Molecules of Life: Understanding Chemistry and Building Blocks

1. PowerLecture:Chapter 2 Molecules of Life

2. Learning Objectives • Understand how protons, electrons, and neutrons are arranged into atoms and ions. • Explain how the distribution of electrons in an atom or ion determines the number and kinds of chemical bonds that can be formed. • Know the various types of chemical bonds, the circumstances under which each forms, and the relative strengths of each type.

3. Learning Objectives (cont’d) • Understand the essential chemistry of water and of some common substances dissolved in it. • Understand how small organic molecules can be assembled into large macromolecules by condensation. Understand how large macromolecules can be broken apart into their basic sub­units by hydrolysis.

4. Learning Objectives (cont’d) • Memorize the functional groups presented and know the properties they confer when attached to other molecules. • Know the general structure of a monosaccharide with six carbon atoms, glycerol, a fatty acid, an amino acid, and a nucleotide. • Know the macromolecules into which these essential building blocks can be assembled by condensation.

5. Learning Objectives (cont’d) • Know where these carbon compounds tend to be located in cells or organelles and the activities in which they participate.

6. Impacts/Issues It’s Elemental

7. It’s Elemental • Life depends on chemical reactions. • An element is a fundamental form of matter that has mass and takes up space. • Organisms consist mostly of carbon, oxygen, hydrogen, and nitrogen. • Trace elements are needed only in small quantities.

8. Elements in the Human Body vs. Earth’s Crust Human Body Earth’s Crust Oxygen 65% Carbon 18 Hydrogen 10 Nitrogen 3 Calcium 2 Phosphorus 1.1 Potassium 0.35 Sulfur 0.25 Sodium 0.15 Chlorine 0.15 Magnesium 0.05 Iron 0.004 Oxygen 46.6% Silicon 27.7 Aluminum 8.1 Iron 5.0 Calcium 3.6 Sodium 2.8 Potassium 2.1 Magnesium 1.5

9. How Would You Vote? To conduct an instant in-class survey using a classroom response system, access “JoinIn Clicker Content” from the PowerLecture main menu. • Many communities add fluoride to drinking water supplies. Do you want it in yours? • a. Yes, screening lets people make informed reproductive decisions about the risk to their children. • b. No, therapies and medications for CF continue to improve; a person with CF can live a full life.

10. Section 1 Atoms, the Starting Point

11. Atoms, the Starting Point • Atoms are composed of smaller particles. • An atom is the smallest unit of matter that is unique to a particular element. • Atoms are composed of three particles: • Protons (p+) are part of the atomic nucleus and have a positive charge. Their quantity is called the atomic number (unique for each element). • Electrons (e-) have a negative charge. Their quantity is equal to that of the protons. They move around the nucleus. • Neutrons are also a part of the nucleus; they are neutral. Protons plus neutrons = atomic mass number.

13. Fig. 2.1, p. 16

14. Atoms, the Starting Point • Electron activity is the basis for organization of materials and the flow of energy in living things. • Isotopes are varying forms of atoms. • Atoms with the same number of protons (e.g., carbon has six) but a different number of neutrons (carbon can have six, seven, or eight) are called isotopes (12C, 13C, 14C). • Some radioactive isotopes are unstable and tend to decay into more stable atoms. • They can be used to date rocks and fossils. • Some can be used as tracers to follow the path of an atom in a series of reactions or to diagnose disease.

15. Section 2 Medical Uses for Radioisotopes

16. Medical Uses for Radioisotopes • Radioisotopes have many important uses in medicine. • Tracers are substances containing radioisotopes that can be injected into patients to study tissues or tissue function. • Radiation therapy uses the radiation from isotopes to destroy or impair the activity of cells that do not work properly, such as cancer cells. • For safety, clinicians usually use isotopes with short half-lives (the time it takes the isotope to decay to a more stable isotope).

17. Example of Radioactive Iodine Figure 2.2

18. Section 3 What Is a Chemical Bond?

19. What Is a Chemical Bond? • Interacting atoms: Electrons rule! • In chemical reactions, an atom can share electrons with another atom, accept extra electrons, or donate electrons. • Electrons are attracted to protons, but are repelled by other electrons. • Orbitals can be thought of as occupying shells around the nucleus, representing different energy levels.

20. Electron Arrangements Figure 2.4

21. What Is a Chemical Bond? • Chemical bonds join atoms. • A chemical bond is a union between the electron structures of atoms. • Having a filled outer shell is the most stable state for atoms. • The shell closest to the nucleus has one orbital holding a maximum of two electrons. • The next shell can have four orbitals with two electrons each for a total of eight electrons. • Atoms with “unfilled” orbitals in their outermost shell tend to be reactive with other atoms—they want to “fill” their outer shell with the maximal eight electrons allowed.

22. Shell Model Figure 2.5

23. What Is a Chemical Bond? • Atoms can combine into molecules. • Molecules may contain more than one atom of the same element; N2 for example. • Compounds consist of two or more elements in strict proportions. • A mixture is an intermingling of molecules in varying proportions.

25. Section 4 Important Bonds in Biological Molecules

26. Important Bonds in Biological Molecules • An ionic bond joins atoms that have opposite charges. • When an atom loses or gains one or more electrons, it becomes positively or negatively charged—an ion. • In an ionic bond, (+) and (–) ions are linked by mutual attraction of opposite charges, for example, NaCl.

27. Example of an Ionic Bond Figure 2.7a

28. Important Bonds in Biological Molecules • Electrons are shared in a covalent bond. • A covalent bond holds together two atoms that share one or more pairs of electrons. • In a nonpolarcovalent bond, atoms share electrons equally; H2 is an example. • In a polar covalent bond, because atoms share the electron unequally, there is a slight differ­ence in charge (electronegativity) between the two atoms participating in the bond; water is an example.

29. Examples of Covalent Bonds Figure 2.7b

30. Important Bonds in Biological Molecules • A hydrogen bond is a weak bond between polar molecules. • In a hydrogen bond, a slightly negative atom of a polar molecule interacts weakly with a hydro­gen atom already taking part in a polar covalent bond. • These bonds impart structure to liquid water and stabilize nucleic acids and other large molecules.

31. Example of a Hydrogen Bond Figure 2.7c

33. Section 5 Antioxidants

34. Antioxidants • Free radicals are formed by the process of oxidation. • Oxidation is the process whereby an atom or molecule loses one or more electrons. • Oxidation can produce free radicals that may “steal” electrons from other molecules. • In large numbers, free radicals can damage other molecules in a cell, such as DNA.

35. Antioxidants • Antioxidants are chemicals that can give up an electron to a free radical before it does damage to a DNA molecule. Figure 2.8

36. Section 6 Life Depends on Water Figure 2.9c

37. Life Depends on Water • Hydrogen bonding makes water liquid. • Water is a polar molecule because of a slightly negative charge at the oxygen end and a slightly positive charge at the hydrogen end. • Water molecules can form hydrogen bonds with each other. Figure 2.9a-b

38. Life Depends on Water • Polar substances are hydrophilic (water loving); nonpolar ones are hydrophobic (water dreading) and are repelled by water.

39. Life Depends on Water • Water can absorb and hold heat. • Water tends to stabilize temperature because it has a high heatcapacity—the ability to absorb considerable heat before its temperature changes. • This is an important property in evaporative and freezing processes.

40. Life Depends on Water • Water is a biological solvent. • The solvent properties of water are greatest with respect to polar molecules because “spheres of hydration” are formed around the solute (dissolved) molecules. • For example, the Na+ of salt attracts the negative end of water molecules, while the Cl- attracts the positive end. Figure 2.10

41. Section 7 Acids, Bases, and Buffers: Body Fluids in Flux

42. Acids, Bases, and Buffers • The pH scale indicates the concentration of hydrogen ions. • pH is a measure of the H+ concentration in a solution; the greater the H+ the lower the value on the pH scale. • The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).

43. The pH Scale Figure 2.11

44. Acids, Bases, and Buffers • Acids give up H+ and bases accept H+. • A substance that releases hydrogen ions (H+) in solution is an acid—for example, HCl. • Substances that release ions such as (OH-) that can combine with hydrogen ions are called bases (example: baking soda). • High concentrations of strong acids or bases can disrupt living systems both internal and external to the body. Figure 2.12

45. Acids, Bases, and Buffers • Buffers protect against shifts in pH. • Buffer molecules combine with, or release, H+ to prevent drastic changes in pH. • Bicarbonate is one of the body’s major buffers.

46. Acids, Bases, and Buffers • A salt releases other kinds of ions. • A salt is an ionic compound formed when an acid reacts with a base; example: HCl + NaOH  NaCl + H2O. • Many salts dissolve into ions that have key functions in the body; for example, Na, K, and Ca in nerve and muscles.

47. Section 8 Molecules of Life

48. Molecules of Life • Biological molecules contain carbon. • Only living cells synthesize the molecules characteristic of life—carbohydrates, lipids, proteins, and nucleic acids. • These molecules are organic compounds, meaning they consist of atoms of carbon and one or more other elements, held together by covalent bonds.

49. Molecules of Life • Carbon’s key feature: versatile bonding. • Living organisms are mostly oxygen, hydrogen, and carbon. • Much of the hydrogen and oxygen are linked as water. • Carbon can form four covalent bonds with other atoms to form organic molecules of several configurations.

50. Molecules of Life • Functional groups affect the chemical behavior of organic compounds. • By definition a hydrocarbon has only hydrogen atoms attached to a carbon backbone. • Functionalgroups—atoms or groups of atoms covalently bonded to a carbon backbone—convey distinct properties, such as solubility, to the complete molecule.