The Chemical Context of Life Chapter 2 The Chemical Context of Life

Ants & the Duroia Trees Ants use formic acid to prevent other plants from growing so that the Duroia trees can serve as their home.

You Must Know The three subatomic particles and their significance. The types of bonds, how they form, and their relative strengths.

A patient is diagnosed with anemia resulting from iron deficiency A patient is diagnosed with anemia resulting from iron deficiency. What is the best way to supplement the patient’s diet with iron? The patient should add fine metallic iron filings to his morning cereal. The patient should periodically suck on rusty nails. The patient should cook with a cast-iron skillet and eat vegetables with high iron content, such as spinach. The patient should eat more red meat. Answer c should increase the uptake of iron into the patient’s body and red blood cells. Answer d may also help, but may have other undesirable effects such as increased fat and cholesterol intake. Choice a will be ineffective, as the reduced (metallic) form of iron is not available to cells; choice b is only marginally better, and unpleasant. This question could lead to a discussion about biologically active forms (ionization states) of the elements. Based on Concept 2.1 on essential elements and Concept 2.3 on ionization. 4

I. Matter vs. Energy Matter Energy Has mass & takes up space Affected by gravity Consists of elements and compounds Energy Moves matter Potential, kinetic Ability to do work Conversions Sound, light, heat

Element Compound “pure” substance Can’t be broken down by “ordinary” means to another substance Ex. hydrogen (H), nitrogen (N) Compound 2 or more different elements combined in a fixed ratio Ex. H2O, CO2

Elements of Life 25 elements Hint: Remember CHNOPS 96% : O, C, H, N ~ 4% : P, S, Ca, K & trace elements (ex: Fe, I) Hint: Remember CHNOPS

II. Atomic Structure Atom = smallest unit of matter that retains properties of an element Subatomic particles: Mass (dalton or AMU) Location Charge neutron 1 nucleus proton +1 electron negligible shell -1

He 4 2 Mass # (protons + neutrons) symbol Atomic # (protons or electrons)

What do elements with atomic numbers 6, 14, and 22 have in common? A) same number of electrons B) same atomic mass C) same valence and will form the same number of covalent bonds D) all of the above E) none of the above Answer: c This question focuses on Concept 2.2. It highlights the fact that these elements have the same basic structures and therefore the same basic properties. 12

Isotopes # neutrons varies, but same # of protons Radioactive isotopes used as tracers (follow molecules, medical diagnosis) Uncontrolled exposure causes harm

More than one of the above options is correct. Water is a polar molecule because of the presence of ___________ bonds. ionic covalent polar covalent hydrogen More than one of the above options is correct. Answer: c This question focuses on the properties that result from different bonding patterns in molecules. 14

III. Chemical Bonds Strongest Bonds: Covalent: sharing of e- Polar: covalent bond between atoms that differ in electronegativity Nonpolar: e- shared equally; eg. O2 or H2

Based on the periodic table shown here, which elements will most likely form a covalent bond? Na and Cl C and O N and O Si and Cl H and H Answer: e is the best choice This question is aimed at Concept 2.3. It should lead to a discussion of the basic concepts of electronegativity and types of bonds. One way to change this question would be to add C and H as a choice. This could be used to lead into a more detailed discussion. 16

Na and Cl C and O, and N and O Si and Cl, and H and H all of the above Based on the periodic table shown here, which elements will most likely form a polar covalent bond? Na and Cl C and O, and N and O Si and Cl, and H and H all of the above none of the above Answer: b is the best choice This question is aimed at Concept 2.3. It should lead to a discussion of the basic concepts of electronegativity and types of bonds. 17

III. Chemical Bonds Strongest Bonds: Ionic: 2 ions (+/-) bond (givers/takers) Na+Cl- Affected by environment (eg. water)

Na and Cl, and Li and F C and O N and O Si and Cl all of the above Based on the periodic table shown here, which elements will most likely form an ionic bond? Na and Cl, and Li and F C and O N and O Si and Cl all of the above Answer: a is the best choice This question is aimed at Concept 2.3. It should lead to a discussion of the basic concepts of electronegativity and types of bonds. 19

Weaker Bonds: Hydrogen: H of polar covalent molecule bonds to electronegative atom of other polar covalent molecules

Weaker Bonds: Van der Waals Interactions: slight, fleeting attractions between atoms and molecules close together Weakest bond Eg. gecko toe hairs + wall surface

Bonds Covalent Ionic Hydrogen All important to life Form cell’s molecules Quick reactions/ responses H bonds to other electronegative atoms Strong bond Weaker bond (esp. in H2O) Even weaker Made and broken by chemical reactions

is an electrical attraction. is a unique chemical attraction. The force of the chemical bond (the attraction between the different elements) is an electrical attraction. is a unique chemical attraction. results from the sharing of electrons. results from atoms filling their outermost valence shell. Answer: a This question focuses on understanding the force that holds atoms together in molecules. Answers c and d are potentially correct but do not answer the question in terms of what creates the attraction. 23

All bonds affect molecule’s SHAPE  affect molecule’s FUNCTION Similar shapes = mimic morphine, heroin, opiates mimic endorphin (euphoria, relieve pain)

Chemical Reactions Reactants  Products Some reactions are reversible: Eg. 6CO2 + 6H2O  C6H12O6 + O2 Some reactions are reversible: Eg. 3H2 + N2 2NH3 Chemical equilibrium: point at which forward and reverse reactions offset one another exactly Reactions still occurring, but no net change in concentrations of reactants/products

Water and the Fitness of the Environment Chapter 3 Water and the Fitness of the Environment

You Must Know The importance of hydrogen bonding to the properties of water. Four unique properties of water, and how each contributes to life on Earth. How to interpret the pH scale. The importance of buffers in biological systems.

The four emergent properties of water that are important for life are: Cohesion, expansion upon freezing, high heat of evaporation, and capillarity Cohesion, moderation of temperature, expansion upon freezing, and solvent properties Moderation of temperature, solvent properties, high surface tension, and capillarity Heat of vaporization, high specific heat, high surface tension, and capillarity Polarity, hydrogen bonding, high specific heat, and high surface tension Answer: b

1. Polarity of H2O O- will bond with H+ on a different molecule of H2O = hydrogen bond H2O can form up to 4 bonds

2. Properties of H2O Cohesion = H-bonding between like molecules Surface Tension = measure of how difficult it is to break or stretch surface of liquid

Which one of the following hypothetical changes in a water molecule would tend to make it more polar? It is a linear molecule, as in H-O-H. Adjacent water molecules form covalent bonds with each other. The electronegativity values for H is increased. The electronegativity value for O is increased. All of the above would make water more polar. Answer: d

2. Properties of H2O Adhesion = bonding between unlike molecules Adhesion of H2O to vessel walls counters ↓ pull of gravity

2. Properties of H2O C. Transpiration = movement of H2O up plants H2O clings to each other by cohesion; cling to xylem tubes by adhesion

3. Moderation of temperature Heat = Total amount of KE in system Temperature = measure intensity of heat due to average KE of molecules Which has higher temp? More heat?

3. Moderation of temperature Water’s high specific heat Change temp less when absorbs/loses heat Large bodies of water absorb and store more heat  warmer coastal areas Create stable marine/land environment Humans ~65% H2O  stable temp, resist temp. change

3. Moderation of temperature Evaporative Cooling Water has high heat of vaporization Molecules with greatest KE leave as gas Stable temp in lakes & ponds Cool plants Human sweat

3. Moderation of temperature Insulation by ice – less dense, floating ice insulates liquid H2O below Life exists under frozen surface (ponds, lakes, oceans) Ice = solid habitat (polar bears)

Water has an unusually high specific heat Water has an unusually high specific heat. This is directly related to which one of the following? At its boiling point, water changes from liquid to vapor. More heat is required to raise the temperature of water. Ice floats in liquid water. Salt water freezes at a lower temperature than pure water. Floating ice can insulate bodies of water. Answer: b

4. Solvent of life Solution = liquid, homogeneous mixture of 2+ substances Solvent = dissolving agent (liquid) Solute = dissolved substance Water = versatile solvent

4. Solvent of life Hydrophilic Hydrophobic “like dissolves like” Affinity for H2O Repel H2O Polar, ions Nonpolar Cellulose, sugar, salt Oils, lipids Blood Cell membrane

Figure 3.8 A water-soluble protein

Which of the following explains what is happening when sodium chloride dissolves in water? More hydrogen bonds are forming between water molecules. Sodium and chloride atoms are separating from one another. Hydration shells are forming around the sodium and chloride ions. Covalent bonds are breaking and re-forming. Nonpolar substances are mixing with polar substances. Answer: c

5. Acids and Bases H2O H+ + OH- (gains proton) H+ + H2O  H3O+ (hydronium ion) (loses proton) H2O – H+  OH- (hydroxide ion)

5. Acids and Bases 7 14 Basic Acidic pH Scale Acid = increases H+ concentration (HCl) Base = reduces H+ concentration (NaOH) Most biological fluids are pH 6-8 7 14 Basic Acidic pH Scale

Figure 3.10 The pH scale and pH values of some aqueous solutions

Calculating pH [H+][OH-] = 10-14 pH = -log [H+] If [H+] = 10-6 M, then [OH-] = 10-8 pH = -log [H+] If [H+] = 10-2 -log 10-2 = -(-2) = 2 Therefore, pH = 2 If [OH-] = 10-10 [H+] = 10-4 -log 10-4 = -(-4) = 4 Therefore, pH = 4

H2CO3 (carbonic acid)  HCO3- (bicarbonate) + H+ 5. Acids and Bases Buffers: minimize changes in concentration of H+ and OH- in a solution (weak acids and bases) Buffers keep blood at pH ~7.4 If blood drops to 7 or up to 7.8, then death Carbonic Acid – Bicarbonate System: important buffers in blood plasma H2CO3 (carbonic acid)  HCO3- (bicarbonate) + H+

Ocean acidification threatens coral reef ecosystems CO2 mixed with seawater  Carbonic acid (lowers ocean pH)

The effects of acid precipitation on a forest

Scientists are concerned about increased concentrations of atmospheric carbon dioxide due to increased fossil fuel combustion and deforestation. In addition to major effects on global temperatures, increased levels of CO2 can threaten aquatic organisms in which way? forming more carbonic acid in a solution that raises the pH of seawater forming more carbonic acid that decreases the concentration of carbonate ions in seawater increasing photosynthesis rates in aquatic plants and algae decreasing the oxygen available for cellular respiration in aquatic organisms increasing the levels of harmful sulfur oxides and nitrous oxides Answer: b

Examples of Benefits to Life H2O Property Chemical Explanation Examples of Benefits to Life Cohesion polar H-bond like-like ↑gravity plants, trees Adhesion unlike-unlike plants xylem bloodveins Surface Tension diff. in stretch break surface bugswater Specific Heat Absorbs & retains E oceanmod temp protect marine life Evaporation liquidgas KE Cooling Homeostasis Universal Substance Polarityionic Good dissolver solvent