The Stuff of Life Copyright © 2009 Pearson Education, Inc.

Why are chemistry concepts essential to the study of life?  Facts, laws, and theories of the field apply to all living things.  Chemicals are at the base of the biological hierarchy.  Life results from the ordering of atoms into molecules and the interactions of these molecules within cells. Copyright © 2009 Pearson Education, Inc.

I. The Matter of Life ( ) A. Matter 1. Matter is… 2. Matter is composed of chemical elements B. Elements 1. a substance that cannot be broken down to other substances naturally occurring elements elements found in organisms; some found in minute amounts (trace elements) Copyright © 2009 Pearson Education, Inc.

II. Elements can combine to form compounds (2.3) A. Chemical Compound 1. substance consisting of two or more different elements combined in a fixed ratio 2. Most in organisms contain C, H, O, and N (ex. Proteins & DNA) 3. Different arrangements of elements provide unique properties for each compound; different emergent properties appear –Many compounds consist of only two elements, example water (H 2 O) and table salt (NaCl) Copyright © 2009 Pearson Education, Inc.

Sodium Chloride Chlorine Sodium + Check for Understanding: 1.Which four chemical elements are most abundant in living things? 2.How do the compounds water and salt differ from each other? 3.*How is a compound different than a molecule?

B. Each element has its own kind of atom 1. An atom is the smallest unit of matter that still retains the properties of a element –Atoms are made of over a hundred subatomic particles, but only three are important for biological compounds 2. Sub-Atomic Particles –Proton—has a single positive electrical charge –Electron—has a single negative electrical charge –Neutron—is electrically neutral Copyright © 2009 Pearson Education, Inc.

III. Atomic Structure (2.4) A. Nucleus  protons (+) and neutrons B. Energy Levels or Shells  electrons (-) 1 st orbital, max 2e- 2 nd orbital, max 8e- 3 rd orbital, max 8e- C. Valence e- D. An atom has no charge

IV. Periodic Table- Appendix 2 A. Atomic number- # of protons B. Atomic mass number - sum of protons + neutrons C. Element symbol: P, Cl, Mg or He D. Electron Distribution Diagram

Electron cloud Protons 2e – Nucleus Electrons Mass number = 4 Neutrons What element do these diagrams represent? Why do the e- stay near the nucleus?

Check for Understanding On an index card describe the structure of an oxygen atom on an index card. Reference your periodic table for its atomic number. In your answer include the terms electron, proton, neutron. Describe how you would identify the number of neutrons found in an atom of oxygen and state the answer.

Check for Understanding In your notebook draw the atomic structure of oxygen. Include the element symbol, electron configuration, and indicate the number of neutrons and protons at the location where these subatomic particles would be found.

Electron cloud Protons 6e – Nucleus Electrons Mass number = 12 Neutrons What element does this diagram represent?

V. COUNTING ATOMS A. Molecular Formula, H 2 O 1. Subscript 2. Coefficient B. Examples: Water H 2 O Aspirin C 9 H 8 O 4 Acetic Acid (vinegar) 2C 2 H 4 O 2 TNT (explosive)C 7 H 5 (NO 2 ) 3

What differs between Carbon-12, Carbon-13, and Carbon-14?

VI. Isotopes ( ) A. All atoms of an element have the same atomic number, some differ in mass number 1. The variations are isotopes, which have the same numbers of protons and electrons but different numbers of neutrons 2. For example, carbon isotopes –One isotope of carbon has 8 neutrons instead of 6 (written 14 C) –Unlike 12 C, 14 C is an unstable (radioactive) isotope that gives off energy Copyright © 2009 Pearson Education, Inc.

B. Radioactive Isotopes(2.5) 1. Living cells cannot distinguish between isotopes of the same element 2. Use as tracers, detect with imaging instruments Copyright © 2009 Pearson Education, Inc. PET image of healthy brain (left) and Alzheimer’s patient (right). Red and yellow indicate high level of PIB bound to beta-amyloid plaques. PIB contains the RI.

3. Benefits - basic research (study processes such as photosynthesis) - medical diagnosis - radioactive dating using half lives 4. Dangers –Uncontrolled exposure can cause damage to some molecules in a living cell, especially DNA –Chemical bonds are broken by the emitted energy, which causes abnormal bonds to form Copyright © 2009 Pearson Education, Inc.

VII. Electron arrangement determines the chemical properties of an atom (2.6) A. Only e- are involved in chemical activity 1. look at # of e- in the outermost shell 2. atoms want a filled outermost shell - not filled, atom is unstable and reactive - therefore atom will accept, donate, or share e- to become stable - results in attraction between atoms called chemical bonds Copyright © 2009 Pearson Education, Inc.

Magnesium Lithium Hydrogen Third shell First shell Second shell Sodium Beryllium Aluminum Boron Silicon Carbon Phosphorus Nitrogen Sulfur Oxygen Chlorine Fluorine Argon Neon Helium What patterns or trends can you identify from this illustration of the periodic table of elements?

Essential Question: Why do atoms combine to form molecules or compounds? 1.Valence shell not filled  unstable and reactive. 2.Lose/Gain e-  ion (charged atom) will be attracted to oppositely charged ion Remember atoms are electrically neutral unless they gain or lose an electron.

VIII. Ionic Bonding (2.7) A. Ion 1. an atom or molecule with an electrical charge resulting from gain or loss of electrons 2. Cation- atom loses e-, a (+) charge results 3. Anion- atom gains e-, a (-) charge results B. Ionic Bond- attraction holding together a cation and an anion C. Bond easily broken Copyright © 2009 Pearson Education, Inc.

Na Sodium atom Transfer of electron Cl Chlorine atom 1.What will be the charge on the sodium ion? 2.What will be the charge on the chlorine ion? 3.What is a cation? 4.What is an anion? 5.How are ions different from atoms? Understanding Ionic Bonds

Na Sodium atom Transfer of electron Cl Chlorine atom Na + Sodium ion Cl – Chloride ion Sodium chloride (NaCl) + – Understanding Ionic Bonds

Na + Cl – Figure 2.7B A crystal of sodium chloride.

IX. Covalent Bonding (2.8) A. results when atoms share outer-shell electrons B. a molecule is formed when atoms are held together by covalent bonds C. Strong, not easily broken D. Can have: 1. 1 pair share, single bond, H-H, H pair share, double bond, O=O, O pair share, triple bond, N=N, N 2 Copyright © 2009 Pearson Education, Inc. Structural formula -- Molecular formula

What does a structural formula show you that a molecular formula does not?

E. Atoms in a covalently bonded molecule continually compete for shared electrons –The attraction (pull) for shared electrons is called electronegativity –More electronegative atoms pull harder F. In molecules of only one element, the pull toward each atom is equal, b/c each atom has the same electronegativity –bonds formed called nonpolar covalent bonds Copyright © 2009 Pearson Education, Inc.

G. In molecules with different elements, like water, atoms have different electronegativities –Oxygen attracts the shared e- more strongly than hydrogen –shared e- spend more time near oxygen –result is a polar covalent bond H. Polar molecules (2.9) - molecule with unequal distribution of charge - ex, H 2 O the oxygen atom has a slight (-) charge and the hydrogens have a slight (+) charge Copyright © 2009 Pearson Education, Inc.

(–) O HH (+) Check for Understanding: 1.Which element in water is the electronegative atom? 2.What is the overall net charge of a water molecule? 3.How might being polar help water molecules stick together?

Hydrogen bond

X. Hydrogen Bonding (2.0) A. Weaker than covalent bond B. Hydrogen, as part of a polar covalent bond, will share attractions with other electronegative atoms (like O and N) C. B/C the (+) charged region is always a H atom, the bond is called a hydrogen bond Copyright © 2009 Pearson Education, Inc. Animation: Water Structure

XI. Chemical Reactions (2.18) A. Atoms react due to their electron configurations B. Chemical rxns rearrange matter by making and breaking chemical bonds C. All chem rxn accompanied by change in energy 1. exothermic- E (heat) released to surroundings 2. endothermic- E (heat)absorbed from surroundings D. Some rxns can be spontaneous while others require activation energy Copyright © 2009 Pearson Education, Inc.

A + B  AB Reactants Products E. Balancing Chemical Reactions 1. Conservation of Mass 2. # and type of atoms on reactants side must be found on products side 3. H 2 + O 2  H 2 O, balance the equation Copyright © 2009 Pearson Education, Inc. yields

WATER’S LIFE-SUPPORTING PROPERTIES Copyright © 2009 Pearson Education, Inc.

I. H bonds make liquid water cohesive (2.11) A. H bonding causes molecules to stick together, a property called cohesion –Cohesion is much stronger for water than other liquids B. Cohesion is related to surface tension—a measure of how difficult it is to break the surface of a liquid –Hydrogen bonds are responsible for surface tension Copyright © 2009 Pearson Education, Inc.

C. Cohesion is the tendency for _______________________ D. Adhesion is the tendency for _______________________  In what ways does this property of water support life?

Water-conducting cells Adhesion Cohesion 150 µm Direction of water movement

What effect does soap have on surface tension? _________________________ Soap has a water loving end and a water hating end. When it is added to water, it separates the water molecules and reduces surface tension.

II. Water’s H bonds moderate temperature (2.12) A. Due to H bonds, water has a greater ability to resist temperature change than other liquids 1. Heat is the energy associated with movement of atoms and molecules in matter 2. Temperature measures the intensity of heat B. Heat must be absorbed to break H bonds; heat is released when H bonds form Copyright © 2009 Pearson Education, Inc. Q: In what ways does this property of water support life?

III. Ice is less dense than liquid water (2.13) *think about the arrangement of water molecules in a gas, liquid, and solid A. At freezing, a water molecule can make 4 H bonds with neighbors 1. A 3-D crystal results 2. Space between molecules B. Due to H bonds, ice is less dense than water, so it floats Copyright © 2009 Pearson Education, Inc. Q: In what ways does this property of water support life?

Liquid water Hydrogen bonds constantly break and re-form Ice Hydrogen bonds are stable Hydrogen bond

IV. Water is the solvent of life (2.14) A. Solution 1. liquid consisting of a uniform mixture of two or more substances 2. The dissolving agent is the solvent 3. The substance that is dissolved is the solute B. Water is a versatile solvent 1. due to its polarity 2. easily dissolves polar substances and ions Copyright © 2009 Pearson Education, Inc. Q: In what ways does this property of water support life?

Ion in solution Salt crystal Notice the orientation of the water molecules.

Why doesn’t oil dissolve in water? Oil is non polar, so does not interact with water. It forms a single layer above it, sticking its water fearing ends out.

2.15 The chemistry of life is sensitive to acidic and basic conditions  A few water molecules can break apart into ions –Some are hydrogen ions (H + ) –Some are hydroxide ions (OH – ) –Both are extremely reactive –A balance between the two is critical for chemical processes to occur in a living organism Copyright © 2009 Pearson Education, Inc.

2.15 The chemistry of life is sensitive to acidic and basic conditions  Chemicals other than water can contribute H + to a solution –They are called acids –An example is hydrochloric acid (HCl) –This is the acid in your stomach that aids in digestion  An acidic solution has a higher concentration of H + than OH – Copyright © 2009 Pearson Education, Inc.

2.15 The chemistry of life is sensitive to acidic and basic conditions  Some chemicals accept hydrogen ions and remove them from solution –These chemicals are called bases –For example, sodium hydroxide (NaOH) provides OH – that combines with H + to produce H 2 O (water) –This reduces the H + concentration Copyright © 2009 Pearson Education, Inc.

2.15 The chemistry of life is sensitive to acidic and basic conditions  A pH scale (pH = potential of hydrogen) is used to describe whether a solution is acidic or basic –pH ranges from 0 (most acidic) to 14 (most basic) –A solution that is neither acidic or basic is neutral (pH = 7) Copyright © 2009 Pearson Education, Inc.

Acidic solution pH scale Battery acid Lemon juice, gastric juice Grapefruit juice, soft drink, vinegar, beer Tomato juice Rain water Human urine Saliva Pure water 6 7 Human blood, tears Seawater Milk of magnesia Household ammonia Household bleach Oven cleaner Neutral solution Basic solution NEUTRAL [H + ]=OH – ] Increasingly ACIDIC (Higher concentration of H + ) 14 Increasingly BASIC (Lower concentration of H + )

Acidic solution Neutral solution Basic solution

2.16 CONNECTION: Acid precipitation and ocean acidification threaten the environment  When we burn fossil fuels (gasoline and heating oil), air-polluting compounds and CO 2 are released into the atmosphere –Sulfur and nitrous oxides react with water in the air to form acids –These fall to Earth as acid precipitation, which is rain, snow, or fog with a pH lower than 5.6 –Additional CO 2 in the atmosphere contributes to the “greenhouse” effect and alters ocean chemistry Copyright © 2009 Pearson Education, Inc.

2.17 EVOLUTION CONNECTION: The search for extraterrestrial life centers on the search for water  An important question is, has life evolved elsewhere? –Water is necessary for life as we know it  The National Aeronautics and Space Administration (NASA) has evidence that water was once abundant on Mars –Scientists have proposed that reservoirs of water beneath the surface of Mars could harbor microbial life Copyright © 2009 Pearson Education, Inc.

August 1999 September 2005 New deposit

CHEMICAL REACTIONS Copyright © 2009 Pearson Education, Inc.

2 H 2 O2O2 2 H 2 O

electron transfer between atoms creates electron sharing between atoms creates Chemical Bonds atomic number of each element water nonpolar covalent bonds (e) ions (f) (g) (h) attraction between ions creates unequal sharing creates can lead to example is equal sharing creates has important qualities due to polarity and have positively charged have neutral have negatively charged number in outer shell determines formation of number may differ in number present equals (a) Atoms (b) (c) (d)

atomic number of each element have positively charged have neutral have negatively charged number in outer shell determines formation of number may differ in number present equals (a) Atoms (b) (c) (d)

electron transfer between atoms creates electron sharing between atoms creates Chemical Bonds water nonpolar covalent bonds (e) ions (f) (g) (h) attraction between ions creates unequal sharing creates can lead to example is equal sharing creates has important qualities due to polarity and

Potassium atomFluorine atom

You should now be able to 1.Describe the importance of chemical elements to living organisms 2.Explain the formation of compounds 3.Describe the structure of an atom 4.Distinguish between ionic, hydrogen, and covalent bonds 5.List and define the life-supporting properties of water 6.Explain the pH scale and the formation of acid and base solutions 7.Define a chemical reaction and explain how it changes the composition of matter Copyright © 2009 Pearson Education, Inc.