

The concept of entropy helps us understand why certain processes are energetically favorable and occur on their own. It turns out that if a given process, by itself, leads to an increase in entropy, that process can proceed without requiring an input of energy.

Such a process is called a spontaneous process. Note that as we're using it here, the word spontaneous does not imply that the process would occur quickly; rather, the word signifies that it is energetically favorable. (In fact, it may be helpful for you to think of the phrase "energetically favorable" when you read the formal term "spontaneous," the word favored by chemists.) Some spontaneous processes, such as an explosion, may be virtually instantaneous, while others, such as the rusting of an old car over time, are much slower.

This information is immensely interesting to biologists, for it allows us to predict which kinds of change can happen without an input of energy.

Such spontaneous changes can be harnessed to perform work. This principle is very important in the study of metabolism, where a major goal is to determine which reactions can supply energy for cellular work.

Super Resolution

Super-resolution.- On the top is a confocal image of part of a nerve cell, using a fluorescent label that binds to a molecule clustered in small sacs in the cell (vesicles) that are 40 nm in diameter. The greenish-yellow spots are blurry because 40 nm is below the 200-nm limit of resolution for standard light microscopy. Below is an image of the same part of the cell, seen using a new super-resolution technique. Sophisticated equipment is used to light up individual fluorescent molecules and record their position. Combining information from many molecules in different places "breaks" the limit of resolution, resulting in the sharp greenish-yellow dots seen here. (Each dot is a 40-nm vesicle.)

Telophase & cytokinesis

Telophase and Cytokinesis: Telophase • Two daughter nuclei form in the cell. Nuclear envelopes arise from the fragments of the parent cell's nuclear envelope and other portions of the endomembrane system. • Nucleoli reappear. • The chromosomes become less condensed. • Any remaining spindle microtubules are depolymerized. • Mitosis, the division of one nucleus into two genetically identical nuclei, is now complete. Cytokinesis: • The division of the cytoplasm is usually well under way by late telophase, so the two daughter cells appear shortly after the end of mitosis. • In animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches the cell in two.

Myosin motors in muscle cell contraction.

The "walking" of myosin projections (the so-called heads) drives the parallel myosin and actin filaments past each other so that the actin filaments approach each other in the middle (red arrows). This shortens the muscle cell. Muscle contraction involves the shortening of many muscle cells at the same time (TEM).

Second, the ATP yield varies slightly depending on the type of shuttle used to transport electrons from the cytosol into the mitochondrion

The 2 electrons of NADH captured in glycolysis must be conveyed into the mitochondrion by one of several electron shuttle systems.

C4 and CAM photosynthesis compared: (a) Spatial separation of steps. In C4 plants, carbon fixation and the Calvin cycle occur in different types of cells (b) Temporal separation of steps. In CAM plants, carbon fixation and the Calvin cycle occur in the same cell at different times.

The C4 and CAM pathways are two evolutionary solutions to the problem of maintaining photosynthesis with stomata partially or completely closed on hot, dry days. Both adaptations are characterized by (1) preliminary incorporation of CO2 into organic acids, followed by (2) transfer of CO2 to the Calvin cycle.

C4 leaf anatomy and the C4 pathway: The structure and biochemical functions of the leaves of C4 plants are an evolutionary adaptation to hot, dry climates. This adaptation maintains a CO2 concentration in the bundle sheath that favors photosynthesis over photorespiration.

The C4 pathway (1)In mesophyll cells, the enzyme PEP carboxylase adds CO2 to PEP, forming a fourcarbon compound. (2) The four-carbon compound (such as malate) moves into a bundle-sheath cell via plasmodesmata. (3)In bundle-sheath cells, CO2 is released and enters the Calvin cycle.

The maintenance of calcium ion concentrations in an animal cell.

The Ca2+ concentration in the cytosol is usually much lower (beige) than in the extracellular fluid and ER (green). Protein pumps in the plasma membrane and the ER membrane, driven by ATP, move Ca2+ from the cytosol into the extracellular fluid and into the lumen of the ER. Mitochondrial pumps, driven by chemiosmosis (see Concept 9.4), move Ca2+ into mitochondria when the calcium level in the cytosol rises significantly.

Phase 1: Carbon fixation.

The Calvin cycle incorporates each CO2 molecule, one at a time, by attaching it to a fivecarbon sugar named ribulose bisphosphate (abbreviated RuBP). The enzyme that catalyzes this first step is RuBP carboxylase-oxygenase, or rubisco. (This is the most abundant protein in chloroplasts and is also thought to be the most abundant protein on Earth.) The product of the reaction is a six-carbon intermediate that is short-lived because it is so energetically unstable that it immediately splits in half, forming two molecules of 3-phosphoglycerate (for each CO2 fixed).

What does the ER consist of ?

The ER consists of a network of membranous tubules and sacs called cisternae (from the Latin cisterna, a reservoir for a liquid). The ER membrane separates the internal compartment of the ER, called the ER lumen (cavity) or cisternal space, from the cytosol. And because the ER membrane is continuous with the nuclear envelope, the space between the two membranes of the envelope is continuous with the lumen of the ER

A particular human cell might undergo one division in 24 hours. Of this time, the M phase would occupy less than 1 hour, while the S phase might occupy 10-12 hours, or about half the cycle. The rest of the time would be apportioned between the G1 and G2 phases.

The G2 phase usually takes 4-6 hours; in our example, G1 would occupy about 5-6 hours. G1 is the most variable in length in different types of cells. Some cells in a multicellular organism divide very infrequently or not at all. These cells spend their time in G1 (or a related phase called G0, to be discussed later in the chapter) doing their job in the organism—a cell of the pancreas secretes digestive enzymes, for example

What does the Golgi apparatus do?

The Golgi apparatus consists of a group of associated, flattened membranous sacs—cisternae—looking like a stack of pita bread (Figure 6.12). A cell may have many, even hundreds, of these stacks. The membrane of each cisterna in a stack separates its internal space from the cytosol. Vesicles concentrated in the vicinity of the Golgi apparatus are engaged in the transfer of material between parts of the Golgi and other structures.

The Golgi apparatus

The Golgi apparatus consists of stacks of associated, flattened sacs, or cisternae. Unlike the ER cisternae, these sacs are not physically connected, as you can see in the cutaway diagram. A Golgi stack receives and dispatches transport vesicles and the products they contain. A Golgi stack has a structural and functional directionality, with a cis face that receives vesicles containing ER products and a trans face that dispatches vesicles. The cisternal maturation model proposes that the Golgi cisternae themselves "mature," moving from the cis to the trans face while carrying some proteins along. In addition, some vesicles recycle enzymes that had been carried forward in moving cisternae, transporting them "backward" to a less mature region where their functions are needed.

In eukaryotic cells, the electron carriers are spatially arranged in the inner mitochondrial membrane in such a way that H+ is accepted from the mitochondrial matrix and deposited in the intermembrane space (see Figure 9.15)

The H+ gradient that results is referred to as a proton-motive force, emphasizing the capacity of the gradient to perform work. The force drives H+ back across the membrane through the H+ channels provided by ATP synthases

Types of Fermentation: Fermentation consists of glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate.

The NAD+ can then be reused to oxidize sugar by glycolysis, which nets two molecules of ATP by substrate-level phosphorylation. There are many types of fermentation, differing in the end products formed from pyruvate. Two types are alcohol fermentation and lactic acid fermentation, and both are harnessed by humans for food and industrial production.

We see green when we look at a leaf because chlorophyll absorbs violet-blue and red light while transmitting and reflecting green light (Figure 10.8).

The ability of a pigment to absorb various wavelengths of light can be measured with an instrument called a spectrophotometer. This machine directs beams of light of different wavelengths through a solution of the pigment and measures the fraction of the light transmitted at each wavelength. A graph plotting a pigment's light absorption versus wavelength is called an absorption spectrum (Figure 10.9).

Upon binding a ligand such as a growth factor, one RTK may activate ten or more different transduction pathways and cellular responses. Often, more than one signal transduction pathway can be triggered at once, helping the cell regulate and coordinate many aspects of cell growth and cell reproduction.

The ability of a single ligand-binding event to trigger so many pathways is a key difference between RTKs and GPCRs, which generally activate a single transduction pathway. Abnormal RTKs that function even in the absence of signaling molecules are associated with many kinds of cancer.

The emergence of cellular functions

The ability of this macrophage (brown) to recognize, apprehend, and destroy Staphylococcus bacteria (orange) is a coordinated activity of the whole cell. Its cytoskeleton, lysosomes, and plasma membrane are among the components that function in phagocytosis (colorized SEM).

The ability to change the lipid composition

The ability to change the lipid composition of cell membranes in response to changing temperatures has evolved in organisms that live where temperatures vary. In many plants that tolerate extreme cold, such as winter wheat, the percentage of unsaturated phospholipids increases in autumn, an adjustment that keeps the membranes from solidifying during winter. Certain bacteria and archaea can also change the proportion of unsaturated phospholipids in their cell membranes, depending on the temperature at which they are growing. Overall, natural selection has apparently favored organisms whose mix of membrane lipids ensures an appropriate level of membrane fluidity for their environment.

Now let's look at the citric acid cycle in more detail. The cycle has eight steps, each catalyzed by a specific enzyme. You can see in Figure 9.12 that for each turn of the citric acid cycle, two carbons (red) enter in the relatively reduced form of an acetyl group (step 1 ), and two different carbons (blue) leave in the completely oxidized form of CO2 molecules (steps 3 and 4 ).

The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate (step 1 ). Citrate is the ionized form of citric acid, for which the cycle is named. The next seven steps decompose the citrate back to oxaloacetate. It is this regeneration of oxaloacetate that makes the process a cycle

An action spectrum is prepared by illuminating chloroplasts with light of different colors and then plotting wavelength against some measure of photosynthetic rate, such as CO2 consumption or O2 release

The action spectrum for photosynthesis was first demonstrated by Theodor W. Engelmann, a German botanist, in 1883. Before equipment for measuring O2 levels had even been invented, Engelmann performed a clever experiment in which he used bacteria to measure rates of photosynthesis in filamentous algae (Figure 10.10c). His results are a striking match to the modern action spectrum shown in Figure 10.10b

Effects of Local Conditions on Enzyme Activity:

The activity of an enzyme—how efficiently the enzyme functions—is affected by general environmental factors, such as temperature and pH. It can also be affected by chemicals that specifically influence that enzyme. In fact, researchers have learned much about enzyme function by employing such chemicals.

How does the mitochondrion (or the plasma membrane in prokaryotes) couple this electron transport and energy release to ATP synthesis?

The answer is a mechanism called chemiosmosis.

chromatin

The associated proteins maintain the structure of the chromosome and help control the activity of the genes. Together, the entire complex of DNA and proteins that is the building material of chromosomes is referred to as chromatin. As you will soon see, the chromatin of a chromosome varies in its degree of condensation during the process of cell division.

Tracking atoms through photosynthesis.

The atoms from CO2 are shown in magenta, and the atoms from H2O are shown in blue.

Cells that are infected, are damaged, or have reached the end of their functional life span often undergo "programmed cell death" (Figure 11.19).

The best-understood type of this controlled cell suicide is apoptosis (from the Greek, meaning "falling off," and used in a classic Greek poem to refer to leaves falling from a tree). During this process, cellular agents chop up the DNA and fragment the organelles and other cytoplasmic components. The cell shrinks and becomes lobed (a change called "blebbing"), and the cell's parts are packaged up in vesicles that are engulfed and digested by specialized scavenger cells, leaving no trace. Apoptosis protects neighboring cells from damage that they would otherwise suffer if a dying cell merely leaked out all its contents, including its many digestive enzymes

In the simplest kind of allosteric regulation, an activating or inhibiting regulatory molecule binds to a regulatory site (sometimes called an allosteric site), often located where subunits join.

The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme.

Membrane structure results in selective permeability

The biological membrane is an exquisite example of a supramolecular structure—many molecules ordered into a higher level of organization—with emergent properties beyond those of the individual molecules.

The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. The first law is also known as the principle of conservation of energy. The electric company does not make energy, but merely converts it to a form that is convenient for us to use. By converting sunlight to chemical energy, a plant acts as an energy transformer, not an energy producer

The brown bear in Figure 8.3a will convert the chemical energy of the organic molecules in its food to kinetic and other forms of energy as it carries out biological processes. What happens to this energy after it has performed work? The second law of thermodynamics helps to answer this question.

Localization of Enzymes Within the Cell

The cell is not just a bag of chemicals with thousands of different kinds of enzymes and substrates in a random mix. The cell is compartmentalized, and cellular structures help bring order to metabolic pathways. In some cases, a team of enzymes for several steps of a metabolic pathway are assembled into a multienzyme complex. The arrangement facilitates the sequence of reactions, with the product from the first enzyme becoming the substrate for an adjacent enzyme in the complex, and so on, until the end product is released. Some enzymes and enzyme complexes have fixed locations within the cell and act as structural components of particular membranes. Others are in solution within particular membraneenclosed eukaryotic organelles, each with its own internal chemical environment.

Cell Walls of Plants

The cell wall is an extracellular structure of plant cells (Figure 6.27). This is one of the features that distinguishes plant cells from animal cells. The wall protects the plant cell, maintains its shape, and prevents excessive uptake of water. On the level of the whole plant, the strong walls of specialized cells hold the plant up against the force of gravity. Prokaryotes, fungi, and some unicellular eukaryotes also have cell walls, as you saw in Figures 6.5 and 6.8, but we will postpone discussion of them until Unit Five.

A Panoramic View of the Eukaryotic Cell

The cell's compartments provide different local environments that support specific metabolic functions, so incompatible processes can occur simultaneously in a single cell. The plasma membrane and organelle membranes also participate directly in the cell's metabolism because many enzymes are built right into the membranes. The basic fabric of most biological membranes is a double layer of phospholipids and other lipids. Embedded in this lipid bilayer or attached to its surfaces are diverse proteins (see Figure 6.6).

inherited lysosomal storage diseases

The cells of people with inherited lysosomal storage diseases lack a functioning hydrolytic enzyme normally present in lysosomes. The lysosomes become engorged with indigestible material, which begins to interfere with other cellular activities. In Tay-Sachs disease, for example, a lipid-digesting enzyme is missing or inactive, and the brain becomes impaired by an accumulation of lipids in the cells. Fortunately, lysosomal storage diseases are rare in the general population.

The ability of a cell to receive new signals depends on reversibility of the changes produced by prior signals. The binding of signaling molecules to receptors is reversible. As the external concentration of signaling molecules falls, fewer receptors are bound at any given moment, and the unbound receptors revert to their inactive form.

The cellular response occurs only when the concentration of receptors with bound signaling molecules is above a certain threshold. When the number of active receptors falls below that threshold, the cellular response ceases. Then, by a variety of means, the relay molecules return to their inactive forms: The GTPase activity intrinsic to a G protein hydrolyzes its bound GTP; the enzyme phosphodiesterase converts cAMP to AMP; protein phosphatases inactivate phosphorylated kinases and other proteins; and so forth. As a result, the cell is soon ready to respond to a fresh signal

The plant cell vacuole.

The central vacuole is usually the largest compartment in a plant cell; the rest of the cytoplasm is often confined to a narrow zone between the vacuolar membrane and the plasma membrane (TEM).

Equilibrium and Metabolism: Reactions in an isolated system eventually reach equilibrium and can then do no work, as illustrated by the isolated hydroelectric system in Figure 8.7

The chemical reactions of metabolism are reversible, and they, too, would reach equilibrium if they occurred in the isolation of a test tube. Because systems at equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead! The fact that metabolism as a whole is never at equilibrium is one of the defining features of life.

plastids

The chloroplast is a specialized member of a family of closely related plant organelles called plastids. One type of plastid, the amyloplast, is a colorless organelle that stores starch (amylose), particularly in roots and tubers. Another is the chromoplast, which has pigments that give fruits and flowers their orange and yellow hues.

The Citric Acid Cycle

The citric acid cycle functions as a metabolic furnace that further oxidizes organic fuel derived from pyruvate. Figure 9.11 summarizes the inputs and outputs as pyruvate is broken down to three CO2 molecules, including the molecule of CO2 released during the conversion of pyruvate to acetyl CoA. The cycle generates 1 ATP per turn by substrate-level phosphorylation, but most of the chemical energy is transferred to NAD+ and FAD during the redox reaction.

The reduced coenzymes, NADH and FADH2, shuttle their cargo of high-energy electrons into the electron transport chain.

The citric acid cycle is also called the tricarboxylic acid cycle or the Krebs cycle, the latter honoring Hans Krebs, the German-British scientist who was largely responsible for working out the pathway in the 1930s.

Components of chloroplast

The contents of a chloroplast are partitioned from the cytosol by an envelope consisting of two membranes separated by a very narrow intermembrane space. Inside the chloroplast is another membranous system in the form of flattened, interconnected sacs called thylakoids. In some regions, thylakoids are stacked like poker chips; each stack is called a granum (plural, grana). The fluid outside the thylakoids is the stroma, which contains the chloroplast DNA and ribosomes as well as many enzymes. The membranes of the chloroplast divide the chloroplast space into three compartments: the intermembrane space, the stroma, and the thylakoid space.

The ability of organisms to produce more of their own kind is the one characteristic that best distinguishes living things from nonliving matter. This unique capacity to procreate, like all biological functions, has a cellular basis. In 1855, Rudolf Virchow, a German physician, put it this way: "Where a cell exists, there must have been a preexisting cell, just as the animal arises only from an animal and the plant only from a plant." He summarized this concept with the Latin saying "Omnis cellula e cellula," meaning "Every cell from a cell."

The continuity of life is based on the reproduction of cells, or cell division. The series of confocal fluorescence micrographs in Figure 12.1, starting at the upper left and reading from left to right, follows the events of cell division as the cells of a two-celled marine worm embryo become four

In effect, the mesophyll cells of a C4 plant pump CO2 into the bundle-sheath cells, keeping the CO2 concentration in those cells high enough for rubisco to bind CO2 rather than O2.

The cyclic series of reactions involving PEP carboxylase and the regeneration of PEP can be thought of as an ATPpowered pump that concentrates CO2. In this way, C4 photosynthesis spends ATP energy to minimize photorespiration and enhance sugar production. This adaptation is especially advantageous in hot regions with intense sunlight, where stomata partially close during the day, and it is in such environments that C4 plants evolved and thrive today.

Note that the peaks of MPF activity correspond to the peaks of cyclin concentration.

The cyclin level rises during the S and G2 phases and then falls abruptly during M phase.

Plasmodesmata between plant cells

The cytoplasm of one plant cell is continuous with the cytoplasm of its neighbors via plasmodesmata, cytoplasmic channels through the cell walls (TEM).

Synthesis of membrane components and their orientation in the membrane

The cytoplasmic (orange) face of the plasma membrane differs from the extracellular (aqua) face. The latter arises from the inside face of ER, Golgi, and vesicle membranes. 1) Membrane proteins and lipids are synthesized in association with the endoplasmic reticulum (ER). In the ER, carbohydrates (green) are added to the transmembrane proteins (purple dumbbells), making them glycoproteins. The carbohydrate portions may then be modified. 2) Inside the Golgi apparatus, the glycoproteins undergo further carbohydrate modification, and lipids acquire carbohydrates, becoming glycolipids. 3) The glycoproteins, glycolipids, and secretory proteins (purple spheres) are transported in vesicles to the plasma membrane 4) As vesicles fuse with the plasma membrane, the outside face of the vesicle becomes continuous with the inside (cytoplasmic) face of the plasma membrane. This releases the secretory proteins from the cell, a process called exocytosis, and positions the carbohydrates of membrane glycoproteins and glycolipids on the outside (extracellular) face of the plasma membrane.

How Ion Pumps Maintain Membrane Potential: All cells have voltages across their plasma membranes. Voltage is electrical potential energy (see Concept 2.2)—a separation of opposite charges.

The cytoplasmic side of the membrane is negative in charge relative to the extracellular side because of an unequal distribution of anions and cations on the two sides. The voltage across a membrane, called a membrane potential, ranges from about -50 to -200 millivolts (mV). (The minus sign indicates that the inside of the cell is negative relative to the outside.)

When were microscopes invented?

The development of instruments that extend the human senses allowed the discovery and early study of cells. Microscopes were invented in 1590 and further refined during the 1600s. Cell walls were first seen by Robert Hooke in 1665 as he looked through a microscope at dead cells from the bark of an oak tree. But it took the wonderfully crafted lenses of Antoni van Leeuwenhoek to visualize living cells. Imagine Hooke's excitement when he visited van Leeuwenhoek in 1674 and the world of microorganisms—what his host called "very little animalcules"—was revealed to him.

Notice in Figure 10.21 that the CAM pathway is similar to the C4 pathway in that CO2 is first incorporated into organic intermediates before it enters the Calvin cycle.

The difference is that in C4 plants, the initial steps of carbon fixation are separated structurally from the Calvin cycle, whereas in CAM plants, the two steps occur within the same cell but at separate times. (Keep in mind that CAM, C4, and C3 plants all eventually use the Calvin cycle to make sugar from carbon dioxide.)

passive transport

The diffusion of a substance across a biological membrane is called passive transport because the cell does not have. The diffusion of a substance across a biological membrane is called passive transport because the cell does not have to expend energy to make it happen. The concentration gradient itself represents potential energy (see Concept 2.2 and Figure 8.5b) and drives diffusion

osmosis

The diffusion of free water across a selectively permeable membrane, whether artificial or cellular, is called osmosis. The movement of water across cell membranes and the balance of water between the cell and its environment are crucial to organisms. Let's now apply what we've learned about osmosis in this system to living cells.

Unless something prevents it, each of these systems will move toward greater stability:

The diver falls, the solution becomes uniformly colored, and the glucose molecule is broken down into smaller molecules.

plant cell walls

The drawing shows several cells, each with a cell wall, large vacuole, a nucleus, and several chloroplasts and mitochondria. The TEM shows the cell walls where two cells come together. The multilayered partition between plant cells consists of adjoining walls individually secreted by the cells.

The distinction between anaerobic respiration & fermentation is that an electron transport chain is used in anaerobic respiration but not in fermentation.

The electron transport chain is also called the respiratory chain because of its role in both types of cellular respiration.)

As in the combustion of methane or gasoline, the fuel (glucose) is oxidized and oxygen is reduced.

The electrons lose potential energy along the way, and energy is released.

Having already discussed the nuclear envelope, we will now focus on the endoplasmic reticulum and the other endomembranes to which the endoplasmic reticulum gives rise. The Endoplasmic Reticulum: Biosynthetic Factory -

The endoplasmic reticulum (ER) is such an extensive network of membranes that it accounts for more than half the total membrane in many eukaryotic cells. (The word endoplasmic means "within the cytoplasm," and reticulum is Latin for "little net.")

Life depends on photosynthesis: The Importance of Photosynthesis: A Review In this chapter, we have followed photosynthesis from photons to food. The light reactions capture solar energy and use it to make ATP and transfer electrons from water to NADP+ , forming NADPH. The Calvin cycle uses the ATP and NADPH to produce sugar from carbon dioxide

The energy that enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds. The entire process is reviewed visually in Figure 10.22, where photosynthesis is also put in its natural context.

Cellular respiration and metabolic pathways play a role of central importance in organisms. Examine Figure 9.2 again to put cellular respiration into the broader context of energy flow and chemical cycling in ecosystems.

The energy that keeps us alive is released, not produced, by cellular respiration. We are tapping energy that was stored in food by photosynthesis. In the next chapter, you will learn how photosynthesis captures light and converts it to chemical energy

Evolutionary relationships between eukaryotic and prokaryotic cells.

The evolutionary relationships between prokaryotic and eukaryotic cells will be discussed later in this chapter, and prokaryotic cells will be described in detail elsewhere (see Chapter 27). Most of the discussion of cell structure that follows in this chapter applies to eukaryotic cells.

cell cycle control system

The experiment shown in Figure 12.14 and other experiments on animal cells and yeasts demonstrated that the sequential events of the cell cycle are directed by a distinct cell cycle control system, a cyclically operating set of molecules in the cell that both triggers and coordinates key events in the cell cycle (Figure 12.15).

The Specificity of Cell Signaling and Coordination of the Response: Consider two different cells in your body—a liver cell and a heart muscle cell, for example. Both are in contact with your bloodstream and are therefore constantly exposed to many different hormone molecules, as well as to local regulators secreted by nearby cells. Yet the liver cell responds to some signals but ignores others, and the same is true for the heart cell. And some kinds of signals trigger responses in both cells—but different responses. For instance, epinephrine stimulates the liver cell to break down glycogen, but the main response of the heart cell to epinephrine is contraction, leading to a more rapid heartbeat. How do we account for this difference?

The explanation for the specificity exhibited in cellular responses to signals is the same as the basic explanation for virtually all differences between cells: Because different kinds of cells turn on different sets of genes, different kinds of cells have different collections of proteins. The response of a cell to a signal depends on its particular collection of signal receptor proteins, relay proteins, and proteins needed to carry out the response. A liver cell, for example, is poised to respond appropriately to epinephrine by having the proteins listed in Figure 11.16 as well as those needed to manufacture glycogen.

The Evolution of Mitosis: Given that prokaryotes preceded eukaryotes on Earth by more than a billion years, we might hypothesize that mitosis evolved from simpler prokaryotic mechanisms of cell reproduction.

The fact that some of the proteins involved in bacterial binary fission are related to eukaryotic proteins that function in mitosis supports that hypothesis.

As we have seen, the response of liver cells to the hormone epinephrine helps regulate cellular energy metabolism by affecting the activity of an enzyme. T

The final step in the signaling pathway that begins with epinephrine binding activates the enzyme that catalyzes the breakdown of glycogen. Figure 11.16 shows the complete pathway leading to the release of glucose 1-phosphate molecules from glycogen. Notice that as each molecule is activated, the response is amplified, a subject we'll return to shortly.

The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells. However, the Calvin cycle is preceded by incorporation of CO2 into organic compounds in the mesophyll cells. See the numbered steps in Figure 10.20, which are also described here:

The first step is carried out by an enzyme present only in mesophyll cells called PEP carboxylase. This enzyme adds CO2 to phosphoenolpyruvate (PEP), forming the four-carbon product oxaloacetate. PEP carboxylase has a much higher affinity for CO2 than does rubisco and no affinity for O2. Therefore, PEP carboxylase can fix carbon efficiently when rubisco cannot—that is, when it is hot and dry and stomata are partially closed, causing CO2 concentration in the leaf to be lower and O2 concentration to be relatively higher.

In alcohol fermentation (Figure 9.17a), pyruvate is converted to ethanol (ethyl alcohol) in two steps.

The first step releases carbon dioxide from the pyruvate, which is converted to the two-carbon compound acetaldehyde. In the second step, acetaldehyde is reduced by NADH to ethanol. This regenerates the supply of NAD+ needed for the continuation of glycolysis. Many bacteria carry out alcohol fermentation under anaerobic conditions. Yeast (a fungus), in addition to aerobic respiration, also carries out alcohol fermentation. For thousands of years, humans have used yeast in brewing, winemaking, and baking. The CO2 bubbles generated by baker's yeast during alcohol fermentation allow bread to rise. During lactic acid fermentation (Figure 9.17b), pyruvate is reduced directly by NADH to form lactate as an end product, regenerating NAD+ with no release of CO2. (Lactate is the ionized form of lactic acid.) Lactic acid fermentation by certain fungi and bacteria is used in the dairy industry to make cheese and yogurt.

Note

The fluorescence micrographs show dividing lung cells from a newt; this species has 22 chromosomes. Chromosomes appear blue, microtubules green, and intermediate filaments red. For simplicity, the drawings show only 6 chromosomes.

NAD1 as an electron shuttle.

The full name for NAD+ , nicotinamide adenine dinucleotide, describes its structure—the molecule consists of two nucleotides joined together at their phosphate groups (shown in yellow). (Nicotinamide is a nitrogenous base, although not one that is present in DNA or RNA; see Figure 5.23.) The enzymatic transfer of 2 electrons and 1 proton (H+ ) from an organic molecule in food to NAD+ reduces the NAD+ to NADH: Most of the electrons removed from food are transferred initially to NAD+ , forming NADH

However, other researchers, working with different cell types or cells from other species, have shown that chromosomes are "reeled in" by motor proteins at the spindle poles and that the microtubules depolymerize after they pass by these motor proteins at the poles.

The general consensus now is that both mechanisms are used and that their relative contributions vary among cell types

How linear electron flow during the light reactions generates ATP and NADPH.

The gold arrows trace the flow of light-driven electrons from water to NADPH. The black arrows trace the transfer of energy from pigment molecule to pigment molecule.

Another surge of epinephrine is needed to boost the cytosolic concentration of cAMP again. Subsequent research has revealed that epinephrine and many other signaling molecules lead to activation of adenylyl cyclase by G proteins and formation of cAMP (Figure 11.12).

The immediate effect of an elevation in cAMP levels is usually the activation of a serine/threonine kinase called protein kinase A. The activated protein kinase A then phosphorylates various other proteins, depending on the cell type. (The complete pathway for epinephrine's stimulation of glycogen breakdown is shown later, in Figure 11.16.)

Wiskott-Aldrich syndrome

The importance of the relay proteins that serve as points of branching or intersection in signaling pathways is highlighted by the problems arising when these proteins are defective or missing. For instance, in an inherited disorder called Wiskott-Aldrich syndrome (WAS), the absence of a single relay protein leads to such diverse effects as abnormal bleeding, eczema, and a predisposition to infections and leukemia. These symptoms are thought to arise primarily from the absence of the protein in cells of the immune system. By studying normal cells, scientists found that the WAS protein is located just beneath the immune cell surface. The protein interacts both with microfilaments of the cytoskeleton and with several different components of signaling pathways that relay information from the cell surface, including pathways regulating immune cell proliferation. This multifunctional relay protein is thus both a branch point and an important intersection point in a complex signal transduction network that controls immune cell behavior. When the WAS protein is absent, the cytoskeleton is not properly organized and signaling pathways are disrupted, leading to the WAS symptoms.

What happens when a potential target cell is exposed to a secreted signaling molecule? The ability of a cell to respond is determined by whether it has a specific receptor molecule that can bind to the signaling molecule.

The information conveyed by this binding, the signal, must then be changed into another form—transduced—inside the cell before the cell can respond. The remainder of the chapter discusses this process, primarily as it occurs in animal cells

An overview of pyruvate oxidation and the citric acid cycle.

The inputs and outputs per pyruvate molecule are shown. To calculate on a per-glucose basis, multiply by 2, because each glucose molecule is split during glycolysis into two pyruvate molecules

cytoplasm

The interior of either type of cell is called the cytoplasm; in eukaryotic cells, this term refers only to the region between the nucleus and the plasma membrane. Within the cytoplasm of a eukaryotic cell, suspended in cytosol, are a variety of organelles of specialized form and function.

Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the reaction can proceed. This contortion can be compared to the bending of a metal key ring when you pry it open to add a new key.

The key ring is highly unstable in its opened form but returns to a stable state once the key is threaded all the way onto the ring

The mitotic spindle at metaphase

The kinetochores of each chromosome's two sister chromatids face in opposite directions. Here, each kinetochore is attached to a cluster of kinetochore microtubules extending from the nearest centrosome. Nonkinetochore microtubules overlap at the metaphase plate (TEMs). Figure 12.8

The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously

The laws of thermodynamics that we've just discussed apply to the universe as a whole. As biologists, we want to understand the chemical reactions of life—for example, which reactions occur spontaneously and which ones require some input of energy from outside. But how can we know this without assessing the energy and entropy changes in the entire universe for each separate reaction?

The Two Stages of Photosynthesis: A Preview The equation for photosynthesis is a deceptively simple summary of a very complex process. Actually, photosynthesis is not a single process, but two processes, each with multiple steps. These two stages of photosynthesis are known as the light reactions (the photo part of photosynthesis) and the Calvin cycle (the synthesis part) (Figure 10.6)

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 (hydrogen ions, H+ ) 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+ (nicotinamide adenine dinucleotide phosphate), where they are temporarily stored.

(The electron acceptor NADP+ is first cousin to NAD+ , which functions as an electron carrier in cellular respiration; the two molecules differ only by the presence of an extra phosphate group in the NADP+ molecule.)

The light reactions use solar energy to reduce NADP+ to NADPH by adding a pair of electrons along with an H+ . The light reactions also generate ATP, using chemiosmosis to power the addition of a phosphate group to ADP, a process called photophosphorylation.

Exergonic reaction

The magnitude of ∆G for an exergonic reaction represents the maximum amount of work the reaction can perform.* The greater the decrease in free energy, the greater the amount of work that can be done. An exergonic reaction proceeds with a net release of free energy (Figure 8.6a). Because the chemical mixture loses free energy (G decreases), ∆G is negative for an exergonic reaction. Using ∆G as a standard for spontaneity, exergonic reactions are those that occur spontaneously. (Remember, the word spontaneous implies that it is energetically favorable, not that it will occur rapidly.)

proton pump

The main electrogenic pump of plants, fungi, and bacteria is a proton pump, which actively transports protons (hydrogen ions, H+ ) out of the cell. The pumping of H+ transfers positive charge from the cytoplasm to the extracellular solution (Figure 7.17)

Diffusion of one solute.

The membrane has pores large enough for molecules of dye to pass through. Random movement of dye molecules will cause some to pass through the pores; this will happen more often on the side with more dye molecules. The dye diffuses from where it is more concentrated to where it is less concentrated (called diffusing down a concentration gradient). This leads to a dynamic equilibrium: The solute molecules continue to cross the membrane, but at roughly equal rates in both directions.

Vescicles

The membranes of this system are related either through direct physical continuity or by the transfer of membrane segments as tiny vesicles (sacs made of membrane).

light microscope (LM)

The microscopes first used by Renaissance scientists, as well as the microscopes you are likely to use in the laboratory, are all light microscopes. In a light microscope (LM), visible light is passed through the specimen and then through glass lenses. The lenses refract (bend) the light in such a way that the image of the specimen is magnified as it is projected into the eye or into a camera (see Appendix D).

interface

The mitotic phase alternates with a much longer stage called interphase, which often accounts for about 90% of the cycle. Interphase can be divided into three phases: the G1 phase ("first gap"), the S phase ("synthesis"), and the G2 phase ("second gap").

Regulation of Cellular Respiration via Feedback Mechanisms: Basic principles of supply and demand regulate the metabolic economy. The cell does not waste energy making more of a particular substance than it needs. If there is a surplus of a certain amino acid, for example, the anabolic pathway that synthesizes that amino acid from an intermediate of the citric acid cycle is switched off.

The most common mechanism for this control is feedback inhibition: The end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway (see Figure 8.21). This prevents the needless diversion of key metabolic intermediates from uses that are more urgent.

Roles of the Cytoskeleton: Support and Motility

The most obvious function of the cytoskeleton is to give mechanical support to the cell and maintain its shape. This is especially important for animal cells, which lack walls. The remarkable strength and resilience of the cytoskeleton as a whole are based on its architecture. Like a dome tent, the cytoskeleton is stabilized by a balance between opposing forces exerted by its elements. And just as the skeleton of an animal helps fix the positions of other body parts, the cytoskeleton provides anchorage for many organelles and even cytosolic enzyme molecules. The cytoskeleton is more dynamic than an animal skeleton, however. It can be quickly dismantled in one part of the cell and reassembled in a new location, changing the shape of the cell.

What does the need for a large surface area enough to accomodate the volume help explain?

The need for a surface area large enough to accommodate the volume helps explain the microscopic size of most cells and the narrow, elongated shapes of others, such as nerve cells

During anaphase, MPF helps switch itself off by initiating a process that leads to the destruction of its own cyclin.

The noncyclin part of MPF, the Cdk, persists in the cell, inactive until it becomes part of MPF again by associating with new cyclin molecules synthesized during the S and G2 phases of the next round of the cycle.

nuclear envelope

The nuclear envelope is a double membrane. The two membranes, each a lipid bilayer with associated proteins, are separated by a space of 20-40 nm. The envelope is perforated by pore structures that are about 100 nm in diameter.

Nuclear pore:

The nuclear pore complex regulates molecular traffic in and out of the nucleus, which is bounded by a double membrane. Among the largest structures that pass through the pore are the ribosomal subunits, which are built in the nucleus.

nucleus

The nucleus contains most of the genes in the eukaryotic cell. (Some genes are located in mitochondria and chloroplasts.) It is usually the most conspicuous organelle (see the purple structure in the fluorescence micrograph), averaging about 5 µm in diameter. The nuclear envelope encloses the nucleus (Figure 6.9), separating its contents from the cytoplasm

Each light-harvesting complex consists of various pigment molecules (which may include chlorophyll a, chlorophyll b, and multiple carotenoids) bound to proteins.

The number and variety of pigment molecules enable a photosystem to harvest light over a larger surface area and a larger portion of the spectrum than could any single pigment molecule alone. Together, these light-harvesting complexes act as an antenna for the reaction-center complex.

Cellular Organization of the Genetic Material: A cell's DNA, its genetic information, is called its genome. Although a prokaryotic genome is often a single DNA molecule, eukaryotic genomes usually consist of a number of DNA molecules.

The overall length of DNA in a eukaryotic cell is enormous. A typical human cell, for example, has about 2 m of DNA—a length about 250,000 times greater than the cell's diameter. Before the cell can divide to form genetically identical daughter cells, all of this DNA must be copied, or replicated, and then the two copies must be separated so that each daughter cell ends up with a complete genome.

When a pigment molecule absorbs a photon, the energy is transferred from pigment molecule to pigment molecule within a lightharvesting complex, like a human "wave" at a sports arena, until it is passed to the pair of chlorophyll a molecules in the reaction-center complex.

The pair of chlorophyll a molecules in the reaction-center complex are special because their molecular environment—their location and the other molecules with which they are associated—enables them to use the energy from light not only to boost one of their electrons to a higher energy level, but also to transfer it to a different molecule—the primary electron acceptor, which is a molecule capable of accepting electrons and becoming reduced.

Receptor Tyrosine Kinases: Receptor tyrosine kinases (RTKs) belong to a major class of plasma membrane receptors characterized by having enzymatic activity. An RTK is a protein kinase—an enzyme that catalyzes the transfer of phosphate groups from ATP to another protein.

The part of the receptor protein extending into the cytoplasm functions more specifically as a tyrosine kinase, an enzyme that catalyzes the transfer of a phosphate group from ATP to the amino acid tyrosine of a substrate protein. Thus, RTKs are membrane receptors that attach phosphates to tyrosines.

The specificity of cell signaling.

The particular proteins a cell possesses determine what signaling molecules it responds to and the nature of the response. The four cells in these diagrams respond to the same signaling molecule (red) in different ways because each has a different set of proteins (purple and teal). Note, however, that the same kinds of molecules can participate in more than one pathway. Cell A. Pathway leads to a single response. Cell B. Pathway branches, leading to two responses. Cell C. Cross-talk occurs between two pathways. Cell D. Different receptor leads to a different response.

In response to a signal relayed by a signal transduction pathway, the cytosolic calcium level may rise, usually by a mechanism that releases Ca2+ from the cell's ER.

The pathways leading to calcium release involve two other second messengers, inositol trisphosphate (IP3) and diacylglycerol (DAG). These two messengers are produced by cleavage of a certain kind of phospholipid in the plasma membrane. Figure 11.14 shows the complete picture of how a signal causes IP3 to stimulate the release of calcium from the ER. Because IP3 acts before calcium in these pathways, calcium could be considered a "third messenger." However, scientists use the term second messenger for all small, nonprotein components of signal transduction pathways.

Peroxisomes: Oxidation

The peroxisome is a specialized metabolic compartment bounded by a single membrane (Figure 6.19). Peroxisomes contain enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen (O2), producing hydrogen peroxide (H2O2) as a by-product (from which the organelle derives its name). These reactions have many different functions. Some peroxisomes use oxygen to break fatty acids down into smaller molecules that are transported to mitochondria and used as fuel for cellular respiration. Peroxisomes in the liver detoxify alcohol and other harmful compounds by transferring hydrogen from the poisonous compounds to oxygen. The H2O2 formed by peroxisomes is itself toxic, but the organelle also contains an enzyme that converts H2O2 to water. This is an excellent example of how the cell's compartmental structure is crucial to its functions: The enzymes that produce H2O2 and those that dispose of this toxic compound are sequestered away from other cellular components that could be damaged

Because their hydrolysis releases energy, the phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds, but the term is misleading.

The phosphate bonds of ATP are not unusually strong bonds, as "high-energy" may imply; rather, the reactants (ATP and water) themselves have high energy relative to the energy of the products (ADP and ~P i). The release of energy during the hydrolysis of ATP comes from the chemical change of the system to a state of lower free energy, not from the phosphate bonds themselves.

centrifuge

The piece of equipment that is used for this task is the centrifuge, which spins test tubes holding mixtures of disrupted cells at a series of increasing speeds. At each speed, the resulting force causes a subset of the cell components to settle to the bottom of the tube, forming a pellet. At lower speeds, the pellet consists of larger components, and higher speeds result in a pellet with smaller components.

The plasma membrane.

The plasma membrane and the membranes of organelles consist of a double layer (bilayer) of phospholipids with various proteins attached to or embedded in it. The hydrophobic parts of phospholipids and membrane proteins are found in the interior of the membrane, while the hydrophilic parts are in contact with aqueous solutions on either side. Carbohydrate side chains may be attached to proteins or lipids on the outer surface of the plasma membrane.

selective permeability

The plasma membrane that surrounds the cell can be considered the edge of life, the boundary that separates a living cell from its surroundings and controls all inbound and outbound traffic. Like all biological membranes, the plasma membrane exhibits selective permeability; that is, it allows some substances to cross it more easily than others. The ability of the cell to discriminate in its chemical exchanges is fundamental to life, and it is the plasma membrane and its component molecules that make this selectivity possible.

arm

The portion of a chromatid to either side of the centromere is referred to as an arm of the chromatid. (An unduplicated chromosome has a single centromere, distinguished by the proteins that bind there, and two arms.)

Alternative fuels from algae

The power of sunlight can be tapped to generate a sustainable alternative to fossil fuels. Species of unicellular algae that are prolific producers of plant oils can be cultured in long, transparent tanks called photobioreactors, such as the one shown here at Arizona State University. A simple chemical process can yield "biodiesel," which can be mixed with gasoline or used alone to power vehicles

Rather than hydrolyzing ATP to pump protons against their concentration gradient, under the conditions of cellular respiration ATP synthase uses the energy of an existing ion gradient to power ATP synthesis.

The power source for ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane.

Photosynthesis converts light energy to the chemical energy of food: The remarkable ability of an organism to harness light energy and use it to drive the synthesis of organic compounds emerges from structural organization in the cell: Photosynthetic enzymes and other molecules are grouped together in a biological membrane, enabling the necessary series of chemical reactions to be carried out efficiently.

The process of photosynthesis most likely originated in a group of bacteria that had infolded regions of the plasma membrane containing clusters of such molecules. In existing photosynthetic bacteria, infolded photosynthetic membranes function similarly to the internal membranes of the chloroplast, a eukaryotic organelle. According to what has come to be known as the endosymbiont theory, the original chloroplast was a photosynthetic prokaryote that lived inside an ancestor of eukaryotic cells. (You learned about this theory in Concept 6.5, and it will be described more fully in Concept 25.3.) Chloroplasts are present in a variety of photosynthesizing organisms (see some examples in Figure 10.2), but here we focus on chloroplasts in plants.

lipid rafts

The proteins are not randomly distributed in the membrane, however. Groups of proteins are often associated in long-lasting, specialized patches, where they carry out common functions. Researchers have found specific lipids in these patches as well and have proposed naming them lipid rafts, but there is ongoing controversy about whether such structures exist in living cells or are an artifact of biochemical techniques. Like all models, the fluid mosaic model is continually being refined as new research reveals more about membrane structure

Living cells require transfusions of energy from outside sources to perform their many tasks—for example, assembling polymers, pumping substances across membranes, moving, and reproducing.

The puffin in Figure 9.1 obtains energy for its cells by feeding upon sand eels and other aquatic organisms; many other animals obtain energy by feeding on photosynthetic organisms such as plants and algae.

Energy profile of an exergonic reaction: The "molecules" are hypothetical, with A, B, C, and D representing portions of the molecules. Thermodynamically, this is an exergonic reaction, with a negative ∆G, and the reaction occurs spontaneously. However, the activation energy (EA) provides a barrier that determines the rate of the reaction

The reactants AB and CD must absorb enough energy from the surroundings to reach the unstable transition state, where bonds can break. After bonds have broken, new bonds form, releasing energy to the surroundings.

The overall decrease in free energy means that EA is repaid with dividends, as the formation of new bonds releases more energy than was invested in the breaking of old bonds

The reaction shown in Figure 8.13 is exergonic and occurs spontaneously (∆G 6 0). However, the activation energy provides a barrier that determines the rate of the reaction. The reactants must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur. For some reactions, EA is modest enough that even at room temperature there is sufficient thermal energy for many of the reactant molecules to reach the transition state in a short time.

A photosystem is composed of a reaction-center complex surrounded by several light-harvesting complexes

The reaction-center complex is an organized association of proteins holding a special pair of chlorophyll a molecules and a primary electron acceptor.

Chromosomes

The replication and distribution of so much DNA are manageable because the DNA molecules are packaged into structures called chromosomes (from the Greek chroma, color, and soma, body), so named because they take up certain dyes used in microscopy (Figure 12.3). Each eukaryotic chromosome consists of one very long, linear DNA molecule associated with many proteins (see Figure 6.9). The DNA molecule carries several hundred to a few thousand genes, the units of information that specify an organism's inherited traits.

scanning electron microscope

The scanning electron microscope (SEM) is especially useful for detailed study of the topography of a specimen (see Figure 6.3). The electron beam scans the surface of the sample, usually coated with a thin film of gold. The beam excites electrons on the surface, and these secondary electrons are detected by a device that translates the pattern of electrons into an electronic signal sent to a video screen. The result is an image of the specimen's surface that appears three-dimensional.

mitochondrial matrix

The second compartment, the mitochondrial matrix, is enclosed by the inner membrane. The matrix contains many different enzymes as well as the mitochondrial DNA and ribosomes. Enzymes in the matrix catalyze some of the steps of cellular respiration. Other proteins that function in respiration, including the enzyme that makes ATP, are built into the inner membrane. As highly folded surfaces, the cristae give the inner mitochondrial membrane a large surface area, thus enhancing the productivity of cellular respiration. This is another example of structure fitting function.

Cyclic AMP.

The second messenger cyclic AMP (cAMP) is made from ATP by adenylyl cyclase, an enzyme embedded in the plasma membrane. Note that the phosphate group in cAMP is attached to both the 5¿ and the 3¿ carbons; this cyclic arrangement is the basis for the molecule's name. Cyclic AMP is inactivated by phosphodiesterase, an enzyme that converts it to AMP.

Other enzymes of the smooth ER help detoxify drugs and poisons, especially in liver cells. Detoxification usually involves adding hydroxyl groups to drug molecules, making them more soluble and easier to flush from the body.

The sedative phenobarbital and other barbiturates are examples of drugs metabolized in this manner by smooth ER in liver cells. In fact, barbiturates, alcohol, and many other drugs induce the proliferation of smooth ER and its associated detoxification enzymes, thus increasing the rate of detoxification. This, in turn, increases tolerance to the drugs, meaning that higher doses are required to achieve a particular effect, such as sedation. Also, because some of the detoxification enzymes have relatively broad action, the proliferation of smooth ER in response to one drug can increase the need for higher dosages of other drugs as well. Barbiturate abuse, for example, can decrease the effectiveness of certain antibiotics and other useful drugs.

An enzyme is not a stiff structure locked into a given shape. In fact, recent work by biochemists has shown that enzymes (and other proteins) seem to "dance" between subtly different shapes in a dynamic equilibrium, with slight differences in free energy for each "pose."

The shape that best fits the substrate isn't necessarily the one with the lowest energy, but during the very short time the enzyme takes on this shape, its active site can bind to the substrate. The active site itself is also not a rigid receptacle for the substrate

movement of phospholipids

The sideways movement of phospholipids within the membrane is rapid. Adjacent phospholipids switch positions about 107 times per second, which means that a phospholipid can travel about 2 µm—the length of many bacterial cells—in 1 second. Proteins are much larger than lipids and move more slowly, but some membrane proteins do drift, as shown in a classic experiment described in Figure 7.4.

The smooth ER also stores calcium ion

The smooth ER also stores calcium ions. In muscle cells, for example, the smooth ER membrane pumps calcium ions from the cytosol into the ER lumen. When a muscle cell is stimulated by a nerve impulse, calcium ions rush back across the ER membrane into the cytosol and trigger contraction of the muscle cell. In other cell types, release of calcium ions from the smooth ER triggers different responses, such as secretion of vesicles carrying newly synthesized proteins.

Functions of Smooth ER

The smooth ER functions in diverse metabolic processes, which vary with cell type. Synthesizes lipids Metabolizes carbohydrates Detoxifies drugs and poisons Stores calcium ions

To treat this life-threatening condition, patients are given a solution to drink containing high concentrations of salt (NaCl) and glucose.

The solutes are taken up by sodiumglucose cotransporters on the surface of intestinal cells and passed through the cells into the blood. This simple treatment has lowered infant mortality worldwide.

Cholesterol

The steroid cholesterol, which is wedged between phospholipid molecules in the plasma membranes of animal cells, has different effects on membrane fluidity at different temperatures (Figure 7.5b). At relatively high temperatures— at 37°C, the body temperature of humans, for example— cholesterol makes the membrane less fluid by restraining phospholipid movement

In general, organic molecules that have an abundance of hydrogen are excellent fuels because their bonds are a source of "hilltop" electrons, whose energy may be released as these electrons "fall" down an energy gradient during their transfer to oxygen.

The summary equation for respiration indicates that hydrogen is transferred from glucose to oxygen. But the important point, not visible in the summary equation, is that the energy state of the electron changes as hydrogen (with its electron) is transferred to oxygen.

A structural role of microfilaments.

The surface area of this nutrient-absorbing intestinal cell is increased by its many microvilli (singular, microvillus), cellular extensions reinforced by bundles of microfilaments. These actin filaments are anchored to a network of intermediate filaments (TEM).

Temperature and pH are environmental factors important in the activity of an enzyme. Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly. Above that temperature, however, the speed of the enzymatic reaction drops sharply

The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures. Each enzyme has an optimal temperature at which its reaction rate is greatest. Without denaturing the enzyme, this temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules. Most human enzymes have optimal temperatures of about 35-40°C (close to human body temperature). The thermophilic bacteria that live in hot springs contain enzymes with optimal temperatures of 70°C or higher (Figure 8.17a).

Contrast

The third parameter, contrast, is the difference in brightness between the light and dark areas of an image. Methods for enhancing contrast include staining or labeling cell components to stand out visually.

An organism's metabolism transforms matter and energy, subject to the laws of thermodynamics

The totality of an organism's chemical reactions is called metabolism (from the Greek metabole, change). Metabolism is an emergent property of life that arises from orderly interactions between molecules

transmission electron microscope

The transmission electron microscope (TEM) is used to study the internal structure of cells (see Figure 6.3). The TEM aims an electron beam through a very thin section of the specimen, much as a light microscope aims light through a sample on a slide. For the TEM, the specimen has been stained with atoms of heavy metals, which attach to certain cellular structures, thus enhancing the electron density of some parts of the cell more than others. The electrons passing through the specimen are scattered more in the denser regions, so fewer are transmitted. The image displays the pattern of transmitted electrons. Instead of using glass lenses, both the SEM and TEM use electromagnets as lenses to bend the paths of the electrons, ultimately focusing the image onto a monitor for viewing

Centromere

The two chromatids, each containing an identical DNA molecule, are typically attached all along their lengths by protein complexes called cohesins; this attachment is known as sister chromatid cohesion. Each sister chromatid has a centromere, a region made up of repetitive sequences in the chromosomal DNA where the chromatid is attached most closely to its sister chromatid. This attachment is mediated by proteins that recognize and bind to the centromeric DNA; other bound proteins condense the DNA, giving the duplicated chromosome a narrow "waist."

In some plant species, alternate modes of carbon fixation have evolved that minimize photorespiration and optimize the Calvin cycle—even in hot, arid climates.

The two most important of these photosynthetic adaptations are C4 photosynthesis and crassulacean acid metabolism (CAM).

Second messengers participate in pathways that are initiated by both G protein-coupled receptors and receptor tyrosine kinases.

The two most widely used second messengers are cyclic AMP and calcium ions, Ca2+ . A large variety of relay proteins are sensitive to changes in the cytosolic concentration of one or the other of these second messengers.

As Figure 10.6 indicates, the thylakoids of the chloroplast are the sites of the light reactions, while the Calvin cycle occurs in the stroma. On the outside of the thylakoids, molecules of NADP+ and ADP pick up electrons and phosphate, respectively, and NADPH and ATP are then released to the stroma, where they play crucial roles in the Calvin cycle.

The two stages of photosynthesis are treated in this figure as metabolic modules that take in ingredients and crank out products. In the next two sections, we'll look more closely at how the two stages work, beginning with the light reactions.

The contractile vacuole of Paramecium

The vacuole collects fluid from canals in the cytoplasm. When full, the vacuole and canals contract, expelling fluid from the cell (LM).

A consequence of the loss of usable energy as heat to the surroundings is that each energy transfer or transformation makes the universe more disordered. We are all familiar with the word "disorder" in the sense of a messy room or a rundown building

The word "disorder" as used by scientists, however, has a specific molecular definition related to how dispersed the energy is in a system, and how many different energy levels are present. For simplicity, we use "disorder" in the following discussion because our common understanding (the messy room) is a good analogy for molecular disorder

Most of the remaining electron carriers between ubiquinone and oxygen are proteins called cytochromes.

Their prosthetic group, called a heme group, has an iron atom that accepts and donates electrons. (The heme group in a cytochrome is similar to the heme group in hemoglobin, the protein of red blood cells, except that the iron in hemoglobin carries oxygen, not electrons.) The electron transport chain has several types of cytochromes, each named "cyt" with a letter and number to distinguish it as a different protein with a slightly different electron-carrying heme group. The last cytochrome of the chain, Cyt a3, passes its electrons to oxygen, which is very electronegative. Each oxygen atom also picks up a pair of hydrogen ions (protons) from the aqueous solution, neutralizing the -2 charge of the added electrons and forming water.

Cell-surface transmembrane receptors play crucial roles in the biological systems of animals. The largest family of human cellsurface receptors is the G protein-coupled receptors (GPCRs).

There are more than 800 GPCRs; an example is shown in Figure 11.7. Another example is the co-receptor hijacked by HIV to enter immune cells (see Figure 7.8); this GPCR is the target of the drug maraviroc, which has shown some success at treating AIDS.

Smooth & Rough ER

There are two distinct, though connected, regions of the ER that differ in structure and function: smooth ER and rough ER. Smooth ER is so named because its outer surface lacks ribosomes. Rough ER is studded with ribosomes on the outer surface of the membrane and thus appears rough through the electron microscope. As already mentioned, ribosomes are also attached to the cytoplasmic side of the nuclear envelope's outer membrane, which is continuous with rough ER.

Evolution of Cell Signaling: One topic cells communicate about is sex. Cells of the unicellular yeast Saccharomyces cerevisiae—which are used to make bread, wine, and beer—identify their sexual mates by chemical signaling.

There are two sexes, or mating types, called a and 훂 (Figure 11.2). Each type secretes a specific factor that binds only to receptors on the other type of cell. When exposed to each other's mating factors, a pair of cells of opposite type change shape, grow toward each other, and fuse (mate). The new a/ cell contains all the genes of both original cells, a combination of genetic resources that provides advantages to the cell's descendants, which arise by subsequent cell divisions.

nuclear matrix

There is also much evidence for a nuclear matrix, a framework of protein fibers extending throughout the nuclear interior. The nuclear lamina and matrix may help organize the genetic material so it functions efficiently.

Another term that describes a state of maximum stability is equilibrium, which you learned about in Concept 2.4 in connection with chemical reactions.

There is an important relationship between free energy and equilibrium, including chemical equilibrium. Recall that most chemical reactions are reversible and proceed to a point at which the forward and backward reactions occur at the same rate. The reaction is then said to be at chemical equilibrium, and there is no further net change in the relative concentration of products and reactants.

In eukaryotes, pyruvate enters the mitochondrion and is oxidized to a compound called acetyl CoA, which enters the citric acid cycle.

There, the breakdown of glucose to carbon dioxide is completed. (In prokaryotes, these processes take place in the cytosol.) Thus, the carbon dioxide produced by respiration represents fragments of oxidized organic molecules.

Based on experimental data, however, most biochemists now agree that the most accurate number is 4 H+

Therefore, a single molecule of NADH generates enough proton-motive force for the synthesis of 2.5 ATP. The citric acid cycle also supplies electrons to the electron transport chain via FADH2, but since its electrons enter later in the chain, each molecule of this electron carrier is responsible for transport of only enough H+ for the synthesis of 1.5 ATP. These numbers also take into account the slight energetic cost of moving the ATP formed in the mitochondrion out into the cytosol, where it will be used.

Each "downhill" carrier is more electronegative than, and thus capable of oxidizing, its "uphill" neighbor, with oxygen at the bottom of the chain

Therefore, the electrons transferred from glucose to NAD+ , which is thus reduced to NADH, fall down an energy gradient in the electron transport chain to a far more stable location in the electronegative oxygen atom

Cofactors: Many enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins.

These adjuncts, called cofactors, may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate. The cofactors of some enzymes are inorganic, such as the metal atoms zinc, iron, and copper in ionic form. If the cofactor is an organic molecule, it is referred to, more specifically, as a coenzyme. Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made.

Genetic research on C. elegans initially revealed two key apoptosis genes, called ced-3 and ced-4 (ced stands for "cell death"), which encode proteins essential for apoptosis. The proteins are called Ced-3 and Ced-4, respectively.

These and most other proteins involved in apoptosis are continually present in cells, but in inactive form; thus, regulation in this case occurs at the level of protein activity rather than through gene activity and protein synthesis.

certain membrane proteins may attach to materials outside the cell.

These attachments combine to give animal cells a stronger framework than the plasma membrane alone could provide. A single cell may have cell-surface membrane proteins that carry out several different functions, such as transport through the cell membrane, enzymatic activity, or attaching a cell to either a neighboring cell or the extracellular matrix.

On a hot, dry day, most plants close their stomata, a response that conserves water but also reduces CO2 levels. With stomata even partially closed, CO2 concentrations begin to decrease in the air spaces within the leaf, and the concentration of O2 released from the light reactions begins to increase.

These conditions within the leaf favor an apparently wasteful process called photorespiration.

The Principle of Redox: In many chemical reactions, there is a transfer of one or more electrons (e- ) from one reactant to another.

These electron transfers are called oxidation-reduction reactions, or redox reactions for short

Other gated channels open or close when a specific substance other than the one to be transported binds to the channel

These gated channels are also important in the functioning of the nervous system, as you'll learn in Concepts 48.2 and 48.3.

Are these membrane bound organelles found in prokaryotic cells?

These membrane bounded structures are absent in almost all prokaryotic cells, another distinction between prokaryotic and eukaryotic cells. In spite of the absence of organelles, though, the prokaryotic cytoplasm is not a formless soup

A more specialized type of local signaling called synaptic signaling occurs in the animal nervous system (Figure 11.5b). An electrical signal along a nerve cell triggers the secretion of neurotransmitter molecules.

These molecules act as chemical signals, diffusing across the synapse—the narrow space between the nerve cell and its target cell—triggering a response in the target cell.

Photoautotrophs

These organisms use light energy to drive the synthesis of organic molecules from carbon dioxide and (in most cases) water. They feed themselves and the entire living world. On land, (a) plants are the predominant producers of food. In aquatic environments, photoautotrophs include unicellular and (b) multicellular algae, such as this kelp; (c) some non-algal unicellular eukaryotes, such as Euglena; (d) the prokaryotes called cyanobacteria; and (e) other photosynthetic prokaryotes, such as these purple sulfur bacteria, which produce sulfur (the yellow globules within the cells) (c-e, LMs). (a) Plants (b) Multicellular alga (c) Unicellular eukaryotes (d) Cyanobacteria (e) Purple sulfur bacteria

The impala in Figure 11.1 flees for its life, racing to escape the predatory cheetah nipping at its heels. The impala is breathing rapidly, its heart pounding and its legs pumping furiously.

These physiological functions are all part of the impala's "fightor-flight" response, driven by hormones released from its adrenal glands at times of stress—in this case, upon sensing the cheetah

CAM Plants: A second photosynthetic adaptation to arid conditions has evolved in many succulent (water-storing) plants, numerous cacti, pineapples, and representatives of several other plant families.

These plants open their stomata during the night and close them during the day, just the reverse of how other plants behave. Closing stomata during the day helps desert plants conserve water, but it also prevents CO2 from entering the leaves. During the night, when their stomata are open, these plants take up CO2 and incorporate it into a variety of organic acids. This mode of carbon fixation is called crassulacean acid metabolism, or CAM, after the plant family Crassulaceae, the succulents in which the process was first discovered.

Endocytosis and exocytosis also provide mechanisms for rejuvenating or remodeling the plasma membrane.

These processes occur continually in most eukaryotic cells, yet the amount of plasma membrane in a nongrowing cell remains fairly constant. The addition of membrane by one process appears to offset the loss of membrane by the other. Energy and cellular work have figured prominently in our study of membranes. In the next three chapters, you will learn more about how cells acquire chemical energy to do the work of life.

Stop and Go Signs: Internal and External Signals at the Checkpoints: Animal cells generally have built-in stop signals that halt the cell cycle at checkpoints until overridden by go-ahead signals. (The signals are transmitted within the cell by the kinds of signal transduction pathways discussed in Chapter 11.) Many signals registered at checkpoints come from cellular surveillance mechanisms inside the cell.

These signals report whether crucial cellular processes that should have occurred by that point have in fact been completed correctly and thus whether or not the cell cycle should proceed. Checkpoints also register signals from outside the cell.

Interestingly, carotenoids similar to the photoprotective ones in chloroplasts have a photoprotective role in the human eye. (Carrots, known for aiding night vision, are rich in carotenoids.) These and related molecules are, of course, found naturally in many vegetables and fruits.

They are also often advertised in health food products as "phytochemicals" (from the Greek phyton, plant), some of which have antioxidant properties. Plants can synthesize all the antioxidants they require, but humans and other animals must obtain some of them from their diets.

How peroxisomes are related to other organelles is still an open question.

They grow larger by incorporating proteins made in the cytosol and ER, as well as lipids made in the ER and within the peroxisome itself. Peroxisomes may increase in number by splitting in two when they reach a certain size, sparking the suggestion of an endosymbiotic evolutionary origin, but others argue against this scenario. Discussion of this issue is ongoing.

Loss of Cell Cycle Controls in Cancer Cells: Cancer cells do not heed the normal signals that regulate the cell cycle. In culture, they do not stop dividing when growth factors are depleted. A logical hypothesis is that cancer cells do not need growth factors in their culture medium to grow and divide.

They may make a required growth factor themselves, or they may have an abnormality in the signaling pathway that conveys the growth factor's signal to the cell cycle control system even in the absence of that factor. Another possibility is an abnormal cell cycle control system. In these scenarios, the underlying basis of the abnormality is almost always a change in one or more genes (for example, a mutation) that alters the function of their protein products, resulting in faulty cell cycle control.

However, unlike normal cellular respiration, photorespiration uses ATP rather than generating it. And unlike photosynthesis, photorespiration produces no sugar. In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle and releasing CO2 that would otherwise be fixed.

This CO2 can eventually be fixed if it is still in the leaf once the CO2 concentration builds up to a high enough level. In the meantime, though, the process is energetically costly, much like a hamster running on its wheel.

As in other types of cellular work, ATP hydrolysis supplies the energy for most active transport. One way ATP can power active transport is when its terminal phosphate group is transferred directly to the transport protein.

This can induce the protein to change its shape in a manner that translocates a solute bound to the protein across the membrane.

Now let's consider the original source of the organic food molecules that provided the necessary chemical energy for these divers to climb the steps.

This chemical energy was itself derived from light energy absorbed by plants during photosynthesis. Organisms are energy transformers.

The hydrogen atoms are not transferred directly to oxygen, but instead are usually passed first to an electron carrier, a coenzyme called nicotinamide adenine dinucleotide, a derivative of the vitamin niacin

This coenzyme is well suited as an electron carrier because it can cycle easily between its oxidized form, NAD1, and its reduced form, NADH.As an electron acceptor, NAD+ functions as an oxidizing agent during respiration.

What does this compartmental organization enables the chloroplast to convert light energy to chemical energy?

This compartmental organization enables the chloroplast to convert light energy to chemical energy during photosynthesis. (You will learn more about photosynthesis in Chapter 10.)

Once absorption of a photon raises an electron to an excited state, the electron cannot stay there long. The excited state, like all high-energy states, is unstable. Generally, when isolated pigment molecules absorb light, their excited electrons drop back down to the ground-state orbital in a billionth of a second, releasing their excess energy as heat.

This conversion of light energy to heat is what makes the top of an automobile so hot on a sunny day. (White cars are coolest because their paint reflects all wavelengths of visible light.) In isolation, some pigments, including chlorophyll, emit light as well as heat after absorbing photons. As excited electrons fall back to the ground state, photons are given off, an afterglow called fluorescence.

Nuclear responses to a signal: the activation of a specific gene by a growth factor

This diagram shows a typical signaling pathway that leads to regulation of gene activity in the cell nucleus. The initial signaling molecule, in this case a growth factor, triggers a phosphorylation cascade, as in Figure 11.10. (The ATP molecules and phosphate groups are not shown.) Once phosphorylated, the last kinase in the sequence enters the nucleus and activates a transcription factor, which stimulates transcription of a specific gene (or genes). The resulting mRNAs then direct the synthesis of a particular protein.

A review of photosynthesis.

This diagram shows the main reactants and products of photosynthesis as they move through the tissues of a tree (left) and a chloroplast (right).

The Calvin cycle.

This diagram summarizes three turns of the cycle, tracking carbon atoms (gray balls). The three phases of the cycle correspond to the phases discussed in the text. For every three molecules of CO2 that enter the cycle, the net output is one molecule of glyceraldehyde 3-phosphate (G3P), a three-carbon sugar. The light reactions sustain the Calvin cycle by regenerating the required ATP and NADPH. View figure 10.19

Cyclic AMP As discussed previously, Earl Sutherland established that, without passing through the plasma membrane, epinephrine somehow causes glycogen breakdown within cells.

This discovery prompted him to search for a second messenger that transmits the signal from the plasma membrane to the metabolic machinery in the cytoplasm.

Electrons lose very little of their potential energy when they are transferred from glucose to NAD+ . Each NADH molecule formed during respiration represents stored energy.

This energy can be tapped to make ATP when the electrons complete their "fall" in a series of steps down an energy gradient from NADH to oxygen.

The distance between the crests of electromagnetic waves is called the wavelength. Wavelengths range from less than a nanometer (for gamma rays) to more than a kilometer (for radio waves).

This entire range of radiation is known as the electromagnetic spectrum (Figure 10.7). The segment most important to life is the narrow band from about 380 nm to 750 nm in wavelength. This radiation is known as visible light because it can be detected as various colors by the human eye.

The genetically engineered cells were thus able to mate with one another but not with cells of the parent population.

This evidence supports a model in which changes in the genes encoding receptor and mating factor proteins can lead to the establishment of new species.

The Splitting of Water: One of the first clues to the mechanism of photosynthesis came from the discovery that the O2 given off by plants is derived from H2O and not from CO2. The chloroplast splits water into hydrogen and oxygen. Before this discovery,the prevailing hypothesis was that photosynthesis split carbon dioxide (CO2 --> C + O2) and then added water to the carbon (C + H2O --> [CH2O]).

This hypothesis predicted that the O2 released during photosynthesis came from CO2. This idea was challenged in the 1930s by C. B. van Niel, of Stanford University. Van Niel was investigating photosynthesis in bacteria that make their carbohydrate from CO2 but do not release O2. He concluded that, at least in these bacteria, CO2 is not split into carbon and oxygen. One group of bacteria used hydrogen sulfide (H2S) rather than water for photosynthesis, forming yellow globules of sulfur as a waste product (these globules are visible in Figure 10.2e).

The Calvin cycle is named for Melvin Calvin, who, along with his colleagues James Bassham and Andrew Benson, began to elucidate its steps in the late 1940s. The cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplast.

This initial incorporation of carbon into organic compounds is known as carbon fixation. The Calvin cycle then reduces the fixed carbon to carbohydrate by the addition of electrons. The reducing power is provided by NADPH, which acquired its cargo of electrons in the light reactions. To convert CO2 to carbohydrate, the Calvin cycle also requires chemical energy in the form of ATP, which is also generated by the light reactions. 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.

endosymbiont theory

This is a widely accepted theory, which we will discuss in more detail in Concept 25.3. This theory is consistent with many structural features of mitochondria and chloroplasts. First, rather than being bounded by a single membrane like organelles of the endomembrane system, mitochondria and typical chloroplasts have two membranes surrounding them. (Chloroplasts also have an internal system of membranous sacs.) There is evidence that the ancestral engulfed prokaryotes had two outer membranes, which became the double membranes of mitochondria and chloroplasts.

An illuminated solution of chlorophyll isolated from chloroplasts will fluoresce in the red part of the spectrum and also give off heat (Figure 10.12).

This is best seen by illuminating with ultraviolet light, which chlorophyll can also absorb (see Figures 10.7 and 10.10a). Viewed under visible light, the fluorescence would be difficult to see against the green of the solution.

Let's transfer the cell to a solution that is hypertonic to the cell (hyper means "more," in this case referring to nonpenetrating solutes). The cell will lose water, shrivel, and probably die.

This is why an increase in the salinity (saltiness) of a lake can kill the animals there; if the lake water becomes hypertonic to the animals' cells, they might shrivel and die

The transport proteins that move solutes against their concentration gradients are all carrier proteins rather than channel proteins.

This makes sense because when channel proteins are open, they merely allow solutes to diffuse down their concentration gradients rather than picking them up and transporting them against their gradients

Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors and activators. It is inhibited by ATP and stimulated by AMP (adenosine monophosphate), which the cell derives from ADP. As ATP accumulates, inhibition of the enzyme slows down glycolysis. The enzyme becomes active again as cellular work converts ATP to ADP (and AMP) faster than ATP is being regenerated. Phosphofructokinase is also sensitive to citrate, the first product of the citric acid cycle. If citrate accumulates in mitochondria, some of it passes into the cytosol and inhibits phosphofructokinase.

This mechanism helps synchronize the rates of glycolysis and the citric acid cycle. As citrate accumulates, glycolysis slows down, and the supply of pyruvate and thus acetyl groups to the citric acid cycle decreases. If citrate consumption increases, either because of a demand for more ATP or because anabolic pathways are draining off intermediates of the citric acid cycle, glycolysis accelerates and meets the demand. Metabolic balance is augmented by the control of enzymes that catalyze other key steps of glycolysis and the citric acid cycle. Cells are thrifty, expedient, and responsive in their metabolism.

The energy released at each step of the chain is stored in a form the mitochondrion (or prokaryotic cell) can use to make ATP from ADP.

This mode of ATP synthesis is called oxidative phosphorylation because it is powered by the redox reactions of the electron transport chain.

Electrons acquired from glucose by NAD+ during glycolysis and the citric acid cycle are transferred from NADH to the first molecule of the electron transport chain in complex I.

This molecule is a flavoprotein, so named because it has a prosthetic group called flavin mononucleotide (FMN). In the next redox reaction, the flavoprotein returns to its oxidized form as it passes electrons to an iron-sulfur protein (Fe # S in complex I), one of a family of proteins with both iron and sulfur tightly bound.

Using the techniques of modern DNA technology to tag the origins of replication with molecules that glow green in fluorescence microscopy (see Figure 6.3), researchers have directly observed the movement of bacterial chromosomes.

This movement is reminiscent of the poleward movements of the centromere regions of eukaryotic chromosomes during anaphase of mitosis, but bacteria don't have visible mitotic spindles or even microtubules. In most bacterial species studied, the two origins of replication end up at opposite ends of the cell or in some other very specific location, possibly anchored there by one or more proteins.

Human muscle cells make ATP by lactic acid fermentation when oxygen is scarce.

This occurs during strenuous exercise, when sugar catabolism for ATP production outpaces the muscle's supply of oxygen from the blood. Under these conditions, the cells switch from aerobic respiration to fermentation. The lactate that accumulates was previously thought to cause the muscle fatigue and pain that occurs a day or so after intense exercise.

How does the binding of a mating factor by the yeast cell surface receptor initiate a signal that brings about the cellular response of mating?

This occurs in a series of steps called a signal transduction pathway. Many such pathways exist in both yeast and animal cells. In fact, the molecular details of signal transduction in yeasts and mammals are strikingly similar, even though it's been over a billion years since they shared a common ancestor. This suggests that early versions of cellsignaling mechanisms evolved hundreds of millions of years before the first multicellular creatures appeared on Earth.

Like most systems, a living cell is not in equilibrium. The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life

This principle is illustrated by the open (and more realistic) hydroelectric system in Figure 8.8a. However, unlike this simple system in which water flowing downhill turns a single turbine, a catabolic pathway in a cell releases free energy in a series of reactions. An example is cellular respiration, illustrated by analogy in Figure 8.8b. Some of the reversible reactions of respiration are constantly "pulled" in one direction—that is, they are kept out of equilibrium. The key to maintaining this lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step; finally, waste products are expelled from the cell. The overall sequence of reactions is kept going by the huge free-energy difference between glucose and oxygen at the top of the energy "hill" and carbon dioxide and water at the "downhill" end

As the substrate enters the active site, the enzyme changes shape slightly due to interactions between the substrate's chemical groups and chemical groups on the side chains of the amino acids that form the active site.

This shape change makes the active site fit even more snugly around the substrate (Figure 8.15b). The tightening of the binding after initial contact—called induced fit—is like a clasping handshake. Induced fit brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.

The Regeneration of ATP: An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP (Figure 8.12). The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell.

This shuttling of inorganic phosphate and energy is called the ATP cycle, and it couples the cell's energy-yielding (exergonic) processes to the energyconsuming (endergonic) ones. The ATP cycle proceeds at an astonishing pace. For example, a working muscle cell recycles its entire pool of ATP in less than a minute.

Toxins and poisons are often irreversible enzyme inhibitors. An example is sarin, a nerve gas. In the mid-1990s, terrorists released sarin in the Tokyo subway, killing several people and injuring many others.

This small molecule binds covalently to the R group on the amino acid serine, which is found in the active site of acetylcholinesterase, an enzyme important in the nervous system. Other examples include the pesticides DDT and parathion, inhibitors of key enzymes in the nervous system. Finally, many antibiotics are inhibitors of specific enzymes in bacteria. For instance, penicillin blocks the active site of an enzyme that many bacteria use to make cell walls.

Surface of nuclear envelope (TEM).

This specimen was prepared by a technique known as freeze-fracture, which cuts from the outer membrane to the inner membrane, revealing both.

Oxidation of Pyruvate to Acetyl CoA: Upon entering the mitochondrion via active transport, pyruvate is first converted to a compound called acetyl coenzyme A, or acetyl CoA (Figure 9.10).

This step, linking glycolysis and the citric acid cycle, is carried out by a multienzyme complex that catalyzes three reactions: 1 )Pyruvate's carboxyl group (—COO- ), already somewhat oxidized and thus carrying little chemical energy, is now fully oxidized and given off as a molecule of CO2. This is the first step in which CO2 is released during respiration. 2) Next, the remaining two-carbon fragment is oxidized and the electrons transferred to NAD+ , storing energy in the form of NADH 3) Finally, coenzyme A (CoA), a sulfur-containing compound derived from a B vitamin, is attached via its sulfur atom to the two-carbon intermediate, forming acetyl CoA. Acetyl CoA has a high potential energy, which is used to transfer the acetyl group to a molecule in the citric acid cycle, a reaction that is therefore highly exergonic.

The sodium-potassium pump: a specific case of active transport.

This transport system pumps ions against steep concentration gradients: Sodium ion concentration ([Na+ ]) is high outside the cell and low inside, while potassium ion concentration ([K+ ]) is low outside the cell and high inside. The pump oscillates between two shapes in a cycle that moves three Na+ out of the cell (steps 1 - 3 ) for every two K+ pumped into the cell (steps 4 - 6 ). The two shapes have different binding affinities for Na+ and K+ . ATP hydrolysis powers the shape change by transferring a phosphate group to the transport protein (phosphorylating the protein). 1) Cytoplasmic Na+ binds to the sodium-potassium pump. The affinity for Na+ is high when the protein has this shape. 2) Na+ binding stimulates phosphorylation by ATP 3) Phosphorylation leads to a change in protein shape, reducing its affinity for Na+, which is released outside. 4) The new shape has a high affinity for K+, which binds on the extracellular side and triggers release of the phosphate group. 5) Loss of the phosphate group restores the protein's original shape, which has a lower affinity for K+. 6) K+ is released; affinity for Na+ is high again, and the cycle repeats.

basal body

Though different in length, number per cell, and beating pattern, motile cilia and flagella share a common structure. Each motile cilium or flagellum has a group of microtubules sheathed in an extension of the plasma membrane (Figure 6.24a). Nine doublets of microtubules are arranged in a ring with two single microtubules in its center (Figure 6.24b). This arrangement, referred to as the "9 + 2" pattern, is found in nearly all eukaryotic flagella and motile cilia. (Nonmotile primary cilia have a "9 + 0" pattern, lacking the central pair of microtubules.) The microtubule assembly of a cilium or flagellum is anchored in the cell by a basal body, which is structurally very similar to a centriole, with microtubule triplets in a "9 + 0" pattern (Figure 6.24c). In fact, in many animals (including humans), the basal body of the fertilizing sperm's flagellum enters the egg and becomes a centriole

Molecular basis of apoptosis in C. elegans

Three proteins, Ced-3, Ced-4, and Ced-9, are critical to apoptosis and its regulation in the nematode. Apoptosis is more complicated in mammals but involves proteins similar to those in C. elegans (a) No death signal. As long as Ced-9, located in the outer mitochondrial membrane, is active, apoptosis is inhibited, and the cell remains alive. (b) Death signal. When a cell receives a death signal, Ced-9 is inactivated, relieving its inhibition of Ced-4. Active Ced-4 activates Ced-3, a protease, which triggers a cascade of reactions leading to the activation of nucleases and other proteases. The action of these enzymes causes the changes seen in apoptotic cells and eventually leads to cell death.

. The subunits of an allosteric enzyme fit together in such a way that a shape change in one subunit is transmitted to all others.

Through this interaction of subunits, a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits.

The structure and hydrolysis of adenosine triphosphate (ATP).

Throughout this book, the chemical structure of the triphosphate group seen in (a) will be represented by the three joined yellow circles shown in (b). (a) The structure of ATP. In the cell, most hydroxyl groups of phosphates are ionized (—O- ). (b) The hydrolysis of ATP. The reaction of ATP and water yields ADP and inorganic phosphate ( ) and releases energy.

This chapter has introduced you to many of the general mechanisms of cell communication, such as ligand binding, protein-protein interactions and shape changes, cascades of interactions, and protein phosphorylation.

Throughout your study of biology, you will encounter numerous examples of cell signaling

. Technically, the term cellular respiration includes both aerobic and anaerobic processes. However, it originated as a synonym for aerobic respiration because of the relationship of that process to organismal respiration, in which an animal breathes in oxygen

Thus, cellular respiration is often used to refer to the aerobic process, a practice we follow in most of this chapter

A Comparison of Chemiosmosis in Chloroplasts and Mitochondria: Chloroplasts and mitochondria generate ATP by the same basic mechanism: chemiosmosis (see Figure 9.15). An electron transport chain pumps protons (H+ ) across a membrane as electrons are passed through a series of carriers that are progressively more electronegative

Thus, electron transport chains transform redox energy to a proton-motive force, potential energy stored in the form of an H+ gradient across a membrane. An ATP synthase complex in the same membrane couples the diffusion of hydrogen ions down their gradient to the phosphorylation of ADP, forming ATP.

The H+ has a tendency to move back across the membrane, diffusing down its gradient. And the ATP synthases are the only sites that provide a route through the membrane for H+ . As we described previously, the passage of H+ through ATP synthase uses the exergonic flow of H+ to drive the phosphorylation of ADP.

Thus, the energy stored in an H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis

Given the many important functions of cell-surface receptors, it is not surprising that their malfunctions are associated with many human diseases, including cancer, heart disease, and asthma.

To better understand and treat these conditions, a major focus of both university research teams and the pharmaceutical industry has been to analyze the structure of these receptors.

Water Balance of Cells Without Cell Walls

To explain the behavior of a cell in a solution, we must consider both solute concentration and membrane permeability. Both factors are taken into account in the concept of tonicity, the ability of a surrounding solution to cause a cell to gain or lose water.

The Need for Energy in Active Transport

To pump a solute across a membrane against its gradient requires work; the cell must expend energy. Therefore, this type of membrane traffic is called active transport

To keep working, the cell must regenerate its supply of ATP from ADP and ~P i (see Figure 8.12).

To understand how cellular respiration accomplishes this, let's examine the fundamental chemical processes known as oxidation and reduction.

About 2% of our own genes are thought to code for protein kinases, a significant percentage. A single cell may have hundreds of different kinds, each specific for a different substrate protein.

Together, protein kinases probably regulate the activity of a large proportion of the thousands of proteins in a cell.

The key to coupling exergonic and endergonic reactions is the formation of this phosphorylated intermediate, which is more reactive (less stable, with more free energy) than the original unphosphorylated molecule (Figure 8.10).

Transport and mechanical work in the cell are also nearly always powered by the hydrolysis of ATP. In these cases, ATP hydrolysis leads to a change in a protein's shape and often its ability to bind another molecule. Sometimes this occurs via a phosphorylated intermediate, as seen for the transport protein in Figure 8.11a

Osmosis

Two sugar solutions of different concentrations are separated by a membrane that the solvent (water) can pass through but the solute (sugar) cannot. Water molecules move randomly and may cross in either direction, but overall, water diffuses from the solution with less concentrated solute to that with more concentrated solute. This passive transport of water, or osmosis, makes the sugar concentrations on both sides more nearly equal. (The concentrations are prevented from being exactly equal due to the effect of water pressure on the higher side, which is not discussed here, for simplicity.)

The iron-sulfur protein then passes the electrons to a compound called ubiquinone (Q in Figure 9.13). This electron carrier is a small hydrophobic molecule, the only member of the electron transport chain that is not a protein.

Ubiquinone is individually mobile within the membrane rather than residing in a particular complex. (Another name for ubiquinone is coenzyme Q, or CoQ; you may have seen it sold as a nutritional supplement.)

Other organisms, including yeasts and many bacteria, can make enough ATP to survive using either fermentation or respiration. Such species are called facultative anaerobes. On the cellular level, our muscle cells behave as facultative anaerobes. In such cells, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes (Figure 9.18).

Under aerobic conditions, pyruvate can be converted to acetyl CoA, and oxidation continues in the citric acid cycle via aerobic respiration. Under anaerobic conditions, lactic acid fermentation occurs: Pyruvate is diverted from the citric acid cycle, serving instead as an electron acceptor to recycle NAD+ . To make the same amount of ATP, a facultative anaerobe has to consume sugar at a much faster rate when fermenting than when respiring.

Abnormal functioning of receptor tyrosine kinases (RTKs) is associated with many types of cancers. For example, breast cancer patients have a poor prognosis if their tumor cells harbor excessive levels of a receptor tyrosine kinase called HER2 (see the end of Concept 12.3 and Figure 18.27).

Using molecular biological techniques, researchers have developed a protein called Herceptin that binds to HER2 on cells and inhibits cell division, thus thwarting further tumor development. In some clinical studies, treatment with Herceptin improved patient survival rates by more than one-third. One goal of ongoing research into these cell-surface receptors and other cell-signaling proteins is development of additional successful treatments.

Tracking Atoms Through Photosynthesis: Scientific Inquiry by which plants make food. Although some of the steps are still not completely understood, the overall photosynthetic equation has been known since the 1800s: In the presence of light, the green parts of plants produce organic compounds and oxygen from carbon dioxide and water.

Using molecular formulas, we can summarize the complex series of chemical reactions in photosynthesis with this chemical equation: 6 CO2 + 12 H2O + Light energy --> C6H12O6 + 6 O2 + 6 H2O. We use glucose (C6H12O6) here to simplify the relationship between photosynthesis and respiration, but the direct product of photosynthesis is actually a three-carbon sugar that can be used to make glucose. Water appears on both sides of the equation because 12 molecules are consumed and 6 molecules are newly formed during photosynthesis.

Only a restricted region of the enzyme molecule actually binds to the substrate. This region, called the active site, is typically a pocket or groove on the surface of the enzyme where catalysis occurs (Figure 8.15a; see also Figure 5.16).

Usually, the active site is formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the shape of the active site. The specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate

Vacuoles: Diverse Maintenance Compartments

Vacuoles are large vesicles derived from the endoplasmic reticulum and Golgi apparatus. Thus, vacuoles are an integral part of a cell's endomembrane system. Like all cellular membranes, the vacuolar membrane is selective in transporting solutes; as a result, the solution inside a vacuole differs in composition from the cytosol.

Vacuoles may also help protect the plant

Vacuoles may also help protect the plant against herbivores by storing compounds that are poisonous or unpalatable to animals. Some plant vacuoles contain pigments, such as the red and blue pigments of petals that help attract pollinating insects to flowers.

What are some fo the varied functions performed by vacuoles?

Vacuoles perform a variety of functions in different kinds of cells. Food vacuoles, formed by phagocytosis, have already been mentioned (see Figure 6.13a). Many unicellular eukaryotes living in fresh water have contractile vacuoles that pump excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside the cell (see Figure 7.13). In plants and fungi, certain vacuoles carry out enzymatic hydrolysis, a function shared by lysosomes in animal cells. (In fact, some biologists consider these hydrolytic vacuoles to be a type of lysosome.) In plants, small vacuoles can hold reserves of important organic compounds, such as the proteins stockpiled in the storage cells in seeds.

. Here is the chemical equation for photosynthesis in these sulfur bacteria: CO2 + 2 H2S --> [CH2O] + H2O + 2 S

Van Niel reasoned that the bacteria split H2S and used the hydrogen atoms to make sugar. He then generalized that idea, proposing that all photosynthetic organisms require a hydrogen source but that the source varies: Sulfur bacteria: CO2 + 2 H2S --> [CH2O] + H2O + 2 S Plants: CO2 + 2 H2O --> [CH2O] + H2O + O2 General: CO2 + 2 H2X --> [CH2O] + H2O + 2 X

Evolution of Differences in Membrane Lipid Composition

Variations in the cell membrane lipid compositions of many species appear to be evolutionary adaptations that maintain the appropriate membrane fluidity under specific environmental conditions. For instance, fishes that live in extreme cold have membranes with a high proportion of unsaturated hydrocarbon tails, enabling their membranes to remain fluid (see Figure 7.5a). At the other extreme, some bacteria and archaea thrive at temperatures greater than 90°C (194°F) in thermal hot springs and geysers. Their membranes include unusual lipids that may prevent excessive fluidity at such high temperatures.

cisternal maturation model

Vesicles move from ER to Golgi. Vesicles coalesce to form new cis Golgi cisternae. Cisternal maturation: Golgi cisternae move in a cisto-trans direction. Vesicles form and leave Golgi, carrying specific products to other locations or to the plasma membrane for secretion. Vesicles transport some proteins backward to less mature Golgi cisternae, where they function. Vesicles also transport certain proteins back to ER, their site of function.

Bulk transport across the plasma membrane occurs by exocytosis and endocytosis:

Water and small solutes enter and leave the cell by diffusing through the lipid bilayer of the plasma membrane or by being pumped or moved across the membrane by transport proteins. However, large molecules—such as proteins and polysaccharides, as well as larger particles—generally cross the membrane in bulk, packaged in vesicles. Like active transport, these processes require energy

Equilibrium and work in an isolated hydroelectric system

Water flowing downhill turns a turbine that drives a generator providing electricity to a lightbulb, but only until the system reaches equilibrium.

osmosis

Water molecules can pass through pores, but sugar molecules cannot. This side has fewer solute molecules and more free water molecules Water molecules cluster around sugar molecules. This side has more solute molecules and fewer free water molecules Water moves from an area of higher to lower free water concentration(lower to higher solute concentration)

Free Energy and Metabolism:

We can now apply the free-energy concept more specifically to the chemistry of life's processes

second law of thermodynamics

We can now state the second law of thermodynamics: Every energy transfer or transformation increases the entropy of the universe. Although order can increase locally, there is an unstoppable trend toward randomization of the universe as a whole

Organization of the Chemistry of Life into Metabolic Pathways

We can picture a cell's metabolism as an elaborate road map of the thousands of chemical reactions that occur in a cell, arranged as intersecting metabolic pathways. A metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product. Each step of the pathway is catalyzed by a specific enzyme:

Most water-soluble signaling molecules bind to specific sites on transmembrane receptor proteins that transmit information from the extracellular environment to the inside of the cell.

We can see how cell-surface transmembrane receptors work by looking at three major types: G protein-coupled receptors (GPCRs), receptor tyrosine kinases, and ion channel receptors. These receptors are discussed and illustrated in Figure 11.8; study this figure before going on.

exergonic reaction example

We can use the overall reaction for cellular respiration as an example:C6H12O6 + 6 O2 S 6 CO2 + 6 H2O ∆G = -686 kcal/mol (-2,870 kJ/mol) For each mole (180 g) of glucose broken down by respiration under what are called "standard conditions" (1 M of each reactant and product, 25°C, pH 7), 686 kcal (2,870 kJ) of energy is made available for work. Because energy must be conserved, the chemical products of respiration store 686 kcal less free energy per mole than the reactants. The products are, in a sense, the spent exhaust of a process that tapped the free energy stored in the bonds of the sugar molecules.

This process, in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP, is called chemiosmosis (from the Greek osmos, push).

We have previously used the word osmosis in discussing water transport, but here it refers to the flow of H+ across a membrane.

Cellular respiration is remarkably efficient in its energy conversion. By comparison, even the most efficient automobile converts only about 25% of the energy stored in gasoline to energy that moves the car.

We humans use some of this heat to maintain our relatively high body temperature (37°C), and we dissipate the rest through sweating and other cooling mechanisms.

Response: Cell signaling leads to regulation of transcription or cytoplasmic activities

We now take a closer look at the cell's subsequent response to an extracellular signal—what some researchers call the "output response." What is the nature of the final step in a signaling pathway?

The Versatility of Catabolism: Throughout this chapter, we have used glucose as an example of a fuel for cellular respiration. But free glucose molecules are not common in the diets of humans and other animals.

We obtain most of our calories in the form of fats, proteins, and carbohydrates such as sucrose and other disaccharides, and starch, a polysaccharide. All these organic molecules in food can be used by cellular respiration to make ATP (Figure 9.19).

Now let's take a closer look at the electrons as they drop in energy level, passing through the components of the electron transport chain in Figure 9.13.

We'll first describe the passage of electrons through complex I in some detail as an illustration of the general principles involved in electron transport.

Another source of electrons for the electron transport chain is FADH2, the other reduced product of the citric acid cycle. Notice in Figure 9.13 that FADH2 adds its electrons from within complex II, at a lower energy level than NADH does. Consequently, although NADH and FADH2 each donate an equivalent number of electrons (2) for oxygen reduction, the electron transport chain provides about one-third less energy for ATP synthesis when the electron donor is FADH2 rather than NADH

We'll see why in the next section. The electron transport chain makes no ATP directly. Instead, it eases the fall of electrons from food to oxygen, breaking a large free-energy drop into a series of smaller steps that release energy in manageable amounts, step by step.

To understand how cell cycle checkpoints work, we'll first identify some of the molecules that make up the cell cycle control system (the molecular basis for the cell cycle clock) and describe how a cell progresses through the cycle.

We'll then consider the internal and external checkpoint signals that can make the clock either pause or continue.

External signals are converted to responses within the cell

What does a cell that is "talking" say to a "listening" cell, and how does the latter cell respond to the message—that is, how do cells communicate? Let's approach these questions by first looking at communication among microorganisms.

Most cell division results in genetically identical daughter cells: The reproduction of a cell, with all of its complexity, cannot occur by a mere pinching in half; a cell is not like a soap bubble that simply enlarges and splits in two.In both prokaryotes and eukaryotes, most cell division involves the distribution of identical genetic material—DNA—to two daughter cells. (The exception is meiosis, the special type of eukaryotic cell division that can produce sperm and eggs.)

What is most remarkable about cell division is the accuracy with which the DNA is passed from one generation of cells to the next. A dividing cell replicates its DNA, distributes the two copies to opposite ends of the cell, and then splits into daughter cells.

In C. elegans, a protein in the outer mitochondrial membrane, called Ced-9 (the product of the ced-9 gene), serves as a master regulator of apoptosis, acting as a brake in the absence of a signal promoting apoptosis.

When a death signal is received by the cell, signal transduction involves a change in Ced-9 that disables the brake, and the apoptotic pathway activates proteases and nucleases, enzymes that cut up the proteins and DNA of the cell. The main proteases of apoptosis are called caspases; in the nematode, the chief caspase is the Ced-3 protein.

The initials MPF stand for "maturation-promoting factor," but we can think of MPF as "M-phase-promoting factor" because it triggers the cell's passage into the M phase, past the G2 checkpoint.

When cyclins that accumulate during G2 associate with Cdk molecules, the resulting MPF complex is active—it phosphorylates a variety of proteins, initiating mitosis (Figure 12.16b)

Photosynthetic Pigments: The Light Receptors

When light meets matter, it may be reflected, transmitted, or absorbed. Substances that absorb visible light are known as pigments. Different pigments absorb light of different wavelengths, and the wavelengths that are absorbed disappear. If a pigment is illuminated with white light, the color we see is the color most reflected or transmitted by the pigment. (If a pigment absorbs all wavelengths, it appears black.)

Water Balance of Cells with Cell Walls: The cells of plants, prokaryotes, fungi, and some unicellular eukaryotes are surrounded by cell walls (see Figure 6.27).

When such a cell is immersed in a hypotonic solution—bathed in rainwater, for example—the cell wall helps maintain the cell's water balance. Consider a plant cell. Like an animal cell, the plant cell swells as water enters by osmosis (Figure 7.12b).

To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings.

When the new bonds of the product molecules form, energy is released as heat, and the molecules return to stable shapes with lower energy than the contorted state.

Substrate Specificity of Enzymes: The reactant an enzyme acts on is referred to as the enzyme's substrate. The enzyme binds to its substrate (or substrates, when there are two or more reactants), forming an enzyme-substrate complex.

While enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product (or products) of the reaction. The overall process can be summarized as follows: ( view page 155) Most enzyme names end in -ase. For example, the enzyme sucrase catalyzes the hydrolysis of the disaccharide sucrose into its two monosaccharides, glucose and fructose (see the diagram at the beginning of Concept 8.4)

In some bacteria, the process of cell division is initiated when the DNA of the bacterial chromosome begins to replicate at a specific place on the chromosome called the origin of replication, producing two origins. As the chromosome continues to replicate, one origin moves rapidly toward the opposite end of the cell (Figure 12.12).

While the chromosome is replicating, the cell elongates. When replication is complete and the bacterium has reached about twice its initial size, proteins cause its plasma membrane to pinch inward, dividing the parent bacterial cell into two daughter cells. In this way, each cell inherits a complete genome.

The Golgi manufactures and refines its products in stages, with different cisternae containing unique teams of enzymes. Until recently, biologists viewed the Golgi as a static structure, with products in various stages of processing transferred from one cisterna to the next by vesicles.

While this may occur, research from several labs has given rise to a new model of the Golgi as a more dynamic structure. According to the cisternal maturation model, the cisternae of the Golgi actually progress forward from the cis to the trans face, carrying and modifying their cargo as they move. Figure 6.12 shows the details of this model. The reality probably lies somewhere between the two models; recent research suggests the central regions of the cisternae may remain in place, while the outer ends are more dynamic.

The electromagnetic spectrum

White light is a mixture of all wavelengths of visible light. A prism can sort white light into its component colors by bending light of different wavelengths at different angles. (Droplets of water in the atmosphere can act as prisms, causing a rainbow to form.) Visible light drives photosynthesis.

The signal that triggers apoptosis can come from either outside or inside the cell. Outside the cell, signaling molecules released from other cells can initiate a signal transduction pathway that activates the genes and proteins responsible for carrying out cell death.

Within a cell whose DNA has been irretrievably damaged, a series of protein-protein interactions can pass along a signal that similarly triggers cell death. Considering some examples of apoptosis can help us to see how signaling pathways are integrated in cells.

As an alternative to respiratory oxidation of organic nutrients, fermentation is an extension of glycolysis that allows continuous generation of ATP by the substrate-level phosphorylation of glycolysis. For this to occur, there must be a sufficient supply of NAD+ to accept electrons during the oxidation step of glycolysis.

Without some mechanism to recycle NAD+ from NADH, glycolysis would soon deplete the cell's pool of NAD+ by reducing it all to NADH and would shut itself down for lack of an oxidizing agent. Under aerobic conditions, NAD+ is recycled from NADH by the transfer of electrons to the electron transport chain. An anaerobic alternative is to transfer electrons from NADH to pyruvate, the end product of glycolysis.

We can simplify the equation by indicating only the net consumption of water: 6 CO2 + 6 H2O + Light energy --> C6H12O6 + 6 O2

Writing the equation in this form, we can see that the overall chemical change during photosynthesis is the reverse of the one that occurs during cellular respiration (see Concept 9.1). Both of these metabolic processes occur in plant cells. However, as you will soon learn, chloroplasts do not synthesize sugars by simply reversing the steps of respiration.

Human cells from lining of uterus (colorized TEM)

Yeast cells: reproducing by budding (above, colorized SEM) and a single cell (right, colorized TEM)

Cyclic Electron Flow: In certain cases, photoexcited electrons can take an alternative path called cyclic electron flow, which uses photosystem I but not photosystem II.

You can see in Figure 10.16 that cyclic flow is a short circuit: The electrons cycle back from ferredoxin (Fd) to the cytochrome complex, then via a plastocyanin molecule (Pc) to a P700 chlorophyll in the PS I reaction-center complex. There is no production of NADPH and no release of oxygen that results from this process. On the other hand, cyclic flow does generate ATP

Animal Cell

a) ENDOPLASMIC RETICULUM (ER): network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions. Rough ER & Smooth ER. b) Nucleus:Chromatin: material consisting of DNA and proteins; visible in a dividing cell as individual condensed chromosomes Nucleolus: nonmembranous structure involved in production of ribosomes; a nucleus has one or more nucleoli Nuclear Envelope: double membrane enclosing the nucleus; perforated by pores; continuous with ER

An introduction to electron transport chains.

a) Uncontrolled reaction. The one-step exergonic reaction of hydrogen with oxygen to form water releases a large amount of energy in the form of heat and light: an explosion. (b) Cellular respiration. In cellular respiration, the same reaction occurs in stages: An electron transport chain breaks the "fall" of electrons in this reaction into a series of smaller steps and stores some of the released energy in a form that can be used to make ATP. (The rest of the energy is released as heat.)

Figure 7.7 illustrates six major functions performed by proteins of the plasma membrane. Some functions of membrane proteins. In many cases, a single protein performs multiple tasks.

a)Some functions of membrane proteins. In many cases, a single protein performs multiple tasks. b) Enzymatic activity. A protein built into the membrane may be an enzyme with its active site (where the reactant binds) exposed to substances in the adjacent solution. In some cases, several enzymes in a membrane are organized as a team that carries out sequential steps of a metabolic pathway. c)Signal transduction. A membrane protein (receptor) may have a binding site with a specific shape that fits the shape of a chemical messenger, such as a hormone. The external messenger (signaling molecule) may cause the protein to change shape, allowing it to relay the message to the inside of the cell, usually by binding to a cytoplasmic protein (see Figure 11.6). d)Cell-cell recognition. Some glycoproteins serve as identification tags that are specifically recognized by membrane proteins of other cells. This type of cell-cell binding is usually short-lived compared to that shown in (e).Intercellular joining. Membrane proteins of adjacent cells may hook together in various kinds of junctions, such as gap junctions or tight junctions (see Figure 6.30). This type of binding is more long-lasting than that shown in (d). (f)Attachment to the cytoskeleton and extracellular matrix (ECM). Microfilaments or other elements of the cytoskeleton may be noncovalently bound to membrane proteins, a function that helps maintain cell shape and stabilizes the location of certain membrane proteins. Proteins that can bind to ECM molecules can coordinate extracellular and intracellular changes (see Figure 6.28).