1. Overview Chapters 2

2. Atoms & Molecules Element - pure substance made up of only one kind of atom Compound - pure substance made up of only one kind of molecule, but two or more different kinds of atoms Mixture - not a pure substance Elementary Chemistry

3. Atomic number – number of protons Atomic mass - # protons + # neutrons Isotopes – extra neutrons NEUTRONS DON’T AFFECT CHEMISTRY ! Elementary Chemistry

4. Particlelocationchargemass Proton nucleuspositive1 amu Neutronnucleusneutral1 amu Electronorbitalsnegativeapprox. 0 Sub-Atomic Particles

5. Affinity for electrons Will determine type(s) of bonds Will determine bond distances Electronegativity

6. Atoms can be grouped into molecules because of the way they attract and join other atoms. There are three kinds of bonds between atoms: – Covalent bonds – Ionic bonds – Hydrogen bonds Chemical Bonds

7. Covalent bonds are formed when two atoms share a pair of electrons between them. Each is attracted to the pair of electrons, and therefore to each other. Chemical Bonds

8. Two smallest atoms Hydrogen has one proton and one electron Helium has two protons, two neutrons, and two electrons. Helium’s orbital is full; it is not reactive... Hydrogen and Helium

9. Lithium, Beryllium, Boron…the next three elements... Carbon has 6 protons, 6 neutrons, 6 electrons. Its outer orbital has 4 electrons;it needs 4 more to make 8... Next Elements

10. Nitrogen has 5 outer electrons; needs 3 more Oxygen has 6 outer electrons; needs 2 more Fluorine has 7 outer electrons; needs only 1 more (not shown here) Neon is full; it’s non-reactive. Next Elements

11. The hydrogen atoms on the left each need an electron to complete the outer orbital. If they overlap their orbitals, they can share one electron each and form the hydrogen molecule on the right. Sharing Electrons The stick in our model represents the bond, a shared pair of electrons:

12. The sodium atom on the left needs 7 electrons to complete its outer orbital. There’s just no way. The chlorine on the right needs only 1. Chlorine is so strongly attracted to the electron, and sodium is so weakly attracted, that the electron is transferred from one to the other, resulting in charged atoms, which attract each other. (Opposite charges attract.) Ionic Bonds

13. that the electron is transferred from one to the other, resulting in charged atoms, which attract each other. (Opposite charges attract.) Ionic Bonds

14. Hydrogen bonding is a result of slightly positive and slightly negative charges on parts of a molecule attracting each other. Water’s cohesive properties come from the fact that it is a polar molecule... Hydrogen Bonds

15. Hydrogen Bonding

16. Synthesis - small molecules into larger ones (Energy: anabolic - energy in) Decomposition- large molecules to small ones (Energy: catabolic - energy out) (Rearrangement…) combined reaction of both of the above. (reaction coupling) Chemical reactions

17. Dehydration - removal of water (usually in a synthesis reaction) e.g. dehydration synthesis Hydrolysis - using water to break down large molecules (usually in a decomposition reaction) Chemical reactions

18. Inorganic molecules - those that do not contain Carbon Organic - Carbon-containing molecules (Some chemists do not consider Carbon dioxide to be organic. They say there must be at least one Carbon-Hydrogen bond in the molecule…) Inorganic/Organic

19. Chemical properties of water – Polar molecule – Will dissolve polar molecules (hydrophilic) – Ionizable - dissociates in itself! Physical properties of water – Clear, liquid (0° C - 100°C) – Solid form less dense (ice floats) – High capacity for heat Properties of Water

20. Surface tension - a measure of how difficult it is to stretch or break the surface of a liquid. Cohesion – attraction between molecules of the same kind. Adhesion – attraction between different kinds of molecules. Hydrogen Bonding

21. Energy required for phase changes. Heat of vaporization (evaporate/condense). Heat of fusion (freeze/melt) Physical Properties

22. Hydrogen Bonding

23. Hydrophilic – water seeking Hydrophobic – water “fearing” Membranes

24. Water molecules will arrange themselves about ions in solution. This will buffer the charges in solution. Spheres of Hydration

25. Below is a phospholipid. It is made of two fatty acid chains (green), which are neutral, and a phosphate head (purple), which is negative. Membrane Composition

26. Here’s how the phospholipids will arrange themselves with respect to water: MICELLE CELL MEMBRANE

27. Solution – Aqueous solution – Solvent = what is doing the dissolving – Solute = what is being dissolved Solutions

28. Ionization of salt… NaCl Na + + Cl - Ionization

29. Ionization of water in solution… Ionization of Water A proton comes off the molecule… H +

30. Measure of the hydrogen ion concentration: [H + ] pH H2OH2O H + + OH - 1x10 -7 pH = - (exponent of [H + ]) pH = -(-7) = 7

31. Thousands of protein “words” Functions – Cell structures – Chemical messengers – receptors on cell membranes – Immunity – ENZYMES Thousands of protein “words” Functions – Cell structures – Chemical messengers – receptors on cell membranes – Immunity – ENZYMES Proteins

32. smallest unit of proteins (monomer) Contains: smallest unit of proteins (monomer) Contains: Amino Acids Amino group Acid group “R” group NC H C H O OH H

33. To form larger molecules the acid end of one amino acid and the amino end of another dehydrate to form a larger molecule... Dehydration Synthesis

34. That is called a dipeptide. The bond between the two original amino acids is a covalent bond called a peptide bond. Dipeptide

35. A string of amino acids is called a polypeptide. The backbone (NCCNCCNCCNCC) is made of covalent bonds. This backbone is called the primary structure of a protein. Primary Structure

36. The polypep-ide is coiled into its secondary structure. The coil is held in shape by hydrogen bonds... The polypep-ide is coiled into its secondary structure. The coil is held in shape by hydrogen bonds... Secondary Structure Alpha Helix

37. There is another way to organize primary protein chains. These are parallel primary chains linked by hydrogen bond. Another Secondary Beta Pleated Sheet

38. 2ndary Structure Combinations within Tertiary Structure Alpha helixes Beta pleated sheet Sulfur bridge

39. Next the secondary structure is wrapped on itself in the tertiary (globular) form. This is held together by – Hydrogen bonds – Sulfur bridges – Weak electrostatic bonds Next the secondary structure is wrapped on itself in the tertiary (globular) form. This is held together by – Hydrogen bonds – Sulfur bridges – Weak electrostatic bonds Tertiary Structure

40. Finally, some tertiary proteins are joined with others to form quaternary proteins. Quaternary Structure This one is hemo- globin. The red disks are heme.

41. Numerous diagrams of tertiary and quaternary proteins Several types of chaperonins “Molecules of the year” What do you mean biologists are geeks? Web Sites - Proteins A.P. Biology Salesianum School PDV / 2004 http://www.rcsb.org/pdb/molecules/molecule_list_2002.html http://kuchem.kyoto-u.ac.jp/kozo/home/structure.html

42. Enzymes - Active Site Enzyme specificity allows for binding of substrate at active site. Active site = “groove / pocket” on enzyme. Enzyme interaction with substrate causes a conformational change in which the enzyme changes shape slightly - active site fits “snugly” around substrate “Induced Fit”

43. Induced fit

44. Environment & Enzyme Activity Temperature affects 3D shape of enzyme (structure) / bonding Salt concentration affects chemical bonds within protein structure pH affects protein structure -> [H+]

45. Other Factors Affecting Enzyme Activity Cofactors = non-protein “helpers” Coenzyme = organic molecule

46. Allosteric Inhibition

47. Inhibition: Permanent or Temporary? Irreversible = covalent bonding Reversible = weak/hydrogen bonds Depends on Concentrations – Substrate vs. Inhibitor molecule

48. Inhibition and Cell Metabolism Use of reversible inhibitors “Negative feedback”= metabolic reaction is blocked by its products. Energy saving device – Ex: ATP