Chapter 2 – Atoms, Molecules and Life 2.1 What Are Atoms? 2.2 How Do Atoms Interact to Form Molecules? 2.3 Why Is Water So Important to Life?

Figure: 2-CO Title: Atoms, Molecules, and Life Caption: The basilisk lizard and this child learning to ice skate have something in common: both are "walking on water."

2.1 What Are Atoms? Atoms are the fundamental structural units of matter Atoms are composed of a nucleus, protons, neutrons and electrons We use models to simplify talking about atoms

electron shell e- e- p+ p+ p+ n n e- nucleus Hydrogen (H) Helium (He) Figure :2-1 Title: Atomic models Caption: Structural representations of the two smallest atoms, (a) hydrogen and (b) helium. In these simplified models, the electrons are represented as miniature planets, circling in specific orbits around a nucleus that contains protons and neutrons. e- nucleus Hydrogen (H) Helium (He)

Figure :2-T1 Title: Common Elements Important in Living Organisms Caption:

Radioactivity in Research Isotope is a form of an element where there is a different number of neutrons than protons Some isotopes are radioactive which means the nucleus is unstable and will break down releasing radiation

PET = positron emission tomography detector ring Figure: E2-1 Title: How positron emission tomography works PET = positron emission tomography

Atoms Positive and negative attract Electrons are in held around the nucleus in “shells” The first “shell” holds two electrons The next “shells” hold eight electrons

Copyright © 2005 Pearson Prentice Hall, Inc. FIGURE 2-2 Electron shells in atoms Most biologically important atoms have at least two shells of electrons. The first shell, closest to the nucleus, can hold two electrons; the next shell holds a maximum of eight electrons. More-distant shells can hold larger numbers of electrons. Copyright © 2005 Pearson Prentice Hall, Inc.

Energy Capture and Release Life depends on electrons capturing and releasing energy Electron shells correspond to energy levels Energy exciting an atom causes an electron jump from a lower- to higher-energy shell Later, the electron falls back into its original shell, releasing the energy Copyright © 2005 Pearson Prentice Hall, Inc.

Copyright © 2005 Pearson Prentice Hall, Inc. FIGURE 2-3 Energy capture and release Copyright © 2005 Pearson Prentice Hall, Inc.

Copyright © 2005 Pearson Prentice Hall, Inc. FIGURE 2-3 Energy capture and release Copyright © 2005 Pearson Prentice Hall, Inc.

Copyright © 2005 Pearson Prentice Hall, Inc. FIGURE 2-3 Energy capture and release Copyright © 2005 Pearson Prentice Hall, Inc.

2.2 How Do Atoms Interact to Form Molecules? A molecule consists of two or more atoms of the same or different elements A compound means two different elements Inert vs. reactive

Reactive Inert (Nobel Gases) electron shell e- e- p+ p+ p+ n n e- Figure :2-1 Title: Atomic models Caption: Structural representations of the two smallest atoms, (a) hydrogen and (b) helium. In these simplified models, the electrons are represented as miniature planets, circling in specific orbits around a nucleus that contains protons and neutrons. e- nucleus Hydrogen (H) Helium (He) Reactive Inert (Nobel Gases)

2.2 How Do Atoms Interact to Form Molecules? Chemical bonds are atoms gaining stability by losing, gaining or sharing electrons Chemical bonds are attractive forces Chemical reactions are the making or breaking of chemical bonds

Ions interact to form ionic bonds Sodium atom (neutral) Na Chlorine atom (neutral) Cl 11p+ 11n 17p+ 18n Atoms that have lost or gained 1 or 2 electrons are charged and called ions Ions interact to form ionic bonds 11p+ 11n 17p+ 18n Sodium ion (+) Chloride ion (–) Cl– Na+ Caption: (a) Sodium has only one electron in its outer electron shell; chlorine has seven. (b) Sodium can become stable by losing an electron, and chlorine can become stable by gaining an electron. Sodium becomes a positively charged ion and chlorine a negatively charged ion. (c) Because oppositely charged particles attract one another, the resulting sodium ions (Na+) and chloride ions (Cl–) nestle closely together in a crystal of salt, NaCl. An ionic compound: NaCl Na+ Cl–

2.2 How Do Atoms Interact to Form Molecules? Uncharged atoms can become stable by sharing electrons, forming covalent bonds Covalent bonds vary in strength but are always stronger than ionic bonds Nonpolar vs. polar covalent bonds

Nonpolar covalent bonding Hydrogen (H–H or H2) Figure :2-4 part a Title: Covalent bonds involve shared electrons part a Nonpolar covalent bonding Caption: In hydrogen gas (top), an electron from each hydrogen atom is shared, forming a single nonpolar covalent bond. In oxygen gas (bottom), two oxygen atoms share four electrons, forming a double nonpolar covalent bond. 8p+ 8p+ 8n 8n Oxygen (O=O or O2)

Polar covalent bonding (slightly negative) 8p+ 8n Figure :2-4 part b Title: Covalent bonds involve shared electrons part b Polar covalent bonding Caption: Oxygen lacks two electrons to fill its outer shell, so oxygen can form polar covalent bonds with two hydrogen atoms, creating water. Oxygen exerts a greater pull on the electrons than does hydrogen, so the “oxygen end” of the molecule has a slight negative charge and the “hydrogen” end has a slight positive charge. Question In water's polar bonds, why is oxygen's pull on electrons greater than hydrogen's? (slightly positive) Water (H–O–H or H2O)

Figure :2-T2 Title: Chemical Bonds Caption:

Figure :2-UN3 Title: Bonding patterns of atoms commonly found in biological molecules Caption:

Figure :2-T3 Title: Bonding Patterns of Atoms Commonly Found in Biological Molecules Caption:

Free Radicals A molecule with an unpaired electron Steals electrons from other molecules Free radicals contribute to cancer and Alzheimer’s disease Free radicals can be increased by exposure to the sun (radiation) and many chemicals

Antioxidants React with free radicals to render them harmless Vitamin C and Vitamin E Many can be found in a healthy diet Your risk of cancer can be lowered 50% simply by eating 5 fruits and veggies a day

O (–) H (+) H (+) H (+) O (–) H (+) hydrogen bonds Figure :2-5 Title: Caption: The partial charges on different parts of water molecules produce weak attractive forces called hydrogen bonds (dotted lines) between the oxygen and hydrogen atoms in adjacent water molecules. H (+) H (+) O (–) H (+) hydrogen bonds

2.3 Why Is Water So Important to Life? Water interacts with many other molecules A solvent is capable of dissolving a wide range of substances Water is a polar solvent and can dissolve proteins, salts and sugars

solutes solution Water as a solvent Na+ H Cl– O– H Cl– H H Na+ O Na+ Figure :2-6 Title: Water as a solvent Caption: When a salt crystal is dropped into water, the water surrounds the sodium and chloride ions with oppositely charged poles of its molecules. Thus insulated from the attractiveness of other molecules of salt, the ions disperse, and the whole crystal gradually dissolves. H H Na+ O Na+ solution Water as a solvent

Polar vs. Nonpolar Ions and polar molecules are hydrophilic (Greek for “water-loving”) Uncharged and nonpolar molecules are hydrophobic (“water-fearing”) Think of oil and vinegar

Copyright © 2005 Pearson Prentice Hall, Inc. FIGURE 2-12 Oil and water don't mix Yellow oil has just been poured into this beaker of water and is rising to the surface. Oil floats because it is lighter than water, and it forms droplets in water because it is a hydrophobic, nonpolar molecule that is not attracted to the water's polar molecules. Copyright © 2005 Pearson Prentice Hall, Inc.

water hydrogen bond glucose hydroxyl group Figure :2-7 Title: Water dissolves many biological molecules Caption: Many biological molecules dissolve in water because they have polar parts—for example, OH– (hydroxyl) groups—that can form hydrogen bonds with water molecules. Here, sugar dissolves because hydrogen bonds form between the hydroxyl groups on a glucose molecule (a simple sugar) and surrounding water molecules. Question Why is it important to human physiology that sugars dissolve easily in water?

2.3 Why Is Water So Important to Life? Cohesion is the tendency of molecules to stick together Water’s high cohesion creates surface tension (Water also has a high specific heat)

Figure :2-8 Title: Cohesion among water molecules Caption: (a) Buoyed by surface tension, the fishing spider rushes across the surface of a pond to capture an insect. (b) In giant redwoods, cohesion holds water molecules together in continuous strands from the roots to the topmost leaves as high as 300 feet above the ground.

(–) (+) O + H O H H H water (H2O) hydroxide ion (OH–) hydrogen ion Figure: 2-UN1 Title: Ionization of Water Caption: Although water is generally regarded as a stable compound, a small fraction of water molecules are ionized—that is, broken apart into hydrogen ions (H+) and hydroxide ions (OH–). hydroxide ion (OH–) hydrogen ion (H+)

2.3 Why Is Water So Important to Life? Water-Based Solutions Can Be Acidic, Basic, or Neutral If H+ exceeds OH-, the solution is acidic If OH- exceeds H+, the solution is basic If they are equal, the solution is neutral

Figure :2-9 Title: The pH scale Caption: H+ concentration (moles/liter) pH value 100 1-molar hydrochloric acid (HCI) 10–1 1 stomach acid lime juice 10–2 2 lemon juice 10–3 3 "acid rain" (2.5–5.5) vinegar, cola, orange juice, tomatoes increasingly acidic (H+ > OH–) 10–4 4 beer 10–5 5 black coffee, tea normal rain (5.6) urine (5.7) 10–6 – 6 6 neutral (H+ = OH–) 10–7 – 7 7 pure water (7.0) saliva blood, sweat (7.4) 10–8 – 8 8 seawater (7.8 – 8.3) Figure :2-9 Title: The pH scale Caption: The pH scale expresses the concentration of hydrogen ions in a solution on a scale of 0 (very acidic) to 14 (very basic). Each unit of change on the scale represents a tenfold change in the concentration of hydrogen ions. Lemon juice, for example, is about 10 times more acidic than orange juice, and the most severe acid rains in the northeastern United States are almost 1000 times more acidic than normal rainfall. Except for the inside of your stomach, nearly all the fluids in your body are finely adjusted to a pH of about 7.4. The color-coding shown corresponds to a common pH indicator dye, bromthymol blue. 10–9 – 9 9 baking soda 10–10 – 10 10 phosphate detergents chlorine bleach milk of magnesia increasingly basic (H+ < OH–) 10–11 – 11 11 household ammonia some detergents (without phosphates) 10–12 – 12 12 washing soda 10–13 – 13 13 oven cleaner 10–14 – 14 14 1-molar sodium hydroxide (NaOH)

2.3 Why Is Water So Important to Life? A buffer helps maintain a solution at a relatively constant pH (homeostatis) Water moderates the effects of temperature changes (due to high specific heat) 1 calorie of energy will rise the temperature of water 1 ºC (only 0.6 calories are needed for alcohol, 0.2 for salt, 0.02 for granite)

Water forms an unusual solid -> ICE Figure: 2-UN2 Title: Comparison of liquid and solid phases of water Water forms an unusual solid -> ICE

Figure :E2-2 Title: Chocolate Caption: Cocoa powder is derived from cacao beans (inset), which grow on trees in tropical regions of the Americas.