Midterm Bio Textbook Content PDF

for more ebook/ testbank/ solution manuals requests: email [email protected]. T C e cell is the simplest entity that can exist as an independent unit of life. Every known living organism is either a single cell or an ensemble of a few to many cells (Fig. 1.9). Most bacteria like those in Pasteur's experiment, yeasts, and the tiny algae that oat in oceans and ponds spend their lives as single cells. In contrast, plants and animals contain billions to trillions of cells that function in a coordinated fashion. FIG. 1.9 Unicellular and multicellular organisms. All living organisms are made up of cells: (a) bacteria; (b) brewer's yeast; (c) algae; (d) cheetahs; (e) humans. Most cells are tiny, with dimensions that are well below the threshold of detection by the naked eye (Fig. 1.10). e cells that make up the layers of your skin (Fig. 1.10a) average about 30 micrometers (mm), or 0.03 mm, in diameter, which means that nearly 20 would t in a row across the period at the end of this sentence. Many bacteria are less than a micrometer long. Certain specialized cells, however, can be uite large. Some nerve cells in humans, like the ones pictured in Fig. 1.10b, extend slender projections known as axons for short and long distances, and the cannonball-sized e of an ostrich in Fig. 1.10c is a single giant cell. FIG. 1.10 Cell diversity. Cells vary greatly in size and shape: (a) skin cells; (b) nerve cells; (c) ostrich egg. e types of cell just mentioned -- bacteria, yeasts, skin cells, nerve cells, and an e -- seem very di erent, but all are organized along broadly similar lines. In general, all cells have a discrete boundary that separates the interior of the cell from its external environment; they contain a stable blueprint of information in molecular form; and they have the ability to harness materials and energy from the environment. Membranes define cells and spaces within cells. e rst essential feature of all cells is a cell membrane, or plasma membrane, that separates the living material within the cell from the nonliving environment around it (Fig. 1.11). is boundary between inside and outside does not mean that cells are closed systems independent of the environment. On the contrary, there is an active and dynamic interplay between cells and their surroundings that is mediated by the cell membrane. All cells re uire sustained contributions from their surroundings, both simple ions and the building blocks re uired to manufacture macromolecules. Cells also release waste products into the environment. As you will learn in Chapter 3, the cell membrane controls the movement of materials into and out of the cell. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 1.11 The cell membrane. The cell membrane surrounds all cells and controls the exchange of material with the environment. In addition to the cell membrane, many cells have internal membranes that divide the cell into discrete compartments, each specialized for a particular function. A notable example of such a compartment is the nucleus, which houses the cell's DNA. Like the cell membrane, the nuclear membrane selectively controls movement of molecules into and out of it. As a result, the nucleus occupies a discrete space within the cell, separate from the space outside the nucleus, called the cytoplasm. Not all cells have a nucleus. In fact, cells can be grouped into two broad classes depending on whether they have a nucleus. Cells without a nucleus are called prokaryotes, and cells with a nucleus are eukaryotes. e rst cells that emerged about 4 billion years ago were prokaryotic. eir descendants include the familiar bacteria, found today nearly everywhere that life can persist. Some prokaryotes live in peaceful coexistence with humans, inhabiting our gut and aiding digestion (Case 5 e Human Microbiome). Others cause disease -- salmonellosis, tuberculosis, and cholera are familiar examples of such bacterial diseases. e success of prokaryotes depends in part on their small size, their ability to reproduce rapidly, and their ability to obtain energy and nutrients from diverse sources. Most prokaryotes live as single-celled organisms, but some have simple multicellular forms. Eukaryotes evolved much later, roughly 2 billion years ago, from prokaryotic ancestors. Eukaryotes include familiar groups such as animals, plants, and fungi, along with a wide diversity of single-celled microorganisms called protists. Eukaryotic organisms exist as single cells like yeasts or as multicellular organisms like humans. In multicellular organisms, cells may specialize to perform di erent functions. For example, in humans, muscle cells contract; red blood cells carry oxygen to tissues; and skin cells provide an external barrier. e terms "prokaryotes" and "eukaryotes" are useful in drawing attention to a fundamental distinction between these two groups of cells. However, today, biologists recognize three major groups, or domains of life -- Bacteria, Archaea, and Eukarya (Chapters 24 and 25). Bacteria and Archaea are mostly single-celled microorganisms that lack a nucleus and are therefore prokaryotes, whereas Eukarya have a nucleus and are eukaryotic. Many Archaea ourish under seemingly hostile conditions, such as those found in the extreme heat of the hot springs in Yellowstone National Park. Nucleic acids store and transmit information needed for growth, function, and reproduction. e second essential feature of a cell is its ability to store and transmit information. To accomplish this, cells re uire a stable archive of information that encodes and helps determine their physical attributes. Just as the construction of a house re uires a blueprint that de nes the walls, plumbing, and electrical wiring, organisms re uire an accessible and reliable archive of information that helps determine their structure and metabolic activities. is information can be transmitted to other cells through cell division. To divide, cells must be able to copy their archive of information rapidly and accurately. In all living organisms, the information archive is a remarkable molecule known as deoxyribonucleic acid, or DNA (Fig. 1.12). FIG. 1.12 A molecule of DNA. DNA is a double helix made up of varying sequences of four diﬀerent subunits. In cells, DNA takes the form of a double helix, with each strand made up of varying se uences of four di erent kinds of molecules connected end to end. ese molecular subunits provide a four-letter alphabet that encodes cellular information. Speci cally, the information encoded in DNA is used as a model, or template, for the synthesis of a closely related molecule called ribonucleic acid, or RNA. Specialized molecular structures then "read" the RNA molecule to determine which building blocks to use to build a protein. Proteins are molecules that provide structure and do much of the work of the cell. Virtually every aspect of the cell -- its internal architecture, its shape, its ability to move, and its various chemical reactions -- depends on proteins. e synthesis of RNA from a DNA template is called transcription, a term that describes the copying of information from one form into another. e synthesis of proteins from an RNA template is called translation. is process converts information in the language of nucleic acids to information in the language of proteins. e pathway from DNA to RNA (speci cally to a form of RNA called messenger RNA, or mRNA) to protein is known as the central dogma of molecular biology (Fig. 1.13). e central dogma describes the basic ow of information in a cell, and, while there are exceptions, it constitutes a fundamental principle in biology. As proteins are ultimately encoded by DNA, we can de ne speci c stretches or segments of DNA according to the proteins that they encode. is is the simplest de nition of a gene: the DNA se uence that corresponds to a functional product, such as a protein. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 1.13 The central dogma of molecular biology. The central dogma defines the usual flow of genetic information from DNA to RNA to protein in cells. DNA has another remarkable feature. In addition to storing information that can be used for the synthesis of proteins, it is easily copied, or replicated. DNA replication allows genetic information to be passed from cell to cell or from an organism to its progeny. Each organism's DNA archive can be stably and reliably passed from generation to generation in large part because of its double-stranded helical structure. During replication, each strand of the double helix serves as a template for a new strand. Replication is necessarily precise and accurate because mistakes introduced into the cell's information archive may be lethal to the cell. at said, errors in DNA can and do occur during the process of replication, and environmental insults can damage DNA as well. Such changes to DNA se uence are known as mutations. ey can spell death for the cell, or they can lead to the variations that underlie the diversity of life and the process of evolution. Metabolism is the set of chemical reactions that sustains life. A third key feature of cells is the ability to harness energy from the environment. Let's go back to our introductory example of eating an apple. e apple contains sugars, which store energy in their chemical bonds. By breaking down sugar, our cells harness this energy and convert it into a form that can be used to do the work of the cell. Energy from the food we eat allows us to grow, move, communicate, and do all the other things that we do. Organisms ac uire energy from just two sources -- the sun and chemical compounds. e term metabolism describes chemical reactions by which cells convert energy from one form to another and build or break down molecules. ese reactions are re uired to sustain life. Regardless of their source of energy, all organisms use chemical reactions to break down molecules, in the process releasing energy that is stored in a chemical form called adenosine triphosphate, or ATP. ATP provides a readily accessible form of chemical energy, enabling cells to carry out all sorts of work, including growth, division, and moving substances into and out of the cell. Many metabolic reactions are highly conserved among organisms, meaning the same reactions are found in many di erent species. is observation su ests that the reactions evolved early in the history of life and have been maintained for billions of years because of their fundamental importance to cellular biochemistry. Self-Assessment Questions What does it mean to say that a cell is life's functional unit? a cell is what makes up life. All living things are made from cells.. M C B Atoms can combine with other atoms to form molecules, which are groups of two or more atoms attached together that act as a single unit. When two atoms form a molecule, the individual atoms interact through what is called a chemical bond, a form of attraction between atoms that holds them together. e ability of atoms to form bonds with other atoms explains in part why just a few types of element can come together in many di erent ways to make a variety of molecules that can carry out diverse functions in a cell. ere are several ways in which atoms can interact with one another, and therefore many di erent types of chemical bond. A covalent bond results when two atoms share electrons. e ability of atoms to combine with other atoms is determined in large part by the electrons farthest from the nucleus -- those in the outermost orbitals of an atom. ese electrons are called valence electrons, and as discussed earlier, they are at the highest energy level of the atom. When atoms combine with other atoms to form a molecule, the atoms share valence electrons with each other. Speci cally, when the outermost orbitals of two atoms come into proximity to each other, two atomic orbitals each containing one electron merge into a single orbital containing a full complement of two electrons. e merged orbital is called a molecular orbital, and each shared pair of electrons constitutes a covalent bond that holds the atoms together. We can represent a speci c molecule by its chemical formula, which is written as the letter abbreviation for each element followed by a subscript giving the number of that type of atom in the molecule. Among the simplest molecules is hydrogen gas, illustrated in Fig. 2.5, which consists of two covalently bound hydrogen atoms as indicated by the chemical formula H. Each hydrogen atom has a single electron 2 in a spherical orbital. When the atoms join to create a molecule, the two orbitals merge into a single molecular orbital containing two electrons that are shared by the hydrogen atoms. A covalent bond between atoms is denoted by a single line connecting the two chemical symbols for the atoms, as shown in the structural formula at the top of Fig. 2.5. FIG. 2.5 A covalent bond. A covalent bond is formed when two atoms share a pair of electrons in a molecular orbital. Two adjacent atoms can sometimes share two pairs of electrons, forming a double bond, denoted by a double line connecting the two chemical symbols for the atoms. In this case, four orbitals, each occupied by a single electron, merge to form two molecular orbitals. Molecules tend to be most stable when the two atoms forming a bond share enough electrons to ll the outermost shell. e outermost shell of a hydrogen atom can hold two electrons; by comparison, this shell can hold eight electrons in carbon, nitrogen, and oxygen atoms. e tendency of elements to prefer eight electrons in this shell, thus allowing for the formation of stable molecules, is known as the octet rule, and it applies to many, but not all, elements. For example, as shown in Fig. 2.6, one carbon atom (C, with four valence electrons) combines with four hydrogen atoms (H, with one valence electron each) to form CH (methane); nitrogen (N, with ve valence electrons) combines 4 for more ebook/ testbank/ solution manuals requests: email [email protected] with three H atoms to form NH (ammonia); and oxygen (O, with six valence electrons) combines with two H atoms to form H 3 2O (water). Interestingly, the elements in the next row of any column behave similarly. is is just one example of the recurring, or periodic, behavior of the elements. FIG. 2.6 Four molecules. Atoms tend to combine in such a way as to complete the complement of electrons in the outer shell. A polar covalent bond is characterized by unequal sharing of electrons. In hydrogen gas (H ), the electrons are shared e ually by the two hydrogen atoms. In many bonds, however, the electrons are not shared 2 e ually by the two atoms. e result is that part of the molecule has a slight positive charge, denoted as d , and another part has a slight + negative charge, denoted as d. A notable example is the bonds in a water molecule (H [?] 2O) : it consists of two hydrogen atoms, each covalently bound to a single oxygen atom (Fig. 2.7). FIG. 2.7 A polar covalent bond. In a polar covalent bond, like the bonds shown here for a water molecule, the two atoms do not share electrons equally. In a molecule of water, the electrons are more likely to be located near the oxygen atom. e une ual sharing of electrons results from a di erence in the ability of the atoms to attract electrons, a property known as electronegativity. Electronegativity tends to increase across a row in the periodic table; as the number of positively charged protons across a row increases, negatively charged electrons are held more tightly to the nucleus. erefore, oxygen is more electronegative than hydrogen and attracts electrons more readily than does hydrogen. In a molecule of water (Fig. 2.7), oxygen has a slight negative charge (d ), while the two hydrogen atoms have a slight positive charge (d ). When [?] + electrons are shared une ually between the two atoms, the resulting interaction is described as a polar covalent bond. A covalent bond between atoms that have the same, or nearly the same, electronegativity is described as a nonpolar covalent bond, which means that the atoms share the bonding electron pair almost e ually. Nonpolar covalent bonds include those in gaseous hydrogen (H ) and 2 oxygen (O ), as well as carbon-carbon (C[?]C) and carbon-hydrogen (C[?]H) bonds. Molecules held together by nonpolar covalent bonds are 2 important in cells because they do not mix well with water. An ionic bond forms between oppositely charged ions. In a molecule of water, the di erence in electronegativity between the oxygen and hydrogen atoms leads to une ual sharing of electrons. In more extreme cases, when an atom of very high electronegativity is paired with an atom of very low electronegativity, the di erence in electronegativity is so great that the electronegative atom "steals" the electron from its less electronegative partner (Fig. 2.8). In this case, the atom with the extra electron has a negative charge and is a negative ion. e atom that has lost an electron has a positive charge and is a positive ion. e two ions are not covalently bound, but because opposite charges attract, they associate with each other in an ionic bond (Fig. 2.8a). FIG. 2.8 An ionic bond. (a) Sodium chloride (salt, NaCl) is formed by the attraction of two ions. (b) In solution, the ions are surrounded by water molecules. When sodium chloride is placed in water, the salt dissolves to form sodium ions (Na + ) that have lost an electron and so are positively charged and chloride ions (Cl [?] ) that have gained an electron and so are negatively charged. In solution, the two ions are pulled apart and become surrounded by water molecules. e negatively charged ends of water molecules are attracted to the positively charged sodium ion, and the positively charged ends of other water molecules are attracted to the negatively charged chloride ion (Fig. 2.8b). Only as the water evaporates do the concentrations of Na and Cl increase to the point where the ions join and precipitate as salt crystals. + [?] A chemical reaction involves breaking and forming chemical bonds. e chemical bonds that link atoms in molecules can change in a chemical reaction. During a chemical reaction, atoms keep their identity, but the atoms to which they are bonded change. e starting substances are called reactants and the ending ones are called products. erefore, during a chemical reaction, reactants are transformed into products. For example, two molecules of hydrogen gas (2H ) and one molecule of oxygen gas (O ) can react to form two molecules of water (2H 2 2 , as 2O) shown in Fig. 2.9. In this reaction, the numbers of each type of atom are conserved, but their arrangement is di erent in the reactants and the products. Speci cally, the H[?]H bond in hydrogen gas and the O=O bond in oxygen are broken. At the same time, each oxygen atom forms new covalent bonds with two hydrogen atoms, forming two molecules of water. In fact, this reaction is the origin of the word "hydrogen," which literally means "water former." e reaction releases a good deal of energy and is used in some rockets as a booster in satellite launches. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 2.9 A chemical reaction. During a chemical reaction, atoms retain their identity, but their connections change as bonds are broken and new bonds are formed. In biological systems, chemical reactions provide a way to build and break down molecules for use by the cell, as well as to harness energy, which can be held in chemical bonds (Chapter 6). Self-Assessment Questions From their positions in the periodic table (Fig. 2.3), can you predict how many lithium (Li) atoms and hydrogen atoms can combine to form a molecule? What are the di erences between covalent bonds and polar covalent, hydrogen, and ionic bonds?. O M Chemical processes in the cell depend on just a few classes of carbon-based molecules. Proteins provide structural support and act as catalysts that facilitate chemical reactions. Nucleic acids encode and transmit genetic information. Carbohydrates provide a source of energy and make up the cell wall in bacteria, plants, and algae. Lipids make up cell membranes, store energy, and act as signaling molecules. ese molecules are all large, consisting of hundreds or thousands of atoms, and many are polymers, complex molecules made up of repeated simpler units connected by covalent bonds. Proteins are polymers of amino acids, nucleic acids are polymers of nucleotides, and carbohydrates such as starch are polymers of simple sugars. Lipids are di erent in that they are not de ned by a chemical structure, but instead because they are hydrophobic. Building macromolecules from simple, repeating units provides a means of generating an almost limitless chemical diversity. Indeed, in macromolecules, the building blocks of polymers play a role much like that of the letters in words. In written language, a change in the content or order of letters changes the meaning of the word (or renders it meaningless). For example, by reordering the letters of the word SILENT you can write LISTEN, a word with a di erent meaning. Similarly, rearranging the building blocks that make up macromolecules provides an important way to make a large number of diverse macromolecules whose functions di er from one to the next. e building blocks of polymers are also called subunits or monomers. In the following sections, we focus on the building blocks of these four key molecules of life, reserving a discussion of the structure and function of the macromolecules for Chapters 3-8. Functional groups add chemical character to carbon chains. e simple repeating units of polymers are o en based on a nonpolar core of carbon atoms. Attached to these carbon atoms are functional groups, groups of one or more atoms that have particular chemical properties on their own, regardless of what they are attached to. Among the functional groups fre uently encountered in biological molecules are those listed in Table 2.1. e nitrogen, oxygen, phosphorus, and sulfur atoms in these functional groups are more electronegative than the carbon atoms, and functional groups containing these atoms are polar. e methyl group, by contrast, is nonpolar. TABLE 2.1 Functional Groups Commonly Observed in Biological Molecules. NAME FORMULA STRUCTURE PROPERTIES COMMONLY FOUND IN Amino [?]NH 2 Polar, positively charged at the pH of a cell, behaves as a base, Amino acids, proteins hydrophilic Amide [?]C(=O)NH[?] Polar, hydrophilic Proteins Carboxyl [?]COOH Polar, negatively charged at the pH of a cell, behaves as an acid, Fatty acids, amino acids, proteins hydrophilic for more ebook/ testbank/ solution manuals requests: email [email protected] Carbonyl >C=O Polar, hydrophilic Carbohydrates, proteins Hydroxyl [?]OH [?]O[?]H Polar, hydrophilic Carbohydrates, proteins, nucleic acids Sulfhydryl [?]SH [?]S[?]H Polar, forms S[?]S disulfide bonds The amino acid cysteine, proteins Methyl [?]CH 3 Nonpolar Amino acids, proteins, nucleic acids Phosphate [?]OPO 3 H 2 Polar, negatively charged at the pH of a cell, hydrophilic Phospholipids, nucleic acids, ATP Because many functional groups are polar, molecules that contain these groups -- molecules that would otherwise be nonpolar -- become polar. As a result, these molecules become soluble in the cell's a ueous environment. In other words, they disperse in solution throughout the cell. Moreover, because many functional groups are polar, they are reactive. Notice in the following sections that the reactions joining simpler molecules into polymers usually take place between functional groups. Proteins are composed of amino acids. Proteins do much of the cell's work. Some proteins function as catalysts that accelerate the rates of chemical reactions (in which case they are called enzymes); others act as structural components necessary for cell shape and movement. e human body contains many thousands of distinct types of protein that perform a wide range of functions. Since proteins consist of amino acids linked covalently to form a chain, we need to examine the chemical features of amino acids to understand the diversity and versatility of proteins (Fig. 2.17). FIG. 2.17 Amino acids and peptide bonds. (a) An amino acid contains four groups attached to a central carbon atom. (b) In the environment of a cell, the amino group gains a proton and the carboxyl group loses a proton. (c) Peptide bonds link amino acids to form a protein. e general structure of an amino acid is shown in Fig. 2.17a. Each amino acid contains a central carbon atom, called the a (alpha) carbon, covalently linked to four groups: an amino group ([?]NH ), a carboxyl group ([?]COOH), a hydrogen atom (H), and an R group, or side 2 chain, which di ers from one amino acid to the next. e identity of each amino acid is determined by the structure and composition of the side chain. e side chain of the amino acid glycine is simply H, for example, and that of alanine is CH. In most amino acids, the a carbon is 3 covalently linked to four di erent groups. Glycine is the exception, since its R group is a hydrogen atom. At the pH commonly found in a cell (pH 7.4), the amino and carboxyl groups are ionized (charged) owing to interactions with the surrounding medium. e amino group gains a proton ([?]NH + 3 ) and the carboxyl group loses a proton ([?]COO [?] , as shown in Fig. 2.17b. ) Amino acids are linked in a chain to form a protein (Fig. 2.17c). e carbon atom in the carboxyl group of one amino acid is joined to the nitrogen atom in the amino group of the next by a covalent linkage called a peptide bond. In Fig. 2.17c, the chain of amino acids includes four amino acids. e formation of a peptide bond involves the loss of a water molecule. at is, to form a C[?]N bond, the carbon atom of the carboxyl group releases a hydroxyl group ([?]OH) and the nitrogen atom of the amino group releases a hydrogen atom (H). is hydroxyl group and hydrogen atom then combine to form a water molecule (H 2 O). is type of reaction is called a dehydration reaction and also occurs in the linking of subunits to form other polymers such as complex carbohydrates. Cellular proteins are composed of combinations of 20 di erent amino acids, each of which can be classi ed according to the chemical properties of its R group. e particular se uence, or order, in which amino acids are present in a protein determines how it folds into its three-dimensional structure. e three-dimensional structure, in turn, determines the protein's function. In Chapter 5, we examine how the se uence of amino acids in a particular protein is speci ed and discuss how proteins fold into their three-dimensional shapes. Nucleic acids encode genetic information in their nucleotide sequence. for more ebook/ testbank/ solution manuals requests: email [email protected] Nucleic acids are examples of informational molecules -- that is, large molecules that carry information in the se uence of nucleotides that make them up. is molecular information is much like the information carried by the letters in an alphabet, but in the case of nucleic acids, the information is in chemical form. e nucleic acid deoxyribonucleic acid (DNA) is the genetic material in all cellular organisms. It is transmitted from parents to o spring, and it contains the information needed to specify the amino acid se uence of all the proteins synthesized in an organism. e nucleic acid ribonucleic acid (RNA) has multiple functions; it is a key player in protein synthesis and the regulation of gene expression. DNA and RNA are long molecules consisting of nucleotides bonded covalently one to the next. A nucleotide, in turn, is composed of three components: a 5-carbon sugar, a nitrogen-containing compound called a base, and one or more phosphate groups (Fig. 2.18). e sugar in RNA is ribose, and the sugar in DNA is deoxyribose. e sugars di er in that ribose has a hydroxyl (OH) group on the second carbon (designated the 2 carbon), whereas deoxyribose has a hydrogen atom at this position (hence, deoxyribose). (By convention, the carbons in the sugar are numbered with primes -- 1 , 2 , and so on -- to distinguish them from carbons in the base -- 1, 2, and so on.) ′ ′ FIG. 2.18 Nucleotides. Shown here is a ribonucleotide and a deoxyribonucleotide, the building blocks of RNA and DNA, respectively. e bases are built from nitrogen-containing rings and are of two types (Fig. 2.19). e pyrimidine bases (Fig. 2.19a) have a single ring and include cytosine (C), thymine (T), and uracil (U). e purine bases (Fig. 2.19b) have a double ring and include guanine (G) and adenine (A). DNA contains the bases A, T, G, and C, whereas RNA contains the bases A, U, G, and C. Just as the order of amino acids provides the information carried in proteins, so, too, does the se uence of nucleotides determine the information in DNA and RNA molecules. FIG. 2.19 Pyrimidine bases and purine bases. (a) Pyrimidines have a single-ring structure, and (b) purines have a double-ring structure. In DNA and RNA, each adjacent pair of nucleotides is connected by a phosphodiester bond, which forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide (Fig. 2.20). Like the formation of a peptide bond, the formation of a phosphodiester bond involves the formation and release of a water molecule. FIG. 2.20 The phosphodiester bond. Phosphodiester bonds link successive deoxyribonucleotides, forming the backbone of the DNA strand. DNA in cells usually consists of two strands of nucleotides twisted around each other in the form of a double helix (Fig. 2.21). e sugar- phosphate backbones of the strands wrap like a ribbon around the outside of the double helix, and the bases point inward (Fig. 2.21a). e bases form speci c purine-pyrimidine pairs that are complementary: where one strand carries an A, the other carries a T; and where one strand carries a G, the other carries a C. Base pairing results from hydrogen bonding between the bases (Fig. 2.21b). for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 2.21 The structure of DNA. (a) DNA most commonly occurs in the form of a double helix, with the sugar and phosphate groups forming the backbone and the bases oriented inward. (b) The bases are complementary: A is always paired with T, and G is always paired with C. Base pairing results from hydrogen bonds. e genetic information in DNA is contained in the se uence, or order, in which successive nucleotides occur along the molecule. Successive nucleotides along a DNA strand can occur in any order, so a long molecule could contain any of an immense number of possible nucleotide se uences. is is one reason why DNA is an e cient carrier of genetic information. In Chapter 4, we consider the structure and function of DNA and RNA in greater detail. Complex carbohydrates are made up of simple sugars. Many of us, when we feel tired, reach for a candy bar for a uick energy boost. e energy in a candy bar comes from sugars, which are uickly broken down to release energy. Sugars belong to a class of molecules called carbohydrates, distinctive molecules composed of C, H, and O atoms, usually in the ratio 1:2: 1. Carbohydrates are a major source of energy for metabolism. Sugars (also called saccharides) are the simplest carbohydrates. Simple sugars are linear or, far more commonly, cyclic molecules containing ve or six carbon atoms. All 6-carbon sugars have the same chemical formula (C 6 H 12 O 6 ) and di er only in con guration. Glucose (the product of photosynthesis), galactose (found in dairy products), and fructose (a commercial sweetener) are examples; they share the same formula (C 6 H 12 O 6 ) but di er in the arrangement of their atoms (Fig. 2.22). FIG. 2.22 Structural formulas for some 6-carbon sugars. Glucose and galactose have an aldehyde group, while fructose has a ketone group. A simple sugar is also called a monosaccharide (mono means "one"), and linking two simple sugars together by a covalent bond forms a disaccharide (di means "two"). Sucrose (C , or table sugar, is a disaccharide that combines one molecule each of glucose and fructose. 12 H 22 O 11 ) Simple sugars combine in many ways to form polymers called polysaccharides (poly means "many") that provide long-term energy storage (starch and glycogen) or structural support (cellulose in plant cell walls). Long, branched chains of monosaccharides are called complex carbohydrates. Let's take a closer look at monosaccharides, the simplest sugars. Monosaccharides are unbranched carbon chains with either an aldehyde (HC=O) or a ketone (C=O) group (Fig. 2.22). Monosaccharides with an aldehyde group are called aldoses, and those with a ketone group are known as ketoses. In both types of monosaccharide, the other carbons each carry one hydroxyl ([?]OH) group and one hydrogen (H) atom. When the linear structure of a monosaccharide is written with the aldehyde or ketone group at the top, the carbons are numbered from top to bottom. Almost all of the monosaccharides in cells are in ring form (Fig. 2.23), rather than linear structures. To form a ring, one end of the chain bonds to another part of the chain: the carbon in the aldehyde or ketone group forms a covalent bond with the oxygen of a hydroxyl group carried by another carbon in the same molecule. For example, cyclic glucose is formed when carbon 1, which is part of an aldehyde group, forms a covalent bond with the oxygen atom of the hydroxyl group on carbon 5. e cyclic structure is o en depicted as a planar hexagon like the one shown in Fig. 2.23, with the covalent bonds in the ring indicated by thick lines in the foreground. e groups attached to any carbon project either above or below the ring. When the ring is formed, the aldehyde oxygen becomes a hydroxyl group. e presence of the polar hydroxyl groups through the sugar ring makes these molecules highly soluble in water. FIG. 2.23 Cyclic form of glucose. The cyclic, or circular, form of glucose is formed when the carbon in the aldehyde group forms a covalent bond with the oxygen of a hydroxyl group attached to another carbon of the same molecule. Monosaccharides, especially 6-carbon sugars, are the building blocks of complex carbohydrates. Monosaccharides are attached to each other by covalent bonds called glycosidic bonds (Fig. 2.24). As with peptide bonds, the formation of glycosidic bonds involves the release of a water molecule. A glycosidic bond is formed between carbon 1 of one monosaccharide and a hydroxyl group carried by a carbon atom in a di erent monosaccharide molecule. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 2.24 Glycosidic bonds. Glycosidic bonds link carbohydrate molecules together. In this example, they link glucose monomers together to form the polysaccharide starch. Carbohydrate diversity stems in part from the monosaccharides that make up carbohydrates, similar to the way that protein and nucleic acid diversity stems from the se uence of their subunits. Some complex carbohydrates are composed of a single type of monosaccharide, while others are a mix of di erent kinds of monosaccharide. Starch, for example, is a sugar storage molecule in plants composed completely of glucose molecules, whereas pectin, a component of the cell wall, contains up to ve di erent types of monosaccharide. Lipids are hydrophobic molecules. Proteins, nucleic acids, and carbohydrates all are polymers made up of smaller, repeating units with a de ned structure. Lipids, however, are di erent. Instead of being de ned by a chemical structure, they share a particular property: lipids are all hydrophobic. Because they share a property rather than a structure, lipids are a chemically diverse group of molecules. ey include the familiar fats that make up part of our diet, components of cell membranes, and signaling molecules. Let's brie y consider each in turn. Triacylglycerol is an example of a lipid that is used for energy storage. It is the major component of animal fat and vegetable oil. A triacylglycerol molecule is made up of three fatty acids joined to glycerol (Fig. 2.25). A fatty acid is a long chain of carbon atoms attached to a carboxyl group ([?]COOH) at one end (Figs. 2.25a and 2.25b). Glycerol is a 3-carbon molecule with OH groups attached to each carbon (Fig. 2.25c). e carboxyl end of each fatty acid chain attaches to glycerol at one of the OH groups (Fig. 2.25d), releasing a molecule of water. FIG. 2.25 Triacylglycerol and its components. Triacylglycerol consists of a glycerol molecule covalently linked to three fatty acids. Fatty acids di er in the length of their hydrocarbon chain -- that is, they di er in the number of carbon atoms in the chain. (A hydrocarbon is a molecule composed entirely of carbon and hydrogen atoms.) Most fatty acids in cells contain an even number of carbon atoms because they are synthesized by the stepwise addition of 2-carbon units. Some fatty acids have one or more carbon-carbon double bonds; these double bonds can di er in number and location. Fatty acids that do not contain double bonds are described as saturated. Because there are no double bonds, the maximum number of hydrogen atoms is attached to each carbon atom, so all of the carbon atoms are said to be "saturated" with hydrogen atoms (Fig. 2.25a). Fatty acids that contain carbon-carbon double bonds are unsaturated (Fig. 2.25b). e chains of saturated fatty acids are straight, while the chains of unsaturated fatty acids have a kink at each double bond. Triacylglycerols can contain di erent types of fatty acids attached to the glycerol backbone. e hydrocarbon chains of fatty acids do not contain polar covalent bonds like those in a water molecule. Instead, their electrons are distributed uniformly over the whole molecule, so these molecules are uncharged. As a conse uence, triacylglycerols are all extremely hydrophobic and, therefore, form oil droplets inside the cell. Triacylglycerols are an e cient form of energy storage because, by excluding water molecules, a large number can be packed into a small volume. Although fatty acid molecules are uncharged, the constant motion of electrons leads to regions of slight positive and slight negative charges (Fig. 2.26). ese charges either attract or repel electrons in neighboring molecules, setting up areas of positive and negative charge in those molecules as well. e temporarily polarized molecules weakly bind to one another because of the attraction of opposite charges. ese for more ebook/ testbank/ solution manuals requests: email [email protected] interactions are known as van der Waals forces. e van der Waals forces come into play when atoms are su ciently close to one another, and they are weaker than hydrogen bonds. Even so, many van der Waals forces acting together help to stabilize molecules. FIG. 2.26 Van der Waals forces. Transient asymmetry in the distribution of electrons along fatty acid chains leads to asymmetry in neighboring molecules, resulting in weak attractions. Because of van der Waals forces, the melting points of fatty acids depend on their length and level of saturation. As the length of the hydrocarbon chains increases, the number of van der Waals interactions between the chains also increases. e melting temperature increases because more energy is needed to break the greater number of van der Waals interactions. By contrast, kinks introduced by double bonds reduce the tightness of the molecular packing and, therefore, the number of van der Waals interactions. As a result, the melting temperature is lower. us, an unsaturated fatty acid has a lower melting point than a saturated fatty acid of the same length. Animal fats such as butter are composed of triacylglycerols with saturated fatty acids and are solid at room temperature, whereas plant fats and sh oils are composed of triacylglycerols with unsaturated fatty acids and are li uid at room temperature. Steroids such as cholesterol are a second type of lipid (Fig. 2.27). Like other steroids, cholesterol has a core composed of carbon atoms bonded to form four fused rings, and it is hydrophobic. Cholesterol is a component of animal cell membranes (Chapter 3) and serves as a precursor for the synthesis of steroid hormones such as estrogen and testosterone (Chapters 9 and 37). FIG. 2.27 The chemical structure of cholesterol. This molecule is a major component of cell membranes and is used in the synthesis of essential molecules including hormones. Phospholipids are a third type of lipid. ey are a major component of the cell membrane and are described in Chapter 3. Self-Assessment Questions Take a close look at Fig. 2.22. How is glucose di erent from galactose? What are the essential functions of proteins, nucleic acids, carbohydrates, and lipids? How is diversity achieved in polymers? Use proteins as an example. What are the basic structures of amino acids, nucleotides, monosaccharides, and fatty acids? Sketch your answers.. C T Cells di er in size and shape, but they share many features. e similarity in the microscopic organization of all living organisms led to the development in the middle of the nineteenth century of the cell theory. Based on the work and ideas of Matthias Schleiden, eodor Schwann, Rudolf Virchow, and others, the cell theory became one of the pillars of modern biology. ere is no life without cells, and the cell is the basic unit of life. The cell theory places the cell at the center of life. e cell theory makes three interrelated observations: All organisms are made up of cells. e cell is the fundamental unit of life. Cells come from preexisting cells. e rst observation is the idea that all organisms are made up of cells. Some organisms are unicellular, spending their lives as a single cell. Other organisms are multicellular, made up of hundreds, thousands, millions, or even trillions of cells. In multicellular organisms, cells are specialized to carry out di erent functions. For example, skin cells provide protection from the outside world; skeletal muscle cells help you move about; liver cells metabolize the food you eat; and nerve cells process information and help to control and coordinate the functions of your various organs. e second observation states that the cell is the fundamental unit of life. When we say the "fundamental unit" of life, what we mean is that the cell is the simplest entity that we can de ne as living. Life is di cult to de ne, but it has certain features, such as the ability to reproduce, respond to the environment, harness energy, evolve, and so on. Cells, too, have these features. Anything smaller or simpler, like a membrane or molecule, does not have all of these features and so is not alive. In other words, the cell is the smallest, most basic unit of life, and there is no life without cells. e third observation notes that cells arise from preexisting cells through the process of cell division. When a single parent cell divides, it produces daughter cells. Of course, this begs the uestion of where the rst cell came from, which is the subject of Case 1 Life's Origin. The structure and function of cells are closely related. One of the central ideas of biology is that structure and function are closely related. A close connection between structure and function exists at all levels of scale in biology, from molecules to cells to tissues to organs to organisms. Simply observing cells reveals this relationship. Fig. 3.2 shows di erent types of cells, all with di erent structures and functions. Figure 3.2a shows a red blood cell. It has a distinctive biconcave shape, in which both sides of the cell curve inward toward the cell interior. is unusual shape allows it to alter its shape readily as it passes through narrow blood vessels with diameters smaller than that of the red blood cell itself. In addition, its shape gives it a relatively high surface area compared to its volume, which helps it to pick up and release oxygen throughout the body. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 3.2 Diverse cell types. Cells diﬀer in shape and are well adapted for their various functions. e red blood cell in Fig. 3.2a looks and functions very di erently from the long, slender muscle cells shown in Fig. 3.2b that contract to exert force. A neuron, such as the one in Fig. 3.2c, has long and extensively branched projections that communicate with other cells and organs. It is structurally and functionally uite distinct from a cell lining the intestine, shown in Fig. 3.2d, that absorbs nutrients. Cells can be classified as prokaryotic or eukaryotic. Cells are structurally and functionally diverse, but they all have certain features in common. While all cells have genetic material in the form of DNA, in some cells, this genetic material is housed in a membrane-bound space called the nucleus. Organisms can be divided into two classes based on the absence or presence of a nucleus in their cell (Chapter 1). e cells of prokaryotes, including bacteria and archaea, lack a nucleus; the cells of eukaryotes, including animals, plants, fungi, and protists, have a nucleus. ese two types of cells are shown in Fig. 3.3. FIG. 3.3 Prokaryotic and eukaryotic cells. Prokaryotic cells lack a nucleus and extensive internal compartmentalization. Eukaryotic cells have a nucleus and extensive internal compartmentalization. e rst forms of life were prokaryotic cells. eir genetic material is organized in one circular chromosome with many loops. Instead of a nucleus, this genetic material is concentrated in a discrete region of the cell known as the nucleoid. ey also have a cell wall surrounding the cell membrane, which help to maintain their shape. Some bacteria have agella (singular, agellum), structures that extend from their surface and allow them to move. Although the absence of a nucleus is a de ning feature of prokaryotes, other features also stand out. For example, prokaryotic cells are small, typically just 1-2 micrometers (a micrometer is 1/1,000,000 of a meter) in diameter, much smaller than eukaryotic cells. e small size of prokaryotic cells means that they have a relatively high ratio of surface area to volume, which makes sense for an organism that absorbs nutrients from the environment. In other words, a large amount of membrane surface area is available for absorption relative to the volume of the cell that it serves. Eukaryotic cells are typically much bi er than prokaryotic cells (Fig. 3.3). In addition, they have an extensive internal array of membranes, which are typically lacking in prokaryotes. ese membranes de ne compartments, called organelles, that divide the cell contents into smaller spaces specialized for di erent functions. Such a cell can be compared to a large factory with many di erent departments. Each department has a speci c function and internal organization that contribute to the work of the factory. Similarly, the organelles in eukaryotic cells carry out di erent functions that are important to the life of the cell. One of these organelles is the nucleus. e nucleus houses the vast majority of the cell's DNA, which takes the form of multiple linear chromosomes, in contrast to the single circular chromosome of prokaryotes. e nucleus allows for more complex regulation of gene expression than is possible in prokaryotes (Chapters 1, 4, and 17). In eukaryotes, the processes of transcription and translation are separated in space and time: transcription takes place in the nucleus rst, and translation takes place later in the cytoplasm. Each of these steps can be regulated separately. By contrast, in prokaryotes, translation occurs as soon as the mRNA is transcribed from the DNA template. Transcription and translation also di er in detail between prokaryotes and eukaryotes, and there are di erences in the types of lipids that make up their cell membranes. In spite of these and other di erences between prokaryotes and eukaryotes, it is the absence or presence of a nucleus that de nes the two groups. Although bacteria and archaea are structurally similar and grouped together as prokaryotes, from an evolutionary perspective, archaea and eukaryotes are actually more closely related to each other than either is to bacteria. We explore these relationships in more detail in Chapter 24. Self-Assessment Questions 1.All organisms are made of cells What are the three basic tenets of the cell theory? 2.Cells are the fundamental unit of life 3.all cells come from pre-existing cells What are the major di erences between prokaryotic and eukaryotic cells? Compare their organization, degree of compartmentalization, and relative size. The main difference between prokaryotic and eukaryotic cells are prokaryotic do not have a nucleus, insted a nucloid where their DNA is stored in rings, they also have a cell wall. Eukarotic cells have a nucleus and membrane bound organelle that work together like departments of a factory. for more ebook/ testbank/ solution manuals requests: email [email protected]. S C M All cells -- whether prokaryotic or eukaryotic -- are de ned by membranes. Membranes physically separate cells from their external environment and de ne spaces within many cells that allow them to carry out their diverse functions. Lipids are the main component of cell membranes. ey have properties that allow them to form a barrier in an a ueous (watery) environment. Membranes are not, however, made up of only lipids. Proteins are o en embedded in or associated with the membrane, where they perform important functions such as transporting molecules. Carbohydrates can also be found in cell membranes, usually attached to lipids (glycolipids) and proteins (glycoproteins). Cell membranes are composed of two layers of lipids. e major types of lipids found in cell membranes are phospholipids, which were introduced in Chapter 2. Most phospholipids are made up of a glycerol backbone attached to a phosphate group and two fatty acids (Fig. 3.4). e phosphate head group is hydrophilic ("water loving") because it is polar, enabling it to form hydrogen bonds with water. By contrast, the two fatty acid tails are hydrophobic ("water fearing") because they are nonpolar and do not form hydrogen bonds with water. Molecules with both hydrophilic and hydrophobic regions in a single molecule are termed amphipathic. FIG. 3.4 Phospholipid structure. Phospholipids, the major component of cell membranes, are made up of glycerol attached to a phosphate-containing head group and two fatty acid tails. They are amphipathic because they have both hydrophilic and hydrophobic domains. In an a ueous environment, amphipathic molecules such as phospholipids behave in a particular way. Namely, they spontaneously arrange themselves into various structures in which the polar head groups on the outside interact with water and the nonpolar tails come together on the inside away from water. is arrangement results from the tendency of polar molecules like water to exclude nonpolar molecules or nonpolar groups of molecules. e shapes of the structures formed by phospholipids are determined by the bulkiness of the head group relative to the hydrophobic tails (Fig. 3.5). For example, lipids with bulky heads and a single hydrophobic fatty acid tail are wedge-shaped and pack into spherical structures called micelles (Fig. 3.5a). By contrast, lipids with less bulky head groups and two hydrophobic tails are roughly rectangular and form a bilayer (Fig. 3.5b). A lipid bilayer is a structure formed of two layers of lipids in which the hydrophilic heads are the outside surfaces of the bilayer and the hydrophobic tails are sandwiched in between, isolated from contact with the a ueous environment. When phospholipids are added to a test tube of water at neutral pH (pH 7), they spontaneously form spherical bilayer structures called liposomes that surround a central space, resembling a cell (Fig. 3.5c). FIG. 3.5 Behavior of phospholipids in water. Phospholipids can form (a) micelles, (b) bilayers, or (c) liposomes when placed in water. In liposomes, the bilayers form closed structures with an inner space because free edges would expose the hydrophobic chains to the a ueous environment. is organization in part explains why bilayers are e ective cell membranes. It also explains why membranes are self-healing. Small tears in a membrane are rapidly sealed by the spontaneous rearrangement of the lipids surrounding the damaged region because of the tendency of water to exclude nonpolar molecules. The first cell membranes may have formed spontaneously, capturing macromolecules. e ability of phospholipids to form a liposome when placed in water has important implications for our understanding of how life might have originated. e structure forms spontaneously, dependent solely on the properties of the phospholipid and without the action of an enzyme, as long as the concentration of free phospholipids is high enough and the pH of the solution is neutral, around pH 7. e pH is important because it ensures that the head groups are in their ionized (charged) form and suitably hydrophilic. As the liposomes form, they may capture macromolecules present in solution. for more ebook/ testbank/ solution manuals requests: email [email protected] Such a process may have been at work in the early evolution of life on Earth. Experiments show that liposomes can form, break, and re-form in environments such as tidal ats that are repeatedly dried and ooded with water. e liposomes can even grow, incorporating more and more lipids from the environment, and capture nucleic acids and other molecules in their interiors. Depending on their chemical composition, early membranes might have been either leaky or almost impervious to the molecules of life. Over time, they evolved in such a way as to allow at least limited molecular tra c between the environment and the cell interior. At some point, new lipids no longer had to be incorporated from the environment. Instead, proteins guided lipid synthesis within the cell, although how this switch to protein- mediated synthesis happened remains uncertain. All evidence su ests that membranes formed originally by straightforward physical processes, but that their composition and function evolved over time. Francois Jacob once said that evolution works more like a tinkerer than an engineer, modifying already existing materials rather than designing systems from scratch. It seems that the evolution of membranes is no exception to this pattern. Cell membranes are dynamic. Lipids freely associate with one another because of the extensive van der Waals forces between their fatty acid tails (Chapter 2). ese weak interactions are easily broken and re-formed, so lipid molecules are able to move within the plane of the membrane, sometimes very rapidly: a single phospholipid can move across the entire length of a bacterial cell in less than 1 second. Lipids can also rapidly rotate around their vertical axis, and individual fatty acid chains are able to ex, or bend. As a result, membranes are dynamic: they are continually moving, forming, and re-forming during the lifetime of a cell. Because membrane lipids are able to move in the plane of the membrane, the membrane is said to be uid. e degree of membrane uidity depends on its composition. Two features of the lipids that make up the membrane a ect its uidity: the length and the number of carbon- carbon double bonds in the fatty acid tails. e longer the fatty acid tails, the less uid the membrane. is is because long fatty acid tails have more surface area to participate in van der Waals interactions with one another than short fatty acid tails. ese interactions limit lipids to lateral movement within a single layer of the lipid bilayer. In addition, the fewer the number of carbon-carbon double bonds, the less uid the membrane (Fig. 3.6). Saturated fatty acid tails, which have no carbon-carbon double bonds, are straight and tightly packed, reducing mobility (Fig. 3.6a). Carbon-carbon double bonds in unsaturated fatty acids introduce kinks in the fatty acid tails, reducing the tightness of packing and enhancing lipid mobility in the membrane (Fig. 3.6b). FIG. 3.6 Saturated and unsaturated fatty acids. The degree of saturation of the fatty acid tails of phospholipids aﬀects the tightness of packing and therefore the fluidity of the membrane. In addition to phospholipids, cell membranes o en contain other types of lipids, which can also in uence membrane uidity. For example, cholesterol is a major component of animal cell membranes, representing approximately 30% by mass of the membrane lipids. Like phospholipids, cholesterol is amphipathic, with both hydrophilic and hydrophobic groups being in the same molecule. In cholesterol, the hydrophilic region is simply a hydroxyl group ([?]OH) and the hydrophobic region consists of four interconnected carbon rings with an attached hydrocarbon chain (Fig. 3.7). is structure allows a cholesterol molecule to insert itself into the lipid bilayer so that its head group interacts with the hydrophilic head group of phospholipids, while the ring structure participates in van der Waals interactions with the fatty acid chains. FIG. 3.7 Cholesterol. Cholesterol molecules in the lipid bilayer aﬀect the fluidity of the membrane. e e ect of cholesterol on membrane uidity depends on temperature. At high temperatures, cholesterol decreases membrane uidity, making it more stable. In this case, the rigid ring structure of cholesterol interacts with the phospholipid fatty acid tails, thereby reducing the mobility of the phospholipids. At low temperatures, cholesterol increases membrane uidity by preventing phospholipids from packing tightly with other phospholipids. e e ect of cholesterol on membrane uidity is opposite that of temperature alone, where high temperature increases uidity and low temperature decreases uidity. us, cholesterol helps maintain a consistent state of membrane uidity by preventing dramatic transitions in uidity as the temperature changes. For many decades, it was thought that the various types of lipids found in the membrane were randomly distributed throughout the bilayer. More recent studies show that speci c types of lipids, such as sphingolipids, sometimes assemble into de ned patches called lipid ra s. Cholesterol and other membrane components such as proteins also appear to accumulate in some of these regions. us, membranes are not always a uniform uid bilayer, but instead can contain regions with discrete components. Although lipids are free to move in the plane of the membrane, the spontaneous movement of a lipid between layers of the bilayer, known as lipid ip- op, is very rare. is is not surprising because ip- op re uires the hydrophilic head group to pass through the hydrophobic interior of the membrane. As a result, little exchange of components occurs between the two layers of the membrane, which in turn allows the two layers to di er in composition. In fact, in many membranes, di erent types of lipids are present primarily in one layer or the other. Proteins associate with cell membranes. Most membranes contain proteins as well as lipids. For example, proteins represent as much as 50% by mass of the membrane of a red blood cell. Membrane proteins serve di erent functions (Fig. 3.8). Some act as transporters, moving ions or molecules across the membrane. Other membrane proteins act as receptors, which allow the cell to receive signals from the environment. Still others are enzymes that catalyze chemical reactions or anchors that attach to other proteins and help to maintain cell structure and shape. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 3.8 Membrane proteins. Membrane proteins include transporters, receptors, enzymes, and anchors. e various membrane proteins can be classi ed into two groups depending on how they associate with the membrane (Fig. 3.9). Integral membrane proteins are permanently associated with cell membranes and cannot be separated from the membrane experimentally without destroying the membrane itself. Peripheral membrane proteins are temporarily associated with the lipid bilayer or with integral membrane proteins through weak noncovalent interactions. ey are easily separated from the membrane by simple experimental procedures that leave the structure of the membrane intact. FIG. 3.9 Integral and peripheral membrane proteins. Integral membrane proteins are permanently associated with the membrane. Peripheral membrane proteins are temporarily associated with one side of the membrane or with an integral membrane protein. Most integral membrane proteins are transmembrane proteins that span the entire lipid bilayer, as shown in Fig. 3.9. ese proteins are composed of three regions. ere are two hydrophilic regions, one protruding from each face of the membrane in contact with the a ueous environment inside and outside of the cell. ere is also one hydrophobic region that spans the hydrophobic interior of the membrane. is structure allows for separate functions and capabilities of each end of the protein. For example, the hydrophilic region on the external side of a receptor can interact with signaling molecules, whereas the hydrophilic region of that receptor protein on the internal side of the membrane o en interacts with other proteins in the cytoplasm of the cell to pass along the signal. Peripheral membrane proteins may be associated with either the internal or external side of the membrane (Fig. 3.9). ese proteins interact either with the polar heads of lipids or with integral membrane proteins by weak noncovalent interactions such as hydrogen bonds. Peripheral membrane proteins are only transiently associated with the membrane and can play a role in transmitting information received from external signals. Other peripheral membrane proteins limit the ability of transmembrane proteins to move within the membrane and assist proteins in clustering in lipid ra s. Proteins, like lipids, are o en free to move in the membrane. e mobility of proteins in the cell membrane can be demonstrated using an elegant experimental techni ue called uorescence recovery a er photobleaching (FRAP), described in Fig. 3.10. In this techni ue, membrane proteins are ta ed with a uorescent label so they are visible. A laser is used to bleach an area of the membrane, making it non uorescent. Over time, the bleached area becomes uorescent again, su esting that uorescent proteins that weren't bleached are able to move into the bleached area. H D W K ? F. 3.10 Do proteins move in the plane of the membrane? B Fluorescent recovery a er photobleaching (FRAP) is a technique used to measure mobility of molecules in the plane of the membrane. A fluorescent dye is attached to proteins embedded in the cell membrane in a process called labeling. Labeling all the proteins in a membrane creates a fluorescent cell that can be visualized with a fluorescence microscope. A laser is then used to bleach a small area of the membrane, leaving a nonfluorescent spot on the surface of the cell. H If membrane components such as proteins move in the plane of the membrane, the bleached spot should become fluorescent over time as unbleached fluorescent molecules move into the bleached area. If membrane components do not move, the bleached spot should remain intact. E R Over time, fluorescence appears in the bleached area, telling us that fluorescent proteins that were not bleached moved into the bleached area. C The gradual recovery of fluorescence in the bleached area indicates that proteins move in the plane of the membrane. for more ebook/ testbank/ solution manuals requests: email [email protected] SOURCE Peters, R., et al. 1974. "A Microfluorimetric Study of Translational Diﬀusion in Erythrocyte Membranes." Biochimica et Biophysica Acta 367:282-294. e idea that lipids, proteins, and carbohydrates coexist in the membrane, and that they are able to move in the plane of the membrane, led American biologists S. Jonathan Singer and Garth Nicolson to propose the uid mosaic model in 1972. According to this model, the lipid bilayer is a structure within which molecules move laterally (it is uid) and is a mixture (a mosaic) of di erent types of molecules, including lipids, proteins, and carbohydrates. Self-Assessment Questions How do lipids with hydrophilic and hydrophobic regions behave in an a ueous environment? Like cell membranes, many fats and oils are made up in part of fatty acids. Most animal fats (like butter) are solid at room temperature, whereas plant fats (like canola oil) tend to be li uid. Can you predict which type of fat contains saturated fatty acids and which type contains unsaturated fatty acids? What are two ways in which proteins associate with membranes? What would happen in the FRAP experiment if proteins did not move in the plane of a membrane?. M T Phospholipids with embedded proteins make up the membrane surrounding all cells. is membrane, called the cell membrane or plasma membrane, is a fundamental, de ning feature of all cells. It is the boundary that de nes the space of the cell, separating its internal contents from the surrounding environment. But the cell membrane is not simply a passive boundary or wall. Instead, it serves an active and important function. e environment outside the cell is constantly changing. In contrast, the internal environment of a cell operates within a narrow window of conditions, such as a particular pH range or salt concentration. It is the cell membrane that controls the movement of substances into and out of cells, thereby keeping intracellular conditions compatible with life. The cell membrane maintains homeostasis. e active maintenance of a stable environment within cells and organisms, known as homeostasis, is a critical attribute of cells and of life itself. Chemical reactions and protein folding, for example, are carried out e ciently only within a narrow range of conditions. How does the cell membrane maintain homeostasis? e answer is that it is selectively permeable. is means that the cell membrane lets some molecules in and out freely; it lets others in and out only under certain conditions; and it prevents still other molecules from passing through at all. e membrane's ability to act as a selective barrier is the result of the combination of lipids and embedded proteins of which it is composed. e hydrophobic interior of the lipid bilayer prevents ions and charged polar molecules from moving across it. Furthermore, many macromolecules such as proteins and polysaccharides are too large to cross the cell membrane on their own. By contrast, gases such as oxygen and carbon dioxide, and nonpolar molecules such as lipids, can move across the lipid bilayer. Small uncharged polar molecules, such as water, are able to move through the lipid bilayer to a very limited extent, but this movement is not biologically signi cant. However, protein transporters in the membrane can greatly facilitate the movement of molecules, including ions, water, and nutrients, that cannot cross the lipid bilayer on their own. e identity and abundance of these membrane-associated proteins vary among cell types, re ecting the speci c functions of di erent cells. For example, cells in your gut contain membrane transporters that specialize in the uptake of glucose, whereas nerve cells have di erent types of ion channels that are involved in electrical signaling. Passive transport involves diﬀusion. Molecules are in constant, random motion in most environments. For example, molecules in water at room temperature move around at about 500 m/sec, which means that they can move only about 3 molecular diameters before they run into another molecule, leading to about 5 trillion collisions per second. e fre uency with which molecules collide has important conse uences for chemical reactions, which depend on the interaction of molecules (Chapter 6). Net movement of molecules can occur from one region to another when there is a concentration gradient in the distribution of molecules, meaning that there are areas of higher and lower concentrations. e net movement of substances, such as ions and molecules, from areas of higher to lower concentration is called di usion. When there is no longer a concentration gradient, net movement stops, but random motion of molecules in both directions continues (Fig. 3.11). for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 3.11 Diﬀusion. Diﬀusion is the net movement of substances such as ions and molecules from areas of high to low concentration due to random motion. Passive transport occurs when molecules move across a cell membrane by di usion. ese molecules move as a result of di erences in concentration between the inside and outside of the cell. Some molecules di use directly through the cell membrane, a process called simple di usion. Oxygen and carbon dioxide, for example, move into and out of the cell in this way. Many hydrophobic molecules, such as triacylglycerols (Chapter 2), are also able to di use directly through the cell membrane, which is not surprising because the lipid bilayer is also hydrophobic. Passive transport also occurs when molecules move passively down a concentration gradient through protein transporters. In this case, passive transport works by facilitated di usion. Simple di usion and facilitated di usion both result from the random motion of molecules, and net movement of the substance occurs when there are concentration di erences (Fig. 3.12). In simple di usion, molecules move directly through the lipid bilayer, while in facilitated di usion, molecules move through a membrane transporter. FIG. 3.12 Simple diﬀusion and facilitated diﬀusion. Both simple diﬀusion and facilitated diﬀusion result in movement of molecules down a concentration gradient. In simple diﬀusion, molecules move directly through the cell membrane. In facilitated diﬀusion, molecules move through a channel or carrier. ere are two types of membrane transporters. e rst type is a channel protein, which provides an opening between the inside and outside of the cell through which certain molecules can pass, depending on their shape and charge. Some membrane channels are gated, which means that they open in response to some sort of signal, which may be chemical or electrical (Chapter 9). e second type of membrane transporter is a carrier protein, which binds to and then transports speci c molecules. Membrane carriers exist in two conformations: one that is open to one side of the cell, and another that is open to the other side of the cell. Binding of the transported molecule induces a conformational change in the membrane protein, allowing the molecule to be transported across the lipid bilayer, as shown on the right in Fig. 3.12. Up to this point, we have focused our attention on the movement of molecules (the solutes) in water (the solvent). We now take a di erent perspective and focus instead on water movement across cell membranes. Water moves into and out of cells by passive transport. Although the central part of the phospholipid bilayer is hydrophobic, water molecules are small enough to move passively through the bilayer to a very limited extent by simple di usion. However, this movement does not appear to be biologically signi cant. Instead, water moves through the cell membrane by channel proteins called a uaporins. ese channels allow water to move much more readily across the cell membrane by facilitated di usion than is possible by simple di usion. e net movement of a solvent such as water across a selectively permeable membrane such as the cell membrane is known as osmosis. As in any form of di usion, water moves from regions of higher water concentration to regions of lower water concentration (Fig. 3.13). Because water is a solvent in which solutes such as glucose or ions such as sodium or potassium are dissolved, water concentration decreases as solute concentration increases. erefore, it is sometimes easier to think about water moving from regions of lower solute concentration toward regions of higher solute concentration. Whether expressed in terms of water or solute concentration, the direction of water movement is the same. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 3.13 Osmosis. Osmosis is the net movement of a solvent such as water across a selectively permeable membrane from an area of lower solute concentration to an area of higher solute concentration. During osmosis, the net movement of water toward the side of the membrane with higher solute concentration continues until a concentration gradient no longer exists or until the movement is opposed by another force. is force could be pressure due to gravity (in the case of Fig. 3.13) or the cell wall (in the case of plants, fungi, and bacteria, as described later in this chapter). Osmosis can therefore be prevented by applying a force to the compartment with the higher solute concentration. Osmotic pressure describes the tendency of a solution to draw water in by osmosis (Chapter 40). e higher the solute concentration, the higher the osmotic pressure of that solution. To learn more about Water Chemistry and Movement, go to the Primers in Achieve. Primary active transport uses the energy of ATP. Passive transport works to the cell's advantage only if the concentration gradient is in the right direction, from higher on the outside to lower on the inside for nutrients that the cell needs to take in, and from higher on the inside and lower on the outside for wastes that the cell needs to export. However, many of the molecules that cells re uire are not present at high concentrations in the environment. Although some of these molecules can be synthesized by the cell, others must be taken up from the environment. In other words, cells have to move these substances from areas of lower concentration to areas of higher concentration. e "uphill" movement of substances against a concentration gradient is called active transport. Many substances cross the cell membrane using active transport. Active transport re uires an input of energy, either directly or indirectly. In fact, most of the energy used by a cell goes into keeping the inside of the cell di erent from the outside, a function carried out by the membrane-associated proteins. During active transport, cells move substances through transport proteins embedded in the cell membrane. Some of these proteins act as pumps, using energy directly to move a substance into or out of a cell. A good example is the sodium-potassium pump (Fig. 3.14). Within cells, sodium is kept at concentrations much lower than in the external environment; the opposite is true of potassium. erefore, both sodium and potassium have to be moved against a concentration gradient. e sodium-potassium pump actively moves sodium out of the cell (steps 1 and 2 in Fig. 3.14) and potassium into the cell (steps 3 and 4 in Fig. 3.14). is movement of ions uses energy, which comes from the chemical energy stored in adenosine triphosphate (ATP), which is broken down into adenosine diphosphate (ADP) and inorganic phosphate (P ). Active transport that uses energy of ATP directly in this manner is called primary active transport. Note that the sodium i ions and potassium ions move in opposite directions; protein transporters that work in this way are referred to as antiporters. Other transporters move two di erent molecules in the same direction and are referred to as symporters. FIG. 3.14 Primary active transport. The sodium-potassium pump uses the energy stored in ATP to move sodium and potassium ions against their concentration gradients. Secondary active transport is driven by an electrochemical gradient. Active transport can work in yet another way. Because small ions cannot cross the lipid bilayer, many cells have transport proteins that build up the concentration of a small ion on one side of the membrane. e resulting concentration gradient stores potential energy that can be harnessed to drive the movement of other substances across the membrane against their concentration gradient. is form of active transport is called secondary active transport. An example of secondary active transport is illustrated in Fig. 3.15. Some cells actively pump protons (H + ) across a membrane using ATP (step 1). As a result, in these cells the concentration of protons is higher on one side of the membrane and lower on the other side. In other words, the pump generates a concentration gradient, also called a chemical gradient because the entity forming the gradient is a chemical (step 2 in Fig. 3.15). As we discussed earlier, concentration di erences favor the movement of protons back to the other side of the membrane. By blocking the movement of protons to the other side, the lipid bilayer creates a store of potential energy, just as a dam or battery does. for more ebook/ testbank/ solution manuals requests: email [email protected] FIG. 3.15 Secondary active transport. Protons (H + ) are pumped across a membrane using ATP (step 1), resulting in an electrochemical gradient (step 2), which in turn drives the movement of another molecule against its concentration gradient (step 3). In addition to the chemical gradient, another force favors the movement of protons back across the membrane: a di erence in charge. Because protons carry a positive charge, the side of the membrane with more protons has a higher positive charge than the other side. is di erence in charge is called an electrical gradient. Protons (and other ions) move from areas of like charge to areas of unlike charge, driven by an electrical gradient. A gradient that has both electrical and chemical components is known as an electrochemical gradient. If protons are then allowed to pass through the cell membrane by a transporter protein, they will move down their electrochemical gradient toward the region of lower proton concentration. ese transporter proteins can use the movement of protons to drive the movement of other molecules against their concentration gradient (step 3 in Fig. 3.15). e movement of protons is always from regions of higher to lower concentration, whereas the movement of the coupled molecule is from regions of lower to higher concentration. Because the movement of the coupled molecule is driven by the movement of protons and not by ATP directly, this form of transport is called secondary active transport. Secondary active transport uses the potential energy of an electrochemical gradient to drive the movement of molecules; by contrast, primary active transport uses the chemical energy of ATP directly. e use of an electrochemical gradient as a temporary energy source is a common cellular strategy. For example, cells use a sodium electrochemical gradient generated by the sodium-potassium pump to transport glucose and amino acids into cells. In addition, cells use a proton electrochemical gradient to synthesize ATP, as we discuss later in this chapter and in Chapter 7. Many cells maintain size and composition using active transport. Many cells use active transport to maintain their size. Consider human red blood cells placed in a variety of solutions (Fig. 3.16). If a red blood cell is placed in a hypertonic solution (one with a solute concentration higher than that inside the cell), water leaves the cell by osmosis and the cell shrinks. By contrast, if a red blood cell is placed in a hypotonic solution (one with a solute concentration lower than that inside the cell), water moves into the cell by osmosis and the cell lyses, or bursts. Animal cells solve the problem of water movement in part by keeping the intracellular uid isotonic (that is, at the same solute concentration) with the extracellular uid. Cells use the active transport of ions to maintain e ual concentrations inside and out, and the sodium-potassium pump plays an important role in keeping the inside of the cell isotonic with the extracellular uid. FIG. 3.16 Changes in red blood cell shape due to osmosis. Red blood cells shrink or burst because of net water movement driven by diﬀerences in solute concentration between the inside and the outside of the cell. Another strategy to prevent cell lysis resulting from water movement is seen in some protists, such as Paramecium and other single-celled eukaryotes. ese organisms live in freshwater habitats, where the extracellular environment is hypotonic relative to the cell's interior. As a result, they face the risk of bursting from water moving in by osmosis, just like red blood cells. ese organisms contain contractile vacuoles that solve this problem. Contractile vacuoles are organelles that take up excess water from inside the cell and then, by contraction, expel it into the external environment (Fig. 3.17). FIG. 3.17 Contractile vacuole. The contractile vacuole in a paramecium is shown (a) when full and (b) a er emptying. The cell wall and cytoskeleton help to maintain cell shape. In addition to active transport, cells have other strategies to maintain their shape. For example, many organisms have a cell wall surrounding the cell membrane. ese organisms include bacteria, fungi, many protists, most algae, and all plants. e cell wall plays a critical role in the maintenance of cell size and shape. When Hooke looked at cork through his microscope, what he saw was not living cells, but rather the cell walls devoid of cells. for more ebook/ testbank/ solution manuals requests: email [email protected] e cell wall is made up of many di erent components, including carbohydrates and proteins. e speci c components di er depending on the organism. e plant cell wall is composed of polysaccharides, including cellulose, a polymer of the sugar glucose. Cellulose is the most abundant biological material in nature. Many types of algae have cell walls made up of cellulose, as in plants, but others have cell walls made of silicon or calcium carbonate. Fungi have cell walls made of chitin, another polymer of sugars. In bacteria, the cell wall is made up primarily of peptidoglycan, a polymer of amino acids and sugars. e cell wall provides structural support and protection for the cell. Because the cell wall is rigid and resists expansion, it allows pressure to build up when water enters a cell. e force exerted by water pressing against an object is called turgor pressure. Turgor pressure builds as a result of water moving by osmosis into cells surrounded by a cell wall. Cells contain high concentrations of solutes. Recall that when an animal cell, such as a red blood cell, is placed in a hypotonic solution, it swells until it bursts. By contrast, when a plant cell is placed in a hypotonic solution, water enters the cell by osmosis until the turgor pressure created by the cell wall increases to a level to stop osmosis (Fig. 3.18). Turgor pressure develops because the cell wall resists being stretched and pushes back on the interior of the cell, just as a balloon pushes back on the air inside. FIG. 3.18 Turgor pressure. Turgor pressure results when water enters a plant cell by osmosis and the cell wall pushes back, as shown on the right. In the absence of turgor pressure, the plant visibly wilts, as shown on the le. e pressure exerted by water inside the cell on the cell wall provides structural support for many organisms. In addition, plant and fungal cells have another structure, called a vacuole (di erent from a contractile vacuole), that absorbs water and contributes to turgor pressure. Its function explains why plants wilt when dehydrated: the loss of water from the vacuoles reduces turgor pressure, so the cells can no longer maintain their shape within the cell wall. Plant vacuoles have many other functions and are o en the most conspicuous feature of plant cells. ey also explain in part why plant cells are typically larger than animal cells and can store water, as well as nutrients, ions, and wastes. e shape of a cell also depends in part on a system of protein laments that are collectively called the cytoskeleton. Just as the bones of vertebrate skeletons provide internal support for the body, the protein laments of the cytoskeleton provide internal support for cells. e cytoskeleton is a universal and ancient feature of all cells. In some cells, cytoskeletal elements perform other functions as well, allowing cells to change shape, move about, and transport substances within the cell. We discuss the cytoskeleton in detail in Chapter 10 in the context of cell junctions and tissues. Self-Assessment Questions What are the roles of lipids and proteins in maintaining the selective permeability of membranes? A container is divided into two compartments by a membrane that is fully permeable to water and small ions. Water is added to one side of the membrane (side A), and a 5% solution of sodium chloride (NaCl) is added to the other (side B). In which direction will water molecules move? In which direction will sodium and chloride ions move? When the concentration is e ual on both sides, will movement stop? What is the di erence between passive and active transport? In the absence of the sodium-potassium pump, the extracellular solution becomes hypotonic relative to the inside of the cell. Poisons such as ouabain can interfere with the action of the sodium-potassium pump. What are the conse uences for the cell? What are three di erent ways in which cells maintain size and shape?. C C S DNA Deoxyribonucleic acid (DNA) is a linear polymer of four di erent subunits. It is the molecule by which hereditary information is transmitted from generation to generation. Today the role of DNA is well known, but at one time hardly any biologist would have bet on it. A poll of biologists before about 1950 would have shown overwhelming support for the idea that proteins are life's information molecules. Compared with the seemingly monotonous, featureless structure of DNA, the three-dimensional structures of proteins are highly diverse. Proteins carry out most of the essential activities in a cell, so it seemed logical to assume that they would play a key role in heredity, too. But while proteins do play a role in heredity, they do so by supporting replication, error correction, and readout of the information encoded in DNA. e rst hint that DNA might be the genetic material came in 1928, when Frederick Gri th conducted studies on the transmission of genetic information and showed that macromolecules in extracts from bacteria could transmit genetic information from one bacterial cell to another (Fig. 4.1). Almost 20 years later, experiments carried out by Oswald Avery, Colin MacLeod, and Maclyn McCarty showed that this information-carrying macromolecule is DNA, not RNA or protein (Fig. 4.2). H D W K ? F. 4.1 Can genetic information be transmitted between two strains of bacteria? B In the 1920s, it was not clear which biological molecule carries genetic information. Fred Neufeld, a German microbiologist, identified several strains of the bacterium Streptococcus pneumoniae, which causes pneumonia in mice. One of these strains is virulent -- it causes illness and death when injected into mice (Fig. 4.1a). A second strain is nonvirulent and does not cause illness when injected into mice (Fig. 4.1b). E In 1928, Frederick Griﬀith, another microbiologist who was also interested in bacterial virulence, made a puzzling observation. He noted that live nonvirulent bacteria, when injected into mice, do not cause mice to get sick (Fig. 4.1b). He also noted that virulent bacteria that had been killed by heating, when injected into mice, do not cause mice to get sick (Fig. 4.1c). However, when Griﬀith mixed live nonvirulent bacteria and killed virulent bacteria and injected the mice with this mixture, they became sick and died (Fig. 4.1d). Furthermore, when Griﬀith isolated bacteria from the dead mice, the isolated bacteria appeared to be virulent, even though the mice had been injected with live nonvirulent bacteria. for more ebook/ testbank/ solution manuals requests: email [email protected] R C Griﬀith concluded that the virulent bacteria, although killed, had somehow caused the nonvirulent bacteria to become virulent. He asserted that a molecule that is present in the debris of killed virulent bacteria carries the genetic information for virulence, but he did not identify the molecule. He based this conclusion on the observation that one strain of bacteria (nonvirulent) was transformed into another (virulent) by an unknown molecule from the virulent cells. F U W Griﬀith's experiments were followed up by many researchers, most notably Oswald Avery, Colin MacLeod, and Maclyn McCarty, who identified DNA as the molecule responsible for transforming the bacteria from a nonvirulent strain to a virulent strain (Fig. 4.2). SOURCE Griﬀith, F. 1928. "The Significance of Pneumococcal Types." Journal of Hygiene 27:113-159. H D W K ? F. 4.2 Which molecule carries genetic information? B Following Frederick Griﬀith, researchers Oswald Avery, Colin MacLeod, and Maclyn McCarty also studied virulence in pneumococcal bacteria. In the early 1940s, they recognized the significance of Griﬀith's experiments (Fig. 4.1) and set out to identify the molecule that is responsible for transforming nonvirulent bacterial cells into virulent bacterial cells. E Avery,

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