Midterm Half 1 Chemistry PDF

why is chemistry important for biology chemistry provides the foundational knowledge needed to explore and understand the complexity of biological systems 25 essential el...

why is chemistry important for biology chemistry provides the foundational knowledge needed to explore and understand the complexity of biological systems 25 essential elements of life · the first level in the biological hierarchy is molecules 92 naturally occurring elements but, only · matter is composed of elements Is are essential for life in humans blocks form building can group into : chemical element major elements (96 3 %) · a is a. type of matter composed · lesser elements (3 7 %). of only one atom · trace elements (10 01 %). IMPORTANT A know : the body is mainly made up of, carbon oxygen made up of 96% of our bodies · hydrogen nitrogen why the properties of water is important · all organisms require water more than any other substance. · most cells are surrounded by water cells themselves are made up of fo-95 % water · water is the main reason the earth is habitable. elements definition a pure substance that cannot be broken down into simpler substances O > symbol by chemical means chlorine > name of element 17 > atomic number ex · elements on the periodic table like oxygen (0) , , gold (Au) atoms definition the smallest unit of an element that retains the properties of that element. Lithium atom & eX. a single oxygen atom (0) or O it > electrons a single hydrogen atom (H) ⑨ "neutron W proton compound definition a substance formed when two or # Hy0 more different elements are chemically bonded together. eX. water (H20) carbon dioxide , I It (CO2) sodium chloride (NaCl) CH + , H It isotope isotopes are atoms that have the same number of protons (same atomic number) but different number of neutrons (and mass number) can be stable e... unstable nucleus stays intact over a long nucleus decays spontaneously example and carbon-13 are : carbon-12 period of time. giving off particles and energy. stable where as carbon - It is radio- active. how they can be helpful or harmful...... · cells cannot tell the difference · radioactivity is easily detected and measured between radioactive isotopes by instruments so radioactive isotopes are , and nonradioactive isotopes , used as tracers in medicine + research. so they move through biological systems in the same way. · high levels of exposure to radioactive isotopes can mutate DNA. BUFFER a solution that resists changes in pl when small amounts of acids or bases are added. they help maintain a stable pl environment. how it work..... when acid is added : When base is added : the conjugate base reacts with the the weak acid donates It ions to neutralize added It ions to form the weak the added base , also helping to keep acid reducing impact , on pl. pH stable. structure of an atom an atom is the basic unit of matter and consists of three primary subatomic particles. protons found the nucleus · positively charged particles in · number of protons determines the atomic number and identity of the element. eX hydrogen has I proton carbon has 6. , neutrons · neutral particles also located in the nucleus · the number of neutrons , along with protons contributes , to the atomic mass electrons negatively charged particles that orbit the nucleus in electron shells energy level · or · in a neutral atom the number of electrons = number of protons , , balancing the charge. in · transfer covalent bonds when atoms share electrons Bonds ionic bond ionic bonds happen when one atom transfers electrons to another , creating cations + anions cations anions positively charged protons negatively charged electrons than · more more · , , than electrons protons ex-sodium chloride (NaCk) , sodium (Nat donates an electron to chlorine (CIT nonpolar covalent bond formed when two atoms share electrons due to similar electronegativities equally. molecules such ex. as hydrogen (Hc) and oxygen (02). polar covalent bond when two atoms share electrons due to different occur unequally electronegativities , resulting in partial positive and negative charges. H - · ex. water (H20) where oxygen , is more electronegative j than hydrogen creating a dipole · =. , It' " hydrogen bond a weak interaction that occurs between a hydrogen atom bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom. ex. the attraction between water molecules (H2O) that leads to properties like surface tension. hydrogen bond o O surface tension " "It caused cohesive force between It "X H by > , polar liquid molecules covalent screates an elastic-like layer on waters ItIt surface , allowing some insects to walk on water. examples : sodium reacts w/ chlorine : : Na - : · : · = ionic bond two hydrogen atoms bond with one oxygen atom (water) 2H + 0 = Ho polar cunequal oxygen has covalent , It =H Dmore H than hydrogen) (CHA) methane # H - nonpolar j covalent ⑰ Di H.... H · · shares electrons equally it four emergent properties of water I. cohesion water molecule structure cohesion is when molecules of the same kind O stick together. It If Chydrogen bond hydrogen bonds hold water molecules - together - adhesion is when molecules of different kinds polar covalent bonds it H S stick together. ~ water molecules + other substances ( O It It & 2. moderation of temperature O heat : total Kinetic energy due to molecular motion It It amount of energy being transferred between molecules / g temp : measure of intensity of heat due to average Kinetic of molecules. & H energy water heated water cooled energy is absorbed to disrupt hydrogen hydrogen bonds reform , causing heat to be released bonds before water molecules can move which slows down the cooling process. faster. water temp only increases a little with a lot of energy energy is required to break hydrogen bonds energy , is released when hydrogen bonds reform.. 3 expansion upon freezing · the solid form is more dense than the liquid form. ice floats in liquid water because hydrogen bonds · are more ordered/organized in ice than they are in water · floating ice insulates the liquid below from the colder air from above. S if ice DID NOT float on water what , it would be too cold for the organisms , would be the consequence to the ice would sink into the water n they organisms living in the water ? would not survive. 1 versatile solvent solution is a liquid that is a homogenous mixture of substances : · solvent : dissolving agent of a solution · solute : substance that is dissolved water dissolves many of the solutes necessary for life , including ionic compounds and polar molecules. not all substances dissolve in water... hydrophilic hydrophobic has polarity and has an a non polar and DOES NOT have affinity for water. affinity for water an. # ↓ water-loving watering hating hydrophilic or hydrophobic ?? hydrophilic check the polarity has ionic polar bonds (molecules · or analyze molecular structure proteins hydrophilic · · are hydrophobic nonpolar molecules , like fats or oils (do not mix with water) · many steroids are hydrophobic. acids bases , ACID BASE + a compound that donates I Ions to a compound that accepts H ions and solution. as a result the concentration , removes them from a solution. the concentration of CH ] decreases. + + of CH ] increases. pH scale a scale that measures the acidity or basicity of a solution based on the CH] concentration. acidic solutions have pH 3 · values Iowerthant. a two unit pH is a 100-fold change in It. a three unit plt change is a 1000-fold change. · basic solutions have pH values higher than. 7 Buffer a buffer sulotion consists of a weak acid and its conjugate base OR a weak base and its conjugate acid. · buffers are substances that minimize + pl. H2fOg HCO3 + H changes in carbonic acid bicarbonate weak acid conjugate Elements, Atoms, and Compounds 2.1 Organisms are composed of elements, usually combined into compounds You and all things around you are made of matter-the physi- cal "stuff" of the universe. Matter is defined as anythin g that T Figure 2.18 occupies space and has mass. (In everyday language, we think Elements of t he of mass as an object's weight.) Matter is found on Earth in human body as per· centage of body weight three physical states: solid, liquid, an d gas. (including water) Types of matter as diverse as water, rocks, air, and biology students are all composed of chemical elements. An element is a substance th at cannot be broken down to other substances by ordinary chemical means. Chemists recognize 92 elements that occur in nature; gold, copper, carbon, and oxygen are some examples. Chemists have also made a few dozen syn- thetic elements. Each element has a symbol made up of the first letter or two of its English, Latin, or German name. For example, the symbol 0 comes from the English word oxygen; the symbol for sodium, Na, is from the Latin word natrium. A compound is a substance consisting of two or more dif- ferent elements combined in a fixed ratio. For example, table gen (N): 3.3% salt (sodium chloride, NaCl) has equal parts of the elements sodium (Na) and chlorine (Cl). Pure sodium is a metal and ium (Ca): 1.5% pure chlorine is a poisonous gas. Chemically combined, how- sphorus (P): 1.0% ever, t hey form an edible compound (Figure 2.1A). Hydrogen (H) and oxygen (0) are elements that typically exist as gases. Chemically combined in a ratio of 2:1, however, they form the most abundant compound on the surface of Earth- water (H 20). Water and table salt are examples of organized matter having emergent properties: A compound has characteristics different from those of its elements. Most of the compounds in living organisms contain at least t h ree or four elements. Sugar, for example, is formed of carbon (C), h ydrogen, and oxygen. Proteins, which make up carbohydrates, and lipids. Calcium (Ca) and phosphorus (P) are about 20% of your body, are compounds con taining carbon, the major components of your bones and teeth. Accounting for hydrogen, oxygen, nitrogen (N), and a small amount of most of the remaining 1% of your body, potassium (K), sulfur, sulfur (S). sodium, chlorine, and magnesium (Mg) are involved in func- How m any elements are essential for life? The requirements tions such as nerve signaling and chemical reactions. are similar among organisms, but there is some variation. For What about that last tip of the toe in Figure 2.lB? The example, humans need 25 elements, but plants require only so-called trace elements are present in minute quantities , 17. As you can see in Figure 2.18, six elements- oxygen, car- making up less t han 0.01% of human body weight. They bon, hydrogen, nitrogen, calcium, and phosphorus-make include boron, chromium, cobalt, copper, fluorine, iodine, up about 99% of your body. The first four (0, C, H, and N) are iron, manganese, molybdenum, selenium, silicon, tin, the main ingredients of t he biological molecules proteins, vanadium, and zinc. Iron makes up only about 0.004% of your body weight but is vital for energy processing and for transporting oxygen in your blood. Iron (Fe) is a trace ele- ment needed by all forms of life. Others are required only by certain species. For example , iodine (I) is essential only + - for vertebrates-animals with backbones , which include you. We explore the importance of trace elements to your health next. Sodium Chlorine Sodium chloride n Explain how table salt illustrates the concept of emergent (Na) (Cl) (NaCl) U properties. snouos1od e pue 1elaw e WJO' amd LI! aJe ' aupo14:>.A. Figure 2.1A The emergent properties of table sa lt pue wn!pos ' 11es a1qe110 s1e1s,\Jo a1q!pa a41 dn 1e41 s1uawa1a a41 22 CHAPTER 2 The Chemical Basis of Life  2.2 Trace elements are common additives to food and water Trace elements are required in very small quan- of science and societal ben- H.WHJ11.1;1 tities, but, in some cases, even those small requirements are difficult to fulfil!. efits and interactions. In the early 1900s, a dentist began Iodine is an essential component of a hormone produced searching for the cause of by the thyroid gland. An iodine deficiency in th e diet causes brown-stained teet h (then the thyroid gland to grow to abnormal size, a condition called called Colorado brown stain goiter (Figure 2.2A). The most serious effects of iodine defi- and n ow known as fluoro- ciency take p lace during feta! development and childhood, sis). With the h elp of other leading to miscarriages, poor growth, researchers, h e establish ed and mental impairment. Seafood, the cause as a high concen- i. Figure 2.2C Mouthwash and kelp, dairy products, and dark, leafy tration of fluoride in local toothpaste w ith added fluoride greens are good natural sources. water supplies. But he also Thus, deficiencies are often found noted that stained teeth were correlated with a greatly reduced in inland regions, especially in incidence of cavities and tooth loss. By th e 1940s, scientists at areas where t he soil is lacking in the U.S. National Institutes of Health published several studies iodine. A global strategy to elim- showing that reduced tooth decay was associated with a fluo- inate iodine deficiency involves ride concentration that was low enough n ot to cause fluorosis. universal iodization of all salt A five-year con trolled study of water fluoridation in Grand used for human and animal Rapids, Michigan, showed significant reductions in cavities, consumption. Unfortunately, and by 1951, fluoridation became an official policy of the U.S. about 30% of global house- Public Health Service. Numerous research studies continue h olds still do not have access to show the effectiveness of water fluoridation on reducing i. Figure 2.2A Goit er, a to iodized salt. Although cavities in both children and adults. symptom of iodine deficiency, most common in developing But this public health achievement is not without contro- in a Burmese woman n ations, iodine deficiencies versy. When first introduced in the 1950s, some groups asserted may also result from excessive consumption of highly that fluoridated water, along with the polio vaccine, was part of processed foods (which often use non-iodized salt). a communist conspiracy. Fluoridation efforts in som e U.S. com- A deficiency in an oth er trace element-iron-is the munities have met with strong opposition, based sometimes world's most common nutrition al disorder, with as many as on conflicting studies, a distrust of science, or a strong belief 2 billion people affected, in particular children and women in in individual rights. With the advent of fluoridated toothpaste developing countries. Strategies for addressing the ch allenge and oth er fluoride treatments (Figure 2.2C), some opponents of iron deficiency include food fortification, iron supple- maintain that this public health practice should not be forced ments, and diet diversification and improvement. Figure 2.28 on everyone. Proponents assert that this intervention benefits illustrates some iron-rich foods. In the United States, wh eat those who may be least able to afford proper dental care. As is flour h as been fortified with iron since the 1940s, and iron is often the case, citizens need to educate themselves about all commonly added to processed foods, such as cereal. sides of such controversies and critically evaluate the types But can an excess of trace elements also pose a problem? of scientific evidence on which decisions are based. Recent studies indicate that older Americans are less likely to suffer from iron deficiency than from iron overload, which f t A serving of cereal fortif ied to provide 100% of the can dam age organs and may increase the risk of certain dis- U recommended daily intake contains 18 mg of iron. The recommended tolerable upper intake level is 45 mg (before eases. An d because of the risk of accidental fatal poisoning in causing gastrointestinal upset). How many bowls of cereal children, warning labels are required on iron supplements. before you exceed that level? Trace elements have also been added to water to s:IU!AJaS S" i:. improve public h ealth. Fluoride is a form of fluorin e (F), which is found in small amounts in all water sources. For more than 70 years, t he American Dental Association has supported fluoridation of community drinking water. Indeed, t he Centers for Disease Control an d Prevention (CDC) 23 - listed water fluoridation as one of 10 great public health achievements of the 20th century. The history of water fluoridation illustrates both the process A Figure 2.28 Foods rich in iron Elements, Atoms, and Compounds 2.3 Atoms consist of protons, neutrons, and electrons Each element has its own type of atom, wh ich is different element have the same unique number of protons. This from the atoms of other elemen ts. An atom, named from a number is the element's atomic number. Thus, an atom of Greek word meaning "indivisible," is the smallest unit of mat- helium, with 2 protons, has an atomic number of 2. Unless ter that st ill retains the properties of an element. Atoms are otherwise indicated, an atom has an equal number of protons so small that it would take about a million of them to stretch and electrons, and thus its net electrical charge is 0 (zero). across the period printed at the end of this sentence. What other numbers are associated with an atom? An atom's mass number is the sum of the number of protons Subatomic Particles Physicists have sp lit the atom into and neutrons in its nucleus. For helium, the mass number is 4. more than a hundred types of subatomic particles. However, The mass of a proton and the mass of a neutron are almost only three kinds of particles are relevant here. A p roton is a identical and are expressed in a unit of measurement called the subatomic particle with a single positive electrical charge(+). dalton. Protons and neutrons each have masses close to 1 dal- An electron is a subatomic particle with a single negative ton. An electron has only about 1/2,000 the mass of a proton, charge(- ). A neutron, as its name implies, is electrically so it contributes very little to an atom's mass. Thus, an atom's neutral (has no charge). atomic mass (or weight) is approximately equal to its mass Figure 2.3 shows two very simple models of an atom of the number-the sum of its protons and neutrons-in daltons. element helium (He), the "lighter-than-air" gas that makes balloons rise. Notice that two protons ( + ) and two neutrons Isotopes All atoms of an element have the same atomic (Q) are tightly packed in the atom's central core, or nucleus. number, but some atoms of that element may differ in mass Two rapidly moving electrons ( Q ) form a sort of cloud of neg- number. The different isotopes of an element have the ative charge around the nucleus. The attraction between the same number of protons and behave identically in ch emi- negatively charged electrons and the positively charged pro- cal reactions, but they have different numbers of neutrons. tons holds the electrons near the nucleus. The left-hand model Table 2.3 sh ows the numbers of subatomic particles in the shows the two electrons on a circle around the nucleus. The t hree isotopes of carbon. Note that carbon's atomic number right-hand model, slightly more realistic, represents the elec- is 6-all of its atoms have 6 protons. Carbon -12 (named for trons as a spherical cloud of negative charge. Neither model its mass number), with 6 neutrons, accounts for about 99% is drawn to scale. In real atoms, the electrons are very much of naturally occurring carbon. Most of the remaining 1% smaller than the protons and neutrons, and the electron cloud consists of carbon-13 , with a mass number of 13 and thus is very much bigger compared with the nucleus. Imagine that 7 neutrons. A third isotope, carbon-14, with 8 neutrons, this atom was the size of a baseball stadium: The nucleus would occurs in minute quantities. Of course, all three isotopes be the size of a pea in center field, and the electrons would be have 6 protons- otherwise, t h ey would not be carbon. like two tiny gnats buzzing around inside the stadium. Both carbon-12 and carbon -13 are stable isotopes, mean- ing that t heir nuclei remain intact more or less forever. The Atomic Number and Mass Number So what makes the at- isotope carbon-14, on the other hand, is unstable, or radio- oms of different elements different? All atoms of a particular active. A radioactive isotope is one in which the nucleus decays spontaneously, giving off particles and en ergy. Radiation from decaying isotopes can damage cellular mol- ecules and t hus can pose serious risks to living organisms. Nucleus But radioactive isotopes can be helpful, as in their use in dat- ing fossils (see Module 15.5). They are also used in biological research and medicine, as we see next. Mass Mass Mass Electron/ cloud Protons Neutrons number 12 number 13 :l number 14 Electrons 6 6 6 2 Protons } Nucleus 2 Neutrons 2 9 Electrons ft A nitrogen atom has 7 protons, and its most common U isotope has 7 neutrons. A radioactive isotope of nitrogen has 9 neutrons. What is the atomic number and mass number.A. Figure 2.3 Two models of a helium atom. (Note that t hese models are not to scale; they greatly overestimate the size of the nucleus in of this radioactive nitrogen? relation to the electron cloud.) 9l = Jaqwnu ssew !L = 1aqwnu ::>!WOl';f 24 CHAPTER 2 The Chemical Basis of Life  2.4 Radioactive isotopes can help or harm us Livin g cells cannot readily distinguish between '1'ff'"Qj' [I]" of the same element. Con sequently,. 111 111111 1111 orgam sms take up and use compounds contam- ing radioactive isotopes in the usual way. Because radioactivity is easily detected and measured by instruments, radioactive isotopes are useful as tracers-biological spies, in effect-for monitoring the fate of atom s in living organism s. Basic Research Biologists often use radioactive tracers to follow m olecules as they undergo chemical changes in an organism. For example, research ers h ave u sed carbon dioxide (C02 ) containing the radioactive isotope carbon-14 to study photosynthesis. Using sunlight to power the conversion , plants take in C0 2 from the air and u se it to m ake sugar m ol- '°" Figure 2.48 PET images of brains of a healthy person (left) and a ecules. Radioactively labeled C0 2 has en abled research ers to person with Alzheimer's disease (right). Red and yellow colors indicate high levels of PIB bound to beta-amyloid plaques. trace the sequen ce of molecules m ade by plants in the ch emi- cal route from C02 to sugar. Medical Diagnosis and Treatment Radioactive isotopes on a PET scan. Figure 2.48 shows PET images of the brain s of may also be u sed to tag chemicals t h at accumulate in specific a h ealthy person (left) and a person with Alzh eimer's (right) areas of the body, su ch as phosphorus in bon es. After injec- injected with PIB. Notice that the brain of the Alzh eimer's tion of such a tracer, a special cam era produces an image p atien t h as high levels of PIB (red and yellow areas), whereas of wh ere the radiation collects. In m ost diagn ostic uses, t h e unaffected person's brain h as lower levels (blue). New the patient receives only a tiny am ount of an isotope. t h erapies are focu sed on limiting the production of beta- Som etimes radioactive isotopes are used for treatment. amyloid or clearing it from the brain. A diagn ostic test usin g As you learned in Module 2.2, the body uses iodine to m ake PIB would allow research ers to m onitor t he effectiven ess of a thyroid h ormone. Because radioactive iodine accumulates n ew drugs in people living wit h the disease. in the thyroid, it can be used to kill can cer cells there. Substan ces that the body m etabolizes, such as glucose Dangers Although radioactive isotopes have many bene- or oxygen , m ay also be labeled with a radioactive isotope. ficial uses, uncontrolled exposure to h igh levels of radiation Figure 2.4A sh ows a patient being examined by a PET can be lethal. The particles and en ergy thrown off by radio- (positron-emission tomography) scanner, which can produce act ive atom s can da mage molecules, esp ecially DNA. The images of areas of th e body with high metabolic activity. PET explosion of a nuclear reactor in Chernobyl, Ukraine, in 1986 is useful for diagn osing certain h eart disorders and cancers released large amounts of radioactive isotopes into the en- and for basic research on t h e brain. vironment, which drifted over large areas of Russia, Belarus, The early detection of Alzh eimer's d isease m ay be a n ew and Eu rope. A few dozen people died from acute radiation use for such techniques. Th is devastating illness gradually poisoning within a few weeks of t h e acciden t, and more than destroys a person 's m em ory and ability to think. As the 100,000 people were evacuated from t he area. Increased rates disease progresses, t he brain becomes riddled with dep osits o f thyroid cancer in children exposed to the radiation have (plaques) of a protein called beta-amyloid. Researchers have been reported. Likewise, scientists will carefully m onitor th e synthesized a radioactively labeled protein m olecule called long-term h ealth con sequences of t he 20ll post-tsunami PIB that binds to beta-amyloid plaques and can be detected Fukushima nuclear disaster in Japan, particularly for th e 150 em ergency workers at the plant. Natural sources of radiation can also pose a threat. Radon , a radioactive gas, is t h e second-leading cause of lung cancer in the United States. Radon can contaminate buildings in region s wh ere un derlying rocks naturally contain uran ium , a radioactive element. Hom eown ers can buy a radon detector or hire a company to test their h ome to en sure that radon levels are safe. If levels are fou nd to be un safe, tech nology exists to remove radon from homes. f t Why are radioactive isotopes useful as tracers in research 25 - U on the chemistry of life? ·.(poq a1..n u1 suoneoo1 Jo si solution is (pH stands for potential o f hyd rogen ). As shown c 0 in Figure 2.14, the scale ranges from 0 (m ost acidic) to 14 ():;::; 9 (m ost basic). Each pH unit represents a 10-fold chan ge in en- the co n centration of H+ in a solut ion. For example, lem on 10 juice at pH 2 h as 10 times m ore H+ t h an an equal amount ->-o c Milk of magnesia owow o f a cola at p H 3 an d 100 t imes m ore H+ than tomato juice Ul J: 11 ow wow at pH 4. Household ammonia ow Pure water and aqueous solution s that are n either acidic 12 OW W OW nor basic are said to be n eutral; t h ey h ave a pH of 7, and the Household bleach con centrations of H+ and OH- are equal. Th e pH inside m ost 13 Basic solution cells is close to 7. Oven cleaner Th e pH of human blood is very close to 7.4. A person can - 14 not survive for m ore than a few minutes if the blood pH drops.A. Figure 2.14 The pH scale, which reflects the relative concentrations to 7.0 or rises to 7.8. How can your body m aintain a relatively of H+ and OW constant pH in your cells an d blood? Biological fluids contain buffers, substances that minimize changes in pH. They do ft Compared to a basic solution at pH 9 , the same volume so by accepting H+ when it is in excess and donating H+ wh en U of an acidic solution at pH 4 has times more H+. it is depleted. ooo'ooi: 2.15 Scientists study the effects of rising atmospheric C02 on coral reef ecosystems Carbon dioxide is the m ain product of fossil t his century. As an examp le of t h e importance of the t h eme IWMfMWI fuel and its stea_dil_y increasing of iilii#@[,]M, scientists are studying t he effects of such - 1 11 - release m to the atmosphere 1s lm ked Will rising ch anges on m arine organism s and ecosystem s. to climate change (see Modules 7.14 and 38.4). Several studies investigating the impact of a About 25% of this C02 is absorbed by t he ocean s- atmospheric C02 lower pH on coral reef ecosystems h ave looked and this n aturally occurring rem edy to excess C02 harm coral reefs? at t he process called calcification , in which coral would seem to be a good t h ing. However, as C02 levels on animals com bine calcium and carbonate ions to form their the plan et continue to rise, the in creasing absorption of C02 calcium carbon ate skeleton s. As seawater acidifies, t h e extra is threatening to h arm m arine life and ecosystem s. hydrogen ion s (H1 combine with carbonate ions (C03 21 to In ocean acidification, C02 dissolving in seawater form bicarbonate ion s (HC0 3l. Th is reaction reduces the lowers the pH of the ocean. Recent studies estimate that the carbon ate ion con centration available to corals and oth er p H of the oceans is 0.1 pH unit lower n ow than at any time sh ell-buildin g animals. Scientists predict that ocean acidifi- in the past 420 ,000 years and m ay rapidly drop an oth er cation will cau se the carbonate ion concentration to decrease 0.3- 0. 5 p H unit from t he current level of 8.1 by the en d of by 40% by t he year 2100. 32 CHAPTER 2 The Chemical Basis of Life  220 240 260 280 "" Figure 2.158 A "champagne' reef with bubbles of C02 rising from [Co}-l (µmol/kg of seawater) a volcanic seep Sourc e: Adaptation of figure 5 from "Effect of Calcium Carbonate Saturation S tate on the Calcification Rate of an Experimental Coral Reef" by C. Langdon, et al., from Global Biogeochemical Cycles , June 2000, Volume 14(2). American Geophysical Union. A 2011 study looked at three volcanic seeps in Papua New "" Figure 2.15A The effect of carbonate ion concentration Guinea. As you can see in Figure 2.158, bubbles of C02 are on calcification rate in an artificial coral reef system released from underwater volcanoes around such "champagne reefs," lowering the pH of the water. Researchers surveyed three study sites in which the pH naturally varied from 8.1 to 7.8. Scientists have looked at the effect of decreasing carbon- They found reductions in coral diversity and t he attachment ate ion concentration on t he rate of calcium deposition of juvenile coral as th e pH of the sites declined, both of which by reef organisms. The Biosphere 2 aquarium in Arizona undermine the resiliency of a reef community. Researchers also con tains a large coral reef system t hat behaves like a nat- found a shift to less structurally complex and slower-growing ural reef. Researchers measured how the calcification rate corals. The structural complexity of coral reef ecosystems ch anged with differing amounts of dissolved carbonate ions. makes them havens for a great diversity of organisms. Figure 2.15A presents the results of one set of experiments, Scientists often synthesize their conclusions using multi- in which pH, temperat ure, and calcium ion concentration p le lines of evidence. The results from both controlled exper- were held constant while the carbonate ion concen tration imental studies and observational field studies of sites where of th e seawater was varied. As you can see from t h e graph, pH naturally varies have dire implications for the health of the lower t h e concentration of carbonate ions, t he lower coral reefs and the diversity of organisms they support. the rate of calcification, an d thus, the slower the growth of coral animals. Controlled experiments such as this one have provided ft Identify the independent and dependent variables in the evidence that ocean acidification and the resulting reduction U experiment depicted in Figure 2.15A. in carbonate ion concentration will negatively affect coral ·1uaw1eaJ1 1e1uaw1Jadxa a41 01 puodsaJ Jo.uo puadap, 01 pap1paJd seM pue luaw1iadxa aLn LI! pamseaw seM le4M s1-s1xe ,{ aln uo uM04s 'a1eJ uone:>111:>1e:> reefs. But scientists have also looked to natural habitats to aLn-a1qe!JeA lUapuadap a1u ·pa1e1nd!uew sJa4:>masaJ aLn 4014M 'suo1 a1e study how ocean acidification affects coral reef ecosystems. ·uoqrn:> !D uo11eJ1ua:>uo:> aLn S! s1xe x a41 uo uM04s a1qe1JeA lUapuadapu1 aLu 2.16 The search for extraterrestrial life centers on the search for water When astrobiologists search for signs of life on Evidence of water has also come from the Mars MHffl:Mj'(,)!I distant planets, they_ look_ for evidence of water. Reconnaissance Orbiter. In 2011, high-resolution images sent 111 - Why? As we've seen m this chapter, the emer- to Earth revealed distin ctive streaks along steep slopes during gent properties of water support life on Earth in many ways. the Mars sprin g and summer, which then vanish during the Is it possible t hat some form of life has evolved on other winter, indicating that seasonal streams form when subsur- planets that have water in the environment? Scientists with face ice melts during the warm season. Then, in 2015, NASA the National Aeronautics and Space Administration (NASA) announced that refined chemical readings taken from the are exploring this question. orbiter identified waterlogged molecules in those streaks, Like Earth , Mars has an ice cap at both poles, and scientists providing evidence for liquid water on Mars' surface. These have found signs that water may exist elsewhere on the plan et. exciting finds have reinvigorated the search for signs of life, In 2008, the robotic spacecraft Phoenix landed on Mars and past or present, on Mars and other planets. If any life-forms or sent back images showin g ice present just under Mars's sur- fossils are found, their study will shed light on the process of face. The Curiosity rover, which landed on Mars in 2012, has evolution from an entirely n ew perspective. measured a high percentage of water in its soil samples. And in 2013, the Opportunity rover, which has far outlasted its ft Why is the presence of water important in the search 3- three-month mission begun in 2004, spotted types of clay U for extraterrestrial life? in an ancient rock that suggest that n eutral-pH water once ·ai!I JO 1ua 1os a41 se llu1uo1pun1 011aue1d a41 uo sam1eJadwa1 flowed in t he area. llu11eJapow WOJJ 'I! aM se arn U! sa10J 1uepodw1 sile1d Ja1eM Water's Life-Supporting Properties  2 a: UJ I- For practice quizzes, BioFlix animations, MP3 tutorials, video tutors, and REVIEW C.. S!P 01 s1snua!:>S JO.(1!1!qe a1..n aseaJ:>U! Aew ways, but not without consequen ces. Technology h as helped sa1lio1ou4oa1 Mau :sa1lio1ou4oa1 Mau 01 pear.\ew sa11aAoos1p 01muaps MaN The Process of Scie nce Five Unifying Themes in Biology Biology is a subject of enormous scope. Within this ever-growing body of knowledge, however, we can identify some unifying themes. In the next few modules, we'll describe the themes of evolution, information, structure and function, energy and matter, and interactions. We'll also help you recognize them as they recur throughout your study of biology. 1.9 Theme: Evolution is the core theme of biology Life is distinguished by both its unity and its diversity. Darwin's second point was to propose a m echanism Multiple lines of evidence point to life's unity, from the simi- for evolution, which he called natural selection. larities seen am ong and between fossil and living organisms, Darwin started with two observations, from which he drew to common m etabolic processes, to the universal molecule of two inferen ces. inheritance, DNA. The amazing diversity of life is on display OBSERVATION # 1: Individual variation. Individuals in a all around you and is documented in zoos, n ature shows, population vary in their traits, many of which seem to be and natural history museums. The scientific explanation h eritable (passed on from parents to offspring). for this unity and diversity is evolution, the process of change that has transformed life on Earth from its earliest OBSERVATION #2: Overproduction ofoffspring. All species forms to the vast array of organisms living today. can produce far more offspring than the environm ent can support. Competition for resources is thus inevitable, and Darwin's Theory of Evolution The history of life, as many of t hese offspring fail to survive and reproduce. documented by fossils and other evidence, is the saga of INFERENCE # 1: Unequal reproductive success. Individuals a changing Earth b illions of years old, inhabited by an with inherited traits best suited to the local environment evolving cast o f living forms. This evolutionary view of are more likely to survive and reproduce than are less well- life cam e into sharp focus in November 1859, wh en suited individuals. Charles Darwin published one of the most influential INFERENCE #2: Accumulation of favorable traits over books ever written , entitled On the Origin of Species by time. As a result of this unequal reproductive success Means ofNatural Selection. over m an y gen eration s, a h igh er and h igh er proportion How does Darwin's work illustrate the process of science o f ind ividuals in the population will h ave the advanta- you just learned about? As a young man, Darwin made key geou s traits. observations that greatly influenced his thinking. During a five-year, around-th e-world voyage, he collected and documented plants, animals, and fossils in widely vary- ing locations-from the isolated Galapagos Islands to the h eights of the Andes m ountains to the rain forests of Brazil. He was particularly struck by the adapta- tio ns of these varied organism s that made them well suited to their diverse h abitats. After returning to England, Darwin sp ent m ore than two decades con - tinuin g his observations, performing experiments, corresponding with other scientists, and refining his thinking before h e finally published his work. The first of two main p oints that Darwin presented in The Origin ofSpecies was that species living today arose from a su ccession o f ancestors that were differ- ent from them. Darwin called this process "descent with modification." This insightful phrase captures both the unity of life (descent from a common an- cestor) and the diversity of life (modification s that evolved as species diverged from their ancestors). Figure 1.9A illustrates this unity and diversity am ong American flamingo birds. The flamingo, penguin, and hummingbird all.A. Figure 1.9A Unity and diversity among birds h ave a common "bird" body plan of wings, beak, feet, and feathers, but these structures are highly specialized for each TRY THIS For each bird, describe some adaptations that fit it to its environment and way of life. bird's unique lifestyle. 10 CHAPTER 1 Biology: Exploring Life 0 Population with varied inherrted traits. f) Elimination of individuals with certain E) Increasing frequency of traits traits and reproduction of survivors. that enhance survival and reproductive success..t. Figure 1.98 An example of natural selection in action TRY THIS Predict what might happen if some of these beetles colonized a sand dune habitat. Figure 1.98 uses a simple example to show h ow natural and racoons are placed in three separate families. Red pan- selection works. 0 An imaginary beetle population has das are now classified as t he sole living species of the family colonized an area wh ere the soil has been blackened by a Ailuridae. recent brush fire. Initially, the population varies extensively The theory of evolution by natural selection is supported in the inherited coloration of individuals, from very light by multiple lines of evidence- t h e fossil record, experiments, gray to charcoal. f) A bird eats the beetles it sees most easily, observations of natural selection in action, and ever- the light-colored ones. This selective predation reduces the in creasing numbers of DNA comparisons. Evolution is the number of ligh t-colored beetles and favors the survival and central theme that makes sen se of everything we know and reproductive success of the darker beetles, which pass on t he learn about biology. Th roughout this text, we'll see many e genes for dark coloration to their offspring. After several more examples of both the process and products of evolu- gen erations, the population is quite different from th e origi- tion. To emphasize evolution as the cent ral t h em e of biolo- nal on e. As a result of n atural selection, the frequency of t h e gy, we include an Evolution Conn ection m odule, called out darker-colored beetles in the population h as increased. with a green icon , in each chapter. Darwin realized that numerous small ch anges in popula- f t Explain the cause and effect of unequal reproductive tions as a result of natural selection could eventually lead to U success. major alterations of species. He proposed that n ew species ·uo1te1ndod a1.n LI! saseaJ:>U! Sl!eJl aAndepe asa1.n !O uO!lJOdoJd could evolve as a result of the gradual accumulation of ch ang- aln..e a1e 1e1n:>n1ed ua4M pue o:ua4M-UO!Ssa1dxa of nucleotides in the RNA is translated into a ch ain of aual! s1oaue 1uawuoJ!AUa 1euJa1xa pue 1euJa1u1 a41 woJj uo11ewJ01u1 protein building blocks. Once completed, t he chain forms a specific protein with a unique shape and function. This process is called gen e expr essi on. All forms of life use essentially the same chemical language to translate the information stored in DNA into proteins. Called t he genetic code, this universal language is a strong Q Signal: piece of evidence that all living organisms are related. The high blood universal genetic code also makes it possible to engineer glucose level cells to produce proteins normally found on ly in some other organism. Thus, bacteria can be used to produce insulin for f) Pancreatic the treatment of diabetes by inserting a gene for human insu- Glucose cell releases insulin 0 Normal blood glucose level lin into bacterial cells. removes signal, insulin Signaling Information Wh at Figure l.llB does not show release stops is th at the flow of genetic in formation from DNA to RNA to protein is usually linked with information from the external Q Insulin binding and internal environment. For example, the information your stimulates body receives includes external stimuli such as light, sound, or body cells to chemicals, and internal stimuli such as food in your stomach take up glucose or an excess of sugar in your blood. The stimulus is usually re- Normal blood ceived by some type of receptor and its information is relayed g lucose level within your body in the form of nervous signals, hormones, or other types of signals. This flow of information u ltimately.A. Figure 1.11C The flow of information in t he regulation of the level 13 - of glucose in the blood reaches individual cells and influences t h eir behavior, often by chan ging the activity of existing proteins or by regulating TRY THIS Describe the action of insulin as a signaling molecule in this regulatory pathway. gen e expression and the production of specific proteins. Five Unifying Themes in Biology 1.12 Theme: Structure and function are related A third theme that pervades all of biology is the correlation of structure and function. When considering useful objects around your home, you may note that form generally fits function. A screwdriver tightens or loosens screws, a h ammer pounds nails. Because of their form, these tools can't do each other's jobs. You use a spoon to eat soup, but if you are spear- ing a piece of meat, you use a fork. Similarly, in biological sys- tems, structure (the shape of something) and function (what it does) are almost always related, with each providing insight into t he other. The relationship between structure and function can be observed at every level of life. At the molecular level, the structure of a protein correlates with its function , wheth er it is part of the strong ligaments holding your bones together or the hemoglobin m olecules transporting oxygen in your blood. On the cellular level, the long extensions of n erve cells enable them to transmit impulses from your spinal cord to your toes. The long, thin cells of fungi enable them to extend through their food source and absorb nutrients. Th e thick walls surrounding plant cells provide structural support to.A. Figure 1.128 A red panda grasping bamboo; a CT scan showing the "false thumb" of a red panda (inset) the plant leaf p ictured in Figure 1.12A, just as the tough exoskeleton of the beetle supports its body. Let's consider the red panda's hand as an other example. it grasp bamboo. By studyin g the fossil record, scientists In Figure 1.128, you can see a red panda holding som e bam- propose that this projection originally evolved in the red boo. Scientists using an X-ray technique known as computed panda's carnivorous ancestor as an adaptation that enabled tomography (CT) produced a scan of the hand and wrist it to move along bran ches in trees. Secon darily, this pro- of a red panda (upper left part of the figure) to highlight jection enabled the plant-eating red pan da to h old on to t he small bone protruding from the wrist, called the radial bamboo. In the evolutionary history of life, we will encoun- sesamoid. In red pandas, this bone is much larger than in ter many examples of the rem od elin g of existing structures related animals and is often referred to as a "false thumb." to new functions. What might be its function? Just as your t humbs are useful Interestingly, the giant pan da also has a "false thumb," yet in grasping objects, the red panda's wrist projection h elps much larger. As discussed in Module 1.6, this shared "panda thumb" and bamboo diet on ce led biologists to classify t h e red panda and the giant panda as close relatives. However, evidence from fossils and comparisons of DNA indicate t hat these similar structural adaptations evolved separately in the two distinct lineages. The close m atch of form and function in the structures of life can be explained by natural selection. The organisms whose structures best performed their functions would h ave been most likely to h ave reproductive success, thereby passing those adaptations o n to their offspring. Given t h at existing structures are often rem odeled for new functions, h owever, we don 't expect evolutionary adapt ations to be perfect (see t he introduction to Ch apter 20). Through out the text we will see how the them e of struc- ture and function applies to life at all levels of organization, from m olecules and cells, to the internal organization of plants and animals, to whole ecosystems. To help you recog- nize this theme, specific examples will be highlighted with this icon: STRUCTURE AND FUNCTION ft Look at the structure of your hand and explain how its.A. Figure 1.12A Structural adaptations in the form of plant cell walls U structure supports its function. and insect exoskeletons that function in physical support ·sioafqo a1e1nd1uew 01 noA Mone Sl!li!P a1qesoddo pue s1u1of Jallu11 14 CHAPTER 1 Biology: Exploring Life 1.13 Theme: Life depends on the transfer and transformation of energy and matter The activities of life- movement, growth, reproduction, As illustrated in Figure 1.13, the dynamics of ecosystems regulation, and most cellular processes- require energy. The can be summarized wit h two major processes- the flow of input of energy, primarily from the sun, and the conver- energy and the cycling of matter. An ecosystem gains and sion of energy from one form to another make life possible. loses en ergy constantly. Energy flows into most ecosystems Figure 1.13 is a simplified diagram of the transfer and trans- as sunlight (yellow arrow), and photosynthetic organisms formation s of energy and matter taking place in a forest in convert it into the ch emical energy in sugars and other Canada. Plants are the producers that provide the food for energy-rich molecules. Ch em ical energy in food (orange a typical terrestrial ecosystem. A tree, for example, absorbs arrow) is then passed through a series of consumers and, water (H2 0) and min erals through its roots, and its leaves take eventually, to decomposers, powering each organism in turn. in carbon dioxide (C0 2) from the air. In the process of p hoto- In the process of these energy conversions between and with- synthesis, energy from sunlight is stored as chemical energy in organisms, some energy is always converted to h eat, which as th e atoms in C02 and H2 0 are rearranged into sugar mole- is then lost from the ecosystem (red arrow). Th us, energy cules that are rich in ch emical energy. flows through an ecosystem in one direction, entering as light The consumers in an ecosystem eat plants and other ani- and exiting as heat. By contrast , matter cycles within an eco- mals. The moose in Figure 1.13 eats the grasses and tender system, from the air and soil to producers, to consumers and shoots and leaves of trees in the forest ecosystem. To release decomposers, and back to the air and soil (shown by the blue the ch emical energy in food, animals (as well as plants and arrows in the figure). most other organisms) use the process of cellular respiration, This "chemical square d ance" in which molecules swap taking in 0 2 from the air and releasing C02. Consumers use chemical partners as they receive, convert, and release energy both the energy and the atoms (matter) obtained from food is never-ending in all forms of life. Throughout your study to build new molecules. For example, proteins in the moose's of biology, you will see many examples of t his theme, from fur were assembled from atoms that were once in its food. An microscopic cellular processes to ecosystem-wide cycles animal's wastes return matter to the en vironment. of carbon and oth er nutrients. To h elp you recognize this Vital parts of this ecosystem are the small animals, fungi, t heme, some examples will be highligh ted with this icon : and bacteria in the soil t hat decompose wastes and the ENERGY AND MATTER remains of dead organisms. These decomposers act as recy- clers, changing complex matter in to simpler ch emicals that return to the environment and are once again available to 0 Describe how photosynthesis transforms energy and m atter. 1e=>1wa4:> paJois Lll!M sa1n=ia1ow producers. Jel!ns OIU! pa1JaAUOO aJe (Janew) o'H pue