CHAPTER 2 Small Molecules: Structure and Behavior

1. CHAPTER 2Small Molecules: Structure and Behavior

2. Atoms: The Constituents of Matter • Matter is composed of atoms with positively charged nuclei of protons and neutrons surrounded by negatively charged electrons.

3. Figure 2.1 Main Elements Found in Living Organisms

4. Figure 2.2 Isotopes of an element differ in numbers of neutrons Some isotopes are unstable and are termed radioactive. These radioisotopes are useful for many purposes.

5. Electrons are distributed in shells of orbitals Each orbital contains a max of 2 electrons

6. Figure 2.5 Orbital Shell Representations for Several Atoms

7. Table 2.1 Interaction of atoms via sharing of electrons generates molecules via bonding

8. Covalent Bonds Figure 2.6 Covalent bonds form when two atomic nuclei share one or more pairs of electrons. They have spatial orientations that give molecules three-dimensional shapes

9. Figure 2.7 Covalent Bonds Combining electrons in all the orbitals in a particular level often occurs. sp3 bonds of carbon are the combination of the 2s orbital and the 3 2p orbitals to form 4 sp3 orbitals which each have a single electron that is shared with the single electron in H’s 1s orbital

10. table 02-02.jpg Table 2.2 Table 2.2

11. Chemical Bonds: Linking Atoms Together • Nonpolar covalent bonds form when the electronegativities of two atoms are approximately equal • Polar covalent bond in which one end is d+ and the other is d– forms when atoms with strong electronegativity (such as oxygen) bond to atoms with weaker electronegativity (such as hydrogen) • Hydrogen bonded to a strongly electronegative atom can be donated to a H-bond

12. Figure 2.8 figure 02-08.jpg Polarity in bonding

13. table 02-03.jpg Table 2.3 Table 2.3

14. Figure 2.10 Ionic bonds Complete gain/loss of electron to form a charged species Oppositely charged ions then interact electrostatically

15. figure 02-09.jpg Hydrogen bonds • Hydrogen bonds form between a d+ hydrogen atom in one molecule and a d– nitrogen, oxygen or sulfur atom in another molecule or in another part of a large molecule.

16. Figure 2.11 Polar solvents dissolve ionic & polar substances

17. Polar & Non-polar Molecules • Nonpolar molecules do not interact directly with polar substances. They are attracted to each other by very weak bonds called van der Waals forces. • Van der Waals forces are the weak sharing of electons between orbitals of molecules

18. Water: Structure and Properties • Water’s molecular structure and capacity to form hydrogen bonds give it unusual properties significant for life.

19. Water: Structure and Properties • Cohesion of water molecules results in a high surface tension. Water’s high heat of vaporization assures cooling when it evaporates. • Solutions are substances dissolved in water. Concentration is the amount of a given substance in a given amount of solution. Most biological substances are dissolved at very low concentrations.

20. Chemical Reactions: Atoms Change Partners • In chemical reactions, substances change their atomic compositions and properties. Energy is either released or added. Matter and energy are not created or destroyed, but change form.

21. Acids, Bases, and the pH Scale • Acids are substances that donate hydrogen ions. Bases are those that accept hydrogen ions. • The pH of a solution is the negative logarithm of the hydrogen ion concentration. • pH=-log[H+] • Values lower than pH 7 indicate an acidic solution. • Values above pH 7 indicate a basic solution

22. Figure 2.18 pH Scale

23. Acids, Bases, and the pH Scale • Buffers are systems of weak acids and bases that limit the change in pH when hydrogen ions are added or removed.

24. The Properties of Molecules • Molecules vary in size, shape, reactivity, solubility, and other chemical properties. • Functional groups make up part of a larger molecule and have particular chemical properties. • The consistent chemical behavior of functional groups helps us understand the properties of the molecules that contain them.

25. Figure 2.20 – Part 1 Functional Groups

26. Figure 2.20 – Part 2 Functional Groups

27. Optical Isomers Figure 2.21 Isomers • Optical isomers • rotate plain polarized light in opposite directions • Structural isomers • Differ in position of functional groups

28. CHAPTER 3Macromolecules: Their Chemistry and Biology

29. Macromolecules: Giant Polymers • Macromolecules are formed by covalent bonds between monomers and include polysaccharides, proteins, and nucleic acids. • Lipids are crucial biomolecules, but are not considered ‘macromolecules’

30. table 03-01.jpg Table 3.1 Fatty Acid Triglyceride Phospholipid

31. Macromolecules: Giant Polymers • Macromolecules have specific three-dimensional shapes. • Different functional groups give local sites on macromolecules specific properties.

32. Condensation Reactions • Monomers are joined by condensation reactions. Hydrolysis reactions break polymers into monomers. • Joining of monomers is typically called polymerization

33. Proteins: Polymers of Amino Acids • Functions of proteins include support, protection, catalysis, transport, defense, regulation, and movement. They sometimes require an attached prosthetic group.

34. Proteins: Polymers of Amino Acids • Twenty amino acids are found in proteins. • Each consists of an amino group, a carboxyl group, a hydrogen, and a side chain bonded to the a carbon atom.

35. table 03-02a.jpg Amino Acids Table 3.2 – Part 1

36. table 03-02bc.jpg Amino Acids

37. Proteins: Synthesis • Amino acids are covalently bonded together by peptide linkages or peptide bond • Chemically this is an amide bond • Each amino acid is called a residue • Reaction proceeds leaving the amino terminus of the 1st aa and the carboxyl terminus of the last aa unmodified (free)

38. Proteins: Structure • Polypeptide chains of proteins are folded into specific three-dimensional shapes • There are 4 levels of structure • Primary (1o) – amino acid sequence • Secondary (2o) – localized structures of adjacent residues • Tertiary (3o) – folding of units of secondary structure • Quaternary – association of multiple individual proteins (subunits) to form a functional complex

39. Protein Structure H-bonds stabilize 2o structures

40. Protein Structure 3.5 – Part 2 Figure 3.5 – Part 2 Covalent bonds (disulfide bridges), H-bonds & ionic bonds (salt bridges) stabilize 3o and 4o structures

41. figure 03-03.jpg Protein Structure Figure 3.3 The SH groups of cysteine residues can form disulfide bridges that link distant regions of proteins together

42. figure 03-07.jpg 3.7 Figure 3.7

43. Proteins: Structure • Chemical interactions important for binding of proteins to other molecules. • H-bonds • Van der Waals interactions • Ionic interactions

44. Proteins: Structure • Proteins can be denatured • heat, acid, or chemicals • Loss of tertiary and secondary structures and biological function.

45. Proteins: Structure • Proper folding of proteins is critical for their function • Chaperonins assist protein folding

46. Carbohydrates: Sugars and Sugar Polymers • Monosaccharides • 3-carbons – trioses • 5-carbons - pentoses • 6-carbons – hexoses • Disaccharides • Two monosaccharides • Maltose • Sucrose • Lactose • Oligosaccharide • <10 glycoside residues • Polysaccharide • >10 glycoside residues

47. Carbohydrates: Structures Hemiacetal forms

48. Glyceraldehyde Carbohydrates Structure 4 carbon sugar is erythrose

49. figure 03-12b.jpg Carbohydrates Structure Isomers

50. Carbohydrate Polymerization Glycosidic linkages may have either a or b orientation in space Numbering of bond refers to carbon position of hemiacetal ring