1. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chapter 2 – Chemical Context of Life Biology is a multi-disciplined science – In order to understand biology, an understanding of basic chemistry is needed

2. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Some Basic Definitions Matter – anything that takes up space and has mass Element – a substance that can’t be broken down to other substances by chemical reaction – 92 found in nature Compound – substance containing two or more different elements combined in a fixed ratio – Has characteristics different from those of its elements

3. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Compound An example of a compound is table salt (NaCl) – Sodium is a metal – Chlorine (chloride) is a poisonous gas (liquid) SodiumChloride Sodium Chloride +

4. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Elements in Biology Only 25 of the 92 natural elements are needed for life Of those 25, 4 make up 96% of all living matter – O, C, H, N Other 4% are Trace Elements – elements required by an organism in small quantities Table 2.1

5. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Atoms Atom – smallest unit of matter that still retains the properties of the element – Three sub-atomic particles are of interest to us Protons Neutrons Electrons

6. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Sub-Atomic Particles Protons – Positively charged – Located in the nucleus – Mass of about 1 dalton Each atom of an element has a unique number of protons in its nucleus

7. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Sub-Atomic Particles Neutrons – No charge – Located in nucleus – Mass of about 1 dalton – Number may vary

8. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Sub-Atomic Particles Electrons – Negative charge – Located in cloud around the nucleus – Mass is negligible – Important to bonding

9. Copyright © 2006 Cynthia Garrard publishing under Canyon Design 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

10. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Atomic Number and Atomic Mass Atomic Number – number of protons in the nucleus

11. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Atomic Number and Atomic Mass Atomic mass – sum of protons and neutrons in the nucleus of an atom – Atomic mass – atomic number = # of neutrons For our purposes, Atomic mass is the same as Mass number

12. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Assume atoms are neutral in charge – The Atomic number (# of protons or positive charges) = the number of electrons (or negative charges).

13. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Isotopes Isotopes – atoms of the same element that differ in the number of neutrons Radioactive isotopes – one in which the nucleus decays spontaneously, giving off particles and energy

14. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical Reactions Only electrons are involved in chemical reactions Nuclei never get close enough to one another to react

15. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Energy Energy – the capacity to cause change (by doing work) Potential energy – the energy that matter possesses because of location or structure In order to restore potential energy (slinky to the top of the stairs), work must be done (slinky must be brought to the top of the stairs)

16. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Energy The more distant an electron is from the nucleus, the more potential energy it has An electron’s energy level is related to its average distance from the nucleus – Energy level – the different states of potential energy that an electron has in an atom Represented symbolically by electron shells

17. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical Behavior of Atoms Chemical behavior of atoms is determined by the distribution of electrons in the atom’s electron shells Electron shells are filled in a specific order: – First shell holds maximum of 2 electrons – Second shell holds maximum of 8 – Third shell holds maximum of 8 Each lower level must be filled before an electron can be in a higher shell

18. Copyright © 2006 Cynthia Garrard publishing under Canyon Design 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 Figure 2.7B

19. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical Behavior of Atoms Chemical behavior depends mostly on the number of electrons in the outermost shell, known as the valence shell and the electrons in the valence shell are know as valence electrons An atom with a completed valence shell is non- reactive

20. Copyright © 2006 Cynthia Garrard publishing under Canyon Design

21. Chemical Behavior of Atoms Reactivity of atoms arise from unpaired electrons in the valence shell It is these unpaired electrons that interact to form bonds

22. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Bonds Chemical bonds - attraction between atoms resulting in either sharing or transferring of valance shell electrons There are several types of bonds – Covalent – Ionic – Hydrogen – van der Waals interactions

23. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Covalent Bonds Covalent bond – sharing of a pair of valence electrons by two atoms By sharing, each atom has a completed valence shell for part of the time This is the strongest type of bond Hydrogen atoms (2 H) Hydrogen molecule (H 2 ) + + + + ++

24. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Covalent Bond A molecule – Consists of 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

25. Copyright © 2006 Cynthia Garrard publishing under Canyon Design (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

26. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Covalent Bond Electronegativity – Is the attraction of a particular kind of atom for the electrons in a covalent bond The more electronegative an atom – The more strongly it pulls shared electrons toward itself

27. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Covalent Bond Types Non-polar covalent bond – Equal sharing of electrons is – Atoms have similar electronegativities – Ex: H-HO=O Polar covalent bond – Unequal sharing – Resulting molecule has areas of relative charge

28. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polar Covalent Bond 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

29. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Polar Covalent Bond Oxygen is one of the most electronegative elements, attracting shared electrons more strongly than hydrogen does Result is an unequal sharing

30. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Ionic Bonds In some cases, two atoms are so unequal in their attraction for valence shell electrons, the more electronegative atom strips the electron away from its bonding partner This results in two ions or charged particles – Cation – positively charged particle (has less electrons) – Anion – negatively charged particle (has more electrons)

31. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Ionic Bonds 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

32. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Ionic Bonds The transfer of an electron is not the formation of a bond, but it allows an ionic bond to form because the resulting ions are attracted to each other

33. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Ionic Bonds Na + Cl – Figure 2.14 Ionic compounds – Are often called salts, which may form crystals

34. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Ionic Bonds Ionic bonds are not as strong as covalent bonds One reason is that the bond can be affected by the envionment

35. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Weak Chemical Bonds Several types of weak chemical bonds are important in living systems

36. Copyright © 2006 Cynthia Garrard publishing under Canyon Design 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

37. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Van der Waals Interactions Van der Waals interactions – Occur when transiently positive and negative regions of molecules attract each other

38. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Weak Bonds Weak chemical bonds – Reinforce the shapes of large molecules – Help molecules adhere to each other

39. Copyright © 2006 Cynthia Garrard publishing under Canyon Design 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 electrons in the molecule’s atoms

40. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Molecular shape – Determines how biological molecules recognize and respond to one another with specificity

41. Copyright © 2006 Cynthia Garrard publishing under Canyon Design 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

42. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical Reactions A Chemical reaction – Is the making and breaking of chemical bonds – Leads to changes in the composition of matter – Can not create or destroy matter

43. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical reactions – Convert reactants to products

44. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical Reactions Some reactions continue to completion – That is, all the reactants are used up to make products Most reactions are reversible – That is, the products of the forward reaction become the reactants of the backward reaction – 3H 2 + N 2 2NH 3

45. Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chemical Reactions Chemical equilibrium – Is reached when the forward and reverse reaction rates are equal – The reactions are still occurring, but there is no net effect on the concentrations