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. Outline and Key Questions • What Are the Distinctive Properties of Living Systems? • What Kinds of Molecules Are Biomolecules? • What is the Structural Organization of Complex Biomolecules? • How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition? • What is the Organization and Structure of Cells? • What are Viruses?

3. On Life and Chemistry… • “Living things are composed of lifeless molecules.” (Albert Lehninger) • “Chemistry is the logic of biological phenomena.” (Garrett and Grisham)

4. 1.1 – What Are the Distinctive Properties of Living Systems? • Organisms are complicated and highly organized • Biological structures serve functional purposes • Living systems are actively engaged in energy transformations • Living systems have a remarkable capacity for self-replication

5. Energy-rich molecules Organisms capture energy in the form of special energized molecules such as ATP and NADPH. Steady state – the appearance of consistency over time, but not at equilibrium Equilibrium – the appearance of consistency over time due to equal and opposite forces

6. Covalent Bond Formation by H, C, N, and O Makes Them Suitable to the Chemistry of Life

7. The Fidelity of Self-Replication Resides Ultimately in the Chemical Nature of DNA All due to complementary forces!!

8. 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

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?

11. 1.3 What is the Structural Organization of Complex Biomolecules?

12. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition • Macromolecules and their building blocks have a “sense” or directionality • Macromolecules are informational • Biomolecules have characteristic three-dimensional architecture • Weak forces maintain biological structure and determine biomolecular interactions

13. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Amino acids build proteins

14. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Polysaccharides are built by joining sugars together

15. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Nucleic acids are polymers of nucleotides

16. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

17. 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

18. Biomolecules Have Characteristic Three-Dimensional Architecture Antigen-binding domain of immunoglobulin G (IgG).

19. 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

20. Van der Waals Forces Are Important to Biomolecular Interactions Van der Waals packing is enhanced in molecules that are structurally complementary.

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

22. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition

23. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Some biologically important H bonds

24. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Ionic bonds in the Mg-ATP complex

25. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Ionic bonds contribute to the stability of proteins

26. 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

27. Biomolecular Recognition is Mediated by Weak Chemical Forces 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.

28. Biomolecular Recognition is Mediated by Weak Chemical Forces

29. Biomolecular Recognition is Mediated by Weak Chemical Forces

30. Biomolecular Recognition is Mediated by Weak Chemical Forces Large energy changes can cause problems for the cell. Small, step reaction are necessary to prevent things like denaturation.

31. 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

32. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition Cells release the energy of glucose in a stepwise fashion, capturing it in the formation of ATP

33. 1.4 – Properties of Biomolecules Reflect Their Fitness to the Living Condition The Time Scale of Life: • The processes of life have durations ranging over 33 orders of magnitude • From 10-15 sec (for electron transfer reactions) • To 1018 sec (the period of evolution, from the first appearance of organisms to today) • The processes and lifetimes described in Table 1.5 will be discussed throughout the text and course

34. 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.

35. How Many Genes Does a Cell Need?

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

37. 1.5 What is the Organization and Structure of Cells? This figure diagrams a cell in the leaf of a higher plant

38. Cellular Features • Tables 1.7, 1.8 and 1.9 outline the major features of prokaryotic, eukaryotic, and plant cells. It is important that if you are not familiar with these general features that you carefully read these tables.

39. 1.6 What Are Viruses? Viruses are genetic elements enclosed in a protein coat. Viruses are not free-living organisms and can reproduce only within cells. (a) adenovirus; (b) bacteriophage T4 on E.coli; (c) a plant virus, tobacco mosaic virus.

40. 1.6 What are Viruses? The virus life cycle. Viruses are mobile bits of genetic information encapsulated in a protein coat.

41. Questions • You should be able to complete questions 1-14 and 16-17 at the end of the chapter. While they will not be graded, they would be excellent practice.