2 Chapter 1 The Facts of Life:Chemistry Is the Logic of Biological Phenomen polymerie moccarhitcur in t nree sugars and amino acids.Indeed.the complex three-dimensional strusture of a macro molecule.known as its conformation,is a consequence of interactions between the structure functional char cteristic of biological structures that separatest ence s,an pattems:that is.to ask what functional role they serve within the oreanism. Third,living systems are actively engaged in energy transformations.Maintenance of the highly organized st e sun. mery low5o的ht cnergy。 nivorous predators at the apex of the food pyramid(Figure 1.2).The biosphere is thus a system through which energy flows Organisms capture some of this energy.be it from ADPH d,by forming spe monly used abbreviation cover of this book.)ATP and NADPH are energized biomolecules because they repre sent chemically useful forms of stored energy.We explore the chemi asis of thi mat whe etically unfavor sses That is.ATP.NADPH.and related compounds are the power sources that drive the energy-requiring activities of the cell.including biosyn cence).Only upon maintain its intricate order and activity far removed from equilibrium with its surround
2 Chapter 1 The Facts of Life: Chemistry Is the Logic of Biological Phenomena polymeric molecules, called macromolecules. These macromolecules themselves show an exquisite degree of organization in their intricate three-dimensional architecture, even though they are composed of simple sets of chemical building blocks, such as sugars and amino acids. Indeed, the complex three-dimensional structure of a macromolecule, known as its conformation, is a consequence of interactions between the monomeric units, according to their individual chemical properties. Second, biological structures serve functional purposes. That is, biological structures play a role in the organism’s existence. From parts of organisms, such as limbs and organs, down to the chemical agents of metabolism, such as enzymes and metabolic intermediates, a biological purpose can be given for each component. Indeed, it is this functional characteristic of biological structures that separates the science of biology from studies of the inanimate world such as chemistry, physics, and geology. In biology, it is always meaningful to seek the purpose of observed structures, organizations, or patterns; that is, to ask what functional role they serve within the organism. Third, living systems are actively engaged in energy transformations. Maintenance of the highly organized structure and activity of living systems depends on their ability to extract energy from the environment. The ultimate source of energy is the sun. Solar energy flows from photosynthetic organisms (organisms able to capture light energy by the process of photosynthesis) through food chains to herbivores and ultimately to carnivorous predators at the apex of the food pyramid (Figure 1.2). The biosphere is thus a system through which energy flows. Organisms capture some of this energy, be it from photosynthesis or the metabolism of food, by forming special energized biomolecules, of which ATP and NADPH are the two most prominent examples (Figure 1.3). (Commonly used abbreviations such as ATP and NADPH are defined on the inside back cover of this book.) ATP and NADPH are energized biomolecules because they represent chemically useful forms of stored energy. We explore the chemical basis of this stored energy in subsequent chapters. For now, suffice it to say that when these molecules react with other molecules in the cell, the energy released can be used to drive energetically unfavorable processes. That is, ATP, NADPH, and related compounds are the power sources that drive the energy-requiring activities of the cell, including biosynthesis, movement, osmotic work against concentration gradients, and, in special instances, light emission (bioluminescence). Only upon death does an organism reach equilibrium with its inanimate environment. The living state is characterized by the flow of energy through the organism. At the expense of this energy flow, the organism can maintain its intricate order and activity far removed from equilibrium with its surroundings, yet exist in a state of apparent constancy over time. This state of apparent constancy, or so-called steady state, is actually a very dynamic condition: Energy and Figure 1.1 (a) Gelada (Theropithecus gelada), a baboon native to the Ethiopian highlands. (b) Tropical orchid (Masdevallia norops), Ecuador. Herbert Kehrer/Corbis Science Photo Library/Alamy (a) (b) Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
1.1 What Are the Distinctive Properties of Living Systems? 3 Carnivore product (0.4 g) Consumers Herbivore product (6g) ary pr tivity (270 g) 1'Producers material are consumed by the organism and used to maintain its stability and order.in contrast.inanimate matter.as exemplified by the universe in totality,is moving to a condition of increasing disorder or,in thermodynamic terms,maximum entropy identical copies of themsehves Thi rtosxuarproduction n plantsandanimas but in everyase it is characterized byan astounding degree of fidelity(Figure 1.4).Indeed.if the accuracy of self-replication were significantly greater,the evolution of organisms would be hampered.This is so because in the chemical nature of the genetic material.This substance consists of polymeric chains of deoxyribonucleic acid,or DNA.which are structurally complementary to one another (Figure 1.5).These molecules can generate new copies of themselves in a rigorously T FIGURE1 ATP and NADPH,two biochemically important NADPH n eecu
1.1 What Are the Distinctive Properties of Living Systems? 3 material are consumed by the organism and used to maintain its stability and order. In contrast, inanimate matter, as exemplified by the universe in totality, is moving to a condition of increasing disorder or, in thermodynamic terms, maximum entropy c. Fourth, living systems have a remarkable capacity for self-replication. Generation after generation, organisms reproduce virtually identical copies of themselves. This selfreplication can proceed by a variety of mechanisms, ranging from simple division in bacteria to sexual reproduction in plants and animals; but in every case, it is characterized by an astounding degree of fidelity (Figure 1.4). Indeed, if the accuracy of self-replication were significantly greater, the evolution of organisms would be hampered. This is so because evolution depends upon natural selection operating on individual organisms that vary slightly in their fitness for the environment. The fidelity of self-replication resides ultimately in the chemical nature of the genetic material. This substance consists of polymeric chains of deoxyribonucleic acid, or DNA, which are structurally complementary to one another (Figure 1.5). These molecules can generate new copies of themselves in a rigorously Entropy c A thermodynamic term used to designate that amount of energy in a system that is unavailable to do work. hν Carnivores 2° Consumers 1° Consumers 1° Producers Carnivore product (0.4 g) Herbivore product (6 g) Primary productivity (270 g) Herbivores Photosynthesis Productivity per square meter of a Tennessee eld Figure 1.2 The food pyramid. Photosynthetic organisms at the base capture light energy. Herbivores and carnivores derive their energy ultimately from these primary producers. OCH2 O H H N H H OH OH O O P O– –O N N N NH2 ATP N NADPH O O P O– O P O– OHOH O P O HH –O O O P –O O CH2 O P –O O– O CH2 C NH2 O N N NH2 N N OOH O Figure 1.3 ATP and NADPH, two biochemically important energy-rich compounds. Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
4 Chapter 1 The Facts of Life:Chemistry Is the Logic of Biological Phenomen ucleotide rise to structural complementarity. 1.2 What Kinds of Molecules Are Biomolecules? The elemental co gen constitute more than9%of the atoms in the human body,with most of the Hand
4 Chapter 1 The Facts of Life: Chemistry Is the Logic of Biological Phenomena executed polymerization process that ensures a faithful reproduction of the original DNA strands. In contrast, the molecules of the inanimate world lack this capacity to replicate. A crude mechanism of replication must have existed at life’s origin. 1.2 What Kinds of Molecules Are Biomolecules? The elemental composition of living matter differs markedly from the relative abundance of elements in the earth’s crust (Table 1.1). Hydrogen, oxygen, carbon, and nitrogen constitute more than 99% of the atoms in the human body, with most of the H and O occurring as H2O. Oxygen, silicon, aluminum, and iron are the most abundant atoms in the earth’s crust, with hydrogen, carbon, and nitrogen being relatively rare (less than Figure 1.4 Organisms resemble their parents. (a) The Garrett lineage. Top-to-bottom, left-to-right: Reg Garrett; sons Jeffrey, Randal, and Robert; grandchildren Jackson, Bella, Reggie, and Ricky. (b) Orangutan with infant. (c) The Grisham family. Topto-bottom, left-to-right: Charles and Rosemary; son David, daughter Emily with granddaughters Annie and May, son Andrew. (a) Reginald H. Garrett (c) Charles M. Grisham Randal Harrison Garrett (b) A G C A A A A A 3' 5' 5' 3' T T T T T C C T C C C G G G G G Figure 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity. Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
1.2 What Kinds of Molecules Are Biomolecules? 5 AComposition of the Earth's Crust,Seawater,and the Human Body Earth's Crust Seawater Human Bodyt Atoms pairing Element % Compound my Element % H+H→H:HH-H 436 63 G+H一GH-C-H 28 Na 470 25 Al 7.9 Mg 54 9.5 Fe 4.5 s0,2 28 1.4 e.+c.-.c:c.-c-e- Ca 3.5 Ca2 10 Ca 037 Na 25 K 10 022 +N:一:N:-C-N 292 K 35 HCO 0.08 Mg 0.01 006 0.46 HPO <0.001 G+0:一G0: --0 0.2 Na 0.19 Mg 0.01 g+c一ccc=c 615 G+N:一cN:c=N 615 found in the human body serving essential biological functions include Mn.Fe.Co.Cu.Zn.Mo.I.Ni +:一coc=o 686 +0:一00.-0-o 02%each)nitr 0+0:一0o 0=0 is also abundant in the atmosphere and in the oceans.What property unites H.O.C. and Nand renders these to the chemistry of is their ability to N+N:一NN: H.( are amo N+H一NH N-H is inversely proportional to the atomic of the atoms involved,H.C.N.and O form the strongest covalent bonds.Two other 0+H一-0-H 460 covalent bond-forming elements,phosphorus (as phosphate [-OPO]derivatives) FIGURE1.Covaknt bond formation byepair and sulfur,also play important roles in biomolecules sharing. 1.2a Biomolecules Are Carbon Compounds All biomolecules contain carbon(C).The prevalence of C is due to its unparalleled versatility in forming stable covalent bonds through electron-pair sharing.Carbon by sharing cch ofth four oms.A ms common uting its single elec n to the formation of an electr on nair ox with two unpaired electrons in its outer shell,can participate in two covalent bonds.and Frogen,whicn has unsnared clectrons.can form three sucn covaent bonds. hermore. in share two ele Two properties of carbon covalent bonds merit particular attention.One is the abil ity of carbon to form covalent bonds with itself.The other is the tetrahedral nature of the four tbonds whe carbon alo ossibilities for includin N O,and H atoms in these compounds(Figure 1.7).We can therefore envision the ability of Cto generate complex structures in three dimensions.These structures,by virtue of
1.2 What Kinds of Molecules Are Biomolecules? 5 0.2% each). Nitrogen as dinitrogen (N2) is the predominant gas in the atmosphere, and carbon dioxide (CO2) is present at a level of 0.04%, a small but critical amount. Oxygen is also abundant in the atmosphere and in the oceans. What property unites H, O, C, and N and renders these atoms so suitable to the chemistry of life? It is their ability to form covalent bonds by electron-pair sharing. Furthermore, H, C, N, and O are among the lightest elements of the periodic table capable of forming such bonds (Figure 1.6). Because the strength of covalent bonds is inversely proportional to the atomic weights of the atoms involved, H, C, N, and O form the strongest covalent bonds. Two other covalent bond-forming elements, phosphorus (as phosphate [OOPO3 22] derivatives) and sulfur, also play important roles in biomolecules. 1.2a Biomolecules Are Carbon Compounds All biomolecules contain carbon (C). The prevalence of C is due to its unparalleled versatility in forming stable covalent bonds through electron-pair sharing. Carbon can form as many as four such bonds by sharing each of the four electrons in its outer shell with electrons contributed by other atoms. Atoms commonly found in covalent linkage to C are C itself, H, O, and N. Hydrogen can form one such bond by contributing its single electron to the formation of an electron pair. Oxygen, with two unpaired electrons in its outer shell, can participate in two covalent bonds, and nitrogen, which has three unshared electrons, can form three such covalent bonds. Furthermore, C, N, and O can share two electron pairs to form double bonds with one another within biomolecules, a property that enhances their chemical versatility. Carbon and nitrogen can even share three electron pairs to form triple bonds. Two properties of carbon covalent bonds merit particular attention. One is the ability of carbon to form covalent bonds with itself. The other is the tetrahedral nature of the four covalent bonds when carbon atoms form only single bonds. Together these properties hold the potential for an incredible variety of linear, branched, and cyclic compounds of C. This diversity is multiplied further by the possibilities for including N, O, and H atoms in these compounds (Figure 1.7). We can therefore envision the ability of C to generate complex structures in three dimensions. These structures, by virtue of appropriately included N, O, and H atoms, can display unique chemistries suitable to the living state. Thus, we may ask, is there any pattern or underlying organization that brings order to this astounding potentiality? Composition of the Earth’s Crust, Seawater, and the Human Body* Earth’s Crust Seawater Human Body† Element % Compound mM Element % O 47 Cl2 548 H 63 Si 28 Na1 470 O 25.5 Al 7.9 Mg21 54 C 9.5 Fe 4.5 SO4 22 28 N 1.4 Ca 3.5 Ca21 10 Ca 0.31 Na 2.5 K1 10 P 0.22 K 2.5 HCO3 2 2.3 Cl 0.08 Mg 2.2 NO3 2 0.01 K 0.06 Ti 0.46 HPO4 22 ,0.001 S 0.05 H 0.22 Na 0.03 C 0.19 Mg 0.01 *Figures for the earth’s crust and the human body are presented as percentages of the total number of atoms; seawater data are in millimoles per liter. Figures for the earth’s crust do not include water, whereas figures for the human body do. †Trace elements found in the human body serving essential biological functions include Mn, Fe, Co, Cu, Zn, Mo, I, Ni, and Se. table 1.1 H + H H H Atoms e– pairing Covalent bond Bond energy (kJ/mol) C + H C + C + N N + O O O + C C C N N O O + O O + N N + H N H + H O H 414 343 292 351 615 615 686 142 402 946 393 460 H H C C C C C C + NC + OC OO + OO NN N H HO C C C C C C C O OO NN N O H H C C C N C C C OO O 436 Figure 1.6 Covalent bond formation by e2 pair sharing. Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
6 Chapter 1 The Facts of Life:Chemistry Is the Logic of Biological Phenomen LINEAR ALIPHATIC Stearic acid HOOC-(CH2)s-CHs CH 888 CYCLIC Cholestero CH BRANCHED 3-Carotene PLANAR: Chlorophylla CH CH CH CH:-CHz-CH:-CH-CH2-CH:-CH2-CH-CH:-CH:-CH:-CH-CH
6 Chapter 1 The Facts of Life: Chemistry Is the Logic of Biological Phenomena LINEAR ALIPHATIC: Stearic acid HOOC (CH2)16 CH3 O CH2 C CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH2 OH BRANCHED: -Carotene H3C CH3 CH3 CH3 CH3 CH3 CH3 H3C CH3 H3C CYCLIC: Cholesterol H C CH2 CH3 HO H3C H3C CH2 CH2 C CH3 H CH3 PLANAR: Chlorophyll a N N N Mg 2+ H3C CH2CH3 CH3 O C OCH3 O CH2 H3C H3C 2C HCH CH2 C O CH2 CH CH C 2 CH2 CH2 CH3 CH CH2 CH2 CH2 CH3 CH CH2 CH2 CH2 CH3 CH CH3 CH3 O N Figure 1.7 Examples of the versatility of COC bonds in building complex structures: linear, cyclic, branched, and planar. Copyright 2017 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it