Chapter 1 The Facts of Life: Chemistry is the Logic of Biological Phenomena

1. Chapter 1The Facts of Life: Chemistry is the Logic of Biological Phenomena

2. Energy-rich molecules Organisms capture energy in the form of special energized molecules such as ATP. Figure 1.3

3. Energy-rich molecules Organisms capture energy in the form of special energized molecules such as NADPH. Figure 1.3

4. The Fidelity of Self-Replication Resides Ultimately in the Chemical Nature of DNA Figure 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity.

5. 1.2 What Kinds of Molecules are Biomolecules?

6. 1.2 What Kinds of Molecules are Biomolecules? • H, O, C and N make up 99+% of atoms in the human body. • What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life ? • Answer: Their ability to form covalent bonds by electron-pair sharing.

7. 1.2 What Kinds of Molecules are Biomolecules? • What are the bond energies of covalent bonds?

8. 1.2 What Kinds of Molecules are Biomolecules? Covalent bond formation by e- pair sharing.

9. 1.3 What is the Structural Organization of Complex Biomolecules? Examples of the versatility of C-C bonds in building complex structures.

10. 1.3 What is the Structural Organization of Complex Biomolecules? Examples of the versatility of C-C bonds in building complex structures.

11. 1.3 What is the Structural Organization of Complex Biomolecules? Examples of the versatility of C-C bonds in building complex structures.

12. 1.3 What is the Structural Organization of Complex Biomolecules? Examples of the versatility of C-C bonds in building complex structures.

13. 1.3 What is the Structural Organization of Complex Biomolecules?

14. 1.3 What is the Structural Organization of Complex Biomolecules? Simple Molecules are the Units for Building Complex Structures • Metabolites and Macromolecules • Organelles • Membranes • The Unit of Life is the Cell

15. 1.3 What is the Structural Organization of Complex Biomolecules?

16. 1.3 What is the Structural Organization of Complex Biomolecules?

17. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition There are four classes of biomolecules The first three are covalent polymers: 1. Proteins. 2. Polysaccharides (Carbohydrates). 3. Nucleic acids. 4. Lipids form large macromolecular structures (membranes) using noncovalent interactions.

18. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Proteins are made from amino acids. A unit in the polymer is called a residue due to the loss of water. The attachment between residues is a peptide bond. Proteins are written N-term  C-Term.

19. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Polysaccharides are made from monosaccharides (sugars). A unit in the polymer is called a residue due to the loss of water. The attachment between residues is a glycosidic bond. Polysaccharides are written nonreducing  reducing.

20. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Nucleic acids are polymers of nucleotides. Nucleic acids are made from nucleotides. A unit in the polymer is called a residue due to the loss of water. The attachment between residues is a phosphodiester bond. Nucleic acids are written 5' 3'.

21. Macromolecule Representations

22. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition • Covalent bonds hold atoms together so that molecules are formed. • Weak forces profoundly influence the structures and behaviors of all biological molecules. • Weak forces create interactions that are constantly forming and breaking under physiological conditions. • Energies of weak forces range from 0.4 to 30 kJ/mol. • Weak forces include: • van der Waals interactions. • Hydrogen bonds. • Ionic interactions. • Hydrophobic interactions.

23. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition • Know these important numbers: • Van der Waals Interactions: 0.4-4.0 kJ/mol • Hydrogen Bonds: 12-30 kJ/mol • Ionic Interactions: 20 kJ/mol • Hydrophobic Interactions: <40 kJ/mol • These interactions influence profoundly the nature of biological structures

24. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Two Important Points about Weak Forces • Biomolecular recognition is mediated by weak chemical forces • Weak forces restrict organisms to a narrow range of environmental conditions

25. Van der Waals Forces Are Important to Biomolecular Interactions Figure 1.12 Van der Waals packing is enhanced in molecules that are structurally complementary. Gln121, a surface protuberance on lysozyme, is recognized by the antigen-binding site of an antibody against lysozyme.

26. Van der Waals Forces Are Important to Biomolecular Interactions Figure 1.13 The van der Waals interaction energy profile as a function of the distance, r, between the centers of two atoms.

27. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

28. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Some biologically important H bonds.

29. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Some biologically important H bonds.

30. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Ionic bonds in the Mg-ATP complex.

31. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Ionic bonds contribute to the stability of proteins.

32. Biomolecular Recognition is Mediated by Weak Chemical Forces Figure 1.16 Structural complementarity: The antigen on the right (gold) is a small protein, lysozyme, from hen egg white. The antibody molecule (IgG) (left) has a pocket that is structurally complementary to a surface feature (red) on the antigen.

33. Biomolecular Recognition is Mediated by Weak Chemical Forces Figure 1.16 Structural complementarity: The antigen on the right (gold) is a small protein, lysozyme, from hen egg white. The antibody molecule (IgG) (left) has a pocket that is structurally complementary to a surface feature (red) on the antigen.

34. Biomolecular Recognition is Mediated by Weak Chemical Forces Figure 1.16 Puzzles and locks in keys are models of structural complementarity.

35. Biomolecular Recognition is Mediated by Weak Chemical Forces Figure 1.17 Denaturation and renaturation of the intricate structure of a protein.

36. Energy of Metabolism Energy distribution 1/3 2/3 nutrients ----> pool molecules -----> CO2, H2O, NH3  biomolecules

37. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Cells release the energy of glucose in a stepwise fashion, forming ATP.

38. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Combustion of glucose in a calorimeter yields energy in its least useful form, heat.

39. Enzymes Catalyze Metabolic Reactions Figure 1.19 Carbonic anhydrase, a representative enzyme.

40. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

41. 1.5 What is the Organization and Structure of Cells? • Prokaryotic cells • A single (plasma) membrane • No nucleus or organelles • Eukaryotic cells • Much larger in size than prokaryotes • 103-104 times larger! • Nucleus plus many organelles • ER, Golgi, mitochondria, etc.

42. Archaea and Bacteria Have a Relatively Simple Structural Organization Figure 1.20 This bacterium is Escherichia coli, a member of the coliform group of bacteria that colonize the intestinal tract of humans. (See Table 1.7.)

43. The Structural Organization of Eukaryotic Cells Is More Complex Than That of Prokaryotic Cells Figure 1.21 This figure diagrams a rat liver cell, a typical higher animal cell.

44. 1.5 What is the Organization and Structure of Cells? Figure 1.22 This figure diagrams a cell in the leaf of a higher plant.

45. 1.5 What is the Organization and Structure of Cells?

46. 1.5 What is the Organization and Structure of Cells?

47. 1.5 What is the Organization and Structure of Cells?

48. 1.6 What Are Viruses? Figure 1.23 Viruses are genetic elements enclosed in a protein coat. Viruses are not free-living organisms and can reproduce only within cells. Viruses show an almost absolute specificity for their particular host cells, infecting and multiplying only within those cells. Viruses are known for virtually every kind of cell. Shown here are examples of (a) an animal virus, adenovirus; (b) bacteriophage T4 on E.coli; and (c) a plant virus, tobacco mosaic virus.

49. 1.6 What are Viruses? Figure 1.24 The virus life cycle. Viruses are mobile bits of genetic informationencapsulated in a protein coat.

50. End Chapter 1Introduction to Biochemistry