Microscopic Structure of living organisms Flashcards

Question

Micelles and Bilayers

Answer 1

Lipid molecules form such structures spontaneously in water. The shape of the lipid molecule determines which of these structures is formed. Wedge-shaped lipid molecules form **micelles**, whereas cylindershaped phospholipid molecules form **bilayers**

Answer 2

* **Biological membranes**: double layer of lipid molecules in which various membrane proteins are embedded. * This lipid bilayer is **fluid**, with individual lipid molecules able to diffuse rapidly within their own monolayer. * Most types of **lipid molecules**, however, very rarely flipflop spontaneously from one monolayer to the other. * There are three major classes of membrane lipid molecules - **phospholipids, cholesterol, and glycolipids** - and the lipid compositions of the inner and outer monolayers are different, reflecting the different functions of the two faces of a cell membrane. * **Different mixtures of lipids** are found in the membranes of cells of different types, as well as in the various membranes of a single eucaryotic cell. Some membrane-bound proteins require specific lipid head groups in order to function,

Answer 3

* Lipid molecules are **insoluble in water** but dissolve readily in organic solvents. They constitute about **50%** of the mass of most animal cell membranes * Lipid molecules are amphipathic (or amphiphilic) that is, they have a **hydrophilic**("water-loving," or polar) end and a **hydrophobic**("water-hating," or nonpolar) end. * **Phospholipids** are most abundant, these have a **polar head group and two hydrophobic hydrocarbon tails**.The tails are usually fatty acids, and they can differ in length ( 14 - 24 carbon atoms). One tail usually has one or more cis-double bonds (that is, it is unsaturated), while the other tail does not (that is, it is saturated). * **Differences in the length and saturation of the fatty acid tails** are important because they influence the ability of phospholipid molecules to pack against one another, and for this reason they affect the fluidity of the membrane * It is the **shape and amphipathic nature of the lipid molecules** that cause them to form bilayers spontaneously in aqueous solution. * When lipid molecules are surrounded on all sides by water, they tend to aggregate so that their **hydrophobic tails** are buried in the interior and their **hydrophilic heads** are exposed to water. * Depending on their shape, they can do this in either of two ways: they can form **spherical micelles**, with the tails inward, or they can form bimolecular sheets, or bilayers, with the **hydrophobic tails** sandwiched between the hydrophilic head groups * Because of their cylindrical shape, membrane phospholipid molecules spontaneously form bilayers in aqueous environments and lipid bilayers tend to close on themselves to form sealed compartments, thereby eliminating free edges where the hydrophobic tails would be in contact with water. * For the same reason compartments formed by lipid bilayers tend to reseal when they are torn. A lipid bilayer has other characteristics besides its self-sealing properties that make it an ideal structure for cell membranes. One of the most important of these is its fluidity, which is crucial to many membrane functions.

Answer 4

* **Carrier proteins** bind specific solutes and transfer them across the lipid bilayer by undergoing conformational changes that expose the solute binding site sequentially on one side of the membrane and then on the other. * Some **carrier proteins** simply transport a single solute "downhill," whereas others can act as pumps to transport a solute "uphill" against its electrochemical gradient, using energy provided by ATP hydrolysis or by a "downhill" flow of another solute (such as Na+) to drive the requisite series of conformational changes. * Carrier proteins belong to a small number of families, each of which comprises proteins of similar amino acid sequence * The family of cation transporting ATPases, which includes the ubiquitous Na+-K+ pump, is an important example; each of these ATPases contains a large catalytic subunit that is sequentially phosphorylated and dephosphorylated during the pumping cycle. * The superfamily of ABC transporters is especially important clinically: it includes proteins that are responsible for cystic fibrosis, as well as for drug resistance in cancer cells and in malaria-causing parasites * Carrier proteins functioning as **uniports, symports, and antiports**

Answer 5

* Whereas the rate of the former is always proportional to the solute concentration, the rate of the latter reaches a maximum **(Vmax)** when the carrier protein is **saturated**. * The solute concentration when transport is at half its **maximal value** approximates the binding constant **(KM)** of the carrier for the solute and is analogous to the KM of an enzyme for its substrate. .

Answer 6

* **Conformational change** in a carrier protein could mediate the facilitated diffusion of a solute. * The **carrier protein** shown can exist in **two conformational states**: * In state "pong" the binding sites for solute A are exposed on the outside of the bilayer; * in state "ping" the same sites are exposed on the other side of the bilayer. * Therefore, if the concentration of A is higher on the outside of the bilayer, more A will bind to the carrier protein in the pong conformation than in the ping conformation, and there will be a net transport of A down its **electrochemical gradient.**

Answer 7

* The binding of Na+ **(1)** and the subsequent phosphorylation by ATP of the cytoplasmic face of the ATPase **(2)** induce the protein to undergo a conformational change that transfers the Na+ across the membrane and releases it on the outside **(3)**. Then the binding of K+on the extracellular surface **(4)** and the subsequent dephosphorylation **(5)** return the protein to its original conformation, which transfers the K+ across the membrane and releases it into the cytosol **(6)**. * These changes in conformation are analogous to the ping pong transitions except that here the Na+- dependent phosphorylation and the K+-dependent dephosphorylation of the protein cause the conforma-tional transitions to occur in an orderly manner, enabling the protein to do useful work. Although for simplicity only one Na+- and one K+-binding site are shown, in the real pump there are thought to be three Na+- and two K+-binding sites. Moreover, although the ATPase is shown as alternating between two conformational states, there is evidence that it goes through a more complex series of conformational changes during the actual pumping cycle.

Answer 8

* This **carrier protein** actively pumps Na+ out of and K+ into a cell against their electrochemical gradients. * For every molecule of ATP hydrolyzed inside the cell, three Na+ are pumped out and two K+ are pumped in. * The specific pump inhibitor ouabain and K+ compete for the same site on the external side of the ATPase.

Answer 9

* Response of a human red blood cell to changes in osmolarity (also called tonicity) of the extracellular fluid. * Because the plasma membrane is freely permeable to water, water will move into or out of cells down its concentration gradient, a process called osmosis. * If cells are placed in a hypotonic solution (i.e., a solution having a low solute concentration and therefore a high water concentration), there will be a net movement of water into the cells, causing them to swell and burst (Lyse) * Hypertonic solution, they will shrink.

Answer 10

* The transcellular transport of glucose across an intestinal epithelial cell **depends on the asymmetrical distribution of transport proteins in the cell's plasma membrane.** * **Glucose** is pumped into the cell through the apical domain of the membrane by a Na+-powered glucose symport, and glucose passes out of the cell (down its concentration gradient) by facilitated diffusion mediated by a different glucose carrier protein in the basal and lateral membrane domains. * The Na+ gradient driving the glucose symport is maintained by the Na+-K+ ATPase in the basal and lateral plasma membrane domains, which keeps the internal concentration of Na+ low. * **Adjacent cells** are connected by impermeable junctions (called tight junctions). The **junctions** have a **dual function** in the transport process illustrated: **1.** they prevent solutes from crossing the epithelium between cells, allowing a concentration gradient of glucose to be maintained across the cell sheet **2.** they also serve as diffusion barriers within the plasma membrane, which help confine the various carrier proteins to their respective membrane domains

Answer 11

* The inner membrane is the cell's plasma membrane. * Between the inner and outer lipid bilayer membranes there is a highly porous, rigid peptidoglycan composed of protein and polysaccharide that constitutes the bacterial cell wall; it is attached to lipoprotein molecules in the outer membrane and fills the periplasmic space(only a little of the peptido-glycan is shown).This space also contains a variety of soluble protein molecules. * **Polysaccharide chains** of the special lipopolysaccharide molecules that form the external monolayer of the outer membrane; for clarity, only a few of these chains are shown. * **Bacteria with double membranes** are called **gram negative** because they do not retain the dark blue dye used in the gram staining procedure. * **Bacteria with single membranes** (but thicker cell walls), such as staphylo-cocci and streptococci, retain the blue dye and therefore are called gram positive; their single membrane is analogous to the inner (plasma) membrane of gramnegative bacteria

Answer 12

* **Porins:** The solute diffuses through channel-forming proteins in the outer membrane and binds to a *periplasmic substrate-binding protein.* * As a result, the substrate binding protein undergoes a conformational change that enables it to bind to a **transport ATPase** in the plasma membrane, which then picks up the solute and actively transfers it across the bilayer in a reaction driven by **ATP hydrolysis**. * The **peptidoglycan** is omitted for simplicity; its porous structure allows the substrate-binding proteins and water-soluble solutes to move through it by simple diffusion

Answer 13

* The transporter consists of **four domains**: * two highly hydrophobic domains, each with six putative membrane-spanning segments that somehow form the translocation pathway, and two ATP-binding catalytic domains (or cassettes). * In some cases the two halves of the transporter are formed by a single polypeptide (as shown), whereas in other cases they are formed by two separate polypeptides. * Sugar transporters: passive glucose transporters in mammalian cells some H+-driven sugar transporters in bacteria * Cation-transporting ATPases Na+-K+ ATPases; Ca2+ ATPases * ABC transporters multidrug resistance (MDR) ATPase in mammalian cells; periplasmic substrate-binding-protein-dependent ATPases in bacteria; chloroquine-resistance ATPase in P. falciparum; mating pheromone exporter in yeast; peptide pump in vertebrate ER membrane; cystic fibrosis transmembrane regulator (CFTR) protein

Answer 14

* **Anion (Cl--HCO3 -) antiporters** band 3 in red blood cells; anion exchangers in other cells * **Cation antiporters** Na+-H+exchanger * **Cation/anion antiporters** Na-dependent Cl--HCO3 - exchanger Na+-driven symporters Na+-glucose symporter in intestinal cells; Na+-proline symporter in bacteria; * **Na+-HCO3 - symporter** in glial cells

Answer 15

* **Channel proteins** form aqueous pores across the lipid bilayer and allow inorganic ions of appropriate size and charge to cross the membrane down their electrochemical gradients at rates that are about **1000 times** greater than those achieved by any known carrier. * These **ion channels** are "gated" and usually open transiently in response to a specific perturbation in the membrane, such as a change in membrane potential (voltage-gated channels) or the binding of a neurotransmitter (transmitter-gated channels) * **K+-selective leak channels** play an important part in determining the resting membrane potential across the plasma membrane in most animal cells. * **Voltage-gated cation channels** are responsible for the generation of self-amplifying action potentials in electrically excitable cells such as neurons and skeletal muscle cells. * **Transmitter-gated ion channels** convert chemical signals to electrical signals at chemical synapses: **excitatory neurotransmitters**, such as acetylcholine and glutamate, open transmitter-gated cation channels and thereby depolarize the postsynaptic membrane toward the threshold potential for firing an action potential; **inhibitory neurotransmitters**, such as GABA and glycine, open transmitter-gated Cl- channels and thereby suppress firing by keeping the postsynaptic membrane polarized. * Gap junctions * A subclass of **glutamate-gated ion channels**, called **NMDA-receptor channels**, are highly permeable to Ca2+, which can trigger the long-term changes in synapses that are thought to be involved for some forms of learning and memory * **Ion channels** work together in complex ways to control the behavior of electrically excitable cells. A typical neuron, for example, receives thousands of excitatory and inhibitory inputs, which combine by spatial and temporal summation to produce a grand postsynaptic potential (PSP) in the cell body. The magnitude of the grand PSP is translated into the rate of firing of action potentials by a mixture of cation channels in the membrane of the axon hillock.

Answer 16

* **Ion channel**, which fluctuates between closed and open conformations. * **A transmembrane protein complex:** forms a hydrophilic pore across the lipid bilayer only when the gate is open. * Polar amino acid side chains are thought to line the wall of the pore, while hydrophobic side chains interact with the lipid bilayer. The pore narrows to atomic dimensions in one region (the "ion-selective filter"), where the ion selectivity of the channel is largely determined. * Gated ion channels: Voltage gated, Ligand-gated extracellular ligand, Ligand-gated intracellular ligand, mechanically gated

Answer 17

* A small flow of ions carries sufficient charge to cause a large change in the membrane potential. * The ions that give rise to the membrane potential lie in a thin surface layer close to the membrane, held there by their electrical attraction to their oppositely charged counterparts (counterions) on the other side of the membrane. * 1 microcoulumb of charge:(6 x 1012 univalent ions)

Answer 18

* **Vertebrate neuron:** The single axon conducts signals away from the cell body, while the multiple dendrites receive signals from the axons of other neurons. The nerve terminals end on the dendrites or cell body of other neurons or on other cell types, such as muscle or gland cells.

Answer 19

Firing frequency of an axon increases with an increase in the grand PSP

Answer 20

Each presynaptic action potential arriving at a synapse produces a small postsynaptic potential, or PSP (black lines). When successive action potentials arrive at the same synapse, each PSP produced adds to the tail of the preceding one to produce a larger combined PSP (green lines). The greater the frequency of incoming action potentials, the greater the size of the combined PSP

Answer 21

Many thousands of nerve terminals synapse on the cell body and dendrites. These deliver signals from other parts of the organism to control the firing of action potentials along the single axon of this large cell

Answer 22

These gated ion channels are essential for the stimulation of muscle contraction by a nerve impulse.

Answer 23

* Five homologous subunits ( α, α, β, γ, δ) combine to form a transmembrane aqueous pore. * The pore is lined by a ring of five transmembrane α helices, one contributed by each subunit. * The ring of α helices is probably surrounded by a continuous rim of transmembrane β sheet, made up of the other transmembrane segments of the five subunits. * In its closed conformation the pore is thought to be occluded by the hydrophobic side chains of five leucine residues, one from each α helix, which form a gate near the middle of the lipid bilayer. * The negatively charged side chains at either end of the pore ensure that only positively charged ions pass through the channel. * Both of the α subunits contain an acetylcholine binding site; when acetylcholine binds to both sites, the channel undergoes a conformational change that opens the gate, possibly by causing the leucine residues to move outward.

Answer 24

* The binding of two acetylcholine molecules opens this transmitter-gated ion channel. * But even with acetylcholine bound, the receptor is thought to stay in the open conformation only briefly, before the channel recloses. * The acetylcholine then dissociates from the receptor, which enables the receptor to return to its original conformation.

Answer 25

* When an action potential reaches the nerve terminal, it stimulates the terminal to release its **neurotrans-mitter**; the neurotransmitter is contained in synaptic vesicles and is released to the cell exterior when the vesicles fuse with the plasma membrane of the nerve terminal. * The released neurotransmitter binds to and opens the transmitter-gated ion channels concentrated in the **plasma membrane** of the target cell at the synapse. * The resulting ion flows alter the membrane potential of the target cell, thereby transmitting a signal from the excited nerve

Answer 26

* Major functional domains of the polypeptide chain of one subunit, with the six putative transmembrane α helices labeled 1 to 6. * Four such subunits, each having about 600 amino acids, are thought to assemble to form a transmembrane pore * In voltage-gated Na+ and Ca2+ channels the four subunits are domains of a single very large polypeptide chain, but otherwise the overall structure is thought to be similar. * The 20 amino acid segment contained in the region linking helices 5 and 6, is thought to extend across the membrane as two antiparallel β strands to line the pore as shown. * The fourth α helix (blue) has positively charged residues at every third position, which is thought to allow this helix to serve as a voltage sensor. In at least some K+ channels, the amino-terminal domain is involved in rapid channel inactiva-tion,

Answer 27

* The action potential is triggered by a brief pulse of current which partially depolarizes the membrane, as shown in the plot of membrane potential versus time * The membrane potential would have simply relaxed back to the resting value after the initial depolarizing stimulus if there had been no voltage-gated ion channels in the membrane; this relatively slow return of the membrane potential to its initial value of -70 mV in the absence of open Na+ channels is automatic because of the efflux of K+ through K+ channels, which drives the membrane back toward the K+ equilibrium potential. The red curve shows the course of the action potential that is caused by the opening and subsequent inactivation of voltage-gated Na+ channels, whose state is shown at the bottom. The membrane cannot fire a second action potential until the Na+ channels have returned to the closed conformation (see Figure11-21); until then the membrane is refractory to stimulation

Answer 28

* The mitochondrion carries out most cellular oxidations and produces the bulk of the animal cell's ATP. * The mitochondrial matrix space contains a large variety of enzymes, including those that convert pyruvate and fatty acids to acetyl CoA and those that oxidize this acetyl CoA to CO2 through the citric acid cycle. * Large amounts of NADH (and FADH2) are produced by these oxidation reactions. * The energy available from combining oxygen with the reactive electrons carried by NADH and FADH2 is harnessed by an electron-transport chain in the mitochondrial inner membrane called the respiratory chain. * The respiratory chain pumps H+ out of the matrix to create a transmembrane electrochemical proton (H+) gradient, which includes contributions from both a membrane potential and a pH difference. * The transmembrane gradient in turn is used both to synthesize ATP and to drive the active transport of selected metabolites across the mitochondrial inner membrane. * The combination of these reactions is responsible for an efficient ATPADP exchange between the mitochondrion and the cytosol that keeps the cell's ATP pool highly charged, so that ATP can be used to drive many of the cell's energy-requiring reactions. * mitochondria tend to be aligned along microtubules

Answer 29

* **Localization of mitochondria** near sites of high ATP utilization in cardiac muscle and a sperm tail. * During the development of the flagellum of the sperm tail, microtubules wind helically around the axoneme, where they are thought to help localize the mitochondria in the tail; these microtubules then disappear * **In fractionation:** Allows the processing of large numbers of mitochondria at the same time, takes advantage of the fact that in media of low osmotic strength water flows into mitochondria and greatly expands the matrix space (yellow). While the cristae of the inner membrane allow it to unfold to accommodate the expansion, the outer membranewhich has no folds to begin withbreaks, releasing a structure composed of only the inner membrane and the matrix

Answer 30

* Contains highly concetrated mix of enzymes required for oxidation of pyruvate and fatty acids and citric acid cycle * Several identical copies of mitochondrial DNA genome, mitochondrial ribosomes, tRNAs and various enzymes required for expression of mitochondrial genes

Answer 31

* folded into cristae which increases surface area * contains proteins that have 3 functions 1. carry out oxidation reactions of the respiratory chain 2. ATP synthase complex that makes ATP in the matrix 3. Transport proteins regulating the passage of metabolites into and out of the cell * Electrochemical gradient that drives ATP synthase is established by respiratory chain and the membrane must be impermeable to small ions

Answer 32

* Porin(large channel forming protein) * permeable to all molecules 5000 daltons or less * enzymes involved in mitochondrial lipid synthesis and those that convert lipid substrates into forms metabolized by matrix

Answer 33

contains several enzymes that use ATP passing out of the matrix to phosphorolate other nucleotides

Answer 34

In the liver an estimated 67% of the total mitochondrial protein is located in the matrix, 21% is located in the inner membrane, 6% in the outer membrane, and 6% in the intermembrane space

Answer 35

* This central intermediate is produced during the breakdown of foodstuffs in the mitochondrion. * The sulfur atom (S) forms a thioester linkage to acetate. Because this is a "high-energy" linkage, which releases a large amount of free energy when it is hydrolyzed, the acetate group can be readily transferred to other molecules, such as oxaloacetate

Answer 36

* lipid droplet in the cytoplasm; the droplet contains triacylglycerols, the main form of stored fat * Fat droplets in a cardiac muscle cell. The droplets are surrounded by mitochondria that oxidize the fatty acids derived from their triacylglycerols * The fatty acid oxidation cycle. The cycle is catalyzed by a series of four enzymes in the mitochondrial matrix. Each turn of the cycle shortens the fatty acid chain by two carbons (shown in red), as indicated, and generates one molecule of acetyl CoA and one molecule each of NADH and FADH2. The NADH is freely soluble in the matrix. The FADH2, in contrast, remains tightly bound to the enzyme fatty acyl-CoA dehydrogenase;its two electrons will be rapidly transferred to the respiratory chain in the mitochondrial inner membrane, regenerating FAD

Answer 37

Glycogen is the major storage form of carbohydrate in vertebrate cells. It is a polymer of glucose, and each glycogen granule is a single, highly branched molecule. The synthesis and degradation of glycogen are catalyzed by enzymes bound to the granule surface, including the synthetic enzyme glycogen synthase and the degradative enzyme glycogen phosphorylase.

Answer 38

* The complex converts **pyruvate to acetyl CoA** in the **mitochondrial matrix** * NADH is also produced in this reaction. * Three enzymes **pyruvate decarboxylase, lipoamide reductase-transacetylase, and dihydrolipoyl dehydrogenase**, whose activities are coupled * The structure of the complex, which is larger than a ribosome * The complex also contains a **protein kinase** and **a protein phosphatase** that regulate its activity, turning it off whenever ATP levels are high

Answer 39

* The intermediates are shown as their free acids, although the carboxyl groups are actually ionized. * Each of the indicated steps is catalyzed by a different enzyme located in the **mitochondrial matrix**. * The two carbons from **acetyl CoA** that enter this turn of the cycle will be converted to CO2in subsequent turns of the cycle * **Three molecules of NADH** are formed. * The **GTP** molecule produced can be converted to ATP by the exchange reaction **GTP + ADP → GDP + ATP.** * The molecule of **FADH2** formed remains protein-bound as part of the succinate dehydrogenase complex in the mitochondrial membrane; this complex feeds the electrons acquired by FADH2 directly to ubiquinone

Answer 40

In this process of **oxidative phosphorylation**, the mitochondrial inner membrane serves as a device that converts one form of chemical bond energy to another, changing a major part of the energy of **NADH (and FADH2)** oxidation into phosphate-bond energy in ATP.

Answer 41

* **Pyruvate and fatty acids** enter the mitochondrion, are **broken down to acetyl CoA**, and are then metabolized by the citric acid cycle, which **produces NADH and FADH2** * In the process of **oxidative phosphorylation**, high energy **electrons** from **NADH (and FADH2)** are then passed to oxygen by means of the **respiratory chain** in the inner membrane, producing **ATP** by a chemiosmotic mechanism. * **NADH** generated by **glycolysis** in the **cytosol** also passes electrons to the respiratory chain. * Since **NADH** cannot pass across the mitochondrial inner membrane, the electron transfer from cytosolic NADH must be accomplished indirectly by means of one of several "shuttle" systems that transport another reduced compound into the mitochondrion; after being oxidized, this compound is returned to the cytosol, where it is reduced by NADH again

Answer 42

* Most of the **energy** that would be **released as heat** if **hydrogen** were **burned** is instead harnessed and stored in a form useful to the cell by means of the electron-transport chain in the mitochondrial inner membrane * The rest of the **oxidation energy** is released as heat by the mitochondrion. In reality, the protons and electrons shown are removed from hydrogen atoms that are covalently linked to NADH or FADH2 molecules

Answer 43

* The components of **two complete hydrogen atoms** are lost from the alcohol: **a hydride ion is transferred to NAD+, and a proton escapes to the aqueous solution** * Only the **nicotinamide ring portion** of the NAD+ and NADH molecules is shown here * The steps occur on a **protein surface**, being catalyzed by specific chemical groups on the enzyme alcohol dehydrogenase

Answer 44

The total proton-motive force across the mitochondrial inner membrane consists of a large force due to the membrane potential (traditionally designated ∆Y by experts, but designated ∆ V in this text) and a smaller force due to the H+ concentration gradient (∆pH). Both forces act to drive H+ into the matrix space.

Answer 45

* As a high-energy electron is passed along the electron-transport chain, some of the energy released is used to drive three respiratory enzyme complexes that pump H+ out of the matrix space. * The resulting electrochemical proton gradient across the inner membrane drives H+ back through the ATP synthase, a transmembrane protein complex that uses the energy of the H+ flow to synthesize ATP from ADP and Pi in the matrix

Answer 46

* The respiratory chain in the inner mitochondrial membrane contains three major enzyme respiratory complexes through which electrons pass on their way from NADH to O2. * Each of these can be purified, inserted into synthetic lipid vesicles, and then shown to pump H+ when electrons are transported through it. * In the native membrane the mobile electron carriers ubiquinone and cytochrome c complete the electron-transport chain by shuttling between the enzyme complexes. * The path of electron flow is NADH → NADH dehydrogenase complex → ubiquinone → b-c1 complex → cytochrome c → cytochrome oxidase complex → molecular oxygen (O2). * The respiratory enzyme complexes couple the energetically favorable transport of electrons to the pumping of H+ out of the matrix. * The resulting electrochemical proton gradient is harnessed to make ATP by another transmembrane protein complex, ATP synthase, through which H+ flows back into the matrix. * The ATP synthase is a reversible coupling device that normally converts a backflow of H+ into ATP phosphate-bond energy by catalyzing the reaction ADP + Pi → ATP, but it can also work in the opposite direction and hydrolyze ATP to pump H+ if the electrochemical proton gradient is reduced. * Its universal presence in mitochondria, chloroplasts, and bacteria testifies to the central importance of chemiosmotic mechanisms in cells

Answer 47

By combining a light-driven bacterial proton pump (bacteriorhodopsin), an ATP synthase purified from ox heart mitochondria, and phospholipids, vesicles were produced that synthesized ATP in response to light

Answer 48

* ATP synthase is a reversible coupling device that interconverts the energies of the electrochemical proton gradient and chemical bonds. * The ATP synthase can either synthesize ATP by harnessing the proton-motive force or pump protons against their electrochemical gradient by hydrolyzing ATP . * The direction of operation at any given instant depends on the net free-energy change for the coupled processes of H+translocation across the membrane and the synthesis of ATP from ADP and Pi * Free-energy change (∆ G) for ATP hydrolysis depends on the concentrations of the three reactants ATP, ADP, and Pi; the ∆ G for ATP synthesis is the negative of this value

Answer 49

* The porphyrin ring. * There are five different cytochromes in the respiratory chain. * Because the hemes in different cytochromes have slightly different structures and are held by their respective proteins in different ways, each of the cytochromes has a different affinity for an electron

Answer 50

* Cytochrome C: an electron carrier in the electrontransport chain. * This small protein contains just over 100 amino acids and is held loosely on the membrane by ionic interactions * The iron atom on the bound heme can carry a single electron * The structures of two types of iron-sulfur centers. (A) A center of the 2Fe2S type. (B) A center of the 4Fe4S type. Although they contain multiple iron atoms, each iron-sulfur center can carry only one electron at a time. There are more than six different iron-sulfur centers in the respiratory chain

Answer 51

* Each of these electron carriers in the respiratory chain picks up one H+ from the aqueous environment for every electron it accepts, and it can carry either one or two electrons as part of a hydrogen atom. * When it donates its electrons to the next carrier in the chain, these protons are released. * In mitochondria the quinone is ubiquinone (coenzyme Q), shown here; the long hydrophobic tail, which confines ubiquinone to the membrane, consists of 6 to 10 five-carbon isoprene units, depending on the organism. * The corresponding electron carrier in plants is plastoquinone, which is almost identical. * For simplicity, both ubiquinone and plastoquinone will normally be referred to as quinone and abbreviated as Q

Answer 52

* (A) Under normal conditions, where oxygen is abundant, all carriers are in a partially oxidized state. * Addition of a specific inhibitor causes the downstream carriers to become more oxidized and the upstream carriers to become more reduced. * (B) In the absence of oxygen all carriers are in their respiratory fully reduced state. * The sudden addition of oxygen converts each carrier to its partially oxidized form with a delay that is greatest for the most upstream carriers

Answer 53

During the transfer of two electrons from NADH to oxygen ubiquinone and cytochrome c serve as carriers between the complexes

Answer 54

* The arrangement of electron carriers in cytochrome oxidase. * Subunit I, which has 12 membrane-spanning alpha helices, contains two heme-linked iron atoms; one of these serves as an electron queuing point that feeds electrons into the bimetallic center (boxed), which is formed by the other iron and a closely opposed copper atom. * Note that four protons are pumped out of the matrix for each O2 molecule that reacts and that this requires a total of four electrons. * (B) An enlarged view of the respiratory bimetallic iron-copper center with O2 bound. * (C) An outline of the pathway used for oxygen reduction at the bimetallic center, giving some idea of the complexity of the reactions involved. Electron become incorporated into hydrogen atoms

Answer 55

* **The redox potential** (denoted E' 0 or Eh) increases as electrons flow down the respiratory chain to oxygen. * **The standard free-energy change**, ∆ G°(in kilocalories per mole), for the transfer of the two electrons donated by an NADH molecule * Electrons flow through an enzyme complex by passing in sequence to the four or more electron carriers in each complex. * Part of the favorable free-energy change is harnessed by each enzyme complex to pump H+ across the mitochondrial inner membrane. * Although the number of H+pumped per electron (n) is uncertain, it is estimated that the NADH dehydrogenase and b-c1 complexes each pump two H+ per electron, whereas the cytochrome oxidase complex pumps one. * The two electrons transported from FADH2, generated by fatty acid oxidation and by the citric acid cycle are passed directly to ubiquinone, and they therefore cause less H+ pumping than the two electrons transported from NADH

Answer 56

* This general model for energy-driven H+ pumping is based on the mechanism that is thought to be utilized by bacteriorhodopsin. * The transmembrane protein shown is driven through a cycle of three conformations, denoted here as A, B, and C. * In conformation C the protein has a low affinity for H+, causing it to release an H+ on the outside of the lipid bilayer; in conformation A the protein has a high affinity for H+, causing it to pick up an H+ on the inside of the lipid bilayer. * The transition from conformation B to conformation C is energetically unfavorable but is driven by being coupled to an energetically favorable reaction occurring elsewhere on the protein. * The other conformational changes lead to states of lower energy and proceed spontaneously. The cycle A → B → C → A therefore goes only one way, causing H+ to be pumped from the inside to the outside. For bacteriorhodopsin the energy for the transition B → C is provided by light, whereas in the mitochondria this energy is provided by electron transport

Answer 57

* A proton-motive force generated across the plasma membrane pumps nutrients into the cell and expels sodium. * In (A) the electrochemical proton gradient is generated in an aerobic bacterium by a respiratory chain and is then used by ATP synthase to make ATP and to transport some nutrients into the cell. * In (B) the same bacterium growing under anaerobic conditions can derive its ATP from glycolysis. Part of this ATP is hydrolyzed by ATP synthase to establish the transmembrane proton-motive force that drives transport processes.

Answer 58

* A DNA molecule; long, unbranched, linear polymer that can contain many nucleotides arranged in an irregular but nonrandom sequence and that the genetic information of a cell is contained in the linear order of the nucleotides in its DNA. * DNA molecule packaged in a separate chromosome, and the total genetic information stored in the chromosomes of an organism is said to constitute its genome. * The human genome, in contrast, contains about 3 x 109 nucleotide pairs, organized as 24 chromosomes (22 different autosomes and 2 different sex chromosomes), and thus consists of 24 different DNA molecules - each containing. * Chromosomal DNA even the slightest mechanical force will break them once the chromosomal proteins have been removed. * In diploid organisms, there are two copies of each different chromosome, one inherited from the mother and one from the father (except for the sex chromosomes in males, where a Y chromosome is inherited from the father and an X from the mother). * A typical human cell thus contains a total of 46 chromosomes and about 6 × 109 nucleotide pairs of DNA. Other mammals have genomes of similar size. By comparison, * The chromosomes in a cell change their structure and activities according to the stage of the cell-division cycle: in mitosis, or **M phase**, they are very highly condensed and transcriptionally inactive; in the other, much longer part of the division cycle, called interphase, they are less condensed and are continuously active in directing RNA synthesis.

Answer 59

* Chromosomes are generally decondensed during interphase, so that their structure is difficult to discern. * Notable exceptions are the specialized lampbrush chromosomes of vertebrate oocytes and the polytene chromosomes of insect giant secretory cells. * Studies of these two types of interphase chromosomes suggest that each long DNA molecule in a chromosome is divided into a large number of discrete domains that are folded differently. * In both lampbrush and polytene chromosomes the regions that are actively synthesizing RNA are least condensed. * Likewise, as judged by nuclease sensitivity, about 10% of the DNA in interphase vertebrate cells is in a relatively uncondensed conformation that correlates with DNA transcription in these regions. * Such "active chromatin" is biochemically distinct from the more condensed inactive regions of chromatin. All chromosomes adopt a highly condensed conformation during mitosis. * When they are specially stained, these mitotic chromosomes have a banded structure that allows each individual chromosome to be recognized unambiguously; these bands contain millions of DNA nucleotide pairs, and they reflect a coarse heterogeneity of chromosome structure that is not understood.

Answer 60

Early in oocyte differentiation each chromosome replicates to begin meiosis, and the homologous replicated chromosomes pair to form this highly extended structure containing a total of four replicated DNA molecules, or chromatids. The lampbrush chromosome stage persists for months or years as the oocyte builds up a supply of mRNA and other materials required for its ultimate development into a new individual.

Answer 61

The set of lampbrush chromosomes in many amphibians contains a total of about 10,000 chromatin loops, although most of the DNA in each chromosome remains highly condensed in the chromomeres. Each loop corresponds to a particular DNA sequence. Four copies of each loop are present in each cell, since each of the two chromosomes shown at the top consists of two closely apposed sister chromatids. This fourstranded structure is characteristic of this stage of development of the oocyte

Answer 62

* A model of chromosome structure. A section of a chromosome is shown folded into a series of looped domains, each containing perhaps 20,000 to 100,000 nucleotide pairs of doublehelical DNA condensed in a 30-nm chromatin fiber * A detailed sketch of the entire set of polytene chromosomes in one Drosophila salivary cell. These chromosomes have been spread out for viewing by squashing them against a microscope slide. Drosophilahas four chromosomes, and there are four different chromosome * The Global Structure pairs present. But each chromosome is tightly paired with its homologue (so that each pair appears as a single structure), which is not the case in most nuclei (except in meiosis). * The four polytene chromosomes are normally linked together by regions near their centromeres that aggregate to create a single large "chromocenter" ( colored region); in this preparation, however, the chromocenter has been split into two halves by the squashing procedure used.

Answer 63

* Each sister chromatid contains one of two identical daughter DNA molecules generated earlier in the cell cycle by DNA replication. * Chromosomes 1 through 22 are labeled in the approximate order of their size; a diploid cell contains two of each of these autosomes plus two sex chromosomes - two X chromosomes (female) or an X and a Y chromosome (male). * The 850 bands shown here are G bands, which stain with reagents that appear to be specific for A-T-rich DNA sequences. * The green knobson chromosomes 13, 14, 15, 21, and 22 indicate the positions of the genes that encode the large ribosomal RNAs; the green linesmark the centromere on each chromosome.

Answer 64

* The process of cell division (M phase of the cell cycle) consists of nuclear division (mitosis) followed by cytoplasmic division (cytokinesis). * The nuclear division is mediated by a microtubulebased mitotic spindle, which separates the chromosomes, while the cytoplasmic division is mediated by an actin-filament-based contractile ring. * Mitosis is largely organized by the microtubule asters that form around each of the two centrosomes produced when the centrosome duplicates. * Centrosome duplication begins during the S and G2 phases of the cell cycle, and the duplicated centrosomes separate and move to opposite sides of the nucleus at the onset of M phase to form the two poles of the mitotic spindle. * Large membrane-bounded organelles, such as the Golgi apparatus and the endoplasmic reticulum, break up into many smaller fragments during M phase, which ensures their even distribution into daughter cells during cytokinesis

Answer 65

The mitotic spindle assembles first and segregates the chromosomes. The contractile ring assembles later and divides the cell in two.

Answer 66

* The centriole pair is associated with the centrosome matrix * At a certain point in G1 phase the two centrioles separate by a few micrometers. * During S phase a daughter centriole begins to grow near the base of each old centriole and at a right angle to it. * The elongation of the daughter centriole is usually completed by G2 phase. * The two centriole pairs remain close together in a single centrosomal complex until the beginning of M phase, when the centrosome splits in two and the two halves begin to separate.

Answer 67

* The centrosome in an interphase cell duplicates to form the two poles of a mitotic spindle. * In most animal cells a centriole pair is associated with the centrosome matrix that nucleates microtubule outgrowth. * Centriole duplication begins in G1 and is completed by G2 * Initially, the two centriole pairs and associated centrosome matrix remain together as a single complex. * In early M phase this complex separates into two and each centrosome nucleates a radial array of microtubules, called an aster. * The two asters, which initially lie side by side and close to the nuclear envelope, move apart. * By late prophase the bundles of polar microtubules that interact between the two asters preferentially elongate as the two centers move apart along the outside of the nucleus. * In this way a mitotic spindle is rapidly formed. At metaphase the nuclear envelope breaks down, enabling the spindle microtubules to interact with the chromosomes; at cytokinesis the nuclear envelope reforms around the two sets of segregated chromosomes, excluding the centrosomes.

Answer 68

* The times vary for different cell types and are much shorter in embryonic cell cycles * Cytokinesis begins before mitosis ends. * The beginning of prophase (and therefore of M phase as a whole) is defined as the point in the cell cycle at which condensed chromosomes first become visible - a somewhat arbitrary criterion, since the extent of chromosome condensation appears to increase continuously during late G2. * The beginning of prometaphase is defined as the time when the nuclear envelope breaks down.

Answer 69

* During interphase the centrosome, consisting of matrix associated with a centriole pair, forms the focus for the interphase microtubule array. * By early prophase the single centrosome contains two centriole pairs (not visible); at late prophase the centrosome divides and the resulting two asters move apart. * The nuclear envelope breaks down at prometaphase, allowing the spindle microtubules to interact with the chromosomes. * At metaphase the bipolar spindle structure is clear and all the chromosomes are aligned across the middle of the spindle. * The paired daughter chromosomes, called chromatids, all separate synchronously at early anaphase and, under the influence of the microtubules, begin to move toward the poles. * By late anaphase the spindle poles have moved farther apart, increasing the separation of the two groups of chromosomes. * At telophase the daughter nuclei re-form, and by late telophase cytokinesis is almost complete, with the midbody persisting between the daughter cells

Answer 70

* Prophase: the chromosomes have condensed and are clearly visible in the cell nucleus. * Prometaphase:the nuclear envelope has broken down and the chromosomes are interacting with microtubules that emanate from the two spindle poles. * Plants do not have centrioles, but their spindle poles contain proteins related to those found in the centrosomal matrix of animal cells. * Metaphase: the chromosomes have lined up at the metaphase plate with their kinetochores located halfway between the two spindle poles. * Anaphase: the chromosomes have separated into their two sister chromatids, which are moving to opposite poles. * Telophase: the chromosomes are decondensing to form the two nuclei that are seen later * Cytokinesis: two successive stages in the formation of the cell plate(a new cell wall) are shown; the cell plate appears as a line whose direction of outgrowth is indicated by arrows in (H).

Answer 71

* Mitosis begins with prophase, which is marked by an increase in the phosphorylation of specific proteins, triggered by the activity of the mitosis-inducing protein kinase MPF. * One consequence of this phosphorylation is an unusually dynamic microtubule array nucleated on the duplicated centrosomes that form the spindle poles. * One subset of the microtubules from each centrosome becomes stabilized, apparently by cross-linking to microtubules from the opposite centrosome, to form the polar microtubules, which are thought to push the poles apart. * After the nuclear envelope breaks down in pro-metaphase, the kinetochores on condensed chromosomes can capture and stabilize other subsets of microtubules from the large numbers that continually grow out from each spindle pole. * Kinetochore microtubules from opposite spindle poles pull in opposite directions on the two kinetochores on each duplicated chromosome, creating a tension that stabilizes the kinetochore attachment. * Balanced forces on the kinetochores also bring the chromosomes to the spindle equator to form the metaphase plate. * The tubulin subunits in the spindle microtubules at metaphase undergo a continuous treadmilling from the spindle equator toward the poles * At anaphase sister chromatids suddenly detach from each other and are pulled to opposite poles (the anaphase A movement). * Meanwhile, the two spindle poles move apart (the anaphase B movement). * In telophase, the final stage of mitosis, the nuclear envelope re-forms on the surface of each group of separated chromosomes as the proteins phosphorylated at the onset of M phase are dephosphorylated

Answer 72

astral, kinetochore, polar

Answer 73

* Microtubules in an M-phase cell are much more dynamic, on average, than the microtubules at interphase. * Mammalian cells in culture were injected with tubulin that had been covalently linked to a fluorescent dye. * After the fluorescent tubulin had become incorporated into the cell's microtubules, all of the fluorescence in a small region was bleached by an intense laser beam. * The recovery of fluorescence in the bleached region of microtubules, caused by their replacement by microtubules formed from unbleached fluorescent tubulin from the soluble pool, was then monitored as a function of time. * The time for 50% recovery of fluorescence (t½) is thought to be equal to the time required for half of the microtubules in the region to depolymerize and re-form.

Answer 74

* New microtubules grow out in random directions from two nearby centrosomes. T * Anchored to the centrosome by their minus ends. * Their plus ends are "dynamically unstable" and switch suddenly from uniform growth (outward-pointing red arrows) to rapid shrinkage (inward-pointing red arrows), during which the entire microtubule often depolymerizes. * When two microtubules from opposite centrosomes interact in an overlap zone, microtubule-associated proteins are thought to cross-link the microtubules together (black beads) in a way that caps their plus ends, stabilizing them by decreasing their probability of depolymerizing. * There is evidence that the cross-linking proteins are plus-end-directed microtubule motor molecules that tend to drive the microtubules in the directions that push the poles of the spindle apart.

Answer 75

* Each kinetochore forms a plaque on the surface of the centromere. The plus ends of the microtubules bind to the kinetochores * A metaphase chromosome stained with human autoantibodies that react with specific kinetochore proteins, showing two kinetochores, one associated with each chromatid. * Electron micrograph of an anaphase chromatid with microtubules attached to its kinetochore. While most kinetochores have a trilaminar structure, the one shown (from a green alga) has an unusually complex structure with additional layers. * The kinetochore binds to the side of a growing microtubule and slides along it toward the spindle pole. * During metaphase, subunits are added to the plus end of a microtubule at the kinetochore and are removed from the minus end at the spindle pole. Thus a constant poleward flux of tubulin subunits occurs, while the microtubules maintain a constant length and remain under tension. * At anaphase the chromatid is released from attachment to its sister at the metaphase plate and the kinetochore moves rapidly up the microtubule, removing subunits from its plus end as it goes. Its attached chromatid is thereby carried to the spindle pole. Part of the chromatid movement is due to the simultaneous loss of tubulin subunits from the minus end of the microtubules at the pole.

Answer 76

* The spindle is constructed from two half-spindles each composed of kinetochore, polar, and astral microtubules. * The polarity of the microtubules is indicated by the arrowheads, which point toward the plus end. * The polar microtubules emanating from opposite spindle poles have a region of overlap where microtubule-associated proteins may cross-link them. * Note that the microtubules are antiparallel in the overlap zone.

Answer 77

* Chromatid separation at anaphase. In the transition from metaphase (A) to anaphase (B), sister chromatids are pulled apart by spindle microtubules * The two processes that separate sister chromatids at anaphase. * In anaphase A the chromatids are pulledtoward opposite poles by forces associated with shortening of their kinetochore microtubules. The force driving this movement is thought to be generated mainly at the kinetochore. * In anaphase B the two spindle poles move apart. It is likely that the forces driving anaphase B are similar to those that cause the centrosome to split and separate into two spindle poles at prophase * There is evidence that two separate forces are responsible for anaphase B: the elongation and sliding of the polar microtubules past one another pushes the two poles apart, and outward forces exerted by the astral microtubules at each spindle pole act to pull the poles away from each other, toward the cell surface.

Answer 78

* Cell division ends as the cytoplasmic contents are divided by the process of cytokinesis and the chromosomes decondense and resume RNA synthesis. * Cytokinesis appears to be guided by organized bundles of actin filaments in eucaryotic cells as diverse as animals, plants, and fungi. * In animal cells the mitotic spindle determines when and where cytokinesis occurs, with the contractile ring of actin and myosin filaments forming midway between the spindle pole asters. * Whereas most cells divide symmetrically, in some cases the spindle is specifically positioned to create an asymmetric cell division: a particular cell can divide into one small cell and one large one, for example, or a specific cytoplasmic component can be moved to one side of a cell prior to cytokinesis so that it is inherited by only one of the two otherwise equal daughter cells. * Cytokinesis occurs by a special mechanism in higher plant cells, where the cytoplasm is partitioned by the construction of a new cell wall, the cell plate, inside the cell. * The position of the cell plate is determined by the position of a preprophase band of microtubules and actin filaments. * The organization of mitosis in some protozoa and in fungi differs from that in animals and plants, suggesting how the complex process of eucaryotic cell division may have evolved.

Answer 79

* Different chromosome separation mechanisms are used by different organisms. Some of these may have been intermediate stages in the evolution of the mitotic spindle of higher organisms. For all of the examples except bacteria, only the central nuclear region of the cell is shown. * Bacteria: daughter chromosomes attached to the plasma membrane are seperated by ingrowth of plasma membrane between them * Typical Dinoflagellates: Several bundles of microtubules pass through tunnels to establish polarity division and chromosomes move apart through the iner nuclear membrane * Hypermastigotes: A single central spindle is formed, chromosomes are attaches by kinetochores to the nuclear membrane and interact with spindle fibres through kineochore microtubules * Yeasts and Diatoms: nuclear envelope remains intact and polar spindle microtubules form inside the nucleus, a single kinetochore molecule attaches each chromosome to a pole * Animals: spindle fibers form outside the nucleus, at prometaphase nuclear membrane breaks down to allow chromosomes to capture spindle microtubules that become kinetochore microtubules

Answer 80

* Many cells in tissues are linked to one another and to the extracellular matrix at specialized contact sites called cell junctions. * Cell junctions fall into three functional classes: occluding junctions, anchoring junctions, and communicating junctions. * Tight junctions are occluding junctions that play a critical part in maintaining the concentration differences of small hydrophilic molecules across epithelial cell sheets by * (1) sealing the plasma membranes of adjacent cells together to create a continuous, impermeable, or semipermeable barrier to diffusion across the cell sheet * (2) acting as barriers in the lipid bilayer to restrict the diffusion of membrane transport proteins between the apical and the basolateral domains of the plasma membrane in each epithelial cell. * The main types of anchoring junctions in vertebrate tissues are adherens junctions, desmosomes, and hemidesmosomes. * Adherens junctions are connecting sites for bundles of actin filaments, whereas desmosomes and hemidesmosomes are connecting sites for intermediate filaments. * Septate junctions also serve as connecting sites for actin filaments, but only in invertebrate tissues. * Gap junctions are communicating junctions composed of clusters of channel proteins that allow molecules smaller than about 1000 daltons to pass directly from the inside of one cell to the inside of the other. Gap junctions are important in coordinating the activities of electrically active cells, and they are thought to play a coordinating role in other groups of cells as well. * Cells connected by such junctions share many of their inorganic ions and other small molecules and are therefore chemically and electrically coupled. * Plasmodesmata are the only intercellular junctions in plants; they function like gap junctions even though their structure is entirely different * Anchoring junctions in an epithelial tissue join cytoskeletal filaments from cell to cell and from cell to extracellular matrix

Answer 81

* Transport proteins are confined to different regions of the plasma membrane in epithelial cells of the small intestine. * This segregation permits a vectorial transfer of nutrients across the epithelial sheet from the gut lumen to the blood. * Tight junctions are thought to confine the transport proteins to their appropriate membrane domains by acting as diffusion barriers within the lipid bilayer of the plasma membrane; these junctions also block the backflow of glucose from the basal side of the epithelium into the gut lumen * Tight junctions allow cell sheets to serve as barriers to solute diffusion * It is postulated that the sealing strands that hold adjacent plasma membranes together are formed by continuous strands of transmembrane junctional proteins, which make contact across the intercellular space and create a seal.

Answer 82

Adhesion belts between epithelial cells in the small intestine. This beltlike anchoring junction encircles each of the interacting cells. Its most obvious feature is a contractile bundle of actin filaments running along the cytoplasmic surface of the junctional plasma membrane. The actin filaments are joined from cell to cell by transmembrane linker proteins (cadherins), whose extracellular domain binds to the extracellular domain of an identical cadherin molecule on the adjacent cell

Answer 83

It is thought that the oriented contraction of the bundle of actin filaments running along adhesion belts causes the epithelial cells to narrow at their apex and that this plays an important part in the rolling up of the epithelial sheet into a tube

Answer 84

The keratin filament networks of adjacent cells are indirectly connected to one another through desmosomes and to the basal lamina through hemidesmosomes.

Answer 85

(A) The cytoplasmic channels of plasmodesmata pierce the plant cell wall and connect all cells in a plant together. (B) Each plasmodesma is lined with plasma membrane common to two connected cells. It usually also contains a fine tubular structure, the desmotubule, derived from smooth endoplasmic reticulum.

Answer 86

Cells dissociated from various tissues of vertebrate embryos preferentially reassociate with cells from the same tissue when they are mixed together. This tissue-specific recognition process in vertebrates is mainly mediated by a family of Ca2+-dependent cell-cell adhesion proteins called cadherins, which hold cells together by a homophilic interaction between transmembrane cadherin proteins on adjacent cells. In order to hold cells together, the cadherins must be attached to the cortical cytoskeleton. Most animal cells also have Ca2+-independent cell-cell adhesion systems that mainly involve members of the immunoglobulin superfamily, which includes the neural cell adhesion molecule N-CAM. As even a single cell type uses multiple molecular mechanisms in adhering to other cells (and to the extracellular matrix), the specificity of cell-cell adhesion seen in embryonic development must result from the integration of a number of different adhesion systems, some of which are associated with specialized cell junctions while others are not.