Water Chemistry Chapter 3 PDF

The Molecule That Supports All of Life a. Water is the biological medium on Earth b. The only common substance to exist in the natural environment in all three physical states of matter c. The structure of the water molecule allows it to interact with other...

The Molecule That Supports All of Life a. Water is the biological medium on Earth b. The only common substance to exist in the natural environment in all three physical states of matter c. The structure of the water molecule allows it to interact with other molecules d. Water’s unique emergent properties help make Earth suitable for life © 2015 Pearson Education Ltd Concept 3.1: Polar covalent bonds in water molecules result in hydrogen bonding a. In the water molecule, the electrons of the polar covalent bonds spend more time near the oxygen than the hydrogen b. The water molecule is thus a polar molecule: the overall charge is unevenly distributed c. Polarity allows water molecules to form hydrogen bonds with each other © 2015 Pearson Education Ltd Figure 3.2  − Hydrogen  bond + Polar covalent bonds   − +   − +   − + © 2015 Pearson Education Ltd  a. Four of water’s properties that facilitate an environment for life are a. Cohesive behavior b. Ability to moderate temperature c. Expansion upon freezing d. Versatility as a solvent © 2015 Pearson Education Ltd Cohesion of Water Molecules a. Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion b. Cohesion helps the transport of water against gravity in plants c. Adhesion is an attraction between different substances, for example, between water and plant cell walls © 2015 Pearson Education Ltd Figure 3.3 H₂O Adhesion Two types of water- conducting cells Direction Cohesion of water 300 movement m H₂O H₂O © 2015 Pearson Education Ltd. BioFlix: Water Transport in Plants © 2015 Pearson Education Ltd  a. Surface tension is a measure of how hard it is to break the surface of a liquid b. Water has an unusually high surface tension due to hydrogen bonding between the molecules at the air- water interface and to the water below © 2015 Pearson Education Ltd Moderation of Temperature by Water a. Water absorbs heat from warmer air and releases stored heat to cooler air b. it can absorb or release a large amount of heat with only a slight change in its own temperature © 2015 Pearson Education Ltd Temperature and Heat a. Kinetic energy is the energy of motion b. The kinetic energy associated with random motion of atoms or molecules is called thermal energy c. Temperature is a measure of energy that represents the average kinetic energy of the molecules in a body of matter d. Thermal energy in transfer from one body of matter to another is defined as heat © 2015 Pearson Education Ltd  a. A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1°C b. The “calories” on food packages are actually kilocalories (kcal), where 1 kcal = 1,000 cal c. The joule (J) is another unit of energy where 1 J = 0.239 cal, or 1 cal = 4.184 J © 2015 Pearson Education Ltd Water’s High Specific Heat a. The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C b. The specific heat of water is 1 cal/g/°C c. Water resists changing its temperature because of its high specific heat © 2015 Pearson Education Ltd  a. Water’s high specific heat can be traced to hydrogen bonding a. Heat is absorbed when hydrogen bonds break b. Heat is released when hydrogen bonds form b. The high specific heat of water minimizes temperature fluctuations to within limits that permit life © 2015 Pearson Education Ltd Evaporative Cooling a. Evaporation is transformation of a substance from liquid to gas b. Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas c. As a liquid evaporates, its remaining surface cools, a process called evaporative cooling d. Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water © 2015 Pearson Education Ltd Floating of Ice on Liquid Water a. Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense than water b. Water reaches its greatest density at 4°C c. If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth © 2015 Pearson Education Ltd Figure 3.6 Hydrogen bond Liquid water: Hydrogen bonds break and re-form Ice: Hydrogen bonds are stable © 2015 Pearson Education Ltd  a. Many scientists are worried that global warming, caused by carbon dioxide and other greenhouse gases, is having a profound effect on icy environments around the globe b. The rate at which glaciers ‫األنهار الجليدية‬and Arctic sea ‫ بحر الشمال‬ice are disappearing is posing an extreme challenge to animals that depend on ice for their survival © 2015 Pearson Education Ltd Water: The Solvent of Life a. A solution is a liquid that is a completely homogeneous mixture of substances b. A solvent is the dissolving agent of a solution c. The solute is the substance that is dissolved d. An aqueous solution is one in which water is the solvent e) Water is a versatile solvent due to its polarity f) When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell © 2015 Pearson Education Ltd Figure 3.7 − Na⁺ + + − − + − − Na⁺ − + + Cl– Cl− + − − + − + − − © 2015 Pearson Education Ltd  a. Water can also dissolve compounds made of nonionic polar molecules b. Even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions © 2015 Pearson Education Ltd Figure 3.8 δ+ δ− δ− δ+ © 2015 Pearson Education Ltd Hydrophilic and Hydrophobic Substances a. A hydrophilic substance is one that has an affinity for water b. A hydrophobic substance is one that does not have an affinity for water c. Oil molecules are hydrophobic because they have relatively nonpolar bonds d. Hydrophobic molecules related to oils are the major ingredients of cell membranes © 2015 Pearson Education Ltd Solute Concentration in Aqueous Solutions a. Most chemical reactions in organisms involve solutes dissolved in water b. When carrying out experiments, we use mass to calculate the number of solute molecules in an aqueous solution © 2015 Pearson Education Ltd  a. Molecular mass is the sum of all masses of all atoms in a molecule b. Numbers of molecules are usually measured in moles, where 1 mole (mol) = 6.02  10²³ molecules c. Avogadro’s number and the unit dalton were defined such that 6.02  10²³ daltons = 1 g d. Molarity (M) is the number of moles of solute per liter of solution © 2015 Pearson Education Ltd Concept 3.3: Acidic and basic conditions affect living organisms a. A) A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other a. The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H⁺) b. The molecule that lost the proton is now a hydroxide ion (OH−) c. The molecule with the extra proton is now a hydronium ion (H₃O⁺), though it is often represented as H⁺ B )Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed © 2015 Pearson Education Ltd Figure 3.UN01 + − 2 H₂O Hydronium Hydroxide ion (H₃O⁺) ion (OH−) a. Though statistically rare, the dissociation of water molecules has a great effect on organisms b. Changes in concentrations of H⁺ and OH− can drastically affect the chemistry of a cell © 2015 Pearson Education Ltd  a. Concentrations of H⁺ and OH− are equal in pure water b. Adding certain solutes, called acids and bases, modifies the concentrations of H⁺ and OH− c. Biologists use something called the pH scale to describe whether a solution is acidic or basic © 2015 Pearson Education Ltd Acids and Bases a. An acid is any substance that increases the H⁺ concentration of a solution b. A base is any substance that reduces the H⁺ concentration of a solution c. Strong acids and bases dissociate completely in water d. Weak acids and bases reversibly release and accept back hydrogen ions, but can still shift the balance of H⁺ and OH− away from neutrality © 2015 Pearson Education Ltd The pH Scale a. In any aqueous solution at 25°C the product of H⁺ and OH− is constant and can be written as [H⁺][OH−] = 10− ¹⁴ b. The pH of a solution is defined by the negative logarithm of H⁺ concentration, written as c. For a neutral aqueous solution, pH = − log [H⁺] [H⁺] is 10−7, so pH = −(− 7) = 7 © 2015 Pearson Education Ltd  a. Acidic solutions have pH values less than 7 b. Basic solutions have pH values greater than 7 c. Most biological fluids have pH values in the range of 6 to 8 © 2015 Pearson Education Ltd Figure 3.10 pH Scale 0 1 2 3 Battery acid 4 5 6 Gastric juice, lemon juice Increasingly Acidic 7 H⁺ 8 [H⁺] > [OH−] H⁺ H⁺ 9 H⁺ OH 10 Vinegar, wine, OH – H⁺ H⁺ 11 cola – H⁺ H⁺ 12 13 Tomato juice Acidic 14 solution Beer Black coffee Rainwater Urine OH Saliva OH – Neutral H⁺– H⁺ OH Pure water OH OH– [H⁺] = [OH−] Human blood, tears – H⁺ – H⁺ H⁺ Neutral Seawater Inside of small intestine solution Increasingly Basic [H⁺] < [OH−] OH Milk of magnesia – OH OH H⁺– OH – OH OH – Household ammonia – H⁺– OH – Basic solution Household bleach Oven cleaner © 2015 Pearson Education Ltd Figure 3.10a O O H⁺ O O H⁺ H− H H− H H⁺ O H⁺ O H H− O OH − H− ⁺O ⁺ O H OH − H⁺ O O H− −H H⁺ HH H − H⁺ H− H⁺ H− O H− H⁺ H− ⁺− ⁺ ⁺ Basic Neutral Acidic solution solution solution © 2015 Pearson Education Ltd Buffers a. The internal pH of most living cells must remain close to pH 7 b. Buffers are substances that minimize changes in concentrations of H⁺ and OH− in a solution c. Most buffer solutions contain a weak acid and its corresponding base, which combine reversibly with H⁺ ions © 2015 Pearson Education Ltd Acidification: A Threat to Water Quality a. Human activities such as burning fossil fuels threaten water quality b. CO₂ is the main product of fossil fuel combustion c. About 25% of human-generated CO₂ is absorbed by the oceans d. CO₂ dissolved in sea water forms carbonic acid; this process is called ocean acidification © 2015 Pearson Education Ltd  a. As seawater acidifies, H⁺ ions combine with carbonate ions to produce bicarbonate b. Carbonate is required for calcification (production of calcium carbonate) by many marine organisms, including reef-building corals c. We have made progress in learning about the delicate chemical balances in oceans, lakes, and rivers © 2015 Pearson Education Ltd  BIOLOGY TENTH EDITION Global Edition A Global Approach Campbell Reece Urry Cain Wasserman Minorsky Jackson 4 Carbon: The Basis of Molecular Diversity Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick © 2015 © 2015 Pearson Pearson Education Education Ltd Ltd  Carbon: The Backbone of Life Living organisms consist mostly of carbon- based compounds Carbon has ability to form large, complex, and varied molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds © 2015 Pearson Education Ltd Figure 4.1a Carbon can bond to four other atoms or groups of atoms, making a large variety of molecules possible. © 2015 Pearson Education Ltd  Organic chemistry is the study of compounds that contain carbon Organic compounds range from simple molecules to colossal (huge) ones Most organic compounds contain hydrogen atoms in addition to carbon atoms © 2015 Pearson Education Ltd  Vitalism was the belief in a life force away from physical and chemical laws It was thought that organic compounds could only be produced in living organisms Vitalism was disproved when chemists were able to synthesize organic compounds.Stanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compounds Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life © 2015 Pearson Education Ltd Figure 4.2 “Atmosphere” CH₄ Water vapor Electrode NH ₃ H₂ Condenser Cooled “rain” containing Cold organic water molecules H₂O “sea” Sample for chemical analysis © 2015 Pearson Education Ltd  Pioneers of organic chemistry helped shift the mainstream of biological thought from vitalism to mechanism Mechanism is the view that physical and chemical laws govern all natural phenomena © 2015 Pearson Education Ltd  Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atom’s characteristics Electron configuration determines the kinds and number of bonds an atom will form with other atoms © 2015 Pearson Education Ltd  The Formation of Bonds with Carbon With four valence electrons, carbon can form four covalent bonds with a variety of atoms This ability makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons © 2015 Pearson Education Ltd Figure 4.3 Molecular Structural Space-Filling Molecule Ball-and-Stick Model Formula Formula Model (a) Methane CH₄ (b) Ethane C₂H₆ (c) Ethene (ethylene) C₂H₄ © 2015 Pearson Education Ltd  The electron configuration of carbon gives it covalent compatibility with many different elements The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the building code for the architecture of living molecules © 2015 Pearson Education Ltd Figure 4.4 Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) © 2015 Pearson Education Ltd  Carbon atoms can partner with atoms other than hydrogen; for example: Carbon dioxide: CO₂ Urea: CO(NH₂)₂ © 2015 Pearson Education Ltd  Molecular Diversity Arising from Variation in Carbon Skeletons Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape © 2015 Pearson Education Ltd Figure 4.5 (a) Length (c) Double bond position Ethane Propane 1-Butene 2-Butene (b) Branching (d) Presence of rings Butane 2-Methylpropane Cyclohexane Benzene (isobutane) © 2015 Pearson Education Ltd  Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy © 2015 Pearson Education Ltd Figure 4.6 Nucleus Fat droplets 10 μm (a) Part of a human adipose cell (b) A fat molecule © 2015 Pearson Education Ltd  Isomers Isomers are compounds with the same molecular formula but different structures and properties Structural isomers have different covalent arrangements of their atoms Cis-trans isomers have the same covalent bonds but differ in spatial arrangements Enantiomers are isomers that are mirror images of each other © 2015 Pearson Education Ltd Figure 4.7 (a) Structural isomers Pentane 2-methyl butane (b) Cis-trans isomers cis isomer: The two Xs are trans isomer: The two Xs are on the same side. on opposite sides. (c) Enantiomers CO₂H CO₂H C C H NH₂ NH₂ H CH₃ CH₃ L isomer D isomer © 2015 Pearson Education Ltd Animation: Isomers © 2015 Pearson Education Ltd  Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Usually only one isomer is biologically active Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules © 2015 Pearson Education Ltd Figure 4.8 Effective Ineffective Drug Effects Enantiomer Enantiomer Reduces Ibuprofen inflammation and pain S-Ibuprofen R-Ibuprofen Relaxes bronchial (airway) muscles, Albuterol improving airflow in asthma patients R-AIbuterol S-AIbuterol © 2015 Pearson Education Ltd  Concept 4.3: A few chemical groups are key to molecular function Distinctive properties of organic molecules depend on the carbon skeleton and on the chemical groups attached to it A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules © 2015 Pearson Education Ltd  The Chemical Groups Most Important in the Processes of Life Estradiol and testosterone are both steroids with a common carbon skeleton, in the form of four fused rings These sex hormones differ only in the chemical groups attached to the rings of the carbon skeleton © 2015 Pearson Education Ltd Figure 4.UN03 Estradiol Testosterone Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties © 2015 Pearson Education Ltd  The seven functional groups that are most important in the chemistry of life Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group © 2015 Pearson Education Ltd Figure 4.9 Chemical Group Compound Name Examples Hydroxyl group (—OH) Alcohol Ethanol Carbonyl group ( — — C＝O) Ketone Aldehyde Acetone Propanal Carboxyl group (—COOH) Carboxylic acid, or organic acid Acetic acid Amino group (—NH₂) Amine Glycine Sulfhydryl group (—SH) Thiol Cysteine Phosphate group (—OPO₃2−) Organic phosphate Glycerol phosphate Methyl group (—CH₃) Methylated compound 5-Methyl cytosine © 2015 Pearson Education Ltd  ATP: An Important Source of Energy for Cellular Processes An important organic phosphate is adenosine triphosphate (ATP) ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups ATP stores the potential to react with water, a reaction that releases energy to be used by the cell © 2015 Pearson Education Ltd Figure 4.UN05 Adenosine ATP Reacts with H₂O P P P Adenosine P P P Adenosine Energy ATP Inorganic ADP phosphate © 2015 Pearson Education Ltd  The Chemical Elements of Life: The versatility of carbon makes possible the great diversity of organic molecules Variation at the molecular level lies at the foundation of all biological diversity © 2015 Pearson Education Ltd