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Basic Chemistry, Bonds, etc.

Basic Chemistry, Bonds, etc.

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  • 1. 1<br />Chapter 2<br />The Chemical Context of Life<br />
  • 2. 2<br />Matter<br />Takes up space and has mass<br />Exists as elements (pure form) and in chemical combinations called compounds<br />
  • 3. 3<br />Elements<br />Can’t be broken down into simpler substances by chemical reaction<br />Composed of atoms<br />Essential elements in living things include carbon C, hydrogen H, oxygen O, and nitrogen N making up 96% of an organism<br />
  • 4. 4<br />Other Elements<br />A few other elements Make up the remaining 4% of living matter<br />Trace Elements<br />Table 2.1<br />
  • 5. 5<br />Deficiencies<br />(b) Iodine deficiency (Goiter)<br />(a) Nitrogen deficiency<br />If there is a deficiency of an essential element, disease results<br />Figure 2.3<br />
  • 6. 6<br />Trace Elements<br />Trace elements Are required by an organism in only minute quantities<br />Minerals such as Fe and Zn are trace elements<br />
  • 7. 7<br />Compounds<br />+<br />Sodium<br />Chloride<br />Sodium Chloride<br />Are substances consisting of two or more elements combined in a fixed ratio<br />Have characteristics different from those of their elements<br />Figure 2.2<br />
  • 8. 8<br />Properties of Matter<br />An element’s properties depend on the structure of its atoms<br />Each element consists of a certain kind of atom that is different from those of other elements<br />An atom is the smallest unit of matter that still retains the properties of an element<br />
  • 9. 9<br />Subatomic Particles<br />Atoms of each element Are composed of even smaller parts called subatomic particles<br />Neutrons, which have no electrical charge<br />Protons, which are positively charged<br />Electrons, which are negatively charged<br />
  • 10. 10<br />Subatomic Particle Location<br />Protons and neutrons<br />Are found in the atomic nucleus<br />Electrons<br />Surround the nucleus in a “cloud”<br />
  • 11. 11<br />Simplified models of an Atom<br />Cloud of negative<br />charge (2 electrons)<br />Electrons<br />Nucleus<br />This model represents the<br />electrons as a cloud of<br />negative charge, as if we had<br />taken many snapshots of the 2<br />electrons over time, with each<br />dot representing an electron‘s<br />position at one point in time.<br />(a)<br />In this even more simplified<br />model, the electrons are<br />shown as two small blue<br />spheres on a circle around the<br />nucleus.<br />(b)<br />Figure 2.4<br />
  • 12. 12<br />Atomic Number &amp; Atomic Mass<br />Atoms of the various elements Differ in their number of subatomic particles<br />The number of protons in the nucleus = atomic number<br />The number of protons + neutrons = atomic mass<br />Neutral atoms have equal numbers of protons &amp; electrons (+ and – charges)<br />
  • 13. 13<br />Atomic Number<br />Is unique to each element and is used to arrange atoms on the Periodic table<br />Carbon = 12<br />Oxygen = 16<br />Hydrogen = 1<br />Nitrogen = 17<br />
  • 14. 14<br />Atomic Mass<br /><ul><li>Is an approximation of the atomic mass of an atom
  • 15. It is the average of the mass of all isotopes of that particular element
  • 16. Can be used to find the number of neutrons (Subtract atomic number from atomic mass)</li></li></ul><li>15<br />Isotopes<br />Different forms of the same element<br />Have the same number of protons, but different number of neutrons<br />May be radioactive spontaneously giving off particles and energy<br />May be used to date fossils or as medical tracers<br />
  • 17. 16<br />Energy Levels of Electrons<br />An atom’s electrons Vary in the amount of energy they possess<br />Electrons further from the nucleus have more energy<br />Electron’s can absorb energy and become “excited” <br />Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels<br />
  • 18. 17<br />Energy<br />Energy<br />Is defined as the capacity to cause change<br />Potential energy<br /> - Is the energy that matter possesses because of its location or structure<br />Kinetic Energy<br /> - Is the energy of motion<br />
  • 19. 18<br />Electrons and Energy<br />(a)<br />A ball bouncing down a flight<br />of stairs provides an analogy<br />for energy levels of electrons,<br />because the ball can only rest<br />on each step, not between<br />steps.<br />Figure 2.7A<br />The electrons of an atom<br />Differ in the amounts of potential energy they possess<br />
  • 20. 19<br />Energy Levels<br />Third energy level (shell)<br />Second energy level (shell)<br />Energy<br />absorbed<br />First energy level (shell)<br />Energy<br />lost<br />Atomic<br /> nucleus<br />(b)<br />An electron can move from one level to another only if the energy<br />it gains or loses is exactly equal to the difference in energy between<br />the two levels. Arrows indicate some of the step-wise changes in<br />potential energy that are possible.<br />Figure 2.7B<br />Are represented by electron shells<br />
  • 21. Thermodynamics and Biology<br />First law of thermodynamics<br />In any process, the total energy of the universe remains the same.<br />It can also be defined as: for a thermodynamic cycle the sum of net heat supplied to the system and the net work done by the system is equal to zero.<br />Second law of thermodynamics<br />The entropy (useless energy) of an isolated system will tend to increase over time.<br />In a simple manner, the second law states that &quot;energy systems have a tendency to increase their entropy&quot; rather than decrease it.<br />20<br />
  • 22. 21<br />Periodic table<br />Helium<br />2He<br />Atomic number<br />2<br />He<br />4.00<br />Hydrogen<br />1H<br />Element symbol<br />Atomic mass<br />First<br />shell<br />Electron-shell<br />diagram<br />Beryllium<br />4Be<br />Carbon<br />6C<br />Oxygen<br />8O<br />Neon<br />10Ne<br />Lithium<br />3Li<br />Boron<br />3B<br />Nitrogen<br />7N<br />Fluorine<br />9F<br />Second<br />shell<br />Aluminum<br />13Al<br />Chlorine<br />17Cl<br />Argon<br />18Ar<br />Sulfur<br />16S<br />Sodium<br />11Na<br />Magnesium<br />12Mg<br />Silicon<br />14Si<br />Phosphorus<br />15P<br />Third<br />shell<br />Figure 2.8<br />Shows the electron distribution for all the elements<br />
  • 23. 22<br />Why do some elements react?<br />Valence electrons<br />Are those in the outermost, or valence shell<br />Determine the chemical behavior of an atom<br />
  • 24. 23<br />Electron Orbitals<br />An orbital<br />Is the three-dimensional space where an electron is found 90% of the time<br />
  • 25. 24<br />Covalent Bonds<br />Hydrogen atoms (2 H)<br />In each hydrogen<br />atom, the single electron<br />is held in its orbital by<br />its attraction to the<br />proton in the nucleus.<br />+<br />+<br />1<br />2<br />3<br />When two hydrogen<br />atoms approach each<br />other, the electron of<br />each atom is also<br />attracted to the proton<br />in the other nucleus.<br />+<br />+<br />The two electrons<br />become shared in a <br />covalent bond,<br />forming an H2<br />molecule.<br />+<br />+<br />Hydrogen<br />molecule (H2)<br />Sharing of a pair of valence electrons <br />Examples: H2<br />Figure 2.10<br />
  • 26. 25<br />Covalent Bonding<br />Name<br />(molecular<br />formula)<br />Electron-<br />shell<br />diagram<br />Space-<br />filling<br />model<br />Structural<br />formula<br />Hydrogen (H2). <br />Two hydrogen <br />atoms can form a <br />single bond.<br />H<br />H<br />Oxygen (O2).<br />Two oxygen atoms <br />share two pairs of <br />electrons to form <br />a double bond.<br />O<br />O<br />Figure 2.11 A, B<br />A molecule<br />Consists of two or more atoms held together by covalent bonds<br />A single bond<br />Is the sharing of one pair of valence electrons<br />A double bond<br />Is the sharing of two pairs of valence electrons<br />
  • 27. 26<br />Compounds &amp; Covalent Bonds<br />Name<br />(molecular<br />formula)<br />Electron-<br />shell<br />diagram<br />Space-<br />filling<br />model<br />Structural<br />formula<br />(c)<br />Water (H2O).<br />Two hydrogen<br />atoms and one <br />oxygen atom are<br />joined by covalent <br />bonds to produce a <br />molecule of water.<br />H<br />O<br />H<br />(d)<br />Methane (CH4).<br />Four hydrogen <br />atoms can satisfy <br />the valence of<br />one carbon<br />atom, forming<br />methane.<br />H<br />H<br />H<br />C<br />H<br />Figure 2.11 C, D<br />
  • 28. 27<br />Covalent Bonding<br />In a nonpolar covalent bond<br />The atoms have similar electronegativities<br />Share the electron equally<br />
  • 29. 28<br />Because oxygen (O) is more electronegative than hydrogen (H), <br />shared electrons are pulled more toward oxygen.<br />d–<br />This results in a <br />partial negative <br />charge on the<br />oxygen and a<br />partial positive<br />charge on<br />the hydrogens.<br />O<br />H<br />H<br />d+<br />d+<br />H2O<br />In a polar covalent bond<br />The atoms have differing electronegativities<br />Share the electrons unequally<br />Figure 2.12<br />Covalent Bonding<br />
  • 30. 29<br />Ionic Bonds<br />In some cases, atoms strip electrons away from their bonding partners<br />Electron transfer between two atoms creates ions<br />Ions<br />Are atoms with more or fewer electrons than usual<br />Are charged atoms<br />
  • 31. 30<br />Ions<br />An anion<br />Is negatively charged ions<br />A cation<br />Is positively charged<br />
  • 32. 31<br />Ionic Bonding<br /> The lone valence electron of a sodium<br />atom is transferred to join the 7 valence<br />electrons of a chlorine atom.<br /> Each resulting ion has a completed<br />valence shell. An ionic bond can form<br />between the oppositely charged ions.<br />–<br />+<br />1<br />2<br />Cl<br />Na<br />Na<br />Cl<br />Cl–<br />Chloride ion<br />(an anion)<br />Na+<br />Sodium on<br />(a cation)<br />Na<br />Sodium atom<br />(an uncharged<br />atom)<br />Cl<br />Chlorine atom<br />(an uncharged<br />atom)<br />Sodium chloride (NaCl)<br />An ionic bond<br />Is an attraction between anions and cations<br />Figure 2.13<br />
  • 33. 32<br />Ionic Substances<br />Na+<br />Cl–<br />Figure 2.14<br />Ionic compounds<br />Are often called salts, which may form crystals<br />
  • 34. 33<br />Weak Chemical Bonds<br />Several types of weak chemical bonds are important in living systems<br />
  • 35. 34<br />Hydrogen Bonds<br />H<br />Water<br />(H2O)<br />O<br />A hydrogen<br />bond results <br />from the <br />attraction <br />between the<br />partial positive <br />charge on the <br />hydrogen atom <br />of water and <br />the partial <br />negative charge <br />on the nitrogen <br />atom of <br />ammonia.<br />H<br /> +<br /> –<br />Ammonia<br />(NH3)<br />N<br />H<br />H<br />d+<br />H<br />+<br />Figure 2.15<br />A hydrogen bond<br />Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom<br /> –<br /> +<br /> +<br />
  • 36. 35<br />Van der Waals Interactions<br />Van der Waals interactions<br />Occur when transiently positive and negative regions of molecules attract each other<br />
  • 37. 36<br />Weak Bonds<br />Weak chemical bonds<br />Reinforce the shapes of large molecules<br />Help molecules adhere to each other<br />
  • 38. 37<br />Molecular Shape and Function<br />Structure determines Function!<br />The precise shape of a molecule<br />Is usually very important to its function in the living cell<br />Is determined by the positions of its atoms’ valence orbitals<br />
  • 39. 38<br />Orbitals &amp; Covalent Bonds<br />Hybrid-orbital model<br />(with ball-and-stick<br />model superimposed)<br />Ball-and-stick<br />model<br />Space-filling<br />model<br />Unbonded<br />Electron pair<br />O<br />O<br />H<br />H<br />H<br />H<br />104.5°<br />Water (H2O)<br />H<br />H<br />C<br />C<br />H<br />H<br />H<br />H<br />(b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules<br />H<br />H<br /> Methane (CH4)<br />Figure 2.16 (b)<br />
  • 40. 39<br />Shape and Function<br />Molecular shape<br />Determines how biological molecules recognize and respond to one another with specificity<br />
  • 41. 40<br />Nitrogen<br />Carbon<br />Hydrogen<br />Sulfur<br />Oxygen<br />Natural<br />endorphin<br />Morphine<br />(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.<br />Natural<br />endorphin<br />Morphine<br />Endorphin<br />receptors<br />Brain cell<br />(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.<br />Figure 2.17<br />
  • 42. 41<br />Chemical Reactions<br />Chemical reactions make and break chemical bonds<br />A Chemical reaction<br />Is the making and breaking of chemical bonds<br />Leads to changes in the composition of matter<br />
  • 43. 42<br />Chemical Reactions<br />+<br />2 H2O<br />2 H2<br />O2<br />+<br />Reactants<br />Reaction<br />Product<br />Chemical reactions<br />Convert reactants to products<br />
  • 44. 43<br />Chemical Reactions<br />Photosynthesis<br />Is an example of a chemical reaction<br />Figure 2.18<br />
  • 45. 44<br />

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