Cell Biology Concepts PDF

1-6 The “Facts” of Life. Each of these statements was once diesel fuel. What model system(s) might you use for each of the regarded as a biological fact but is now understood to be untrue. In following aspects of this project? What tools and techniques...

1-6 The “Facts” of Life. Each of these statements was once diesel fuel. What model system(s) might you use for each of the regarded as a biological fact but is now understood to be untrue. In following aspects of this project? What tools and techniques each case, indicate why the statement was once thought to be true would you use? and why it is no longer considered a fact. (a) Determining which genes and enzymes are required to produce the oil (a) Animal and plant cells do not share a common nucleus. (b) Producing large amounts of a certain enzyme for further research (b) Living organisms are not governed by the laws of chemistry and (c) Studying whether any of the cellular enzymes interact with each physics, as is nonliving matter, but are subject to different laws other that are responsible for the formation of organic compounds. (d) Examining the involvement of any cellular organelles in storage (c) Genes most likely consist of proteins because the only other likely or secretion of the oil candidate, DNA, is a relatively uninteresting molecule consisting of only four kinds of monomers (nucleotides) arranged in a rela- 1-9 DATA ANALYSIS Worm Microscopy. With the use of tively repetitive sequence. microscopy, the localization of two proteins (A and B) using (d) Sunlight is the only source of energy in the biosphere. different fluorescent dyes can be examined in the developing C. elegans embryo images shown in Figure 1-11. The images of A 1-7 Wrong Again. Explain why each of the following statements is and B are overlaid in the third image. Which type of microscopy is false. being used—light microscopy or electron microscopy? Are the two (a) Because of the wavelength of light, resolution of cellular struc- proteins likely to be interacting with each other? Provide evidence tures smaller than 200 nm can never be achieved. for your answers. (b) Fluorescence microscopy can allow us to visualize cells but can- not help identify them. (c) Because all DNA molecules have similar chemical composition, it is not possible to separate and characterize individual DNA molecules. (d) The best way to carry out a scientific experiment is to try to prove a hypothesis by varying all the relevant conditions. (e) The flow of genetic information is always from DNA to RNA to protein. Protein A Protein B A and B merged 10 mm 1-8 A New Biofuel. As a recent cell biology graduate, you have just been hired by a biotechnology company to develop Figure 1-11 Localization of C. elegans Proteins Using a biofuel using algal cells that produce an oil very similar to Microscopy. See Problem 1-9. 42 M01_HARD6525_10_GE_C01.indd 42 12/11/21 9:37 A  2 The Chemistry of the Cell + - - - + - + + - - + + - - + + - + + - - + - - + + - + - A Crystal of Salt Dissolves in Water. As a crystal of salt (green S and purple structure) dissolves in water, the tudents just beginning in cell biology are sometimes surprised—and perhaps even oxygen atoms of water (red) surround the positive ions, dismayed—to find that courses and textbooks dealing with cell biology involve a and its hydrogen atoms (blue) surround the negative ions. substantial amount of chemistry. Yet biology in general and cell biology in particular depend heavily on both chemistry and physics. After all, cells and organisms follow all the laws of the physical universe, so biology is really just the study of chemistry and physics in systems that are alive. In fact, everything cells are and do has a molecular and chemical basis. Therefore, we can truly understand and appreciate cellular structure and function only when we can describe cellular structure in molecular terms and express cellular function in terms of chemical reactions and events. Trying to appreciate cellular biology without a knowledge of chemistry would be like trying to appreciate a translation of Chekhov without a knowledge of Russian. Most of the meaning would probably get through, but much of the beauty and depth of appreciation would be lost in the translation. For this reason, we will consider the chemical background necessary for the cell biologist. Specifically, this chapter will provide an overview of Mastering™ Biology www.masteringbiology.com 43 M02_HARD6525_10_GE_C02.indd 43 01/12/21 9:44 P  several chemical principles critical for understanding of all classes of naturally occurring and synthetic carbon- cellular biology and will introduce the major classes containing compounds. Biological chemistry (biochemistry for short) deals specifically with the chemistry of living sys- of macromolecules in cells: proteins, nucleic acids, tems and is, as we have already seen, one of the several histor- carbohydrates, and lipids. ical strands that form an integral part of modern cell biology The main points of this chapter can conveniently be (see Figure 1-3). structured around five principles: The carbon atom (C) is the most important atom in bio- logical molecules. Carbon-containing compounds owe their 1. The importance of carbon. The carbon atom has diversity and stability to specific bonding properties of the several unique properties that make it especially carbon atom. Especially important are the ways that carbon atoms interact with each other and with other chemical ele- suitable as the backbone of biologically important ments of biological importance (Figure 2-1). molecules. An extremely important property of the carbon atom is 2. The importance of water. The water molecule has its valence of four, meaning it can form up to four chemical bonds with other atoms before filling its outer electron shell. several unique properties that make it especially suit- Atoms can bond to each other via their outer electrons, and able as the universal solvent of living systems. atoms are usually the most stable when they are surrounded 3. The importance of selectively permeable by a total of eight electrons, satisfying what is known as the octet rule. The outermost electron orbital of a carbon atom membranes. Membranes define cellular compart- has four electrons and therefore lacks four of the eight elec- ments and control the movements of molecules and trons needed to fill it completely and make it the most stable. ions into and out of cells and organelles. Therefore, carbon atoms associate with each other or with other electron-deficient atoms, allowing adjacent atoms to 4. The importance of synthesis by polymerization of share a pair of electrons, one from each atom, so that each small molecules. Biological macromolecules are polymers formed by linking many similar or identical small molecules known as monomers. (a) Some biologically important 5. The importance of self-assembly. Biological macro- atoms and their valences molecules are often capable of self-assembly into C H O N higher levels of structural organization because the Carbon Hydrogen Oxygen Nitrogen information needed to specify the spatial configura- (valence: 4) (valence: 1) (valence: 2) (valence: 3) tion of the molecule is contained in the polymer. Understanding these five principles will help you (b) Some simple organic molecules with single bonds to appreciate the cellular chemistry necessary before H H H H venturing further into our exploration of what it means H C H H C C O H H C N H to be a cell. H H H H H Methane Ethanol Methylamine (CH4) (CH3 CH2OH) (CH3 NH2) 2.1 The Importance of Carbon (c) Some simple molecules with double bonds To study cellular molecules really means to study compounds containing carbon. Almost without exception, molecules of H H C C O C O importance to the cell biologist have a backbone, or skeleton, H H of carbon atoms linked together covalently in chains or rings. Ethylene Carbon dioxide Actually, the study of carbon-containing compounds is the (CH2 CH2) (CO2) domain of organic chemistry. In its early days, organic chemistry was synonymous with biological chemistry be- cause the carbon-containing compounds that chemists first (d) Some simple molecules with triple bonds investigated were obtained from biological sources (hence N N H C N H C C H the word organic, acknowledging the organismal origins of the compounds). Molecular nitrogen Hydrogen cyanide Acetylene (N2) (HC N) (CH CH) The terms organic chemistry and biological chemistry have long since gone their separate ways, however, because or- Figure 2-1 Electron Configurations of Some Biologically ganic chemists have now synthesized an incredible variety of Important Atoms and Molecules. Electronic configurations are carbon-containing compounds that do not occur naturally in shown for (a) individual atoms and (b–d) some simple molecules. Only the biological world. Organic chemistry therefore is the study electrons in the outermost electron orbital are shown. 44 M02_HARD6525_10_GE_C02.indd 44 01/12/21 9:44 P  atom’s outer orbital has a full set of eight electrons including 1000 shared electrons. (For hydrogen alone, a full set is only two electrons.) Atoms that share electrons in this way are held to- C C gether and are said to be joined by a covalent bond. Because C C Covalent bond four additional electrons are required to fill the outer orbital of car- 100 C H energies bon, stable organic compounds have four covalent bonds for every C C C N carbon atom. This gives carbon-containing molecules great di- E = energy (kcal/mol) versity in molecular structure and function. Carbon atoms are most likely to form covalent bonds with 10 other carbon atoms and with atoms of oxygen (O), hydrogen (H), nitrogen (N), and sulfur (S). The electronic configurations of several of these atoms are shown in Figure 2-1a. Sulfur, like Hydrogen bonds oxygen, has six outer electrons and a valence of two. Notice that, in each case, one or more electrons are required to com- 1 Vibrational plete the outer orbital to a total of eight electrons. The number (thermal) energy of “missing” electrons corresponds in each case to the valence of the atom, which is the number of covalent bonds the atom can form. Because hydrogen’s outermost electron orbital can 0.1 hold only two electrons, it has a valence of one and forms only one covalent bond. Figure 2-2 Energies of Biologically Important Bonds. Notice The sharing of one pair of electrons between atoms re- that energy is plotted on a logarithmic scale to accommodate the wide sults in a single bond. Methane, ethanol, and methylamine range of values shown. are simple examples of carbon-containing compounds con- Chapter 2 taining only single bonds between atoms (Figure 2-1b), as represented by the pair of electrons between any two chemi- We can appreciate the significance of these bond ener- cal symbols. Sometimes two or even three pairs of electrons gies by comparing them with other relevant energy values, | can be shared by two atoms, giving rise to double bonds as shown in Figure 2-2. Most noncovalent bonds in biologi- The Chemistry of the Cell or triple bonds. Ethylene and carbon dioxide are examples cally important molecules, such as the hydrogen bonds we of double-bonded compounds (Figure 2-1c). Notice that, in will see later in this chapter, have energies of only a few ki- these compounds, each carbon atom still forms a total of localories per mole. The energy of thermal vibration is even four covalent bonds, either one double bond and two single lower—only about 0.6 kcal/mol. Covalent bonds are much bonds or two double bonds. Triple bonds are rare but can be higher in energy than noncovalent bonds and are therefore found in molecular nitrogen, hydrogen cyanide, and acety- much more stable. lene (Figure 2-1d). Thus, both the valence and the low atomic The fitness of the carbon-carbon bond for biological weight of carbon give it unique properties that account for chemistry on Earth is especially clear when we compare its en- the diversity and stability of carbon-containing compounds, ergy with that of solar radiation. As shown in Figure 2-3 on giving carbon a preeminent role in biological molecules. page 46, an inverse relationship exists between the wavelength of electromagnetic radiation and its energy content. This figure shows that the visible portion of sunlight (wavelengths of Carbon-Containing Molecules Are Stable 380–750 nm) is lower in energy than the carbon-carbon bond The stability of organic molecules is a property of the favor- is. If this were not the case, visible light would break covalent able electronic configuration of each carbon atom in the bonds spontaneously, and life as we know it would not exist. molecule. This stability is expressed as bond energy—the Figure 2-3 illustrates another important point: the haz- amount of energy required to break 1 mole (about 6 × 1023 ) ard that ultraviolet radiation poses to biological molecules due of such bonds. (The term bond energy is a frequent source of to its high energy. At a wavelength of 300 nm, for example, confusion. Be careful not to think of it as energy that is some- ultraviolet light has an energy content of about 95 kcal/mol. how “stored” in the bond but rather as the amount of energy This is enough to break carbon-carbon bonds spontaneously. needed to break the bond.) Bond energies are usually expressed This threat underlies the current concern about pollutants in calories per mole (cal/mol), where a calorie is the amount of that destroy the ozone layer in the upper atmosphere because energy needed to raise the temperature of 1 gram of water by the ozone layer filters out much of the ultraviolet radiation 1°C and a kilocalorie (kcal) is equal to 1000 calories. that would otherwise reach Earth’s surface and disrupt the co- It takes a large amount of energy to break a covalent valent bonds that hold biological molecules together. bond. For example, the carbon-carbon (C − C) bond has a bond The stability of carbon is evident not only through our energy of 83 kilocalories per mole (kcal/mol). The bond ener- study of organic chemistry here on Earth but also through ex- gies for carbon-nitrogen (C − N), carbon-oxygen (C − O), and citing discoveries on other planets in our solar system. Recent carbon-hydrogen (C − H) bonds are all in the same range: 70, work made possible by the Mars rover Curiosity has demon- 84, and 99 kcal/mol, respectively. Even more energy is required strated the presence of carbon-containing compounds near the to break a carbon-carbon double bond (C = C; 146 kcal/mol) planet surface. The organic matter was detected despite the high or a carbon-carbon triple bond (C ≡ C; 212 kcal/mol), so these levels of ionizing radiation bombarding the Martian planet’s compounds are even more stable. surface, highlighting carbon’s stable nature and suggesting 45 M02_HARD6525_10_GE_C02.indd 45 01/12/21 9:44 P  CH3 CH3 CH3 CH3 CH3 140 Ethane Propane 120 CH2 CH2 CH CH Ethylene Acetylene 100 C—H bond energy (99 kcal/mol) E = energy (kcal/mol) C—C bond energy (83 kcal/mol) 80 H H C—N bond energy (70 kcal/mol) C C H C C H OR OR 60 C C H H 40 Benzene Figure 2-4 Some Simple Hydrocarbon Compounds. 20 Compounds in the top row have single bonds only, whereas those in UV Visible Infrared the second and third rows have double or triple bonds. 0 200 400 600 800 1000 l = wavelength (nm) commercially to promote fruit ripening. However, hydrocar- bons do play an important role in the structure of biological Figure 2-3 The Relationship Between Energy (E) and membranes. The interior of every biological membrane is a Wavelength ( λ ) for Electromagnetic Radiation. The dashed lines nonaqueous environment consisting of the long hydrocarbon mark the bond energies of the C—H, the C—C, and the C—N single “tails” of phospholipid molecules that project into the interior bonds. The bottom of the graph shows the approximate range of wavelengths for ultraviolet (UV), visible, and infrared radiation. of the membrane from either surface. This feature of mem- branes has important implications for their role as permeabil- ity barriers, as we will see shortly. Most biological compounds contain, in addition to car- that more exciting organic compounds could be discovered far- bon and hydrogen, one or more atoms of oxygen and often ther below the surface of Mars where less radiation exists. nitrogen, phosphorus, or sulfur as well. These atoms are usu- ally part of various functional groups, which are specific Carbon-Containing Molecules Are Diverse arrangements of atoms that confer characteristic chemical In addition to their inherent stability, carbon-containing com- properties on the molecules to which they are attached. Some pounds are characterized by the great diversity of molecules of the more common functional groups present in biologi- that can be generated from relatively few different kinds of cal molecules are shown in Figure 2-5. At the near-neutral atoms. Again, this diversity is due to the tetravalent nature pH of most cells, several of these groups form ions, which of the carbon atom and the resulting ability of each carbon are atoms or molecules that are charged because they have atom to form covalent bonds to four other atoms. Because one gained or lost an electron or a proton (a hydrogen atom with- or more of these bonds can be bonds to other carbon atoms, out its electron). molecules consisting of long chains of carbon atoms can be For example, the carboxyl and phosphate groups, which built up. Ring compounds are also common. Further variety is are considered acidic because they have given up a pro- possible by the introduction of branching and the presence of ton, are negatively charged. By contrast, the amino group, double bonds in the carbon-carbon chains. which is considered basic because it has gained a proton, is When only hydrogen atoms are bonded to carbon positively charged. Other groups, such as the hydroxyl, sulf- atoms in linear or branched chains or in rings, the result- hydryl, carbonyl, and aldehyde groups, are uncharged at pH ing compounds are called hydrocarbons (Figure 2-4). values near neutrality. Economically important hydrocarbons such as hexane However, the presence of any oxygen or sulfur atoms (C6 H14 ), octane (C8 H18 ), and decane (C10 H 22 ) are found bound to carbon or hydrogen results in a polar bond due to in gasoline and other petroleum products. The natural gas unequal sharing of electrons. This is because oxygen and sul- that many of us use for fuel is a mixture of methane, eth- fur have higher electronegativity, or affinity for electrons, than ane, propane, and butane, which are hydrocarbons with carbon and hydrogen. Therefore, when “sharing” electrons one to four carbon atoms, respectively. Benzene (C6 H6 ) is a with carbon or hydrogen, an oxygen (or nitrogen) atom will common industrial solvent. have the electron more than half the time, giving it a slightly In biology, on the other hand, hydrocarbons play only a negative charge and giving the hydrogen (or carbon) a slightly limited role because they are essentially insoluble in water, the positive charge. The resulting polar bonds have higher water universal solvent in biological systems. One exception is eth- solubility and chemical reactivity than nonpolar C − C or ylene (C2 H 4 ), a gas that acts as a plant hormone and is used C − H bonds, in which electrons are equally shared. 46 M02_HARD6525_10_GE_C02.indd 46 01/12/21 9:44 P  Plane of symmetry O O C O- O P O- N+H3 1 1 O- Carboxyl Phosphate Amino C C 4 4 (a) Negatively charged groups (b) Positively charged group 2 2 3 3 O O OH SH C C H Hydroxyl Sulfhydryl Carbonyl Aldehyde (c) Neutral but polar groups Figure 2-5 Some Common Functional Groups Found in Biological Molecules. Each functional group is shown in the form that predominates at the near-neutral pH of most cells. They are Left hand Right hand separated into (a) negatively charged, (b) positively charged, and (c) neutral but polar groups. Figure 2-6 Stereoisomers. Stereoisomers of organic compounds occur when four different groups are attached to a tetrahedral carbon Often, carbon-containing compounds will lose electrons to atom. Stereoisomers, like left and right hands, are mirror images of Chapter 2 other molecules such as molecular oxygen. This process is called each other and cannot be superimposed on one another. oxidation and typically involves degradation and releases energy, as in the oxidation of glucose to carbon dioxide and water. The reverse process, by which carbon-containing compounds gain |The Chemistry of the Cell electrons, is known as reduction and typically is biosynthetic and Plane of requires energy, as in the photosynthetic reduction of carbon di- symmetry oxide to glucose. (Oxidation and reduction will be discussed in more detail in Chapter 9; see Equations 9-7 to 9-10.) O O- O O- Given the incredible diversity of chemical compounds C C in cells, you may wonder how it is possible to study individ- ual compounds to determine their structure. Key Technique, H3N+ C H H C +NH 3 pages 48–49, describes the use of mass spectrometry to deter- mine the chemical structure and identity of individual chemi- CH3 CH3 cal compounds in cells. MAKE CONNECTIONS 2.1 L-alanine D-alanine Which strand of cell biology does mass spectrometry align best (a) with? (Fig. 1-3) O Carbon-Containing Molecules Can Form C H Stereoisomers Carbon-containing molecules are capable of still greater diver- H C OH sity because the carbon atom is a tetrahedral structure. When HO C H four different atoms or groups of atoms are bonded to the four corners of such a tetrahedral structure, two different spatial H C OH configurations are possible. Although both forms have the same structural formula, they are not superimposable but are, in fact, H C OH mirror images of each other as shown by the plane of symme- CH2OH try, which represents the mirror. Such mirror-image forms of the same compound are called stereoisomers (Figure 2-6). (b) D-glucose A carbon atom that has four different substituents (atoms or groups attached) is called an asymmetric carbon Figure 2-7 Stereoisomers of Biological Molecules. (a) The atom (Figure 2-7). Because two stereoisomers are possible amino acid alanine has a single asymmetric carbon atom (in boldface) for each asymmetric carbon atom, a compound with n asym- and can therefore exist in two spatially different forms, designated as metric carbon atoms will have 2n possible stereoisomers. As L- and D-alanine. (b) The six-carbon sugar glucose has four asymmetric shown in Figure 2-7, the three-carbon amino acid alanine has carbon atoms (in boldface). 47 M02_HARD6525_10_GE_C02.indd 47 01/12/21 9:44 P  Key Determining the Chemical Fingerprint of a Cell Technique Using Mass Spectrometry 2 The resulting fragments are focused into a beam and 1 The sample is accelerated past a strong ionized and fragmented. electomagnet, which deflects the fragments sideways. Electromagnet X X Sample Electron Detector gun 3 The detector records the presence of each ion and measures its relative adundance in the sample. Figure 2A-1 A Mass Spectrometer. A Scientist Preparing an Injection for Mass Spectrometry. PROBLEM: In cell biology, scientists typically study processes that involve changes in the chemistry of the cell, such as cell Key Tools: Mass spectrometer; an ionized sample; a computer growth and division. Researchers often want to be able to identify to analyze the results. small molecules in a cellular extract, or they may want to deter- mine the chemical structure of a new compound. How is such Details: Mass spectrometry can identify chemical compounds analysis accomplished? within a sample with high resolution, differentiating between com- pounds that can vary by as little as 1 atomic mass unit (amu), the SOLUTION: Mass spectrometry (often called mass spec) is a mass of a hydrogen atom. Analysis of a compound using a mass method used to identify and measure the relative abundance of spectrometer (Figure 2A-1) involves three main steps: ionization individual molecules in a sample, as well as to determine their and fragmentation of the sample, deflection of the ionized frag- chemical structure. Purified molecules are broken into fragments, ments by an electromagnet, and detection of the individual ions and these fragments can be analyzed to determine their masses and measurement of their abundance. and the arrangement of covalent bonds that hold atoms of the Ionization and Fragmentation. Commonly, the sample is molecule together. ionized by bombarding it with a stream of high-energy electrons from an electron gun. The stream has enough energy to knock an a single asymmetric carbon atom (in the center) and thus has Figure 2-7b. Of the six carbon atoms of glucose, the four shown two stereoisomers, called L-alanine and D-alanine (Figure in boldface are asymmetric. (Can you figure out why the other 2-7a). Neither of the other two carbon atoms of alanine is an two carbon atoms are not asymmetric?) With four asymmetric asymmetric carbon atom because one has three identical sub- carbon atoms, the structure shown (D-glucose) is only one of 24 , stituents (hydrogen atoms) and the other has two bonds to a or 16, possible stereoisomers of the C6 H12O6 molecule. single oxygen atom and thus is only bonded to three substitu- ents. Both stereoisomers of alanine occur in nature, but only CONCEPT CHECK 2.1 L-alanine is present as a component of proteins. What properties of the carbon atom make it especially suitable As an example of a compound with multiple asymmetric as the structural basis for nearly all biomolecules? carbon atoms, consider the six-carbon sugar glucose shown in 48 M02_HARD6525_10_GE_C02.indd 48 01/12/21 9:44 P  electron off the sample to form a positively charged molecular ion 100 (M+). Molecular ions are generally unstable and will break up into H O smaller fragments, some of which will be positively charged and 80 Relative abundance (%) others neutral. H2N C C Deflection. The resulting fragments are focused into a fine OH H 60 H beam and accelerated past a powerful electromagnet that sepa- Glycine (Gly) rates them by mass. The mass of each fragment will depend on H2N C which particular covalent bond in the parent ion (M+) was broken. 40 Because each molecule fragments in a predictable pattern, the H specific pattern of fragment masses can be used to identify a 20 compound. As the beam passes by the electromagnet, individual ions are pulled sideways, deflected from a straight path. The amount of 0 15 30 45 60 75 90 deflection depends on the mass of the ion, with lighter ions being Mass-to-charge (m/z) ratio deflected more. The effect is like dropping a large cannonball and a small steel ball (such as can be found in a pinball machine) near Figure 2A-2 The Mass Spectrum of Glycine. The non-ionized a large magnet. The heavy cannonball will be pulled sideways form of glycine is shown. during its flight much less than the smaller ball. The strength of Chapter 2 the electromagnet can be increased (to deflect heavier ions) or decreased (to deflect lighter ions) so that ions of different masses are focused on a detector at the end of the spectrometer. (Only | positively charged particles reach the detector.) The Chemistry of the Cell Detection and Analysis. The detector records the presence plotted relative to the base peak. The base peak typically corre- of each ion and, based on the strength of the magnetic field, sponds to the most stable, hence most abundant, fragment ion. can determine the ion’s mass. It also records the number of ions In this example, the base peak is at m/z = 30, which, for glycine, is having each different mass and calculates their abundance in the a fragment with a single carbon, a nitrogen, and four hydrogens sample. A computer then converts this information into a graph (CH2NH2). By comparing the pattern of the lines to the patterns of showing vertical lines representing a spectrum of mass-to-charge known compounds, a compound can often be identified. For novel ratios (m/z) across the x-axis, with the heights of the lines (also compounds, the pattern of lines helps identify the fragments. By called peaks) showing each ion’s relative abundance (y-axis). determining how the fragments would fit together to form an in- Figure 2A-2 shows mass spectral results for a simple amino tact molecule, a researcher can predict the types and arrangement acid, glycine. of the covalent bonds and determine the overall chemical structure Data Interpretation. The heaviest ion in a mass spectrum of the novel compound. (the one with the highest m/z value) is often the molecular ion. In Figure 2A-2, this is the peak at m/z = 75. (To confirm that a molecular weight of 75 corresponds to glycine, start with its QUESTION: Compare the flights of the ionized molecular elemental formula, C2H5NO2, and sum the atomic weights of its fragments whose paths are shown in blue and red in Figure 2A-1. carbons, 12 amu × 2; nitrogen, 14 amu × 1; oxygens, 16 amu × 2; and hydrogens, 1 amu × 5.) Which fragment has the higher m/z ratio? What factors might The tallest peak in a mass spectrum, called the base peak, is explain why the deflection of that fragment differs from the assigned a y-axis value of 100%. The heights of all other lines are other fragment? 2.2 The Importance of Water addition, many cells depend on an extracellular environment that is essentially aqueous as well. In some cases, this is a body Just as the carbon atom is uniquely significant because of of water—whether an ocean, a lake, or a river—where the cell its role as the universal backbone of biologically important or organism lives, and in other cases, it may be the body flu- molecules, the water molecule commands special attention ids with which the cell is bathed. Therefore, we must always because of its indispensable role as the universal solvent in take into account the presence of water when considering the biological systems. Water is, in fact, the single most abundant ways that a cell functions. component of cells and organisms. Typically, about 75–85% Water is indispensable for life. True, there are life forms of a cell by weight is water, and most cellular processes (like that can become dormant and survive periods of severe water protein folding) take place in this aqueous environment. In scarcity. Seeds of plants and spores of bacteria and fungi are 49 M02_HARD6525_10_GE_C02.indd 49 01/12/21 9:44 P  clearly in this category. Some plants and animals—notably bent rather than linear in shape, with the two hydrogen atoms certain mosses, lichens, nematodes, and rotifers—can also bonded to the oxygen at an angle of 104.5° rather than 180°. undergo physiological adaptations that allow them to dry out It is no overstatement to say that life depends critically on this and survive in a highly dehydrated form, sometimes for sur- angle because of the distinctive properties that the resulting prisingly long periods of time. Such adaptations are clearly asymmetry produces in the water molecule. an advantage in environments characterized by periods Although the water molecule as a whole is uncharged, of drought. Yet all of these are, at best, temporary survival its electrons are unevenly distributed. The oxygen atom is mechanisms. Resumption of normal activity always requires highly electronegative—it tends to draw electrons toward rehydration. it. Therefore, the oxygen atom has a partial negative charge The successful transport of water into and out of cells, as (denoted as δ − , with the Greek letter delta standing for “par- well between cells is also critical. Water can move across cellu- tial”), and each of the two hydrogen atoms has a partial posi- lar membranes based on the concentration of solutes present tive charge (δ + ). This unequal distribution of charge makes in a process called osmosis. Whereas osmosis can be a slow any O − H bond polar and, along with the presence of two process, water is able to move much more quickly through a lone electron pairs, helps explain why water is such a highly specialized channel protein known as an aquaporin (AQP). polar molecule. For example, aquaporins allow water to flow rapidly between cells within certain organs like the kidneys. (You will learn Water Molecules Are Cohesive more detail about the movement of water using both these Because of their polarity, water molecules are attracted to each mechanisms in Chapter 8.) other so that the electronegative oxygen atom of one molecule To understand why water is so uniquely suitable for its is associated with the electropositive hydrogen atoms of adja- role, we need to look at its chemical properties. The most criti- cent molecules. This forms a hydrogen bond (dotted lines in cal attribute of water is its polarity because this property ac- Figure 2-8b), which is a type of noncovalent interaction that counts for its cohesiveness, its temperature-stabilizing capacity, is about one-tenth as strong as a covalent bond. and its solvent properties, all of which have important conse- Each oxygen atom can bond to two hydrogens, and both quences for biological chemistry. of the hydrogen atoms can associate in this way with the oxygen atoms of adjacent molecules. As a result, water is Water Molecules Are Polar characterized by an extensive three-dimensional network of An unequal distribution of electrons gives the water molecule hydrogen-bonded molecules. Although individual hydrogen its polarity, which we can define as an uneven distribution bonds are weak, the combined effect of large numbers of them of charge within a molecule. To understand the polar na- can be quite significant. In liquid water, the hydrogen bonds ture of water, we need to consider the shape of the molecule between adjacent molecules are constantly being broken and (Figure 2-8). As shown in Figure 2-8a, the water molecule is re-formed, with a typical bond having a half-life of a few mi- croseconds. On average, however, each molecule of water in the liquid state is hydrogen-bonded to at least three neighbor d- H molecules at any given time. In ice, the hydrogen bonding is O still more extensive, giving rise to a rigid, hexagonal crystal- O line lattice with every oxygen hydrogen-bonded to hydrogens of two adjacent molecules and every water molecule therefore H d+ H H hydrogen-bonded to four neighboring molecules. It is this tendency to form hydrogen bonds between adja- cent molecules that makes water so highly cohesive. This cohe- O Hydrogen siveness accounts for the high surface tension of water, as well bonds as for its high boiling point, high specific heat, and high heat of H H d+ vaporization. The high surface tension of water allows some in- H sects to move across the surface of a pond without breaking the surface (Figure 2-9). High surface tension is also impor- d- O tant in allowing water to move upward through the conduct- O ing tissues of plants. d+ d+ H + H H d Water Has a High Temperature-Stabilizing 104.5º (a) Polarity of (b) Hydrogen bonding between Capacity water molecule water molecules An important property of water that stems directly from the hydrogen bonding between adjacent molecules is the high Figure 2-8 Hydrogen Bonding Among Water Molecules. (a) The specific heat that gives water its temperature-stabilizing capac- water molecule is polar because it has an asymmetric charge distribution, partly due to the high electronegativity of the oxygen atom. It has a ity. Specific heat is the amount of heat a substance must absorb partial negative charge (δ − ), and each of the two hydrogen atoms has per gram to increase its temperature 1°C. The specific heat of a partial positive charge (δ + ). (b) The extensive association of water water is 1.0 calorie per gram. molecules with one another in either the liquid or the solid state is due to Because of its extensive hydrogen bonding, the specific hydrogen bonds (blue dots). heat of water is much higher than that of most other liquids. 50 M02_HARD6525_10_GE_C02.indd 50 01/12/21 9:44 P  Water Is an Excellent Solvent From a biological perspective, one of the most important prop- erties of water is its excellence as a general solvent. A solvent is a fluid in which another substance, called the solute, can be dissolved. Water is an especially good solvent for biologi- cal purposes because of its remarkable capacity to dissolve a great variety of solutes. It is the polarity of water that makes it so useful as a sol- vent. Many of the molecules in cells are also polar and there- fore form hydrogen bonds with water molecules. Solutes that have an affinity for water and therefore dissolve readily in water are called hydrophilic (“water-loving”). Most small or- ganic molecules found in cells are hydrophilic. Examples are sugars, organic acids, and some of the amino acids. Molecules Figure 2-9 Walking on Water. The high surface tension of water that are not very soluble in water are termed hydrophobic results from the collective strength of vast numbers of hydrogen (“water-fearing”). Among the more important hydrophobic bonds. It enables insects such as this water strider to walk on the compounds found in cells are the lipids and proteins found in surface of a pond without breaking the surface. biological membranes. In general, polar molecules and ions are hydrophilic, and nonpolar molecules are hydrophobic. Some biological macromolecules, notably proteins, have both hydrophobic and hydrophilic regions, so some parts of the In other liquids, much of the energy would cause an increase molecule have an affinity for water whereas other parts of the Chapter 2 in the motion of solvent molecules and therefore an increase molecule do not. in temperature. In water, the energy is used instead to break To understand why polar substances and ions dissolve so hydrogen bonds between neighboring water molecules, buff- readily in water, let’s consider a salt such as sodium chloride ering aqueous solutions against large changes in tempera- (NaCl) (Figure 2-10). Because it is a salt, NaCl exists in crys- |The Chemistry of the Cell ture. This capability is an important consideration for the cell talline form as a lattice of positively charged sodium cations biologist because cells release large amounts of energy as heat ( Na + ) and negatively charged chloride anions (Cl − ). For NaCl during metabolic reactions. If not for the extensive hydrogen to dissolve in a liquid, solvent molecules must overcome the bonding and the resulting high specific heat of water mol- attraction of the Na + cations and Cl − anions for each other. ecules, this release of energy would pose a serious overheating When NaCl is placed in water, both the sodium and chloride problem for cells, and life would not be possible. ions become involved in electrostatic interactions with the water Water also has a high heat of vaporization, which is de- molecules instead of with each other, and the Na + and Cl − fined as the amount of energy required to convert 1 gram of ions separate and become dissolved. Because of their polar- a liquid into vapor. This value is high for water because of the ity, water molecules can form spheres of hydration around both hydrogen bonds that must be disrupted in the process. This Na + and Cl − , thus neutralizing their attraction for each other property makes water an excellent coolant and explains why and decreasing their likelihood of reassociation. people perspire, why dogs pant, and why plants lose water As Figure 2-10a shows, the sphere of hydration around through transpiration. In each case, the heat required to a cation such as Na + involves water molecules clustered evaporate water is drawn from the organism, which is there- around the ion with their negative (oxygen) ends pointing fore cooled in the process. toward it. For an anion such as Cl − , the orientation of the d- d+ d+ O H H H H O d+ d+ d+ d- d+ H d+ d+ H H H d- O Cl- O d- O d- Na+ d- O Figure 2-10 The Solubilization + H d d+ H of Sodium Chloride. Sodium H d- H d+ d+ d+ d+ chloride (NaCl) dissolves in water H H because spheres of hydration are O formed around both (a) the sodium O ions and (b) the chloride ions. The H H oxygen atom and the sodium and d+ d+ d- chloride ions are drawn to scale. (a) Hydration of sodium ion (b) Hydration of chloride ion 51 M02_HARD6525_10_GE_C02.indd 51 01/12/21 9:44 P  HUMAN Connections Taking a Deeper Look: Magnetic Resonance Imaging (MRI) We often take the water content of our bodies for granted. On average, the human body is 55–65% water, depending on age and weight. But the chemistry of water also provides an opportu- nity: each water molecule possesses two hydrogen atoms, which are constantly breaking and re-forming hydrogen bonds with surrounding molecules. In addition, most biological molecules contain hydrogen, and the products of many biological reactions release hydrogen ions into surrounding tissues. It is these hydrogen ions, so plentiful in water and tissue, especially the circulatory sys- tem, that make one of the safest imaging technologies possible: magnetic resonance imaging, or MRI. It is very likely that you or someone you know has had an MRI to diagnose a medical condition, but how does an MRI device exploit water in tissues to produce images of the body? MRI is a noninva- sive method that uses basic principles of chemistry and physics to visualize internal structures of the body. An MRI machine capital- izes on the ability of protons to align with an externally applied magnetic field by placing the patient inside the field of a powerful electromagnet. In the absence of an applied magnetic field, the magnetic fields of individual hydrogens are randomly oriented. When a magnetic field is applied, however, most of the hydrogen atoms in the patient’s body will align in one of two directions: either “up” or “down” with respect to the applied field (Figure 2B-1). Then a second, oscillating magnetic field is applied, which causes the aligned hydrogen atoms to absorb energy, which they subse- quently release in the form of radio waves as the magnetic field changes. By rapidly varying the main magnetic field using a special set of magnetic coils, the release of these radio waves is detected by a receiver and provides relevant spatial information. The rapid switching of these coils on and off gives rise to the familiar repetitive clicking sounds made by an MRI machine. Once the radio waves are detected, a computer creates a spatial map of energy differences to produce an image of the tissue. Figure 2B-2 MRI of Tumor on the Femur. The small tumor All tissues in the body vary in density and water content. is easily visible (red circle). Because an MRI requires a change in orientation of hydrogen ions in a magnetic field, these differences throughout the body actually provide the perfect contrast for visualization. By changing magnetic field strength or the frequency of the radio waves used during an MRI, a specific organ or tissue can be highlighted. For example, water and fluid-containing tissues are bright, whereas fatty tissues with little water are darker. These differences produce striking images of individual organs that can be examined for tu- mors or other abnormalities (Figure 2B-2). For many purposes, the images produced in an MRI scan are far better than those produced by taking multiple X-ray images and reconstructing them (a technique known as computer-aided tomography, or a CAT scan). With the addition of contrast agents injected into a patient’s bloodstream or other tissues, specific structures such as blood ves- sels can be imaged with extraordinary detail using MRI. (a) Before magnetic field applied: (b) After magnetic field The cost of an MRI procedure in the United States can range random orientation of (large arrow) applied: from $1000 to $2000. While more expensive than an X-ray, this proton spins proton spins oriented procedure may be a better choice for many patients due to its potential for more accurate diagnoses. Unlike traditional X-rays, Figure 2B-1 Hydrogen Atom Spin Patterns. (a) The magnetic which can image only dense structures like bone and can cause field orientation of hydrogen atoms in the absence of a magnetic field damage to DNA, an MRI can give a detailed image of soft tissue is random. (b) The magnetic fields of hydrogen atoms align in the such as internal organs, blood vessels, and nerves without posing a presence of an applied magnetic field. significant health risk. 52 M02_HARD6525_10_GE_C02.indd 52 01/12/21 9:44 P  water molecules is reversed, with the positive (hydrogen) Ideally, such a barrier should be impermeable to most of the ends of the solvent molecules pointing in toward the ion molecules and ions found in cells and their surroundings. (Figure 2-10b). Similar spheres of hydration develop around Otherwise, substances could diffuse freely in and out, and charged functional groups (see Figure 2-5a, b), increasing the cell would not really have a defined content at all. On the their solubility. Even uncharged polar functional groups, other hand, the barrier cannot be completely impermeable. such as aldehyde or sulfhydryl groups (see Figure 2-5c), will If it were, necessary exchanges of material between the cell have a sphere of hydration, as the polar oxygen or sulfur and its environment could not take place. The barrier must atoms attract the positively charged ends of the polar water be insoluble in water so that it will not be dissolved by the molecule and increase solubility. aqueous medium of the cell. At the same time, it must be Some biological compounds are soluble in water because readily permeable to water because water is the basic solvent they exist as ions at the near neutral pH of the cell and are system of the cell and must be able to flow into and out of therefore solubilized and hydrated like the ions of Figure 2-10. the cell as needed. Compounds containing carboxyl, phosphate, or amino groups As you might expect, the membranes that surround are in this category (see Figure 2-5). Most organic acids, for cells and organelles satisfy these criteria admirably. A cel- example, are almost completely ionized by deprotonation at a lular membrane is essentially a hydrophobic permeability pH near 7 and therefore exist as anions that are kept in so- barrier that consists of phospholipids, glycolipids, and mem- lution by spheres of hydration, as we have just seen with the brane proteins. In most organisms other than bacteria, the chloride ion in Figure 2-10b. Amines, on the other hand, are membranes also contain sterols—cholesterol in the case of usually protonated at cellular pH and thus exist as hydrated animal cells, ergosterols in fungi, and phytosterols in the mem- cations, and behave like the sodium ion in Figure 2-10a. branes of plant cells. (Don’t be concerned if you haven’t Often, organic molecules have no net charge but are encountered these kinds of molecules before; we’ll meet them nonetheless hydrophilic because they have some regions that all again in Chapter 3.) are positively charged and other regions that are negatively Most membrane lipids and proteins are not simply hy- Chapter 2 charged and thus are soluble in water. Also, compounds con- drophobic or hydrophilic. They typically have both hydro- taining the polar hydroxyl, sulfhydryl, carbonyl, or aldehyde philic and hydrophobic regions and are therefore referred groups shown in Figure 2-5 are also water soluble due to hy- to as amphipathic molecules (the Greek prefix amphi– | drogen bonding of these polar groups with water molecules. means “of both kinds” and pathic means “to feel”). The am- The Chemistry of the Cell Hydrophobic molecules such as hydrocarbons, on the phipathic nature of membrane phospholipids is illustrated other hand, have no such polar regions and therefore show no in Figure 2-11 on page 54, which shows the structure of tendency to interact electrostatically with water molecules. phosphatidylethanolamine, a prominent phospholipid in many In fact, because they disrupt the hydrogen-bonded structure kinds of membranes. The distinguishing feature of amphipa- of water, they tend to be excluded by the water molecules. thic phospholipids is that each molecule consists of a polar Therefore, hydrophobic molecules tend to coalesce as they as- head and two nonpolar hydrocarbon tails. The polarity of the sociate with one another rather than with the water. As we hydrophilic head is due to the presence of a negatively charged will see later in the chapter, such associations of hydrophobic phosphate group that is often linked to a positively charged molecules (or parts of molecules) are a major driving force in group—an amino group, in the case of phosphatidylethanol- the folding of proteins, the assembly of cellular structures, amine and most other phosphoglycerides. (We will learn more and the organization of membranes. about phospholipids in Chapter 3.) Because typical cells are primarily water and most other Soap is a familiar amphipathic molecule that you all biological molecules in cells contain hydrogen, the chemical have likely used to dissolve grease, oil, and other nonpolar and physical properties of the hydrogen atom can be exploited substances. The nonpolar hydrocarbon tails of the soap mol- for medical imaging purposes. The common procedure known ecules interact with and surround the oil or grease, and the as magnetic resonance imaging (MRI) takes advantage of this polar heads interact with water, enabling the oil or grease to abundance of water to image internal body tissues in a nonin- be washed away. In the lab, we often use the amphipathic de- vasive manner (see Human Connections, page 52). tergent sodium dodecyl sulfate (SDS) to isolate insoluble pro- teins and lipids. SDS has a negatively charged sulfate group CONCEPT CHECK 2.2 attached to a single hydrocarbon chain of 12 carbons and How would the properties of water change if the water mol- acts much like the soap described above to solubilize nonpolar ecule were linear rather than bent? Why would it be less satis- and amphipathic molecules. factory as the basis for living cells? A Membrane Is a Lipid Bilayer with Proteins Embedded in It 2.3The Importance of Selectively When exposed to an aqueous environment, amphipathic mol- Permeable Membranes ecules undergo hydrophobic interactions. In a membrane, for example, phospholipids are organized into two layers: their Every cell and organelle needs some sort of physical bar- polar heads face outward toward the aqueous environment rier to keep its contents in and external materials out. A cell on both sides, and their hydrophobic tails are hidden from also needs some means of controlling exchange between its the water by interacting with the tails of other molecules ori- internal environment and the extracellular environment. ented in the opposite direction. The resulting structure is the 53 M02_HARD6525_10_GE_C02.indd 53 01/12/21 9:44 P  H H H Lipid Bilayers Are Selectively Permeable Because of its hydrophobic interior, a lipid bilayer is readily N+ Ethanolamine permeable to nonpolar molecules. However, it is quite imper- CH2 meable to most polar molecules and is highly impermeable to CH2 all ions (Figure 2-13). Because most cellular constituents are either polar or charged, they have little or no affinity for the O membrane interior and are effectively prevented from enter- Phosphate group O P O- ing or escaping from the cell. Small, uncharged molecules are an exception, however. Compounds with molecular weights O below about 100 readily diffuse across membranes, meaning CH2 CH CH2 they can freely and spontaneously pass through membranes, Polar heads regardless of whether they are nonpolar (O2 and CO2) or O O (charged groups) polar (water and ethanol). Water is an especially important C O C O example of a very small molecule that, though polar, diffuses CH2 CH2 CH2 CH2 rapidly across membranes and can readily enter or leave cells. + CH2 CH2 Large, uncharged polar molecules, such as glucose and CH2 CH2 - sucrose, can diffuse across the membrane, but to a lesser ex- CH2 CH2 tent than small molecules. In contrast, even the smallest ions CH2 CH2 CH2 CH2 are effectively excluded from the hydrophobic interior of the CH2 CH2 membrane. For example, a lipid bilayer is at least 108 times CH2 CH2 Nonpolar less permeable to small cations such as Na + or K + than to tails CH2 CH2 (hydrocarbon water. This striking difference is due to both the charge on an CH2 CH2 chains) ion and the sphere of hydration surrounding the ion. CH2 CH2 CH2 CH2 Of course, it is essential that cells have ways of transfer- CH2 CH2 ring not only ions such as Na + and K + but also a wide variety CH3 CH3 of polar molecules across membranes that are not otherwise permeable to these substances. To transport these substances (a) Phospholipid structure (b) Phospholipid into and out of the cell, biological membranes are equipped symbol with a wide variety of transport proteins (which we will dis- Figure 2-11 The Amphipathic Nature of Membrane cuss in