1. The Chemical Context of Life Chapter 2 p. 32-46

2.  Organisms are composed of matter—takes up space, has mass  Matter is made up of elements, substances that cannot be broken down into other substances by chemical reactions ◦ An atom is the smallest unit of matter that still retains the properties of an element  A compound ◦ Consists of two or more elements combined in a fixed ratio ◦ Has characteristics different from those of its elements (Emergent Properties) SodiumChloride Sodium Chloride +

3.  Essential Elements ◦ Carbon, Hydrogen, Oxygen, and Nitrogen ◦ Make up 96% of living matter ◦ A few other elements make up the remaining 4% of living matter (i.e. Ca, P, K – see Table 2.1)  Trace Elements ◦ Are required by an organism in only minute quantities (a) Nitrogen deficiency(b) Iodine deficiency

4. AAtoms of each element ◦A◦Are composed of even smaller parts called subatomic particles PProtons (+ charge) and Neutrons (no charge) ◦A◦Are found in the atomic nucleus EElectrons (- charge) ◦S◦Surround the nucleus in a “cloud” Nucleus Electrons

5.  Atoms of the various elements differ in their number of subatomic particles  The Atomic Number of an element ◦ Is unique to each element ◦ Is the number of protons  The Mass Number of an element ◦ Is an approximation of the atomic mass of an atom ◦ Is the sum of protons plus neutrons in the nucleus of an atom

6. Isotopes of a given element ◦D◦Differ in the number of neutrons in the nucleus ◦H◦Have the same number of protons RRadioactive isotopes ◦S◦Spontaneously give off particles and energy ◦C◦Can be used in biology AAs tracers AAnd to date fossils Cancerous throat tissue

7. Energy ◦I◦Is defined as the capacity to cause change (i.e., to do work) PPotential energy ◦I◦Is the energy that matter possesses because of its location or structure TThe electrons of an atom ◦D◦Differ in the amounts of potential energy they possess FFurther from nucleus = higher in potential energy A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between steps. (a)

8.  Energy levels ◦ Are represented by electron shells Third energy level (shell) Second energy level (shell) First energy level (shell) Energy absorbed Energy lost An electron can move from one level to another only if the energy it gains or loses is exactly equal to the difference in energy between the two levels. Arrows indicate some of the step-wise changes in potential energy that are possible. (b) Atomic nucleus

9. TThe chemical behavior of an atom is determined by the electrons in the outermost electron shell ◦T◦These are referred to as valence electrons ◦E◦Elements w/same # valence electrons have similar properties ii.e. electronegativity 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

10.  A covalent bond ◦ Is the sharing of a pair of valence electrons  A molecule ◦ Two or more atoms held together by covalent bonds  A single bond ◦ Is the sharing of one pair of valence electrons  A double bond ◦ Is the sharing of two pairs of valence electrons

11.  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

12. (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  Single and double covalent bonds

13. 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  Covalent bonding in compounds

14. ◦I◦Is the attraction of a particular kind of atom for the electrons in a covalent bond ◦T◦The more electronegative an atom, the more strongly it pulls shared electrons toward itself IIn a nonpolar covalent bond ◦A◦Atoms have similar electronegativities ◦R◦RESULT: They share electrons equally & the molecule is NONPOLAR IIn a polar covalent bond ◦A◦Atoms have different electronegativities ◦R◦RESULT: Electrons are shared unequally & the molecule is POLAR

15. 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.  Water is a Polar molecule

16.  In some cases, atoms strip electrons away from their bonding partners  Electron transfer between two atoms creates ions  Ions ◦ Are charged atoms ◦ Atoms with a different number of electrons than protons  An anion ◦ Is a negatively charged ion  A cation ◦ Is a positively charged ion

17. 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) AAn ionic bond ◦I◦Is an attraction between anions and cations (weaker than covalent bonds) Ionic compounds Are often called salts, which may form crystals Na + Cl –

18.  Several types of weak chemical bonds are important in living systems  Weak chemical bonds ◦ Reinforce the shapes of large molecules ◦ Help molecules adhere to each other  2 Types: ◦ Hydrogen Bonds ◦ Van der Waals Interactions

19.  A hydrogen bond ◦ Forms between partial charges of molecules, such as water (weak 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. ++ ++

20. VVan der Waals interactions ◦O◦Occur when transiently positive and negative regions of molecules attract each other ◦E◦Electrons bounce around, creating “hot spots” of + and – charges within the same molecule ***Constantly changing

21.  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’ and the weak bonds that form ◦ Determines how biological molecules recognize and respond to one another with specificity  Example: hormones and their receptors

22. 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

23.  A Chemical reaction ◦ Is the making and breaking of chemical bonds ◦ Is the re-arrangement of matter ◦ Leads to changes in the composition of matter ◦ Convert reactants to products Reactant Product 2 H 2 O2O2 2 H 2 O + +