Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 2 The Chemical Context of Life

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 2 Chemistry of Life Overview: Chemical Foundations of Biology – Elemental properties – Chemical bonds – Chemical reactions

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The bombardier beetle uses chemistry to defend itself Figure 2.1

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings SodiumChloride Sodium Chloride + A compound – Is a substance consisting of two or more elements combined in a fixed ratio – Has characteristics different from those of its elements Figure 2.2

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Essential Elements of Life Essential elements – Include carbon, hydrogen, oxygen, and nitrogen – Make up 96% of living matter

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A few other elements – Make up the remaining 4% of living matter Table 2.1

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (a) Nitrogen deficiency(b) Iodine deficiency The effects of essential element deficiencies Figure 2.3

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings An element’s properties depend on the structure of its atoms

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Each element – Consists of a certain kind of atom that is different from those of other elements An atom – Is the smallest unit of matter that still retains the properties of an element

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Subatomic Particles Atoms of each element – Are composed of even smaller parts called subatomic particles

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Relevant subatomic particles include – Neutrons, which have no electrical charge – Protons, which are positively charged – Electrons, which are negatively charged

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Protons and neutrons – Are found in the atomic nucleus Electrons – Surround the nucleus in a “cloud”

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Nucleus (a) (b) In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus. Cloud of negative charge (2 electrons) Electrons This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron‘s position at one point in time. Simplified models of an atom Figure 2.4

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Atomic Number and Atomic Mass Atoms of the various elements – Differ in their number of subatomic particles

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The atomic number of an element – Is the number of protons – Is unique to each element

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The mass number of an element – Is the sum of protons plus neutrons in the nucleus of an atom – Is an approximation of the atomic mass of an atom

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Energy Levels of Electrons An atom’s electrons – Vary in the amount of energy they possess

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Energy – Is defined as the capacity to cause change Potential energy – Is the energy that matter possesses because of its location or structure

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron Configuration and Chemical Properties The chemical behavior of an atom – Is defined by its electron configuration and distribution

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The periodic table of the elements – Shows the electron distribution for all the elements Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Figure 2.8

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron Orbitals An orbital – Is the three-dimensional space where an electron is found 90% of the time

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Covalent Bonds A covalent bond – Is the sharing of a pair of valence electrons

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.10 Formation of a covalent bond Hydrogen atoms (2 H) Hydrogen molecule (H 2 ) In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus. 1 When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus. 2 The two electrons become shared in a covalent bond, forming an H 2 molecule. 3

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (a) (b) Name (molecular formula) Electron- shell diagram Structural formula Space- filling model Hydrogen (H 2 ). Two hydrogen atoms can form a single bond. Oxygen (O 2 ). Two oxygen atoms share two pairs of electrons to form a double bond. HH O O Figure 2.11 A, B Single and double covalent bonds

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Name (molecular formula) Electron- shell diagram Structural formula Space- filling model (c) Methane (CH 4 ). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. Water (H 2 O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. (d) H O H HH H H C Figure 2.11 C, D Covalent bonding in compounds

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In a nonpolar covalent bond – The atoms have similar electronegativities – Share the electron equally

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.12 This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2OH2O –– O H H ++ ++ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. In a polar covalent bond – The atoms have differing electronegativities – Share the electrons unequally

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ionic Bonds In some cases, atoms strip electrons away from their bonding partners

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron transfer between two atoms creates ions Ions – Are atoms with more or fewer electrons than usual – Are charged atoms

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cl – Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium on (a cation) Sodium chloride (NaCl) Figure 2.13 An ionic bond – Is an attraction between anions and cations

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Na + Cl – Figure 2.14 Ionic compounds – Are often called salts, which may form crystals

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrogen Bonds  – –  + +  + + Water (H 2 O) Ammonia (NH 3 ) O H H  + +  – – N H H H A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. ++ ++ Figure 2.15 A hydrogen bond – Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Van der Waals Interactions Van der Waals interactions – Occur when transiently positive and negative regions of molecules attract each other

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Shape and Function The precise shape of a molecule – Is usually very important to its function in the living cell – Is determined by the positions of its atoms’ valence orbitals

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular shape – Determines how biological molecules recognize and respond to one another with specificity

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Natural endorphin Endorphin receptors Morphine Brain cell Figure 2.17

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 2.4: Chemical reactions make and break chemical bonds A Chemical reaction Is the making and breaking of chemical bonds Leads to changes in the composition of matter

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ReactantsReactionProduct 2 H 2 O2O2 2 H 2 O + + Chemical reactions – Convert reactants to products

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Photosynthesis – Is an example of a chemical reaction Figure 2.18

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemical equilibrium – Is reached when the forward and reverse reaction rates are equal