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 <para id="fs-idm56538768">Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of <term id="term-00012">chemical bonds</term>, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the <term id="term-00013">octet rule</term>. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.</para>
 <para id="fs-idm7280128">When an atom does not contain equal numbers of protons and electrons, it is called an <term id="term-00014">ion</term>. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called <term id="term-00015">cations</term>. Negative ions are formed by gaining electrons and are called <term id="term-00016">anions</term>.</para><para id="fs-idp27440032">For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.</para>
 <para id="fs-idp49551552">The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as <term id="term-00017">electron transfer</term>. As <link target-id="fig-ch02_01_04"/> illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.</para>
-<figure id="fig-ch02_01_04"><media id="fs-idp62713856" alt=" Diagram shows electron transfer between elements.">
+<figure id="fig-ch02_01_04"><media id="fs-idp62713856" alt="Diagram shows electron transfer between elements.">
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 <caption>Elements tend to fill their outermost shells with electrons. To do this, they can either donate or accept electrons from other elements.</caption></figure><section id="fs-idp24704704">

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 <title>Moving Against a Gradient</title>
 <para id="fs-idp69579376">To move substances against a concentration or an electrochemical gradient, the cell must use energy. This energy is harvested from ATP that is generated through cellular metabolism. Active transport mechanisms, collectively called pumps or carrier proteins, work against electrochemical gradients. With the exception of ions, small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive changes. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. Because active transport mechanisms depend on cellular metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.</para>
 <para id="fs-idm20132368">Two mechanisms exist for the transport of small-molecular weight material and macromolecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane. The primary active transport system uses ATP to move a substance, such as an ion, into the cell, and often at the same time, a second substance is moved out of the cell. The sodium-potassium pump, an important pump in animal cells, expends energy to move potassium ions into the cell and a different number of sodium ions out of the cell (<link target-id="fig-ch03_06_02"/>). The action of this pump results in a concentration and charge difference across the membrane.</para>
-<figure id="fig-ch03_06_02" class="  "><media id="fs-idp140005312" alt=" This illustration shows the sodium-potassium pump. Initially, the pump’s opening faces the cytoplasm, where three sodium ions bind to it. The pump hydrolyzes ATP to ADP and, as a result, undergoes a conformational change. The sodium ions are released into the extracellular space. Two potassium ions from the extracellular space now bind the pump, which changes conformation again, releasing the potassium ions into the cytoplasm.">
+<figure id="fig-ch03_06_02" class="  "><media id="fs-idp140005312" alt="This illustration shows the sodium-potassium pump. Initially, the pump’s opening faces the cytoplasm, where three sodium ions bind to it. The pump hydrolyzes ATP to ADP and, as a result, undergoes a conformational change. The sodium ions are released into the extracellular space. Two potassium ions from the extracellular space now bind the pump, which changes conformation again, releasing the potassium ions into the cytoplasm.">
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 <title>DNA Repair</title>
 <para id="fs-idm115318592">DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then polymerization continues (<link target-id="fig-ch09_02_06abc"/><emphasis effect="bold">a</emphasis>). Most mistakes are corrected during replication, although when this does not happen, the <term id="term-00012">mismatch repair</term> mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base (<link target-id="fig-ch09_02_06abc"/><emphasis effect="bold">b</emphasis>). In yet another type of repair, <term id="term-00013">nucleotide excision repair</term>, the DNA double strand is unwound and separated, the incorrect bases are removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase (<link target-id="fig-ch09_02_06abc"/><emphasis effect="bold">c</emphasis>). Nucleotide excision repair is particularly important in correcting thymine dimers, which are primarily caused by ultraviolet light. In a thymine dimer, two thymine nucleotides adjacent to each other on one strand are covalently bonded to each other rather than their complementary bases. If the dimer is not removed and repaired it will lead to a mutation. Individuals with flaws in their nucleotide excision repair genes show extreme sensitivity to sunlight and develop skin cancers early in life.</para>
 <figure id="fig-ch09_02_06abc">
-<media id="fs-idm72624736" alt=" Part a shows DNA polymerase replicating a strand of DNA. The enzyme has accidentally inserted G opposite A, resulting in a bulge. The enzyme backs up to fix the error. In part b, the top illustration shows a replicated DNA strand with a G–T base mismatch. The bottom illustration shows the repaired DNA, which has the correct G–C base pairing. Part c shows  a DNA strand in which a thymine dimer has formed. An excision repair enzyme cuts out the section of DNA that contains the dimer so that it can be replaced with a normal base pair.">
+<media id="fs-idm72624736" alt="Part a shows DNA polymerase replicating a strand of DNA. The enzyme has accidentally inserted G opposite A, resulting in a bulge. The enzyme backs up to fix the error. In part b, the top illustration shows a replicated DNA strand with a G–T base mismatch. The bottom illustration shows the repaired DNA, which has the correct G–C base pairing. Part c shows  a DNA strand in which a thymine dimer has formed. An excision repair enzyme cuts out the section of DNA that contains the dimer so that it can be replaced with a normal base pair.">
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 <caption>Proofreading by DNA polymerase (a) corrects errors during replication. In mismatch repair (b), the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base. Nucleotide excision (c) repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced.</caption>

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 <title> Mapping Genomes</title>
 <para id="fs-idp60211744">Genome mapping is the process of finding the location of genes on each chromosome.  The maps that are created are comparable to the maps that we use to navigate streets. A <term id="term-00002">genetic map</term> is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that shows genetic linkage with a trait of interest. The genetic marker tends to be inherited with the gene of interest, and one measure of distance between them is the recombination frequency during meiosis. Early geneticists called this linkage analysis.</para>
 <para id="fs-idp192808912"><term id="term-00003">Physical maps</term> get into the intimate details of smaller regions of the chromosomes (similar to a detailed road map) (<link target-id="fig-ch10_03_01"/>). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses such as cancer, heart disease, and cystic fibrosis, to name a few. In addition, genome mapping can be used to help identify organisms with beneficial traits, such as microbes with the ability to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to methods that produce higher crop yields or to the development of plants that adapt better to climate change.</para>
-<figure id="fig-ch10_03_01"><media id="fs-idp65674256" alt=" A diagram showing a human chromosome with bands revealed with a Giemsa stain. The bands are labeled with Xp and a number on the short arm and Xq and a number on the long arm. Certain genes are found within some of the bands. These genes are labeled on the right: Fanconi anemia B, Wiskott-Aldrich syndrome, Pelizaeus-Merzbacher disease, Fragile X syndrome, and G6PD deficiency[0].">
+<figure id="fig-ch10_03_01"><media id="fs-idp65674256" alt="A diagram showing a human chromosome with bands revealed with a Giemsa stain. The bands are labeled with Xp and a number on the short arm and Xq and a number on the long arm. Certain genes are found within some of the bands. These genes are labeled on the right: Fanconi anemia B, Wiskott-Aldrich syndrome, Pelizaeus-Merzbacher disease, Fragile X syndrome, and G6PD deficiency[0].">
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 <caption>(a) The chimpanzee jaw protrudes to a much greater degree than (b) the human jaw. (credit a: modification of work by "Pastorius"/Wikimedia Commons)</caption></figure><para id="fs-idm241231920">However, unrelated organisms may be distantly related yet appear very much alike, usually because common adaptations to similar environmental conditions evolved in both. An example is the streamlined body shapes, the shapes of fins and appendages, and the shape of the tails in fishes and whales, which are mammals. These structures bear superficial similarity because they are adaptations to moving and maneuvering in the same environment—water. When a characteristic that is similar occurs by adaptive convergence (convergent evolution), and not because of a close evolutionary relationship, it is called an <term id="term-00001">analogous structure</term>. In another example, insects use wings to fly like bats and birds. We call them both wings because they perform the same function and have a superficially similar form, but the embryonic origin of the two wings is completely different. The difference in the development, or embryogenesis, of the wings in each case is a signal that insects and bats or birds do not share a common ancestor that had a wing. The wing structures, shown in <link target-id="fig-ch12_02_03"/> evolved independently in the two lineages.</para>
 <para id="fs-idm96516000">Similar traits can be either homologous or analogous. Homologous traits share an evolutionary path that led to the development of that trait, and analogous traits do not. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.</para>
-<figure id="fig-ch12_02_03" class=" "><media id="fs-idm263472928" alt=" Part A shows a bat wing, part B shows a bat wing, and part C shows a bee wing. All are similar in overall shape. However, the bird wing and bat wing are both made from homologous bones that are similar in appearance. The bee wing is made of a thin, membranous material rather than bone.">
+<figure id="fig-ch12_02_03" class=" "><media id="fs-idm263472928" alt="Part A shows a bat wing, part B shows a bat wing, and part C shows a bee wing. All are similar in overall shape. However, the bird wing and bat wing are both made from homologous bones that are similar in appearance. The bee wing is made of a thin, membranous material rather than bone.">
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 <caption>The wing of a honey bee is similar in shape to a bird wing and a bat wing and serves the same function (flight). The bird and bat wings are homologous structures. However, the honey bee wing has a different structure (it is made of a chitinous exoskeleton, not a boney endoskeleton) and embryonic origin. The bee and bird or bat wing types illustrate an analogy—similar structures that do not share an evolutionary history. (credit a photo: modification of work by U.S. BLM; credit b: modification of work by Steve Hillebrand, USFWS; credit c: modification of work by Jon Sullivan)</caption></figure><note id="fs-idm178594016" class="interactive non-majors">