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© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Chapter 2 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION The Chemical Building Blocks of Life © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Chapter Preview © Jones & Bartlett Learning, LLC 2.1 Organisms Are Composed of Atoms NOT FOR SALE OR DISTRIBUTION 2.2 Chemical Bonds Form Between Reactive Atoms 2.3 All Living Organisms Depend on Water © Jones2.4 & Bartlett Learning, Living Organisms AreLLC Composed of Four NOT FOR SALE DISTRIBUTION TypesOR of Organic Compounds Clinical Case 2: An Outbreak of Salmonella Food Poisoning Investigating the Microbial World 2: © Jones & Bartlett Chemical Evolution © Jones & Bartlett Learning, LLC The origin of life is NOT one ofFOR the great unsolved SALEand OR DISTRIBUTION Learning, LLC FOR SALE MicroInquiry 2: IsNOT Protein or DNA the OR DISTRIBUTION mysteries of science. Researchers believe microGenetic Material? bial life arose on Earth about 3.8 billion years ago, although no one can definitely say how or where life originated. In fact, there are many hypotheses. More Jones & Bartlett Learning, LLC Jonescode, & Bartlett LLC than©likely, a common primitive life form gave rise identical © genetic perhapsLearning, any undiscovered NOT FOR SALE OR DISTRIBUTION OR DISTRIBUTION to bacterial and archaeal cells. If, in fact, this is true, life formsNOT wouldFOR look SALE like prokaryotic cells, but an did such life arise but once or was there opportunity alternate and distinctive biochemistry might single for “life” arising more than once—and in a different them out as “alien.” chemical form? Microbiologists have identified only about 2% Paul Davies is an award-winning physicist and of the microorganisms on Earth. Because we know © Jones & Bartlett Learning, LLC & Bartlett director at Arizona State University of BEYOND:© Jones so little about theLearning, diversity ofLLC these microbes, it is NOT FORCenter SALEfor OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Fundamental Concepts in Science. One possible that there is (or are) other shadow forms of the “big questions” the Center is investigating is dispersed or hidden among the undiscovered. whether “alien” life might be hiding right in front Importantly, that is what science is all about—the of our noses. The hypothesis is that perhaps other field of study that builds knowledge based on testlife arose among the© known life on planet Earth and ing and evidence, and that tries to Jones & Bartlett Learning, LLC © Jones & describe Bartlett and Learning, LLC still exists here today as a so-called “shadow life.” comprehend the nature of the universe in whole or NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION To pursue this controversial idea, scientists have part, wherever that might lead. begun searching high and low (literally up in the air Microorganisms are found in most, if not all, and deep in the crust of the earth) for evidence of habitats on Earth. Some microbes can survive in this shadow life—specifically microorganisms that, alkaline, hypersaline conditions of some lakes, like as the result of a “secondLearning, genesis,” would Mono Lake chapter openingLearning, photo), theLLC acidic © Jones & Bartlett LLC differ © (see Jones & Bartlett chemically from all known microbial life. Because runoff from a ore mine, and high temperatures of a NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION microbes and all known life employ the same hot spring (Figure 2.1). In these cases, as with all chemical building blocks and operate with a nearly environments where microbes and any shadow life Mono Lake, California. © Jones & Bartlett Learning, LLC Olav Lyngfjell/ShutterStock, Inc. NOT FOR© Geir SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 35 © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 35 13/02/17 4:44 pm 36 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC exist, survival depends on cellular chemisNOT might FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION try, the biochemical reactions between atoms and molecules that provide for the unique metabolism found in all organisms. Therefore, studying the basic principles of © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC chemistry will provide you the working knowledge NOTofFOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION to understand the daily lives the microbial workforce, whether in the environment or in your body. For example, in medicine and healthcare, understanding the biochemistry of a pathogen could guide the©development of drugs, like antibiotics, © Jones & Bartlett Learning, LLC Jones & Bartlett Learning, LLC and vaccines to cure or prevent infectious disease. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION This chapter serves as a primer or review of Figure 2.1 Survival in earth’s extreme environments. In the fundamental concepts of chemistry that form the gentle flow of heated water spreading out in terraces, a foundation for the chapters ahead. We will idenorange- and red-pigmented bacterial mats thrive in the tify the elements making up all known substances warm, shallow water toward the edge. »» What other extreme and show how these elementsLLC combine to form the © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, environments can you identify where microbes might survive? major groups of organic compounds NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION found in all Courtesy of Jim Peaco/Yellowstone National Park. “known” forms of life. Chapter Challenge © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION The Earth was formed some 4.5 billion years ago. In that expanse of time, it appears that life only arose once because all life shares the same chemistry. Nonetheless, if some unrecognized, shadow form of microbial life still exists on Earth, it might contain a few unique chemical building blocks that would be used to build large substances. How would we recognize such chemicals and what are the potential markers by which “shadow life” could be detected? Let’s consider some alternatives known chemistry of life! Learning, LLC © Jones & Bartlett Learning, LLC as we investigate the © Jones & Bartlett NOT FOR SALE OR DISTRIBUTION ■ KeY CONCept 2.1 NOT FOR SALE OR DISTRIBUTION Organisms Are Composed of Atoms © Jones & Learning, Bartlett there Learning, are a LLC number of elements AsBartlett far as scientists know,LLC all matter in the physical© JonesIn& addition, in much amounts. These so-called a rock, a tree, or a microbe—is builtNOT needed NOT FORuniverse—be SALE OR it DISTRIBUTION FOR SALE ORsmaller DISTRIBUTION “trace elements” vary from organism to organism, from substances called chemical elements. Chembut often include manganese (Mn), iron (Fe), copper ical elements are the most basic forms of matter (Cu), and zinc (Zn). and they cannot be broken down into simpler substances by ordinary chemical reactions. Ninety-two Atoms Are Composed © ofJones Charged and © Joneshave & Bartlett Learning, LLC & Bartlett Learning, LLC naturally occurring elements been discovered, uncharged Subatomic Particles NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION whereas additional elements have been made in the laboratory or nuclear reactor. An atom is the smallest unit of matter having the Only about 25 of the 92 naturally occurring eleproperties of that element; that is, if you split an ments are essential to the survival of living organatom, like carbon, into simpler parts, it no longer isms.©Many of these are needed in relatively large has the properties Because atomsLLC are so Jones & Bartlett Learning, LLC © Jonesof&carbon. Bartlett Learning, amounts (TABLe 2.1). Note that just six of these small, they often are illustrated using a common but NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION elements—carbon (C), hydrogen (H), nitrogen (N), overly simplified two-dimensional model. oxygen (O), phosphorus (P), and sulfur (S)—make up An atom consists of a positively charged core, about 97% of the weight in both human and bacterial the atomic nucleus that makes up most of the cells. (The acronym CHNOPS is helpful in remematom’s mass (FIGURE 2.2A). The atomic nucleus bering theseLearning, six important elements.) Another five© Jones contains two kinds of tightly packed © Jones & Bartlett LLC & Bartlett Learning, LLC subatomic parelements make up most of the remaining 3%. ticles called protons and neutrons . Although these NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 36 13/02/17 4:44 pm KEY CONCEPT 2.1 Organisms Are Composed of Atoms 37 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION taBLe 2.1 Some of the Major Elements of Bacterial and Human Cells Percent by Mass element Oxygen © Jones & Bartlett Learning, LLC Symbol Bacterial Cell Human Cell NOT FOR SALE OR DISTRIBUTION © JonesMass & Bartlett Atomic Number Number Learning, LLC NOT FOR SALE OR DISTRIBUTION O 72 66 8 Carbon C 12 18 6 12 Hydrogen H 10 10 1 1 © Jones & Bartlett Learning, LLC Nitrogen 3 NOT FOR SALE OR NDISTRIBUTION 16 © Jones & Bartlett Learning, LLC 7 14 NOT FOR SALE OR DISTRIBUTION 3 Phosphorus P 0.6 1 15 31 Sulfur S 0.3 0.3 16 32 © Jones & Bartlett Learning, LLCNa Sodium NOT FOR SALE OR DISTRIBUTION 1.0 Magnesium Mg 0.5 Calcium Ca 0.5 Potassium Chlorine © Jones & LLC 0.2Bartlett Learning, 11 NOT FOR SALE OR DISTRIBUTION 0.1 12 24 1.5 20 40 1.0 © JonesK & Bartlett Learning, LLC 0.4 NOT FOR Cl SALE OR DISTRIBUTION 0.05 0.15 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Electron (e–) p+ n © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 23 19 17 39 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 35 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Atomic nucleus © Jones & Bartlett Learning, LLC NOT FOR SALEElectron OR DISTRIBUTION (A) shells 6p+ © Jones 1p+ & Bartlett Learning, LLC 6n NOT FOR SALE OR DISTRIBUTION + 2e 8e 5e 15pJones © & Bartlett Learning, LLC 16n NOT FOR SALE OR DISTRIBUTION – 8p+ 8n – – 1e– 6e– Hydrogen (H) Carbon (C) Atomic number: 1 Learning, LLC6 © Jones & Bartlett Mass number: 1 12 NOT FOR SALE OR DISTRIBUTION (B) 8e– Oxygen (O) 8© Jones 16 15e– Phosphorus (P) 15 Learning, LLC & Bartlett 31 NOT FOR SALE OR DISTRIBUTION Figure 2.2 Atomic Structure and the Electron Configurations for Four Biologically Important Elements. Using twodimensional models for atomic structure, (A) the atom is composed of protons and neutrons in the atomic nucleus, and electrons in electron shells (not drawn to scale). (B) The atomic structure of four biologically essential elements illustrates that © Jones & LLC © Jones & Bartlett theBartlett number ofLearning, protons equals the number of electrons (though not necessarily equal Learning, to the numberLLC of neutrons). »» Knowing the mass number for an element, what does that tell you about the mass of an electron? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 37 13/02/17 4:44 pm 38 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC particles have about the same mass, each proton NOT FOR SALEMg OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Mg+2 bears one positive electrical charge (value = +1), whereas a neutron has no charge. The number of protons in an atom defines each element. For example, carbon atoms always Jones Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 12p+ 12p+ have six protons. If©there are &seven protons, it is 12n 12n NOT FOR SALE OR DISTRIBUTION NOT FOR ORnitrogen DISTRIBUTION no longer carbon but rather theSALE element (see Table 2.1). The number of protons also represents the atomic number of the atom. As shown in Table 2.1, carbon with six protons has an atomic number of 6. The mass number is the total num© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC ber of protons and neutrons in the nucleus. Because NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION carbon atoms have six protons and usually six neuLost electrons trons, the mass number of carbon would be 12. Figure 2.3 Formation of an ion. Ions can be formed by Surrounding the atomic nucleus is a “cloud” the loss or gain of one or more electrons. Here, a magneof fast- moving, negatively charged electrons sium (Mg) atom has lost two electrons to become a mag(value = –1).Learning, In uncharged © Jones & Bartlett LLCatoms, the number of© Jones & ion Bartlett Learning, nesium (Mg+2). »» For Mg, whatLLC does the superscript (+2) electrons is equal to the number of protons; that is, denote? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the atom has no net electrical charge. Because electrons move so fast, it is impossible at any moment to predict where a particular electron might be located; thus the term “electron cloud” is used. However, ATOMIC STRUCTURE researchers can identify the areas within the cloud © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC where electrons are NOT usually found. These areas are NOT FOR SALE OR DISTRIBUTION involvesFOR SALE OR DISTRIBUTION called electron shells, each shell representing an area that is a different distance from the atomic nucleus Atoms and that has a specific energy level (Figure 2.2B). © Jones & Bartlett Learning, LLC Atoms Can Vary in the Number of Neutrons NOT FOR SALE OR DISTRIBUTION or electrons that consist of the © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Atomic nucleus Electron shells Although the number of protons is the same for all atoms of an element, the number of neutrons in an which is which contain element can vary, which will alter its mass number. As composed of negatively © Jones & Bartlett most Learning, mentioned, carbon LLC atoms have a mass number© Jones & Bartlett Learning, LLC charged 12, whereas some carbon atoms have seven or eightNOT FOR SALE OR DISTRIBUTION NOT FORofSALE OR DISTRIBUTION positively uncharged neutrons, rather than six, resulting in a mass numcharged ber of 13 or 14. Atoms of the same element that have different numbers of neutrons are called isotopes. Electrons Protons Neutrons Therefore, carbon-12, carbon-13, and carbon-14 & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 12 13© Jones 14 (symbolized as C, C, and C, respectively) are the NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION three isotopes of carbon. Such isotopes, though, still the loss or the loss or the loss or gain of which gain of which gain of which have six protons and the same chemical properties. forms a forms an forms an Some isotopes are unstable and give off energy in the form of radiation. Such radioisotopes are use14 ful in©research medicine. For example, Jones and & Bartlett Learning, LLCC atoms © Jones & Bartlett Learning, LLC that have been incorporated into organic substances Different Ion NOT FOR SALE OR DISTRIBUTION NOT FOR Isotope SALE OR DISTRIBUTION element can be used for radiometric (carbon) dating of fossils. Researchers can use isotopes of other elements as radioactive tracers to follow the fate of a substance Figure 2.4 A Concept Map for Atomic Structure. This (see Microinquiry 2 at the end of this chapter). concept map shows the relationship between atoms, eleShould an uncharged LLC atom gain or lose electrons,© Jones © Jones & Bartlett Learning, Bartlett Learning, LLC ments,&isotopes, and ions. »» Which terms in this map apply the resulting atom is called an ion ( Figure 2.3 ). The to atomic number and which apply to mass number? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 38 13/02/17 4:44 pm KEY CONCEPT 2.2 Chemical Bonds Form Between Reactive Atoms 39 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC addition of one or more electrons to an atom means thereSALE are notOR enough electrons to fill the shell, the NOT ifFOR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION there is/are more negatively charged electrons than outermost shell will remain unfilled. positively charged protons. Such a negatively charged Atoms with an unfilled outer electron shell, ion is called an anion. By contrast, the loss of one or called the valence shell, are unstable and the atoms more electrons leaves the atom with fewer electrons tend to be chemically reactive. The valence elec©charged Jonesion, & Bartlett Learning, LLC © Jones Bartlett Learning, LLC and yields a positively called a cation . As trons in the shell can become stable&by interacting NOT Look FOR once SALEagain OR DISTRIBUTION NOTisFOR SALE we will see, ion formation important to OR someDISTRIBUTION forms with another unstable atom. at of chemical bonding. Figure 2.4 provides a concept Figure 2.2B and notice that the carbon atom, with six electrons, has two electrons in its first shell and map that summarizes atomic structure. only four in the valence shell. For this reason, carelectron Distribution Determines bon is extremely reactive in “finding” four more © Jones & Bartlett Learning, © Jones & Bartlett Learning, LLC the Chemical Properties of an AtomLLC electrons and, as we will see, allows carbon to form FOR SALE OR level) DISTRIBUTION NOT FOR SALEwith ORother DISTRIBUTION innumerable combinations elements to EachNOT electron shell (energy can hold a maxfill the valence shell with eight electrons. Therefore, imum number of electrons (see Figure 2.2B). The only atoms with unfilled valence shells participate shell closest to the nucleus can accommodate two in a chemical reaction. electrons, whereas the second and third shells each valence shells of a few elements normally can hold eight. Any additional shells also have © Jones & Bartlett Learning, LLC © JonesThe & Bartlett Learning, LLC are fi lled. Each of these elements, called an “inert numbers but usually no more than 18NOT FOR SALE OR DISTRIBUTION NOT FORmaximum SALE OR DISTRIBUTION gas,” is chemically stable and unreactive. Helium are present in the outermost shell. Because the 25 (atomic number 2) and neon (atomic number 10) essential elements are of lower mass number, only are examples; each has its valence shell filled with 2 the first few shells are of significance to the chemiand 8 electrons, respectively. cal processes of life. Inner shells are filled first and, © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Concept and reasoning Checks 2.1 a. b. c. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Explain how the atomic number differs from the mass number. Describe how an isotope differs from an ion. ©Looking Jones Bartlett © Jones at & Figure 2.2B, doLearning, these atoms LLC have filled valence shells? Explain. NOT FOR SALE OR DISTRIBUTION ■ KeY CONCept 2.2 & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Chemical Bonds Form Between reactive Atoms © Jones & Bartlett Learning, LLC & Bartlett Learning, between sodium and chlorineLLC is an example of how When the valence shells of two unstable atoms come© Jones ions and then form ionic bonds to one the shells overlap, an energyNOT these NOT FORclose SALE OR another, DISTRIBUTION FOR atoms SALEbecome OR DISTRIBUTION when they encounter each other (Figure 2.5). With exchange takes place, and each of the participating atoms assumes a more stable electron configurathe transfer of electrons, both atoms now have tion. When two or more atoms are linked together, their valence shell filled. Because opposite electrithe force holding them is called a chemical bond. cal charges attract, the chloride ions and sodium Jones Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Therefore, chemical©bonds are&the result of atoms ions come together to form stable sodium chloride NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION filling their valence shells. (NaCl)—table salt. The rearrangement of atoms through chemical When two or more different elements interact bonding can occur in one of two ways: atoms, in with one another to achieve stability, they form a the form of ions, can transfer valence electrons; or, compound. Each compound has a definite formula each©reactive atom can share valence electrons with and set of that distinguish it from Jones & Bartlett Learning, LLC © properties Jones & Bartlett Learning, LLCits one or more other reactive atoms. In both cases, the components. For example, sodium (Na) is an exploNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION result is atoms having full valence shells. sive metal and chlorine (Cl) is a poisonous gas, but the compound they form (NaCl) is a solid crystal of ionic Bonds Form Between Oppositely edible table salt. Charged ions Salts are typically formed through ionic bonding. Besides sodium (Na+) andLLC chloride (Cl–), imporIn Bartlett the formation of an ionic bond, one atom gives up© Jones © Jones & Learning, LLC & Bartlett Learning, areOR formed from other ions, including valence electrons to another atom. The reactionNOT tant NOT FORitsSALE OR DISTRIBUTION FORsalts SALE DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 39 13/02/17 4:45 pm 40 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC water OR (H2O), carbon dioxide (CO2), and the NOT such FORasSALE DISTRIBUTION Electron transfer simple sugar glucose (C6H12O6). As shown by these examples, the combination and number of atoms (the subscript) in a molecule are called the molecular formula. (Note that the presence of one atom is © Jones & Bartlett Learning, LLC © Jones“1”.) & Bartlett Learning, LLC represented without the subscript Chlorine atom (Cl) Sodium atom (Na) NOT FOR SALEinORcarDISTRIBUTION NOT FOR SALE OR DISTRIBUTION Covalent bonding occurs frequently bon because this element has four electrons in its Ionic attraction unfilled outer shell. The carbon atom is not strong enough to acquire four additional electrons, but it is 11p 17p sufficiently strong to retain the four it has. It there+ – 12n Learning, © Jones & Bartlett LLC18n © Jones & Bartlett Learning, LLC fore enters into a variety of covalent bonds with NOT FOR SALE OR DISTRIBUTION NOTatoms FORorSALE DISTRIBUTION other reactive groupsOR of atoms. 1. Sodium gives up its valence electron to chlorine, resulting in sodium and chloride ions. 11p 12n 17p 18n Sodium ion (Na+) 2. The stable valence shells bring about the of oppositely Jones attraction & Bartlett Learning, LLC chared ions. © NOT FOR SALE OR DISTRIBUTION Chloride ion (Cl–) Nonpolar Covalent Bonds When electrons between atoms are shared equally, Ionic bond © Jones & Bartlett Learning, LLC An example of a nonpolar covalent bond forms. this type of bonding is methane (natural) gas (CH4), NOT FOR SALE OR DISTRIBUTION which is a byproduct of cellulose digestion by some microbes residing in the ruminant stomach of a cow (Figure 2.6A). For methane, a reactive carbon atom shares each of its four valence electrons with the © JonesSodium & Bartlett © Jones & Bartlett Learning, LLC chloride Learning, LLC valence electron of a reactive hydrogen atom, form(NaCl) FORbonds. SALEBecause OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ing four single nonpolarNOT covalent of the equal sharing of electron pairs, there are no Figure 2.5 ion Formation and ionic Bonding. The transfer of an electron from sodium to chlorine generates oppositely electrical charges (poles) on the molecule; methcharged ions that are attracted to one another, forming an ane, therefore, is a nonpolar molecule. ionic bond through mutual attraction. »» Which ion is a cation Scientists often draw chemical structures as © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC and which is an anion? structural formulas, that is, chemical diagrams NOT FOR SALE OR DISTRIBUTION NOTorder FORand SALE OR DISTRIBUTION showing the arrangement of atoms. In Figure 2.6, each line between carbon and hydrogen calcium (Ca+2), potassium (K+2), magnesium (Mg+2), (C—H) represents a single nonpolar covalent bond and iron (Fe+2 or Fe+3). In medicine, most salts repbetween a pair of shared valence electrons. Other resent electrolytes, which separate into ions when molecules, such as carbon dioxide © Jones & Bartlett Learning, LLC of the human body.© Jones & Bartlett Learning, LLC (CO2), share two they dissolve in the fluids pairs of valence electrons and therefore two lines NOT FORAmong SALEthe ORmost DISTRIBUTION FOR SALE OR DISTRIBUTION important are sodium, potassium,NOT are used to indicate the “double covalent bond”: –3 magnesium, and phosphate (PO4 ). Although ionic O=C=O. In both examples, the atoms now are stabonds in solution are relatively weak, in large numble because the outer electron shell of each atom is bers they play important roles in protein structure filled through this sharing. and the reactions between antigens and antibodies form&hydrocarbons , © Jones & Bartlett Learning, LLCNonpolar covalent bonds © Jones Bartlett Learning, LLC in the immune response. which are molecules consisting solely of hydrogen NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION and carbon. Methane is the simplest hydrocarbon. Covalent Bonds Share electrons When atoms are bonded covalently, they establish a geometric relationship determined largely by the Reactive atoms also can achieve stability by sharelectron configuration. Thus, hydrocarbons can coning valence electrons between interacting atoms, © Jones & Bartlett Learning, LLC strong © Jones & Bartlett Learning, LLC sist of chains of carbon atoms and, in some cases, the the sharing producing a covalent bond. Such NOT SALE ORinDISTRIBUTION NOT FORtoSALE chains can be closed form aOR ringDISTRIBUTION (Figure 2.6B). In bonds are FOR very important biology because the all cases, the nonpolar covalent bonds are distribCHNOPS elements of life usually enter into covauted equally around each carbon atom. Petroleum lent bonds with themselves and one another. hydrocarbons are the primary components in oil A molecule is two or more atoms held together and gasoline and can present quite a challenge to by covalent bonds. Molecules can be composed of © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC an accidental oil microbes (and humans) following only one kind of atom, as in oxygen gas (O2), or they NOT FORcan SALE OR FORasSALE OR in DISTRIBUTION described MiCrOFOCuS 2.1. consist of DISTRIBUTION different kinds of atoms in substancesNOT spill, 11p 12n 17p 18n © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 40 13/02/17 4:45 pm KEY CONCEPT 2.2 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 4 1p + Chemical Bonds Form Between Reactive Atoms © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 6p 6n H Carbon atom Hydrogen atom H C=C H © Jones & Bartlett Learning, LLC H H NOT FOR SALE OR DISTRIBUTION Ethylene Nonpolar covalent bond 1p formed by equal sharing of an electron pair 6p 1p Learning, © Jones & Bartlett 1pLLC 6n NOT FOR SALE OR DISTRIBUTION H – 1p H–C–H H H H C C C H © Jones & Bartlett Learning, LLC H H H NOT PropaneFOR SALE OR DISTRIBUTION H H C H H C H © Jones & Bartlett Learning, LLC C C NOT FOR SALE OR DISTRIBUTION C C H – H 41 Methane (CH4) Benzene (A) © Jones & Bartlett Learning, LLC © Jones &(B) Bartlett Learning, LLC NOT FORFigure SALE2.6 ORChemical DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Bonding and Hydrocarbons. (A) A covalent bond involves the equal sharing of electron pairs between atoms, such as in this simple organic compound methane. (B) The molecular formulas for a few relatively simple hydrocarbons. »» Supply the molecular formula for each of the structural formulas shown in (B). © Jones & Bartlett Learning, LLC MiCrOFOCuS Microbiology NOT2.1: FORenvironmental SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Microbes to the rescue! Jones & the Bartlett Learning, LLCrig, which was working on©aJones & Bartlett Learning, LLC On © April 20, 2010, Deepwater Horizon drilling well for the British Petroleum oil company, blew up in the Gulf of Mexico. For 3 months, oil spilled into the Gulf and contaminated nearby shores and wetlands, NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION making it the largest accidental oil spill in American history. According to federal government estimates, some 5 million barrels, or 795 million liters, were spilled, and it was not until September that the well was declared sealed. Where did all those hydrocarbons go? Petroleum or crude oil consists of a complex mixture of hydrocarbons of various sizes in liquid, gaseous, and solid forms. An oil well, such as the one in the Gulf, produces primarily crude oil, with some natural gas (primarily methane) dissolved in it. For © Jones & decades, Bartlett Learning, LLC Jones (biodegradation) & Bartlett Learning, LLC scientists have tried to use bioremediation, the © breakdown of contaminating compounds using microorganisms, as aNOT naturalFOR method for cleaning NOT FOR SALE OR DISTRIBUTION SALE OR DISTRIBUTION up some of the environment’s worst chemical hazards, including oil spills. In the case of the ruptured Deepwater Horizon well, a natural form of bioremediation came to the rescue. The entry of oil profoundly altered the natural microbial community by significantly stimulating deep-sea, oil-hungry microbes to consume much of the smaller,© dispersed methane gas Jones hydrocarbons & Bartlett and Learning, LLC(see figure). Their © Jones & Bartlett Learning, LLC efficiency was amazing. With bloom sizes of 1023 cells and consisting of more than NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 50 species, within weeks, some areas of the Gulf were nearly free of oil. Overall, the microbes are estimated to have consumed 200,000 tons of oil and methane gas. Still, microbes cannot eliminate or digest all the hydrocarbons present in oil as the spill Bacteria (light-green dots) attached also produced tar-like hydrocarbons that were too large for microbes to digest. Still, to and surrounding oil droplets one biogeochemist gave the microbes a “7 out of 10” for their digestive performance. (three large spheres). © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION (Figure 2.7A). Oxygen has a stronger “pull” on the shared electrons and thus has a slight negative Not all molecules are nonpolar. In fact, water, one charge. The hydrogen atoms are then left with a of Bartlett the most Learning, important molecules to life, is a polar© Jones slight&positive charge. The water molecule therefore © Jones & LLC Bartlett Learning, LLC molecule —it has electrically charged poles (atoms) consists of polar covalent bonds . NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Polar Covalent Bonds © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 41 13/02/17 4:45 pm 42 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 1p 2 8p 8n + + Hydrogen atom © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION – – 8p +H Polar covalent + bonds H – + Polar covalent bond formed by unequal sharing Learning, LLCof an electron pair. © Jones & Bartlett NOT FOR SALE OR DISTRIBUTION (A) – – Water (H2O) Hydrogen bond + © Jones –& Bartlett Learning, LLC O H NOT FOR SALE OR DISTRIBUTION + + – O 8n © Jones & Bartlett Learning, +HLLC + NOT FOR SALE OR 1p DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION – + 1p + Oxygen atom + © +Jones & Bartlett Learning, LLC + NOT FOR SALE OR DISTRIBUTION (B) Figure 2.7 Chemical Bonding and Water. (A) The unequal sharing of electron pairs between oxygen and hydrogen atoms produces a polar molecule. (B) The charged regions of each polar water molecule allow hydrogen bonds to form between the hydrogen atom of one water molecule and the oxygen atom of another water molecule. »» Why is there attraction between a © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, hydrogen atom and an oxygen atom? LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Hydrogen Bonds Form Between Polar groups or Molecules © Jones & Bartlett Learning, LLC A polar molecule, like water, has two positively NOT FOR SALE OR DISTRIBUTION the structure of proteins and nucleic acids, two of the major organic compounds of living cells we will soon encounter in this chapter. Learning, LLC © Jones & Bartlett TABLeNOT 2.2 summarizes types of FOR SALEthe ORdifferent DISTRIBUTION chemical bonds that have been discussed thus far. charged hydrogen atoms and a negatively charged oxygen atom. Therefore, the positive hydrogen Chemical reactions Change Bonding atom on one water molecule will be attracted to Partners the negative oxygen on another water molecule. The opposing charges allow A chemical reaction is a process in which atoms or © Jones & Bartlett Learning, LLCfor the formation of a© Jones & Bartlett Learning, LLC hydrogen bond . Although hydrogen bonds are much molecules interact through making NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION and breaking weaker than covalent bonds, hydrogen bonds prochemical bonds. Different combinations of atoms or vide the “glue” to hold water molecules together molecules result from the reaction; that is, bond(Figure 2.7B). These bonds also are important to ing partners change. However, the total number of © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION taBLe 2.2 Three Types of Chemical Bonds in Living Organisms Type Chemical Basis Strength © Jones & Bartlett Learning, LLC Attraction between oppositely charged ions NOT FOR SALE OR DISTRIBUTION Ionic Covalent Hydrogen Sharing of electron pairs between atoms © Jones & Bartlett Learning, LLC Sodium chloride NOT FOR SALE OR DISTRIBUTION Weak Strong Attraction of a hydrogen nucleus (a proton) to Weak negatively charged oxygen or nitrogen atoms in the same or neighboring molecules © Jones & Bartlett Learning, LLC © Jones & Bartlett NOT FOR SALE OR DISTRIBUTION example Glucose Water Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 42 13/02/17 4:45 pm KEY CONCEPT 2.2 Chemical Bonds Form Between Reactive Atoms 43 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC C6H12O6 + C6H12O6 C12H22O11 interacting atoms remains constant. For chemical NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION reactions, an arrow indicates in which direction the reaction will proceed. By convention, the atoms or molecules drawn to the left of the arrow are the reactants and those to the right are the products of © Jones here: & Bartlett Learning, LLC the reaction, as demonstrated NOT FOR SALE OR DISTRIBUTION A + B ———→ A — B Substrates Product Glucose Glucose H 2O Water Maltose (A) Dehydration reaction C12H22O11 Maltose H2O Water © CJones & Bartlett Learning, LLC 6H12O6 + C6H12O6 NOT FORGlucose SALE OR DISTRIBUTION Glucose (B) Hydrolysis reaction Two types of chemical reactions are common in © Jones & Bartlett Learning, biological compounds: dehydration andLLC hydrolysis. NOT FOR SALE OR DISTRIBUTION Let’s take a look at them. Dehydration reactions In biology, many chemical reactions are based on Figure 2.8 Dehydration and Hydrolysis reactions. © Jones & Bartlett Learning, LLC (A) Dehydration reactions result in building larger moleNOT FOR SALE OR DISTRIBUTION cules with water being one of the products of the reaction. (B) Hydrolysis reactions break down larger molecules into smaller ones, using a water molecule as a reactant. »» Provide proof that the numbers of atoms and types of bonds have not changed because of the chemical reaction in (A) or (B). © Jones & theBartlett assemblyLearning, (synthesis)LLC of larger compounds from© Jones & Bartlett Learning, LLC NOT FORsmaller SALEbuilding OR DISTRIBUTION blocks (Figure 2.8A). In a dehy-NOT FOR SALE OR DISTRIBUTION “break”). The digestion of food molecules would be an example of these reactions. In summary, the new products formed in a chemical reaction have the same number and types © Jones & Bartlett Learning, LLC ©inJones & Bartlett Learning, LLC of atoms that were present the reactants. In formHydrolysis reactions ing new products, chemical reactions only involve NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Many chemical reactions in cells also break a change in the bonding partners. No atoms have (hydrolyze) larger reactants into smaller products been gained or lost from any of these reactions. (Figure 2.8B). Water is one of the reactants used to The sum of all chemical reactions in cells, including break another reactant in what is therefore referred dehydration and hydrolysis reactions, is referred to & Bartlett LLC lysis = © Jones. & Bartlett Learning, LLC to as©a Jones hydrolysis reaction Learning, (hydro = “water”; as cell metabolism dration reaction, when smaller reactants are put together to build larger products, often a water molecule is formed as part of the products. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Concept and reasoning Checks 2.2 a. Construct a diagram to show how the salt calcium chloride (CaCl ) is formed. d. Compare and contrast dehydration and hydrolysis reactions. 2 © Jones & b.Bartlett LLCof electrons? © Jones & Bartlett Learning, LLC Why doLearning, atoms share pairs NOT FOR SALE OR DISTRIBUTION SALE ofOR DISTRIBUTION c. Construct a diagram to show how hydrogen bondingNOT occursFOR in a molecule liquid ammonia (NH3). Chapter Challenge A © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION At this point, you should know that all life (as we know it) is carbon based. With four electrons to share, carbon can form many bonds with other carbon atoms and/or with other elements. Some scientists have proposed that the element silicon (Si) could replace carbon. After all, silicon is the second most abundant element in the Earth’s crust (oxygen is first whereas carbon is fifteenth). In fact, microbes called diatoms (a type of alga) have cell wall & containing silica (hydrated silicon have suggested that the first life on LLC Earth © aJones Bartlett Learning, LLCdioxide; SiO2). A few scientists © Jones & Bartlett Learning, (microbial, we assume) might have been silicon based. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION QueSTiON A: Knowing that silicon (Si) has an atomic number of 14 and a mass number of 28, how similar is silicon to carbon that some individuals would propose it as a potential substitute for carbon in “shadow life”? Draw the structural formula for silane, which is silicon with four hydrogen atoms covalently bonded. How similar is it to methane? As a note: In 2016, researchers were successful in creating a protein isolated from a bacterium that in the lab will bond carbon to silicon. © Jones & You Bartlett LLC can findLearning, answers online in Appendix F. NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 43 13/02/17 4:45 pm 44 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEon ORWater DISTRIBUTION NOT FOR■SALE DISTRIBUTION KeYOR CONCept 2.3 All Living Organisms Depend All organisms are composed primarily of water. Human cells, as well as microbial cells, are about Jones & Bartlett Learning, LLC 70% water by mass.©No organism can survive and FORorganisms, SALE OR DISTRIBUTION grow without water,NOT and many including microbes, live in watery or moist environments. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Na+ Water Has Several unique Properties The water molecule and its Learning, interactionsLLC with other © Jones & Bartlett molecules produces some unique properties. NOT FOR SALE OR DISTRIBUTION universal Solvent Cl– H2O Salt © Jones & Bartlett Learning, LLC crystal NOT FOR SALE OR DISTRIBUTION (solute) Hydrated chloride ion Liquid water is the medium in which all cellular Hydrated chemical reactions occur. Being a polar molecule,© Jones & Bartlett Learning, LLC sodium ion © Jones & Bartlett Learning, LLC water molecules are attracted to other polar molNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ecules. Take, for example, what happens when a crystal of salt is put in water. The salt is hydrophilic, Figure 2.9 Solutes Dissolve in Water. Water molecules meaning it easily dissolves in water into separate separate and surround Na+ and Cl– ions, facilitating their sodium and chloride ions because water molecules dissolving into solution. »» When dissolving, why do the H’s of break the weak ionic©bonds and ion + Jones & surround Bartlett each Learning, LLC ©surround Jonesthe&Na Bartlett Learning, LLC water surround Cl– while the O’s ? in a sphere of waterNOT molecules ( Figure 2.9 ). This NOT FOR SALE OR DISTRIBUTION FOR SALE OR DISTRIBUTION aqueous solution consists of solutes (salt) dissolved in water, which in biology is the universal solvent Water molecules also are reactants or products (MiCrOFOCuS 2.2). By contrast, substances that do in many chemical reactions, including the dehydranot dissolve in water (lipids; see the section coming tion and hydrolysis reactions described in the previ© Jones & Bartlett Learning, LLC © (see Jones & Bartlett Learning, LLC up shortly) are hydrophobic . ous section Figure 2.8 ). NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION MiCrOFOCuS 2.2: Tools The relationship Between Mass Number and Molecular Weight © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Often scientists and students need to make solutions that have a specific concentration of solutes. To make these solutions, they need to know how much a particular molecule or solute weighs, which is referred to as the&molecular © Jones Bartlett Learning, LLC weight. The calculation of the molecular NOT FOR SALE OR DISTRIBUTION weight simply consists of adding together Water the mass number of all the individual atoms (H2O) in the substance of interest. For example, Mass number: 2H= 2 the molecular weight of a water molecule is 1 O = 16 18 daltons,* whereas the molecular weight Jonesmolecule & Bartlett of © a glucose is 180Learning, daltons. OtherLLCMolecular weight: 18 NOT FOR SALE OR DISTRIBUTION (in daltons) molecules can reach astonishing proportions— antibodies of the immune system can have a molecular weight of 150,000 daltons and the bacterial toxin causing botulism is over 900,000 daltons. Carbon dioxide (CO2) 1 C = 12 2 O = 32 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Sodium chloride (NaCl) 1 Na = 23 1 Cl = 35 Glucose (C6H12O6) 6 C = 72 12 H = 12 6 O = 96 Learning, LLC 180 © Jones & Bartlett 44 58 NOT FOR SALE OR DISTRIBUTION © Jones & *Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Dalton: The unit in biology that is used to measure the weight of atomic particles; equivalent to an atomic mass unit used in chemistry (or one-twelfth the weight of an atom of C). NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 12 © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 44 13/02/17 4:45 pm KEY CONCEPT 2.3 All Living Organisms Depend on Water 45 © Jones & Bartlett Learning, LLC NOT FORCohesion SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC purposes, an acid (such as hydrochloric NOT For FORour SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION acid—HCl) is a chemical substance that increases As you have learned, the polar nature of water molthe hydrogen ion concentration ([H+]) of a solution ecules leads to hydrogen bonding. By forming a by donating H+ to a solution. large number of hydrogen bonds, water molecules are held close together, which&isBartlett a property called + Cl– & Bartlett Learning, LLC © Jones Learning, LLC HCl ↔© H+Jones cohesion. However, unique to this bonding that at NOT FOR SALE OR DISTRIBUTION NOT FOR SALE ORisDISTRIBUTION freezing temperatures, the distance between water By contrast, a base (such as sodium hydroxide— molecules expands and there now is more space than NaOH) is a substance that reduces the [H+] in soluthere is between water molecules at liquid tempertion by dissociating into hydroxide ions and cations, atures. Thus, ice floats because the frozen water is or by directly accepting H+. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC less dense than liquid water. This means ice forma– NaOH NOT ↔ Na+FOR + OH–SALE OR OH + H+ ↔ H2O tion NOT insulates deeper water lakes and keeps the FOR SALE OR in DISTRIBUTION DISTRIBUTION water from freezing and, by remaining liquid, life To indicate the concentration of H+ in a solution, (including microbial life) in the water is maintained. the symbol pH (power of hydrogen ions) and the pH scale are used. This numerical scale extends from 0 Temperature Modulation © Jones & Bartlett Learning, LLC © Jones & Bartlett LLC (extremely acidic;Learning, high (H+)) to 14 (extremely basic Because of hydrogen bonding, it takes a large + NOT FOR SALE OR DISTRIBUTION NOT or FOR SALE OR alkaline; low (H DISTRIBUTION )) and is based on actual calculaamount of heat energy to increase the temperations of the number of hydrogen ions present when ture of water. Likewise, a large amount of heat must a substance mixes with water. A substance with a pH be lost before water temperature decreases. So, by of 7, such as pure water, is said to be neutral; solubeing about 70% water, cells are bathed in a solvent tions that gain H+ are said to be “acidic” and have a that maintains a more consistent temperature even © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC pH lower than 7; solutions that lose H+ are “basic” when the environmental temperatures change. NOT FOR SALE NOT FOR SALE OR DISTRIBUTION (or alkaline) and have a pH greater than 7. OR DISTRIBUTION The pH scale is logarithmic; that is, every time Acids and Bases Affect a Solution’s pH the pH changes by one unit, the [H+] changes 10 In an aqueous solution, water molecules can split times. For example, lemon juice (pH 2) and black into hydrogen ions (H+; protons) and hydroxide ions coffee (pH©5)Jones differ in [H+] by a thousandfold (103). Jones & Bartlett Learning, LLCarrow& Bartlett Learning, LLC (OH–© ), only to rapidly recombine (the double Figure 2.10 summarizes the pH values of several FORa reversible SALE ORreaction): DISTRIBUTION NOT FOR SALE OR DISTRIBUTION headNOT indicates common substances. With regard to microorganisms, fungi prefer a slightly acidic environment comH2O ↔ H+ + OH– pared to the more neutral environment preferred by most microbes—although there are some spectacuIn addition to water, other compounds in cells + lar exceptions, as Learning, MiCrOFOCuS 2.3 points out. can dissociate into H when they dissolve in water. © Jones & Bartlett Learning, LLC © Jones & Bartlett LLC Concentrated hydrochloric acid (HCl) Vinegar, Black Seawater wine, pickles coffee Pure water © Jones & Bartlett Learning, LLC Lemon juice Baking Saliva Tomato Milk Blood soda Stomach acid NOT FOR juice SALE OR DISTRIBUTION Extremely acidic Bleach Concentrated sodium hydroxide (NaOH) © Jones & Bartlett Learning, LLC Household Oven ammonia NOT FORcleaner SALE OR DISTRIBUTION Neutral © Jones & Bartlett Learning, LLC 6 1 2 3 4 5 NOT FOR SALE OR DISTRIBUTION pH 0 Optimal growth of most fungi 7 Extremely basic 8 ©9 Jones & Bartlett Learning, LLC 10 11 12 13 14 NOT FOR SALE OR DISTRIBUTION Optimal growth of most other microbes Figure 2.10 A Sample of pH Values for Some Common Substances. Most fungi prefer a slightly acidic pH for growth com- pared to most other microbes. »» On the pH scale, notice that many of the beverages we drink (e.g., wine, tomato juice, coffee) are © Jones & Bartlett Learning, LLC ©solutions Jones(e.g., & Bartlett Learning, LLCPropose an explanaacidic. However, we would never normally drink equally alkaline commercial bleach, ammonia). tion for the statement. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 45 13/02/17 4:45 pm 46 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION MiCrOFOCuS 2.3: environmental Microbiology Just South of Chicago © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC All you need is a map,NOT some FOR pH paper, and a OR few collection vials. When in Chicago, use your map to fiFOR nd theSALE Lake Calumet NOT OR DISTRIBUTION SALE DISTRIBUTION region just southeast of the city. When you arrive, pull out your pH paper, and sample some of the groundwater in the region near the Calumet River. You will be shocked to discover the pH is greater than 12—almost as alkaline as oven cleaner! In fact, this might be one of the most extreme pH environments on Earth. How did the water get this alkaline and could anything possibly live in the groundwater? The groundwater in the areaLearning, near Lake Calumet steel slag that was dumped © Jones & Bartlett LLC became strongly alkaline © because Jonesof&the Bartlett Learning, LLC into the area for more than 100 years. Used to fill the wetlands and lakes, water and air chemically react with the slag to NOTlime FOR SALE OR DISTRIBUTION NOT DISTRIBUTION produce [calcium hydroxide, Ca(OH)2]. It is estimated that 10 trillion cubic feetFOR of slagSALE and the OR resulting lime are what have pushed the pH to such a high value. Now use your collection vials to collect some samples of the water. Back in the lab you will be surprised to find that there are bacterial communities present in the water. Hydrogeologists who have collected such samples have discovered some bacterial species that until then had only been found in Greenland and deep gold mines of South Africa. Other © Jones & identifi Bartlett Learning, LLC Jones & Bartlett Learning, ed species appear to use the hydrogen generated © from the corrosion of the iron for energy. LLC How did these bacterial organisms get there? The hydrogeologists propose that the bacterial species have always NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION been there and have simply adapted to the environment over the last 100 years as the slag accumulated. Otherwise, the microbes must have been imported in some way. So, once again, provide a specific environment and they will come (or evolve)—the microbes that is. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC base can absorb them. Alternatively, if there a NOT FOR SALE ORis DISTRIBUTION FOR to SALE OR DISTRIBUTION Cell Chemistry is NOT Sensitive pH Changes + decrease in H (potential pH increase), the weak acid As microorganisms—in fact all organisms—take up can dissociate, replacing the lost H+. Thus, the give or ingest nutrients and undergo metabolism, chemiand take of H+ maintains the pH. cal reactions occur that use up or produce H+. Therefore,© it Jones is important for all organisms to LLC balance the Potential Potential pH & Bartlett Learning, ©pH Jones & Bartlett Learning, LLC increase drop acidsNOT and bases in cells because chemical reactions FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION and organic compounds are very sensitive to pH Chemical + H required Excessive H+ shifts. Proteins are especially vulnerable, as we will reaction produced soon see. If the internal cellular pH is not maintained, these proteins can be destroyed. Likewise, when most (A) (B) microbes grow in a microbiological nutrient medium,© Jones & Bartlett Learning, © Jones & Bartlett Learning, LLC Acid-base LLC wasteOR products produced can lower the pH of theNOT FOR SALE OR DISTRIBUTION buffer system NOT FORthe SALE DISTRIBUTION medium, which could kill the organisms. H+ absorbed H+ dissociates To prevent pH shifts, cells (and growth media) from acid by base contain buffers, which are substances that maintain Figure 2.11 Hypothetical example for pH Shifts. An acid/ a specific pH. The buffer does not necessarily mainbase buffer system can prevent pH shifts occurring Jones & Bartlett Learning, LLC © Jones & from Bartlett Learning, LLC tain a neutral pH, but©rather whatever pH is required because of a chemical reaction. If the reaction is using up H+ for that environment. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (A), the acid component prevents a pH rise by donating H+ to Most biological buffers consist of a weak acid + offset those used. If the reaction is producing excess H (B), and a weak base (Figure 2.11). If an excessive numthe base can prevent a pH drop by “absorbing” them. »» Prober of H+ is produced (potential pH decrease), the pose what would happen if a chemical reaction continued to © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Concept and reasoning Checks 2.3 release excessive H+ for a prolonged period. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION a. Explain the difference between a solution, a solvent, and a solute. b. What are the properties of acids and bases? & c.Bartlett Learning, © Jones & Bartlett If the pH does drop in LLC a cell, what does that tell you about the buffer system? © Jones NOT FOR SALE OR DISTRIBUTION Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 46 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Chapter Challenge B 47 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION In trying to find “markers” to detect “shadow life,” we run into the problem of microbial diversity. Microbes occupy so many diverse and often extreme habitats (many are called “extremophiles”) that it is hard to know © Jones & Bartlett © Jones & Bartlett Learning, what “shadow life” really means inLearning, the context ofLLC life on Earth. LLC NOT(including FOR SALE OR DISTRIBUTION NOT FOR DISTRIBUTION QueSTiON B: True microbial life (asSALE we knowOR it) can be found, for example, at extreme temperatures substantially above the boiling point of water), extreme pressures (in excess of 1,000 times atmospheric pressure), and extreme pHs (both exceptionally acidic and, as described in MiCrOFOCuS 2.3, tremendously alkaline environments). Are these examples of “extremophiles” representative of “shadow life”? If we do find microbes that use silicon, is that a marker for shadow life or is it just another example of the flexibility of microbes to make the best of their surroundings? If a microbe lost its carbon source, could use silicon it were available? What’s your © itJones & ifBartlett Learning, LLCopinion? © Jones & Bartlett Learning, LLC FOR SALE OR DISTRIBUTION YouNOT can find answers online in Appendix F. NOT FOR SALE OR DISTRIBUTION ■ KeY CONCept 2.4 Living Organisms Are Composed of Four Types of Organic © Jones & Bartlett Learning, LLC Compounds © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION and proteins are essentially stable, unreactive molAs mentioned in the last section, a typical prokaryecules because their outer shells are filled through otic cell is composed of about 70% water. If all the covalent bonding. Why then should these molecules water is evaporated, the predominant “dry weight” Jonescompounds & Bartlett, which Learning, LLC © Jones & Bartlett Learning, LLC take part in chemical reactions to build polymers? remaining consists of©organic are SALEare ORnot DISTRIBUTION NOTtoFOR SALE OR DISTRIBUTION The answer is that NOT these FOR monomers those molecules related or having a carbon basis: entirely stable. Projecting from the carbon skeletons the carbohydrates, lipids, proteins, and nucleic acids are groups of atoms called functional groups, which (Figure 2.12). Except for the lipids, each class reprepresent points where further chemical reactions resents a polymer (poly = “many”; mer = “part”) built can occur©if Jones facilitated by a specifi c enzyme.LLC There from©a Jones very large number of building blocks called & Bartlett Learning, LLC & Bartlett Learning, are only a few functional groups, but their differmonomers (mono = “one”). NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ences and placement on organic compounds make Functional Groups Define Molecular possible a large variety of chemical reactions. The Behavior important functional groups in living organisms are identified in TABLe 2.3. Before we look at the major classes of organic compounds, we need to address one question. The on monomers can interact © Jones & Bartlett Learning, LLC © JonesFunctional & Bartlettgroups Learning, LLC monomers building carbohydrates, nucleic acids, to form larger molecules or polymers through NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Percent dry weight: Phospholipids (8%) Ions, small molecules (4%) © Jones & Bartlett Learning, LLC Nucleic acids (27%) NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Organic compounds (26%) Organic compounds H2O (70%) © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Bacterial cell Proteins (58%) © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Carbohydrates (7%) Figure 2.12 Organic Compounds in Bacterial Cells. Organic compounds are abundant in cells. The approximate compo- © Jones & Bartlett LLC © Jones & Bartlett Learning, sition of theseLearning, compounds in a bacterial cell is similar to the percentages found in other microbes.LLC »» Propose a reason why proteins make up almost 60% of the dry weight of a bacterial cell. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 47 13/02/17 4:45 pm 48 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION taBLe 2.3 Common Functional Groups (and examples) on Organic Compounds Functional group Hydroxyl Carboxyl Carbonyl Structural Formula Shorthand —O—H —OH © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION O —COOH || —C—OH O © Jones & Bartlett Learning, LLC || —C— NOT FOR SALE OR DISTRIBUTION Amino H || —N—H © Jones & Bartlett Learning, LLC —S—H Sulfhydryl NOT FOR SALE OR DISTRIBUTION Phosphate OH || —O—P=O || &OH Bartlett examples Alcohols, simple sugars, amino acids © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Fatty acids, amino acids, proteins —CO— Carbohydrates —NH2 Amino acids, proteins © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION ©—SH Jones & Bartlett Learning, LLC Amino acids, proteins NOT FOR SALE OR DISTRIBUTION —H2PO4 © Jones Learning, LLC NOT FOR SALE OR DISTRIBUTION dehydration reactions. In addition, functional groups can be critical for breaking larger polymers into monomers through hydrolysis reactions.LLC © Jones & Bartlett Learning, IfNOT you are unsure about role of these funcFOR SALE OR the DISTRIBUTION tional groups, do not worry. We will see how specific functional groups interact through dehydration reactions as we now visit each of the four classes of organic compounds. Phospholipids, nucleic acids, ATP © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Sugars The so-called “simple sugars” are the monosac© Jones & Bartlett Learning, LLC charides that consist of a single sugar monomer. FOR SALE ORsugar, DISTRIBUTION Glucose, aNOT six-carbon (hexose) is the most common monosaccharide and is essential for cell metabolism (Figure 2.13). Estimates vary, but many scientists say that half the world’s carbon exists in glucose. Such simple sugars are synthe© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC sized from carbon dioxide and water through the Are Needed for energy NOT FORCarbohydrates SALE OR DISTRIBUTION NOT process FOR SALE OR DISTRIBUTION of photosynthesis . Algae and cyanobacteMetabolism and as Structural Materials ria are microorganisms that have the cellular and Carbohydrates are organic compounds composed chemical machinery for this process. of carbon, hydrogen, and oxygen atoms and include sunlight a variety of sugars and larger sugar polymers. All 6CO2 + 6H2O ⎯⎯⎯→ C6H12&OBartlett + 6O2 Learning, LLC 6 © Jones & Bartlett Learning, LLC © Jones carbohydrates share the same molecular formula FOR SALE OR DISTRIBUTION NOTratio FOR ORto DISTRIBUTION Other simple hexoseNOT sugars include galactose (C6H12O6)n, making the of SALE hydrogen oxyand fructose (see Figure 2.13). A 5-carbon (pentose) gen two to one, the same as in water. The carbohysugar called ribose is important in the structure of drates therefore are considered “hydrated carbon.” nucleic acids. However, the atoms are not present as water moleDisaccharides “two”) are composed LLC of two cules©bound to carbon but rather carbon covalently Jones & Bartlett Learning, LLC © Jones(di&=Bartlett Learning, monosaccharides (double sugars) held together by a bonded to hydrogen atoms and to hydroxyl funcNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION covalent bond resulting from a dehydration reaction tional groups (H–C–OH). (Figure 2.14A). Sucrose (table sugar—C12H22O11), Some carbohydrates function as major fuel the most common disaccharide, is constructed sources in cells, whereas other carbohydrates funcfrom the monosaccharides glucose and fructose. tion as structural molecules present in cell walls and The disaccharide is an additive to many foods and nucleic acids. Often the LLC carbohydrates are termed© Jones © Jones & Bartlett Learning, & Bartlett Learning, LLC is a starting point in wine fermentations. Maltose, saccharides ( sacchar = “sugar”). NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 48 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds © Jones & Bartlett Learning, LLC CH OH CH OH NOT FOR SALE OR DISTRIBUTION C C O O 2 © Jones & Bartlett Learning, LLC by OR yeasts when brewing beer. Lactose, NOT fermented FOR SALE DISTRIBUTION 2 HOCH2 O 49 a third common disaccharide, is composed of the H H OH OH monosaccharides glucose and galactose. Lactose is HO OH H OH C C C C C C known as “milk sugar” because it is the principal OH H H OH H OH disaccharide in milk. In the dairy industry, microorGlucose Galactose Fructose © Jones & Bartlett Learning, LLC & Bartlett Learning, LLC ganisms digest the lactose©inJones milk products, producFigure 2.13 Structural Formulas of Common MonosacFORsour SALE ORand DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ing the lactic acid found NOT in yogurt, cream, charides. Although monosaccharides can exist in linear other sour dairy products. forms, in cells they usually occur as ring structures. »» What H C H H HO C C H H C C H C HO H OH CH2OH is the molecular formula for all three of these monosaccharides? Polysaccharides another disaccharide, is composed of two © Jones & Bartlett Learning, LLCglucose monomers (Figure 2.14B). This disaccharide occurs NOT FOR SALE OR DISTRIBUTION in cereal grains, such as barley, and the sugar is In the microbial world, one of Learning, the major uses © Jones & Bartlett LLCof monosaccharides is as building blocks for large NOT FOR SALE OR DISTRIBUTION polymers. Polysaccharides (poly = “many”) are (A) Monosaccharides © Jones & Bartlett Learning, LLC CH OH NOT FOR SALE OR DISTRIBUTION C O H H H 2 H C HO OH C H + C H OH C HO OH C CH2OH CH3 Glucose O H OH H C C H OH H OH C C H OH C H O C HN CH2OH Glucose C=O HC–CH3 CH3 C=O N-acetylglucosamine (NAG) H2O R © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION N-acetylmuramic acid (NAM) Dehydration reaction H2O H2O (B) Disaccharides CH3 © Jones & Bartlett Learning, C O LLC C O H H H H H H Glucose Glucose NOT FOR SALE OR C C C C DISTRIBUTION HO OH H OH H C C C C H OH H OH O OH C H C=O CH3 CH2OH CH2OH C=O H HN C C H (NAG) H H C Dehydration Learning, LLC reactions H C C O O Dehydration © Jones reactions © Jones & Bartlett NOT FOR SALE (C) ORPolysaccharides DISTRIBUTION CH2OH H HN © Jones & Learning, LLC C O C Bartlett C H H OH CH OH HO H H (NAM) OH C C NOT FOR SALEC OR DISTRIBUTION C O C (NAG) H OH 2 H CH2OH H OH (NAG) H C C H HN C H C=O H H O O C CH2OH C C H HN O HC–CH3 Dehydration Learning, reactions C=O H C=O CH3 R & Bartlett LLC NOT FOR SALE OR DISTRIBUTION CH3 © Jones & Bartlett Learning, LLC Algae Some bacteria Fungi (Glucose) (Glucose)NOT (NAG)n FOR SALE OR DISTRIBUTION n n © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Glycogen H O OH © Jones & Bartlett Learning, LLC Dehydration NOT FOR SALE OR DISTRIBUTION reaction HO O C=O OH H © Jones & Bartlett Learning,CH LLC H HN C H C C HO H NOT FOR HO HSALE OR DISTRIBUTION C C H CH2OH C C Starch Cellulose Chitin © bacteria Jones & Bartlett Learning, LLC Most (NAG—NAM) NOT FOR SALE OR DISTRIBUTION n © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Peptidoglycan Note: The polysaccharides of glucose [(Glucose)n] vary in the carbon bonding between glucose monomers and branching of the polymer chains. © Jones & Bartlett Learning, © Jones & Bartlett LLC used by organisms Figure 2.14 CarbohydrateLLC Monomers Are Built into Polymers. (A) There are manyLearning, monosaccharides that can be combined into disaccharides (B) or assembled into long polymers called polysaccharides (C). »» What type of NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION chemical reaction is required to link glucose into a long polymer such as cellulose? © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 49 13/02/17 4:45 pm 50 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC is much lower. Lipids are used as important “complex carbohydrates” formed by joining hunNOT oxygen FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION stored energy sources by many microorganisms, but dreds of thousands of similar monosaccharides, not bacterial species. The majority of lipids are fats, usually glucose (Figure 2.14C). Covalent bonds phospholipids, and sterols. resulting from the dehydration reactions link the glucose units together. © Jones & Bartlett LLC © Jones & Bartlett Learning, LLC Starch and glycogen are two commonLearning, energy Fats NOT FOR SALE OR DISTRIBUTION NOTinFOR OR DISTRIBUTION storage polysaccharides algalSALE and some bacteA fat (also called a triglyceride) consists of a threeria cells. Cellulose, a structural polysaccharide, is a carbon glycerol molecule and three long-chain fatty component of the cell walls of many single-celled acids (Figure 2.15). Each fatty acid is a long nonalgae and plants. Interestingly, no animals have polar hydrocarbon chain containing between 16 and the enzymes to digest cellulose. Ruminant animals © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 18 carbon atoms, which explains why fats do not mix (e.g., cows and sheep) depend on microbes in their NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION with water. Bonding of each fatty acid to the glycerol gut to break down the cellulose they eat. In humans, molecule occurs by a dehydration reaction between cellulose passes through the digestive system as the hydroxyl functional group on the glycerol and undigested “roughage” (dietary fiber). the carboxyl functional group on a fatty acid. ConOther structural polymers include chitin, which sequently, fats are not considered polymers because is built from chains of another glucose derivative © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC a triglyceride has but four monomers. called N-acetylglucosamine (NAG). Chitin forms the NOT FOR SALE OR DISTRIBUTION NOT FOR ORisDISTRIBUTION A SALE fatty acid saturated if the hydrocarbon cell walls of fungi. In most bacterial cells, the cell chain contains the maximum number of hydrogen wall is composed of peptidoglycan, a carbohydrate atoms extending from the carbon backbone; that modified with protein (peptido). The carbohydrate is, there are no double covalent bonds between car(glycan) building block is a disaccharide of NAG and bon atoms. Animal fats, like lard and&butter that Learning, are N-acetylmuramic acid (NAM) & linked in long poly© Jones Bartlett Learning, LLC © Jones Bartlett LLC solid at room temperature, would be examples. A mer chains. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION fatty acid is unsaturated if the hydrocarbon chain Lipids Play Several roles in Cells contains less than the maximum hydrogen atoms; that is, there is one or more double covalent bonds Lipids are a broad group of nonpolar organic combetween a few carbon atoms (see Figure 2.15). pounds that are hydrophobic; they do not mix with © Like Jones & Bartlett Learning, LLC Jonesplant & Bartlett Examples©include and fish Learning, oils that areLLC liquid water. carbohydrates, lipids are composed of at room temperature. carbon, hydrogen, and oxygen, but the proportion of NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Carboxyl group O H H C OH + HO H C OH C CH2 CH2 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION H C OH Hydroxyl group CH2 CH2 CH2 CH2 CH2 CH2 Dehydration reactions H Glycerol CH2 CH2 CH2 CH2 CH2 C O H C O C CH3 3 H2O © Jones & Bartlett Learning, LLC H NOT FORO SALE OR DISTRIBUTION H CH2 © Saturated Jones & Bartlett Learning, LLC fatty acid NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 O C © Jones & Bartlett Learning, LLC O H C O C CH CH CH CH NOT FOR SALE OR DISTRIBUTION 2 H Covalent bonds 2 2 2 CH2 CH2 CH2 CH A fat (triglyceride) © Jones & Bartlett Learning, LLC Unsaturated fatty acid CHNOT FOR SALE OR DISTRIBUTION C H2 CH 2 CH 2 CH 2 CH 2 CH 3 © Jones & Bartlett Learning, & Bartlett Figure 2.15 Structure forLLC a Simple Lipid. A fat, such as©a Jones triglyceride, consists ofLearning, glycerol and LLC three fatty acids that are saturated or unsaturated. »» Why are the fatty acids referred to as hydrocarbon chains? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 50 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds 51 © Jones & Bartlett Learning, LLC NOT FORPhospholipids SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC inward. This organization forms the NOT pointing FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION basic structure of the membranes found in all cells Another type of lipid found in cell membranes is (Figure 2.16B). the phospholipids, which, unlike fats, have only two fatty acid tails attached to glycerol (Figure 2.16A). Other Lipids In place of the third © fatty acid, there is a polar phosJones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Besides the fats and phospholipids, of phate functional group, which actively interacts NOT FOR other SALEtypes OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION lipids include the waxes and sterols. Waxes are comwith other polar molecules. Some bacterial toxins posed of long chains of fatty acids and form part of are a combination of polysaccharide and lipid, as the cell wall in Mycobacterium tuberculosis, the bacreported in CLiNiCAL CASe 2. terium causing tuberculosis. The waxy wall helps Because one end of the phospholipid is polar © Jones & Bartlett Learning, LLC ©cell Jones Bartlett Learning, LLC protect the from& desiccation. (hydrophilic) and the other end is nonpolar (hydroSterols areFOR structurally veryDISTRIBUTION different from phobic), water the hydrophobic NOTwhen FORmixed SALEin OR DISTRIBUTION NOT SALE OR the other lipids and are included with lipids ends group together, whereas the hydrophilic solely because they too are hydrophobic molecules ends on the outside interact with water. The result (Figure 2.16C). Sterols, such as ergosterol, are is a phospholipid bilayer with the fatty acid tails CH3 N+ H3C Saturated fatty acids (tightly packed) CH3 © CH Jones & Bartlett Learning, LLC CH NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 2 2 Phosphate group Head O –O Unsaturated fatty acids (loosley packed) O P O © Jones Learning, LLC Symbol CH H C & Bartlett CH Glycerol NOT FOR SALE OR DISTRIBUTION O O © Jones & Bartlett Learning, LLC NOT FOR SALE ORCell DISTRIBUTION membrane bilayer 2 2 O C with sterols O C CH2 CH2 CH2 CH2 CH2 CH2 2 2 Phospholipid bilayers © Jones & Bartlett Learning, LLC CH CH NOT FOR SALE ORCHDISTRIBUTION CH 2 2 CH2 CH2 CH2 CH2 CH2 CH CH2 CH2 CH2 CH2 Tails CH © Jones & Bartlett Learning, LLC H3C CH NOT FOR SALE OR DISTRIBUTION CH2 2 CH2 CH2 CH2 Fatty acids 2 3 3 (A) CH CH CH CH 3 3 © Jones & Bartlett Learning, LLC CH CH NOT FOR SALE OR DISTRIBUTION CH3 CH3 CH2 CH © Jones CH & Bartlett Learning, LLC CH CH NOT FOR SALE OR DISTRIBUTIONHO 2 CH CH3 CH2 CH2 CH2 (B) © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION A phospholipid A sterol, ergosterol Learning, LLC © Jones & Bartlett NOT FOR SALE OR DISTRIBUTION (C) Figure 2.16 Phospholipids, Membranes, and Sterols. (A) A phospholipid contains a glycerol molecule attached to two fatty acids and a phosphate head group. Inset: The symbol for the structure of a phospholipid. (B) Phospholipids in biological © Jones & Bartlettform Learning, LLC © Jones membranes a bilayer with the hydrophobic tails pointing inwards. & (C)Bartlett The sterol Learning, like ergosterolLLC can structurally stabilize membranes. »» Why are all these compounds considered “lipids”? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 51 13/02/17 4:45 pm 52 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Clinical Case 2 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION An Outbreak of Salmonella Food Poisoning © Jones & Bartlett Learning, LLC During the morning of October 17, a restaurant NOT FOR SALE ORemployee DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION prepared a Caesar salad dressing, cracking fresh eggs into a large bowl containing olive oil. Anchovies, garlic, and warm water then were mixed into the eggs and oil. The warm water raised the temperature of the mixture © Jones & Bartlett Learning, LLC slightly before the dressing was placed in the refrigerator. Later that day, the Caesar dressing was placed NOT FOR SALE OR DISTRIBUTIONat the salad bar in a cooled compartment having a temperature of about 16°C. The dressing remained at the salad bar until the restaurant closed, a period of 8 to 10 hours. During that time, many patrons helped themselves to the Caesar and the dressing. LLC & salad Bartlett Learning, © © Jones Within OR 3 days, 15 restaurant NOT FOR SALE DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Jones & Bartlett Learning, LLC FOR SALE OR DISTRIBUTION patrons experienced NOT gastrointestinal illness. Symptoms included diarrhea, fever, abdominal cramps, nausea, and chills. Thirteen sought medical care, and eight (all over 65 years of age) required intravenous rehydration. A culture plate of Salmonella. Courtesy of the CDC. © Jones Bartlett LLC ©were Jones & Bartlett Learning, LLC From the stool samples of all 13&patrons whoLearning, sought medical attention, bacterial colonies cultured (see figure) and laboratory tests identifi ed Salmonella enterica serotype Enteritidis as the causative agent. All patrons recovered within NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 7 days. Salmonella enterica serotype Enteritidis produces a lipopolysaccharide toxin that causes the symptoms experienced by all the affected patrons. Questions: Jones Bartlett LLC contamination? (You © & Bartlett a.©What might&have been theLearning, origin of the bacterial canJones find answers online in Learning, Appendix e.) LLC SALE OR DISTRIBUTION NOT FOR SALE ORinDISTRIBUTION b.NOT What FOR conditions would have encouraged the growth of Salmonella? (You can fi nd answers online Appendix e.) c. How could the outbreak have been prevented? (You can find answers online in Appendix e.) d. What types of organic compounds form the lipopolysaccharide toxin? (You can find answers online in Appendix e.) e. Why did so many of the older adult patrons develop a serious illness? (You can find answers online in Appendix e.) For additional information, see www.cdc.gov/nczved/divisions/dfbmd/diseases/salmonella_enteritidis. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Both DNA and RNA are composed of repeating composed of several rings of carbon atoms with monomers called nucleotides. Each nucleotide has side chains. Like cholesterol in animal cells, ergos© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC three components: a sugar molecule, a phosphate terol stabilizes the membranes of protists and fungi. NOT FOR OR in DISTRIBUTION NOT FOR SALE OR DISTRIBUTION group, and a nucleobase (Figure 2.17ASALE ). The sugar Other sterols are found in the cell membrane of the DNA is deoxyribose, whereas in RNA it is ribose. The bacterium Mycoplasma. nucleobases, shown in Figure 2.17B, are nitrogenNucleic Acids Store and Transmit Hereditary containing molecules. In DNA, the double-ringed information purine nucleobases adenineLearning, (A) and guanine © Jones & Bartlett Learning, LLC © Jones &are Bartlett LLC (G) and the single-ringed pyrimidine nucleobases The NOT nucleic acids are unbranched, organic comFOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION are cytosine (C) and thymine (T). In RNA molecules, pounds composed of carbon, hydrogen, oxygen, adenine, guanine, and cytosine also are present, but nitrogen, and phosphorus atoms. Two types, deoxuracil (U) is found instead of thymine. yribonucleic acid (DNA) and ribonucleic acid (rNA), Nucleic acids, like polysaccharides, are polyare the basic genetic material needed to control the mers. DNA and RNA, the LLC nucleotides are cova© Jones & Bartlett Learning, LLC © Jones &InBartlett Learning, complex metabolism within cells of all organisms lently joined through dehydration reactions are the material in viruses. NOT FORand SALE ORgenetic DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 52 13/02/17 4:45 pm KEY CONCEPT 2.4 53 Living Organisms Are Composed of Four Types of Organic Compounds © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC between the sugar of one nucleotide and the phosreports for the first time the NOT research FOR SALE ORdescribing DISTRIBUTION NOT FOR SALE OR DISTRIBUTION phate of the adjacent nucleotide to form a linear polynucleotide. structure of DNA. They described DNA as a molecule consisting of two polynucleotide strands running in opposite directions in a ladder-like arrangement DNA Structure and Function (Figure 2.17C). They also reported that the nucle© Jones & Bartlett Learning, LLC © Jones Bartlett Learning, LLC obases guanine and cytosine always&line up oppoIn 1953, James Watson, Francis Crick, Rosalind NOT FOR SALE oppose OR DISTRIBUTION NOT Wilkins FOR SALE OR DISTRIBUTION site each other, as do thymine and adenine Franklin, and Maurice published three Phosphate © Jones & Bartlett Learning, LLC group O PO–34 CH2 NOT FOR SALE OR DISTRIBUTION C C A H G C C G C G C A T O OH H H C C OH H C H Deoxyribose C C C N H C N C C C H H H C C OH OH H C Guanine (G) H O H3C NH2 Ribose N C C C N C H H Thymine (T) (DNA only) O H C © Jones &A Bartlett Learning, LLC T NOT FOR SALE OR DISTRIBUTION T A N C © JonesH &C Bartlett Learning, LLC O N C NOT FOR SALE OR DISTRIBUTION H H G C N H —C N C Adenine (A) G C O N © Jones & Bartlett Learning, LLCH H —C C C H O N NH2 HOCHNOT FOR 2 N OH SALE OR DISTRIBUTION Cytosine (C) T A H O © Jones & Bartlett Learning, LLC (A) Nucleotides NOT FOR SALE OR DISTRIBUTION C G NH2 N T Learning, LLC A © Jones & Bartlett HOCH2 NOT FOR SALE GORC DISTRIBUTION T C Sugar (pentose) C G © Jones & Bartlett Learning, LLC Purines Pyrimidines NOT FOR SALE OR DISTRIBUTION Nucleobase C H C N © Jones & Bartlett Learning, LLC C C O NOT FOR SALE OR DISTRIBUTION H N H Uracil (U) (RNA only) P Nucleobase T A D © Jones & Bartlett Learning, LLC D P NOT FOR SALE OR DISTRIBUTION P A T P G C Phosphate group D © Jones & Bartlett Learning, LLC P NOT FOR SALE OR DISTRIBUTION D P © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Sugar D D P (B) Nucleobases G C D © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION One nucleotide D P Hydrogen bond ©(C) Jones & Bartlett Learning, LLC DNA double helix NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Figure 2.17 The Molecular Structures of Nucleotide Components and the Construction of DNA. (A) The sugars in nucleo- tides are ribose and deoxyribose, which are identical except for one additional oxygen atom in RNA. (B) For each nucleobase, note the similarities in the structures of the bases and the differences in the side groups. (C) The two polynucleotides of DNA forming the double helix are held together by hydrogen bonds between adenine (A) and thymine (T) and guanine (G) and cytosine (C). »» If a Learning, segment of oneLLC strand of DNA has the bases TTAGGCACG, would be theLearning, sequence of bases © Jones & Bartlett © Joneswhat & Bartlett LLCin the complementary strand? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 53 13/02/17 4:45 pm 54 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC of small RNA molecules control various cellueach other in the two strands. These complemenNOT number FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION lar processes involved with protein synthesis. tary base pairs in the double-stranded DNA are held The chemical nature of nucleic acids makes together by hydrogen bonds. When fully formed, the them prime targets for agents that can alter or kill DNA twists to form a spiral arrangement called the microbial pathogens. For example, ultraviolet (UV) double helix. © Jonesin&DNA Bartlett LLC Jones & Bartlett Learning, LLC light damages DNA and©can be used to control The genetic information existsLearning, in disNOT FOR SALE OR DISTRIBUTION NOT FOR DISTRIBUTION microbes on an environmental surface. Chemicals, crete units of inheritance calledSALE genesOR , which are such as formaldehyde, alter nucleic acids of viruses, sequences of nucleotides that encode information and microbiologists can employ some of these to regulate and synthesize proteins. In prokarychemicals in the preparation of several vaccines. In otic cells, these genes are usually found on a single, addition, certain antibiotics interfere with DNA or circular chromosome, whereas in most eukaryotic © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC RNA function and are used to inhibit or kill bacterial microbes, several hundred genes are located on FORlinear SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION pathogens. eachNOT of several chromosomes. rNA Structure and Function Other roles for Nucleotides Besides having uracil asLLC a base and ribose as the© Jones It also is important to pointLLC out that nucleotides © Jones & Bartlett Learning, & Bartlett Learning, sugar, RNA molecules in cells are single-stranded have other roles in cells besides being the subunit NOT FORpolynucleotides. SALE OR DISTRIBUTION NOT structure FOR SALE OR DISTRIBUTION Biologists once viewed RNAs as for DNA and RNA. Adenine nucleotides the intermediaries, involved in carrying DNA gene with three attached phosphate groups form adeinformation and acting as structural molecules nosine triphosphate (ATP), which is the cellular needed to construct proteins. This certainly is a energy currency in all cells (Figure 2.18). Other major role for RNA but not the & only roles. Learning, LLC adenine nucleotides can © be Jones part of the structureLearning, of © Jones Bartlett & Bartlett LLC In many viruses, including the infl uenza and measome enzymes, such as nicotinamide adenine dinuNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION sles viruses, RNA is the genetic information, not DNA. cleotide (NAD+) and flavin adenine dinucleotide In addition, other so-called noncoding RNA mole(FAD). Both are critical in the process of ATP genercules play key roles in regulating gene activity, while a ation in all cells. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Chapter Challenge C © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION In November 2010, an article was published online in Science that made the news: A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. NASA scientists announced they had found a bacterial organism that they believed used arsenic in place of “traditional” phosphate in the backbone of DNA. The scientists reported that an apparently unusual bacterial organism, called GFAJ-1, discovered in California’s Mono Lake (see chapter opening photo), could© replace phosphorus in its DNA backboneLLC with arsenic if no phosphate was available.&If Bartlett true, it would Jones & Bartlett Learning, © Jones Learning, LLC redefine the chemistry of life as discussed in this chapter. Although this observation has been discredited on further study, NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION it helps us in trying to define a marker for our shadow life. If GFAJ-1 had used arsenic in place of phosphate in DNA, would that represent a marker for “shadow life?” Or, once again, would this just be another example of the power of the microbe to scratch out an existence no matter what extreme conditions are present? © Jones & Bartlett Learning, & Bartlett Learning, QueSTiON C: The atomic number for arsenicLLC is 33 and the mass number is © 75.Jones Draw a segment of a DNA double helixLLC (use Figure 2.17 C as a template) to illustrate how arsenic could replace phosphate. What two other phosphate-containing molecules NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION or structures discussed in this chapter might also be replaced with arsenic? You can find answers online in Appendix F. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 54 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds © Jones & Bartlett Learning, LLC compounds. Here are some of the roles NOT organic FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC H H NOT FOR SALE OR DISTRIBUTION for proteins: N Adenine 55 Structural proteins. Numerous proteins function as structural components of cells and cell walls. C H © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC ▶ C Transport proteins. Many proteins form C NOT FOR SALE OR DISTRIBUTION NOTHFOR SALE OR DISTRIBUTION N N channels or pores through membranes to facilitate the movement of materials into or H O– O– O– out of the cell. O P—O P — O– C— O — P — O ▶ Regulatory proteins. Some proteins bind to C C DNA and help activity © Jones & Bartlett Learning, © Jones ®ulate Bartlettmetabolic Learning, LLCby O OLLC O H H H H switching genes on or off. NOT FOR SALE NOT FOR SALE OR DISTRIBUTION H OR DISTRIBUTION C C Phosphate groups ▶ Receptor proteins. Other proteins in cells act as sensors (receptors) that recognize chemiOH OH cals in the environment. Ribose ▶ Cell motility proteins. Many microbes contain Adenosine © Jones & Bartlett Learning, LLC © Jones & Bartlett flagella orLearning, cilia, whichLLC are protein-containNOT FORFigure SALE2.18 OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ing structures involved with cell movement. The Structure of ATP. The adenosine triphos▶ Immune system proteins. The human immune phate (ATP) molecule is the main energy carrier in all cells. »» Name the three different building blocks (monomers) that build an system uses many different proteins, such ATP molecule. as antibodies, to defend against and eliminate invading pathogens. © Jones & Bartlett Learning, LLC ▶ Enzymes. A large © Jones & Bartlett Learning, LLC number of proteins serve NOTcatalysts FOR SALE DISTRIBUTION NOT FOR SALE OR DISTRIBUTION as enzymes, protein that OR selectively speed up metabolic reactions. ▶ C N C N Proteins Are the “Workhorse” Polymers in Cells © Jones & Bartlett Learning, LLC NOTare FOR SALEofOR DISTRIBUTION Proteins composed carbon, hydrogen, oxygen, nitrogen, and, usually, sulfur atoms. They are the most abundant organic compounds in all living organisms, making up about 58% of a bacterial cell’s dry weight. This high percentage of protein © Jones & Bartlett LLCdiverse roles for these© indicates theLearning, essential and NOT FOR SALE OR DISTRIBUTION Carboxyl group H H Proteins are unbranched polymers built from nitrogen-containing monomers called amino acids. © Jones & amino Bartlett At the center of each acidLearning, is a carbonLLC atom FOR SALE OR DISTRIBUTION attached NOT to two functional groups: an amino group (–NH2) and a carboxyl group (–COOH) (Figure 2.19). Also attached to the carbon is a side chain, called the r group (–r). Each of the 20 amino acids differs only by the atoms composing the R Jones & These Bartlett Learning, LLCbeing functional group. side chains, many NOT FOR SALE OR DISTRIBUTION Amino group Peptide bond R group 2OH ©O Jones & BartlettCHLearning, LLC Dehydration OH reaction NOT FOR SALE OR DISTRIBUTION N — C — C — OH + H H —N—C—C H CH3 H O © JonesAlanine & Bartlett Learning, Serine LLC (Amino acid) (Amino acid) NOT FOR SALE OR DISTRIBUTION Water H OH ©OJones CH & 2Bartlett Learning, LLC OHOR DISTRIBUTION NOT FOR SALE N—C—C — N—C—C H H2O R group H CH3 H H O Dipeptide © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Figure 2.19 Amino Acids and the Dehydration reaction. Amino acids are linked together by dehydration reactions between the carboxyl group of one amino acid and the amino group of the adjacent amino acid. »» What type of chemical bond is the peptide bond? © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 55 13/02/17 4:45 pm 56 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC The ionicOR andDISTRIBUTION hydrogen bonds helping hold groups, are essential in molding the fi nal shape and NOT FOR SALE NOT FOR SALE OR DISTRIBUTION a protein in its 3-D shape are relatively weak function of proteins. associations. As such, these interactions in a In forming a protein, amino acids (someprotein are influenced by environmental conditimes called peptides) are joined together by covations. When subjected to heat, pH changes, or lent (peptide) bonds where the carboxyl group Jonesto&the Bartlett Learning, LLC Jonescan & Bartlett Learning, LLC certain chemicals, these©bonds break, causof one amino acid is©linked amino group of FOR OR DISTRIBUTION FOR SALE ORreaction DISTRIBUTION ing the polypeptide to NOT unfold andSALE lose its bioanother amino acid NOT through a dehydration logical activity. This loss of 3-D shape is referred (Figure 2.19). Peptide (covalent) bonding between to as denaturation. For example, the white of a hundreds of amino acids produces a long polymer boiled egg is denatured egg protein (albumin) called a polypeptide. Because proteins have tremenand cottage cheese is denatured milk protein. dously diverse roles, they come in many sizes and © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Should enzymes be denatured in living cells, the shapes. The final shape depends on the sequence of NOT FOR SALE OR DISTRIBUTION FOR reactions SALE OR DISTRIBUTION importantNOT chemical they facilitate will amino acids in the polypeptide. be interrupted and death of the cell or organism might result. Viruses also can be destroyed Primary Structure by denaturing the proteins that build the virus’ The linear sequence of amino acids in a polypeptide 3-D structure. So, now you should understand © Jones & Bartlett the Learning, represents primary LLC structure (Figure 2.20A).© Jones & Bartlett Learning, LLC the importance of buffers in cells; by preventing NOT FOREach SALE OR DISTRIBUTION protein that has a different function willNOT FOR SALE OR DISTRIBUTION pH shifts, they prevent protein denaturation and have a different primary structure, as each posimaintain protein function. tion along the chain will have one of the 20 amino acids. The sequence of the amino acids is deterQuaternary Structure mined by the sequence of bases (genes) in the © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC DNA. However, the sequence of amino acids alone Many proteins are single polypeptides. However, NOT OR DISTRIBUTION NOT FOR SALE DISTRIBUTION is not sufficient to confer function to aOR protein. other proteins contain two orFOR moreSALE polypeptides to form the complete and functional protein; Secondary Structure this association of polypeptides is called the quaternary structure (Figure 2.20D). Each polyMost proteins have regions folded into a corkscrew peptide chain is folded into itsLearning, tertiary structure © Jones & Bartlett Learning, LLC rep© Jones & Bartlett LLC shape called an alpha helix . These regions and the unique association between separate polyNOT SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION resent partFOR of the protein’s secondary structure peptides produces the quaternary structure. The (Figure 2.20B). Hydrogen bonds between amino same types of chemical bonds are involved as in groups (–NH) and carbonyl groups (–CO) on nearby tertiary structure. amino acids maintain this structure. A secondary The four major classes of organic compounds structure also will form when the hydrogen bonds are in Figure 2.21 © Jones & Bartlett Learning, LLC & Bartlett Learning, LLC. The box iNVeScause portions of the polypeptide chain to zigzag in© Jonessummarized TigATiNg THe MiCrOBiAL WOrLD NOT FORa SALE ORforming DISTRIBUTION flat plane, a pleated sheet. Other regionsNOT FOR SALE OR DISTRIBUTION 2 looks at the origins of the monomers discussed in this chapter, of the protein might not interact and remain in a while MiCrOiNQuirY 2 shows how the radioac“random coil.” tive attributes of two chemical elements can be used to identify whether protein or DNA is the Tertiary Structure © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC genetic material. In conclusion, this chapter atoms NOT described FOR SALE ORand DISTRIBUTION NOTaFOR SALE OR DISTRIBUTION Many proteins also have tertiary structure superelements and their interactions through chemical imposed on the secondary structure (Figure 2.20C). bonding to construct compounds and molecules. Such a three-dimensional (3-D) shape of a protein is The information discussed forms the underlying folded back on itself much like a spiral telephone foundation for many of the topics we will examine cord. Ionic and hydrogen bonds between nearby © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC in microbiology, as growth, metabolism, and R groups on amino acids help form and maintain NOT FOR SALEInOR DISTRIBUTION NOT FORonSALE ORchemical DISTRIBUTION genetics are based cellular reactions. the tertiary structure. addition, covalent bonds, In fact, many microbial pathogens that infect and called disulfide bridges, between sulfhydryl (–SH) damage human cells and tissues do so by means of functional groups in R groups are important in staspecial metabolic reactions they carry out, or by the bilizing tertiary structure. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 56 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC Peptide NOT FOR SALE OR DISTRIBUTION bond H H+ N H H C C R O H R N C C 57 H H N C C H R N C C H H N C C H R N C © Jones & Bartlett Learning, OLLC H H O H O R O R NOT FOR SALE OR DISTRIBUTION O C © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION O– (A) Primary structure: polypeptide chain Hydrogen bond © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION H N C N R H OH C R C C N © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION R O C R C N C H H H O R N H C C C O H N C N R N C C O R H N H C R C R O © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION C C N O H Pleated © Jones & Bartlett Learning, LLC sheet (B) Secondary structure: pleated sheet, alpha NOThelix, FOR SALE OR DISTRIBUTION and random coil in the polypeptide chain N C C © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION O H R H C R N H N C O R O C R C H H C C O O C C H C O C H N N N H H H C O C C O H N H C R H C R O C N H H H C R R R H C O N C H H C H O HO H H C C N N C R O R HO H C R H C N C N C H O H C R O H Alpha Random C N helix coil O H © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION H C Ionic bond CH2 CH2 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION CH2 © Jones & NOT FOR SALE OR DISTRIBUTION CH2 NH3 O C CH2 © Jones & Bartlett Learning, LLC NOT FOR SALE Hydrogen bondOR DISTRIBUTION O CH2 (C) Tertiary structure: bonding between R groups on amino acids in the Bartlett Learning, LLC polypeptide chain O +– OH + – O C CH2 Disulfide bridge (covalent bond) CH2 S S CH2 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION (D) Quaternary structure: Polypeptide chain © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION two or more folded polypeptides bonded together Figure 2.20 Amino Acids and Their Assembly into Polypeptides. (A) As amino acids are linked together by dehydration reactions, the chain gets longer and forms the primary structure. (B) Interaction between amino and carbonyl functional groups on neighboring amino generates the secondary into a tertiary structure LLC through © Jones &acids Bartlett Learning, LLCstructure. (C) The whole polypeptide © Jonesfolds & Bartlett Learning, bonding between R groups. (D) Some proteins consist of more than one polypeptide, forming a quaternary structure. »» Explain NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION why every protein must have three or four levels of folding. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 57 13/02/17 4:45 pm 58 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Electrons Protons Neutrons are built into © Jones & Bartlett Learning, LLC Atoms NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION that form elements, including © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Carbon Hydrogen © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC Oxygen NOT FOR NitrogenSALE OR DISTRIBUTION which can share electrons in covalent bonds to form © Jones & Bartlett Learning, LLC NOTmolecules FOR SALE OR DISTRIBUTION Organic that include © Jones & Bartlett Learning, LLC Large organic compounds NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION such as © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION that are built from that are built from Monosaccharides © Jones & Bartlett and canLearning, be assembled LLC into NOT FOR SALE OR DISTRIBUTION Glycerol © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION that are built from that are built from Nucleotides Amino Acids Fatty acids © Jones & Bartlettand Learning, LLC and are assembled into a are assembled into NOT FOR SALE OR DISTRIBUTION and can be assembled into Polysaccharides Primary structure such as those composed of N-acetylglucosamine Triglycerides Waxes DNA RNA © Jones & Bartlett Learning, LLC OR DISTRIBUTION Phospholipids which arranges into a © Jones & Bartlett Learning, LLC structureOR DISTRIBUTION NOTSecondary FOR SALE N-acetylGlucose NOT FOR SALE muramic acid and then folds into a Chitin Lipid-related molecules Peptidoglycan © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Glycogen Starch Cellulose including Tertiary structure © Jones & Bartlett Learning, LLC NOT FOR SALE OR two orDISTRIBUTION more of which may link into a Sterols Quaternary structure © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Figure 2.21 A Concept Map Summarizing Atoms, elements, and Organic Compounds. »» Finish the concept map by filling in NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the four empty rectangles with the correct type of organic compound. © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 58 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds 59 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION investigating the Microbial World 2 Chemical evolution © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Life today is full of organic monomers thatOR assemble into larger organic compounds that NOT are characteristic of all life,DISTRIBUTION FOR SALE OR NOT FOR SALE DISTRIBUTION including microorganisms. Knowing this, in the 1920s, Aleksandr Oparin, a Russian biochemist, and J. B. S. Haldane, a British geneticist, wondered whether these small monomers could have nonliving (abiotic) origins that were then used to build the first cell, a precursor to the prokaryotic cell. OBSERVATION: Because the primitive atmosphere of Earth contained hydrogen and other substances that readily provide © Jones & Bartlett Learning, LLCOparin and Haldane suggested © Jones & Bartlett Learning, LLC electrons (an atmosphere lacking oxygen gas), independently that with an appropriate supply of energy, such as lightning or ultraviolet light, a variety of organic monomers might be formed. In 1953, this NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION suggestion for chemical evolution was put to the test by Stanley Miller, an American chemist/biologist, and Harold Urey, a physical chemist. 3. Electrical sparks represent © Jones & Bartlett Learning, LLC lightning as the energy source for the chemical reactions. NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC 2. The water vapor enters the + Electrodes “atmosphere” flask containing NOT FOR SALE OR DISTRIBUTION – the mixture of primordial gases. H 20 CH4 4. The water vapor condenses, sending water and any organic molecules formed back to the “ocean” flask. NH3 1. The boiling water H2 the “ocean” flask © Jones & Bartlett Learning, LLC in represents water Gases (primitive atmosphere) vapor. NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Condenser Cold water © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Water (ocean) 5. Periodically samples can be collected for analysis. Heat source Trap © Jones & Bartlett Learning, LLC Miller-Urey apparatus NOT FOR SALE ORThe DISTRIBUTION probe ©Sampling Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Adapted from: Miller, S. L. 1953. Science 117(3046): 528–529; Johnson, A. P., et al. 2008. Science 322(5900):404. Identification of known amino acids © Jones & Bartlett Learning, LLC Results of experiment © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Lysine Arginine and Histidine Glycine Alanine Valine Leucine and Serine Proline © Jones &Threonine Bartlett Learning, LLC Isoleucine Cysteine NOT FOR SALE OR DISTRIBUTION Glutamine Phenylalanine Asparagine Tryptophan © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Identification of known amino acids and results of experiment. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Adapted from: Miller, S. L. 1953. Science 117(3046):528–529; Johnson, A.P., et al. 2008. Science 322(5900):404. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (continues) © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 59 13/02/17 4:45 pm 60 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION investigating the Microbial World 2 (Continued ) Chemical evolution © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC QUESTION: Can organic monomers formedOR in anDISTRIBUTION atmosphere mimicking the conditions on theNOT primitive Earth? FOR SALE OR DISTRIBUTION NOT FOR be SALE HYPOTHESIS: Organic monomers, specifically amino acids, can be formed using the prebiotic atmospheric conditions of early Earth. If so, a combination of the prebiotic atmospheric gases, along with an energy source to drive the reactions, should give rise to a variety of amino acids. EXPERIMENTAL DESIGN: The apparatus illustrated on the previous page depicts the design of a closed environment © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC to mimic the prebiotic conditions believed to represent Earth’s primitive atmosphere [methane (CH4), ammonia (NH3), NOT (H FOR SALE OR NOT FOR SALE OR DISTRIBUTION hydrogen ), and water (H O)].DISTRIBUTION 2 2 EXPERIMENT: The water in the closed apparatus was boiled, allowing the water vapor to mix with the three gases and the electrical discharge. The reaction was run continuously for one week. Then, the contents of the water in the apparatus were analyzed for the presence of amino acids. the run, the water in the apparatus turned and then a cloudy deep red. The redLLC color was presumably © Jones & RESULTS: BartlettDuring Learning, LLC ©pink Jones & Bartlett Learning, due to the presence of organic molecules. The fi gure shows the results for amino acid detection (right figure) along with NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the pattern for known amino acids (left figure). CONCLuSiONS: QUESTION 1: Was the hypothesis validated? QUESTION 2: What acids detected? © amino Jones & were Bartlett Learning, LLC © Jones & Bartlett Learning, LLC QUESTION 3: How do you know SALE that the amino acids detected were not produced by living bacterial apparatus? NOT cells FORin the SALE OR DISTRIBUTION NOT FOR OR DISTRIBUTION You can find answers online in Appendix E. Note: Science often is a process of repetition and refinement. The validity of the Miller-Urey experiment was later questioned when evidence suggested that Earth’s primitive atmosphere was actually composed of different gases, ones sulfur&dioxide (SO2)]. However, modern released from volcanic eruptions [CO2, nitrogen © Jones & Bartlett Learning, LLC(N2), hydrogen sulfide (H2S), © and Jones Bartlett Learning, LLC experiments using these gases, along with those used in the original Miller-Urey experiment, have produced up to 22 amino NOT SALE OR DISTRIBUTION NOTtheFOR OR DISTRIBUTION acids, all fiFOR ve nucleobases in DNA and RNA, and the sugar ribose. So, whatever gases,SALE chemical evolution and abiotic synthesis of organic molecules appear to be validated as at least one source for organic monomers. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION MiCrOiNQuirY 2 © the Jones & Bartlett Learning, LLC is Protein or DNA genetic Material? NOT FOR SALE OR DISTRIBUTION In the early 1950s, there were scientists who still debated whether protein or DNA was the genetic material in cells. To settle the controversy, in 1952 Alfred Hershey and Martha Chase carried out a series of experiments to trace the©fates of protein and DNA Learning, and in so doing settled the Jones & Bartlett LLC debate. FOR SALE ORviruses DISTRIBUTION ItNOT was known that some that infect bacterial cells were composed of DNA and protein and that the virus genetic material had to enter the bacterial cells to direct the production of more viruses. Because the viruses left a viral coat on the surface, what actually entered the cells—protein & orBartlett Learning, LLC © DNA? Whichever did must be the genetic material. © Jones NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Several biologically important elements have isotopes that are radioactive. The table to the right lists a few such elements. Hershey and Chase decided to radioactively label the viruses such that the protein and DNA could be identified by unique les. ©their Jones &radioactive Bartlett profi Learning, LLC 2a. Which NOT of the FOR radioactive elements would only label SALE OR DISTRIBUTION protein? 2b. Which of the radioactive elements would only label DNA? 2c. Could 3H or 14C have been used to label the viruses? JonesExplain. & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 60 13/02/17 4:45 pm KEY CONCEPT 2.4 Living Organisms Are Composed of Four Types of Organic Compounds © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION A. Viruses containing radioactive isotope are mixed with bacteria so that infection can occur. B. After infection, the C. The mixture is D. Radioactivity in the mixture is placed in centrifuged in a test pellet and liquid is a blender to separate tube to separate the measured. viruses outside the cells from the viruses. cells from the bacterial Learning, © Jones & Bartlett cells. LLC DNA Protein Bacterial © virus Jones & Bartlett NOT FOR SALE OR DISTRIBUTION Empty Experiment 1: Viruses are produced that have radioactive sulfur (35S) incorporated into the virus protein. 61 Learning, LLC NOT FOR SALE OR DISTRIBUTION viral coat Bacterial cell © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Liquid (viral coats) Experiment 1 results: All radioactivity is 35S and it is detected in the liquid. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Centrifuge Pellet (bacterial cells and contents) © Jones & Bartlett Learning, LLC Experiment 2: Viruses NOT FOR SALE OR DISTRIBUTION are produced that have © Jones & Bartlett Learning, LLC Experiment 2 results: NOT FOR SALE OR DISTRIBUTION All radioactivity is radioactive phosphorus (32P) incorporated into the virus DNA. 32P and it is detected in the pellet (bacterial cells). © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONCentrifuge © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Pellet © Jones & Bartlett Learning, The Hersey-Chase Experiment LLC NOT FOR SALE OR DISTRIBUTION taBLe Some Radioactive Isotopes Common radioactive © Jones & Bartlett element Learning, Form LLC Form NOT FOR SALE OR DISTRIBUTION 1 3 Hydrogen H H (tritium) C 14 P 32 Carbon 12 Phosphorus 31 Sulfur 32 C P © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION The Hershey and Chase experiment is outlined above. From the two experiments, they could then measure the radioactivity in the pellet (bacterial cells) and the fluid (virus coats) and determine which radioactive isotope was associated withLearning, the bacterial LLC cells. Jones & Bartlett © If protein theDISTRIBUTION genetic material, which NOT 2d. FOR SALE isOR should be associated with the pellet? isotope 2e. If DNA is the genetic material, which isotope should be associated with the pellet? 2f. Did the experiments carried out by& Hershey 35 Jones & Bartlett Learning, LLC © Jones Bartlettand Learning, LLC S Chase support or refute the hypothesis that DNA was NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the genetic material? Explain. S© You can find answers online in Appendix E. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 61 13/02/17 4:45 pm 62 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC NOT FOR SALE ORand DISTRIBUTION Concept reasoning Checks 2.4 a. b. c. d. e. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION What is common to all functional groups except the carbonyl group? Discuss how stable monosaccharides are assembled into energy storage and structural polymers. Give examples. © Jones & Bartlett Learning, LLC © Jones & Bartlettare Learning, LLC Explain why lipids are not considered polymers whereas polysaccharides, polynucleotides, and polypeptides polymers. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION How does the structure of DNA differ from that of RNA? Why does a denatured protein no longer have biological activity? © Jones & Bartlett Learning, LLC NOT FOR SALE Challenge OR DISTRIBUTION Chapter D © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION In this chapter challenge, we have been investigating how we might chemically detect whether another form of life—”shadow life”—arose in a different chemical form on Earth. If there truly is a molecule capable of making life different chemically, it might be in the amino acids used to make proteins. Most all known © Jones & life Bartlett Learning, LLC © Jones & Bartlett Learning, LLC uses the same 20 amino acids to synthesize proteins. However, other amino acids exist and some, like isovaline and NOT FOR SALE OR DISTRIBUTION NOTis FOR SALE DISTRIBUTION pseudoleucine, have been identified in meteorites. Therefore, it possible that OR a marker for shadow life microbes could be unusual amino acids in their proteins? QueSTiON D: The Miller-Urey experiment described in the box iNVeSTigATiNg THe MiCrOBiAL WOrLD 2 might have produced more than the 20 traditional amino acids. If one or more of the rare amino acids were formed in the primordial Earth, and incorporated into protein, would the existing organisms be candidates for “shadow life”? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Scientists have found some bacterial organisms like Salmonella can become antibiotic resistant if they synthesize and NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION use a rare form of the amino acid lysine when making proteins. Some extremophile members of the prokaryotic world that make methane gas possess an unusual amino acid called pyrrolysine. So, in concluding this chapter challenge, does there appear to be any evidence of shadow life on Earth? Explain. You can find answers online in Appendix F. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION subsequent information easier and prepare you for a metabolism they inhibit in the infected cells and tisrewarding learning experience as you continue your sues. Realize the time invested now to understand © Jones & Learning, Learning, study&ofBartlett the microbial world. LLC or Bartlett refresh your memory LLC about chemistry will make© Jones NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 62 13/02/17 4:45 pm Chapter Self-Test 63 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ■ SUMMarY OF KeY CONCeptS Concept 2.1 Organisms Are Composed of Atoms © Jones & Bartlett Learning, 1. 2. Acids donate hydrogen ions (H ), LLC © Jones & whereas Bartlettbases Learning, LLC + acquire H from a solution. The pH scale indicates the Atoms consist of an atomic nucleus (with neutrons NOTand FOR SALE DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONnumber of H+ in a solution denotes the OR relative and positively charged protons) surrounded by a cloud of negatively charged electrons. (Figure 2.2) 2. Isotopes of an element have different numbers of neutrons. Some unstable isotopes, called radioisotopes, are useful in research and medicine. If an atom ©gains Jones & Bartlett Learning, LLC or loses electrons, it becomes an electrically NOT FOR ORare DISTRIBUTION charged ion.SALE Many ions important in microbial metabolism. (Figure 2.3) 3. Each electron shell holds a maximum number of electrons. If atoms have an unfilled valence shell, they chemically react with other reactive atoms. + 3. acidity of a solution. (Figure 2.10) Buffers are a mixture of a weak acid and a weak base that maintain acid/base balance in cells. (Figure 2.11) Jones BartlettAre Learning, Concept © 2.4 Living & Organisms ComposedLLC of Four TypesNOT of Organic Compounds FOR SALE OR DISTRIBUTION 1. The building of large organic compounds depends on the functional groups present on the monomers. Functional groups interact through dehydration reactions to form a covalent bond between 2.3) © Jones & Bartlett Learning, LLC © Jones &monomers. Bartlett(Table Learning, LLC 2. Carbohydrates include simple sugars (monosacConcept 2.2 Chemical Bonds Form Between NOT FOR SALE OR DISTRIBUTION NOT FORcharides SALE) OR DISTRIBUTION such as glucose and double sugars Reactive Atoms (disaccharides) such as sucrose. Monosaccharides 1. ionic bonds result from the attraction of oppositely and disaccharides can be linked into polysacchacharged ions. Compounds called salts result. rides that represent energy and structural molecules. (Figure 2.5) (Figures 2.13, 2.14) 2. Most atoms achieve stability through a sharing of © Jones & Bartlett Learning, LLC Jones Bartlett Learning, LLC 3. Lipids serve as energy© sources and&can be saturated electrons, forming covalent bonds. The equal sharor unsaturated. Phospholipids part of the structure NOT form FOR SALE OR DISTRIBUTION FOR SALEmolecules OR DISTRIBUTION ing of electronsNOT produces nonpolar (no in cell membranes. Other lipids include the sterols. net electrical charge). Atomic interactions between (Figures 2.15, 2.16) hydrogen and oxygen (or hydrogen and nitrogen) 4. The genetic instructions for living organisms are produce unequal sharing of electrons, which gencomposed of two types of nucleic acids: deoxyrierates polar molecules (have electrical charges). bonucleic acid (DNA ), which stores and encodes ©(Figures Jones2.6&, 2.7 Bartlett Learning, LLC © Jones & Bartlett Learning, LLCthe ) hereditary information; and ribonucleic acid (rNA), 3. NOT Separate polar molecules, like water, are electrically FOR SALE OR DISTRIBUTION NOT FORthe SALE OR DISTRIBUTION which transmits information to make proteins, attracted to one another and form hydrogen bonds, controls genes, and helps regulate genetic activity. involving positively charged hydrogen atoms and (Figure 2.17) negatively charged oxygen atoms. (Figure 2.7) 5. Proteins are used as enzymes and as structural 4. In a chemical reaction, the atoms in the reactant components of cells. They are composed of linear change bonding partners in forming one or more © Jones & Bartlett Learning, LLC Bartlett Learning, LLC by peptide bonds. chains of amino acids connected products . Two common chemical reactions in cells© Jones & , and tertiary structures form the are OR dehydration reactions and hydrolysis reactionsNOT . NOT FOR SALE DISTRIBUTION FORPrimary, SALE secondary OR DISTRIBUTION functional shape of many proteins, which can unfold (Figure 2.8) by denaturation. Many proteins are the result of two or more polypeptides bonding together (quaternary Concept 2.3 All Living Organisms Depend on Water structure). (Figures 2.19, 2.20) 1. All chemical reactions in organisms occur in liquid water. Being a © polar molecule, water has unique Jones & Bartlett Learning, LLC properties. These include its role as a universal NOT FOR SALE OR DISTRIBUTION solvent, in cohesion between water molecules and in temperature modulation. (Figure 2.9) © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION ■ Chapter SeLF-teSt © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC For Steps , youSALE can find OR answers to questions and problems in AppendixNOT D. NOTA–D FOR DISTRIBUTION FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 63 13/02/17 4:45 pm 64 CHAPTer 2 THE CHEMICAL BUILDING BLOCKS OF LIFE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ■ Step a: review OF FaCtS aND terMS Multiple Choice © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT before FOR selecting SALE OR DISTRIBUTION Read each question carefully the one answer that best fits the question or statement. 8. A nurse is preparing an IV drip for a patient. In the These positively charged particles are found in the saline solution she is using, the salt represents a atomic nucleus. _____. A. Protons A. solvent B. Electrons © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC B. hydrophobic molecule C. Protons and neutrons NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION C. solute D. Neutrons D. nonpolar molecule 2. Atoms of the same element that have different num9. If the saline solution mentioned in the previous quesbers of neutrons are called ______. tion has a pH of 5.5, it is mildly _____. A. isotopes A. buffered B. ions © Jones & Bartlett Learning, LLC © Jones &B.Bartlett alkaline Learning, LLC C. acids C. acidicOR DISTRIBUTION D. inert elements NOT FOR SALE OR DISTRIBUTION NOT FOR SALE D. basic 3. If an element has two electrons in the first shell and 10. Which one of the following statements about buffers seven in the second shell, the element is said to be is false? what? A. They work inside cells. A. Stable B. They consist of a weak acid and weak base. B. Unreactive © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC C. They prevent pH shifts. C. Unstable NOT reactions. FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIOND. They speed up chemical D. Inert 11. A functional group designated-COOH is known as a/ 4. The transfer of one or more electrons between interan ______. acting atoms results in what type of bond? A. carboxyl A. Hydrogen B. carbonyl B. Ionic ©C.Jones & Bartlett Learning, LLC Jones & Bartlett Learning, LLC C. © amino Peptide D. hydroxyl D. Covalent NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 12. Which one of the following is not a polysaccharide? 5. The covalent bonding of atoms forms a/an ______. A. Chitin A. molecule B. Glycogen B. ion C. Cellulose C. element D. Triglyceride D. isotope © Jones & 6. Bartlett Learning, Bartlett Learning, LLC 13. & How do the lipids differ from the other organic comThe ______ bond is LLC a weak bond that can exist© Jones between poles of adjacent molecules. NOT FOR SALE OR DISTRIBUTION NOT FORpounds? SALE OR DISTRIBUTION A. They are the largest organic compounds. A. hydrogen B. They are nonpolar compounds. B. ionic C. They are the product of hydrolysis reactions. C. polar covalent D. They are not used for energy storage. D. nonpolar covalent 14. Both DNA and RNA are©composed 7. In what type of © chemical reaction are the products Jones & Bartlett Learning, LLC Jones of & ______. Bartlett Learning, LLC A. polynucleotides of water removed during the formation of covalent NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION B. genes bonds? C. polysaccharides A. Hydrolysis D. polypeptides B. Ionization 15. The ______ structure of a protein is the sequence of C. Dehydration amino acids. D. Decomposition © Jones & Bartlett Learning, LLC Jones & Bartlett Learning, LLC A. © primary B. NOT secondary NOT FOR SALE OR DISTRIBUTION FOR SALE OR DISTRIBUTION C. tertiary D. quaternary 1. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 64 13/02/17 4:45 pm Step D: Questions for Thought and Discussion © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION ■ Step B: CONCept review 65 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 19. Predict the chemical reactivity potential for a mole16. Assess the importance of the three types of atomic groups versus one having particles to atomic reactivity. (Learning, Key Con© structure Jones and & Bartlett LLC cule having five functional © Jones & Bartlett Learning, LLC only one functional group. Explain your prediction. cept 2.1) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (Key Concept 2.4) 17. Explain the difference between nonpolar covalent 20. Construct a table providing the name of each type of bonds, polar covalent bonds, and ionic bonds in organic compound and its function or functions. (Key terms of electron interactions between atoms. (Key Concept 2.4) Concept 2.2) 18. Support the statement: “Life as we know it could not ©exist Jones & water.” Bartlett © Jones & Bartlett Learning, LLC without (Key Learning, Concept 2.3) LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ■ Step C: appLiCatiONS aND prOBLeM SOLviNG 21. You want to grow an acid-loving bacterial species; 24. Use the following list to identify the structures (in 25Bartlett i–v) drawnLearning, below. that is, Learning, one that grows best in very acidic environ-© Jones & © Jones & Bartlett LLC LLC A. Amino acid ments. Would you want to grow it in a culture that NOT FOR SALE NOT FOR B.SALE OR DISTRIBUTION Disaccharide has OR a pH DISTRIBUTION of 2.0, 6.8, or 11.5? Explain. ED: insert structures? C. Lipid 22. You are given two beakers of a broth growth medium. D. Monosaccharide However, only one of the beakers of broth is buffered. e. Nucleotide How could you determine which beaker contains the F. Polysaccharide buffered broth solution? Hint: You are provided with © Jones & Bartlett LLC g. Sterol © Jones & Bartlett Learning, LLC a bottle of concentrated HCl and pH papersLearning, that indi25. Identify all functional groups eachSALE structure (i–v). cate a solution’s NOT pH. FOR SALE OR DISTRIBUTION NOT on FOR OR DISTRIBUTION (i) (ii) (iii) (iv) (v) 23. The microbial community in a termite’s gut contains the enzyme cellulase. How does this benefit the termite and the termite’s microbial community? © Jones Bartlett Learning, © Jones & Bartlett Learning, LLC ■ Step D:&QUeStiONS FOrLLC thOUGht aND DiSCUSSiON NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 30. The toxin associated with the foodborne disease bot26. Propose a reason why organic molecules tend to be ulism is a protein. To avoid botulism, home canners so large. are advised to heat preserved foods to boiling for at 27. Bacterial cells do not grow on bars of soap (that are least 12 minutes. How does the heat help to avoid the very alkaline) even though the soap is wet and covered with bacterial organisms after one has washed. © Jones & Bartlett Learning, LLC © Jones &disease? Bartlett Learning, LLC 31. The late Isaac Asimov, an American author and proExplain this observation. NOT FOR 28. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION fessor of biochemistry, once said, “The significant Suppose you had the choice of destroying one class chemicals in living tissue are rickety and unstable, of organic compounds in bacterial cells to prevent which is exactly what is needed for life.” How does their spread. Which class would you choose? Why? this quote apply to the atoms, molecules, and organic 29. Milk production typically has the bacterium Lactobacompounds described in this chapter? cillus added to the milk before it is delivered to mar& produces Bartlettlactic Learning, LLC © Jones & Bartlett Learning, LLC ket. In the milk, © theJones organism acid. (a) Why would this organism added toOR the milk and NOT FOR SALE OR DISTRIBUTION NOT FORbeSALE DISTRIBUTION (b) why was this particular bacterium chosen? Concept Mapping See pages xxix-xxx on how to construct a concept map. © Jones & Bartlett Learning, LLC 32. NOT Construct Chemical Bonds, using FORa concept SALE map OR for DISTRIBUTION the following terms. Hydrocarbon Methane Hydrogen bonds NaCl Ionic bonds Nonpolar covalent bonds © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Polar covalent bonds Salts Water © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 9781284101041_CH02_PASS02.indd 65 13/02/17 4:45 pm
