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CHAPTER 2

CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE. ESLRS: Core Learning Critical Thinking Communication Community. STANDARDS: Investigation & Experimentation: 1 a,b,c,d,j Chemistry: 1 a,d,e; 2 a-h; 5 a-d; more… Cell Biology: 1 b, f, g, & h. Figure 2.0 Bombardier beetle.

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CHAPTER 2

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  1. CHAPTER 2 THE CHEMICAL CONTEXT OF LIFE

  2. ESLRS:Core LearningCritical ThinkingCommunicationCommunity STANDARDS: Investigation & Experimentation: 1 a,b,c,d,j Chemistry: 1 a,d,e; 2 a-h; 5 a-d; more… Cell Biology: 1 b, f, g, & h

  3. Figure 2.0 Bombardier beetle This bomardier beetle illustrates the interdisciplinary nature of scientific research... Focus today is CHEMISTRY

  4. Matter- anything that takes up space and has mass. Element- substance that cannot be broken down to other substances by chemical reactions. 92 elements exist in nature LIFE REQUIRES 25 C, H, N, O - 96% P, S, Ca, K - 4% and trace elements

  5. Table 2.1 Naturally Occurring Elements in the Human Body

  6. What kinds of molecules will an animal, plant, or bacterium take up as necessary building blocks and excrete as waste products?What elements are these molecules made of?DISCUSS.

  7. Water- solvent of lifeCarbohydratesLipidsProteinsNucleic AcidsCarbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

  8. Which elements are most essential for life? • 96%: • Carbon • Hydrogen • Oxygen • Nitrogen

  9. The other 4%? • Phosphorus • Sulfur • Calcium • Potassium

  10. I. Elements essential to life C carbon H hydrogen N nitrogen O oxygen P phosphorus S sulfur Ca calcium K potassium

  11. And trace elements… I iodine Fe iron specific to the species Enlarged thyroid gland

  12. Goiter- Caused by iodine deficiency. Swollen thyroid gland. Hormones thyroxine and triiodotyronine (T3)contain Iodine. Figure 2.4 Goiter

  13. Figure 2.3 Nitrogen deficiency

  14. Atomic structure determines the behavior of an atom. A. STRUCTURE OF ATOMS Electron- negative charge Proton- positive charge Neutron- no charge

  15. ATOM = the entire stadium NUCLEUS = pencil eraser on the pitcher’s mound ELECTRONS = gnats buzzing around stadium

  16. Figure 2.11 Electron orbitals Electron Orbitals are the three-dimensional space where an electron is found 90% of the time. No more than 2 electrons can occupy the same orbital. You don’t need to remember this 1s, 2s, 2p etc. stuff for AP Bio

  17. 2 electrons fit in the first energy shell Outer shells can hold up to 8 electrons This is the “octet rule” Figure 2.10 Electron configurations of the first 18 elements Valence electrons are the outermost electrons- they determine the bonding behavior of the atom. Atoms with unpaired electrons are reactive.

  18. HONK! • Hydrogen - 1 • Oxygen - 2 • Nitrogen - 3 • Carbon - 4 What are the valences of the “essential” elements? This tells you how many bonds each needs to make.

  19. PHOTON is a packet of radiation from the sun. Electrons exist at fixed levels of potential energy called electron shells. Outer shells have more energy. Electrons can shift energy level by absorbing or releasing energy. Ex. Photons of light can cause a quantum leap- electrons jump shells Heat is released when the electrons fall back to the lower energy level.

  20. Isotopes have the same # of P & E but a different # of neutrons.

  21. In nature, an element occurs as a mixture of its isotopes.

  22. Radioactive isotopes • Are unstable. • The nucleus decays spontaneously, giving off particles and energy. • When the decay changes the # of PROTONS, it transforms the element. • Half-life is the length of time required for half of a given number of initial number of atoms of that isotope to be transformed to the decay element. a) CAN BE USED TO DATE FOSSILS • Radioactive Carbon 14 decays to Nitrogen 14 through beta decay half-life = 5730 years so used in archaeology to determine the age of carbonaceous materials up to 60,000 years old. • Uranium-238 decays to Lead…half-life = 4.5 billion years… used to date OLD OLD fossils, like 1st cells.

  23. b) CAN BE USED TO TRACE ATOMS THROUGH METABOLISM • Radioactive tracers are important diagnostic tools in medicine. • Used to follow atoms through metabolism, the chemical processes of an organism • ex. Old “breath” test for ulcers caused by Heliobacter pylori used C14 labeled urea- which will be converted to ammonia and radioactive carbon dioxide. • ex: kidney disorders can be detected by measuring the radioactivity of urine w/ a scintillation counter. • ex. Metabolic activity (brain activity) can be observed using a PET scanner.

  24. The Calvin Cycle Used C14

  25. Phosphorus 32 has a half-life of 14 days Part of DNA nucleotides Used in biotech research. Figure 2.6 Using radioactive isotopes to study cell chemistry

  26. Radiation from decaying isotopes damages cellular molecules. Mutates DNA causing cancer, birth defects, death. Figure 2.8 The Tokaimura nuclear accident Danger: Nuclear Power Plant disasters.

  27. Unless the atom is a noble gas, it will react with other atoms. • Chemical bonds are interactions between atoms that allow them to complete their valence shells. • Ionic and Covalent bonds are strong. • Ionic bonds are weak in the presence of water. • Hydrogen bonds are weak- but plentiful. • Van der Waals interactions are extremely weak and only occur when molecules are close together. II. the glue of life: chemical bonds

  28. Ions are charged atoms. Unequal Protons & Electrons. cation anion Ionic bonds happen when one electron is transferred to Another atom making a + and - ion. Opposites attract. Figure 2.14 Electron transfer and ionic bonding “electrostatic attraction” Ionic bond = Ionic attraction

  29. Ionic compound Figure 2.15 A sodium chloride crystal

  30. A Molecule is a collection of two or more atoms bonded together. Ex. Oxygen O=O Water H-O-H Salt Na+Cl-

  31. A compound is a substance consisting of two or more Elements combined in a fixed ratio. Sodium Chloride- edible compound Sodium- a metal Chlorine- poisonous gas

  32. Notice the EMERGENT PROPERTY of “flavor enhancement” … the compound formed has different qualities than the elements below in a level of organization of matter! Sodium Chloride- edible compound Sodium- a metal Chlorine- poisonous gas

  33. Covalent Bonds = When atoms share electrons. The goal is to get the valence shells full. Hydrogen - 1 bond Oxygen- 2 bonds Nitrogen- 3 bonds Carbon- 4 bonds Figure 2.12 Covalent bonding in four molecules

  34. Methane CH4 Carbon & Hydrogen Share the electrons Evenly. NONPOLAR COVALENT BOND Figure 2.12x Methane Smells bad. Contributes to global warming.

  35. HARRIS RANCH

  36. POLAR COVALENT BOND = unequal sharing of electrons Water is a polar covalent molecule. The oxygen is more electronegative than hydrogen… the shared electrons spend more time around the Oxygen nucleus than the Hydrogen resulting in “partial” negative and positive charge. Figure 2.13 Polar covalent bonds in a water molecule

  37. Is the attraction of a particular kind of atom for the electrons of a covalent bond. • Carbon & Hydrogen are =‘ly electronegative. • So molecules that are composed only of these elements are nonpolar- they have no charge. • OXYGEN & NITROGEN are EXTREMELY ELECTRONEGATIVE • So molecules that have these elements in them are polar where the N or O is bonded. • Will you remember this? • NO!!!!! I mean yes. Electronegativity

  38. form when a partially positive hydrogen atom covalently bonded to one electronegative atom is also bonded to a partially negative electronegative atom on another molecule. Bond from the + Hydrogen of one Polar molecule Bonding to the - part of the other. These are weak bonds Drawn as a dotted line. Hydrogen bonds

  39. Water molecules H bonded Water

  40. DNA- hydrogen bonds hold the two strands together(via nitrogen containing bases).

  41. Notice how all of these Bonds function in various Biological phenomena: Ex. #1 Immune System Antigen-Antibody Specificity Van der Waals interactions (negative and positive “hot spots”) are weak and only occur when molecules are very close together.

  42. Ex. #2 Neurotransmitter Stimulating Next neuron Figure 2.18 Molecular shape and brain chemistry

  43. Both block pain receptors from sending signal Figure 2.19 A molecular mimic Man made Endorphin = endo + morphine

  44. CHAPTER 3 Water and the Fitness of the Environment

  45. Figure 3.0 Earth

  46. Figure 3.x1 Water

  47. Hydrogen bonding of water results in these Emergent Properties Versatility as a solvent Cohesive behavior Ability to stabilize temperature Expansion upon freezing The polarity of water results in hydrogen bonding

  48. Solute + Solvent Solution Water can form hydration shells around ions & break Ionic bonds. Note- the Cl- is surrounded by the + hydrogen parts of water & the Na+ is surrounded by the - oxygen parts of water. Water is the “universal solvent”… it dissolves better than most things… but not everything- it is the solvent of life.

  49. Water, as the universal solvent, supports chemical reactions that occur within cells.

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