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Chapter 3: WATER The Molecule That Supports All of Life • Water is the biological medium on Earth • All living organisms require water more than any other substance for life processes • Most cells are surrounded by water, and cells themselves are about 70-95% water • The abundance of water is the main reason the Earth is habitable – Why? Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The polarity of water molecules results in hydrogen bonding • The water molecule is a polar molecule: The opposite ends have opposite charges • Polarity allows water molecules to form hydrogen bonds with each other Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrogen bonds Four emergent properties of water contribute to Earth’s fitness for life • Four of water’s properties that facilitate an environment for life: Cohesive behavior – it sticks together Ability to moderate temperature – it regulates the temperature on the Earth Expansion upon freezing – causes ice to float, allowing it to insulate the temperatures of the water below the ice Versatility as a solvent – many biologically important molecules are soluble, or able to dissolve, in water Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cohesion • Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion • Cohesion helps the transport of water against gravity in plants • Adhesion of water to plant cell walls also helps to counter gravity • Surface tension is a measure of how hard it is to break the surface of a liquid • Surface tension is related to cohesion as the water is held together, the surface is harder to break Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Moderation of Temperature • Water absorbs heat from warmer air and releases stored heat to cooler air, thus regulating the temperature – Think of the shore!!! • Water can absorb or release a large amount of heat with only a slight change in its own temperature • The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC • Water’s high specific heat minimizes temperature fluctuations to within limits that permit life Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Note how the ocean moderates the temperature of the coast! Santa Barbara 73° Los Angeles (Airport) 75° 70s (°F) 80s San Bernardino 100° Riverside 96° Santa Ana Palm Springs 84° 106° Burbank 90° Pacific Ocean 90s 100s San Diego 72° 40 miles Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evaporative Cooling • Evaporation is transformation of a substance from liquid to gas • Heat of vaporization is the heat a liquid must absorb for 1 gram to be converted to gas • As a liquid evaporates, its remaining surface cools, a process called evaporative cooling • Evaporative cooling of water helps stabilize temperatures in organisms (sweating) and bodies of water Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Insulation of Bodies of Water by Floating Ice • Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense • If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth • Marine organisms would not survive as the water would freeze, and the food chains would be destroyed, the temperature would not be regulated, and fresh water is REQUIRED for life! Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Solvent of Life • A solution is a liquid that is a homogeneous mixture of substances • A solvent is the dissolving agent of a solution • The solute is the substance that is dissolved • Water is a versatile solvent due to its polarity • An aqueous solution is one in which water is the solvent • Water is an effective solvent because it readily forms hydrogen bonds • When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules, a hydration shell Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings So, in salt water, NaCl is the solute and water is the solvent – Na+ + + – – + – – Na+ – + + Cl– Cl– + – + + – – – – Water can also dissolve compounds made of nonionic polar molecules • Even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions Lysozyme molecule in a nonaqueous environment. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Lysozyme molecule in an aqueous environment. Hydrophilic and Hydrophobic Substances • A hydrophilic substance is one that has an affinity for water – philic = loves water • A hydrophobic substance is one that does not have an affinity for water – phobic = ‘scared’ of, or doesn’t like water – Oil is a VERY hydrophobic substance Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Solute Concentration in Aqueous Solutions MOLARITY • As you might imagine, since water makes up the majority of the mass of a cell, most biochemical reactions occur in water • Chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution • Molecular mass is the sum of all masses of all atoms in a molecule • Numbers of molecules are usually measured in moles, with one mole being 6.02 x 1023 molecules – this is known as Avogadro’s number • Molarity is the number of moles of solute per liter of solution Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Dissociation of water molecules leads to acidic and basic conditions that affect living organisms • A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other: – The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) – The molecule with the extra proton is now a hydronium ion (H3O+) – The molecule that lost the proton is now a hydroxide ion (OH-) Hydronium ion (H3O+) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydroxide ion (OH–) Effects of changes in pH • The process can be described in a simplified way as the separation of a water molecule into a hydrogen ion (H+) and a hydroxide ion (OH-) • Though statistically rare, the dissociation of water molecules has a great effect on organisms • Changes in concentrations of H+ and OH- can drastically affect the chemistry of a cell • Concentrations of H+ and OH- are equal in pure water • Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH- • An acid is any substance that increases the H+ concentration of a solution • A base is any substance that reduces the H+ concentration of a solution • Biologists use something called the pH scale to describe how acidic or basic (the opposite of acidic) a solution is Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The pH Scale 1 The pH of a solution is determined by the relative concentration of hydrogen (H+) ions • Acidic solutions have pH values less than 7 • Basic solutions have pH values greater than 7 Increasingly Acidic [H+] > [OH–] • pH Scale 0 Neutral [H+] = [OH–] Battery acid 2 Digestive (stomach) juice, lemon juice 3 Vinegar, beer, wine, cola 4 Tomato juice 5 Black coffee Rainwater 6 Urine 7 Pure water Human blood 8 Most biological fluids have pH values in the range of 6 to 8 Seawater Increasingly Basic [H+] < [OH–] • 9 10 Milk of magnesia 11 Household ammonia 12 Household bleach 13 Oven cleaner Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 14 Buffers • The internal pH of most living cells must remain close to pH 7 • Buffers are substances that minimize changes in concentrations of H+ and OH- in a solution • Most buffers consist of an acid-base pair that reversibly combines with H+ Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Threat of Acid Precipitation • Acid precipitation refers to rain, snow, or fog with a pH lower than 5.6 • Acid precipitation is caused mainly by the mixing of different pollutants with water in the air • Acid precipitation can damage life in lakes and streams • Effects of acid precipitation on soil chemistry are contributing to the decline of some forests • The LA basin routinely has fogs made up of moisture with a pH of 2.2-4 • The lowest recorded rainfall was in Wheeling, WV pH = 1.5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 More acidic Acid rain Normal rain More basic Chapter 4: Carbon—The Backbone of Biological Molecules • Although cells are 70–95% water, the rest consists mostly of carbonbased compounds • Carbon is unparalleled in its ability to form large, complex, and diverse molecules • Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Organic chemistry is the study of carbon compounds • Organic compounds range from simple molecules to colossal ones • Most organic compounds contain hydrogen atoms in addition to carbon atoms • Vitalism, the idea that organic compounds arise only in organisms, was shown to be false when chemists synthesized many organic compounds in the laboratory • Mechanism is the view that all natural phenomena are governed by physical and chemical laws Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Carbon atoms can form diverse molecules by bonding to four other atoms • An atom’s electron configuration is the key to its characteristics • Electron configuration determines the kinds and number of bonds an atom will form with other atoms • With four valence electrons, carbon can form four covalent bonds with a variety of atoms • This tetravalence 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 molecule has a flat shape Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Basic structures of Carbon containing molecules Molecular Formula Structural Formula Methane PowerPoint Lectures for Ethane Biology, Seventh Edition Neil Campbell and Jane Reece Ethene (ethylene) Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ball-and-Stick Model Space-Filling Model Carbon can form bonds with atoms of many different elements • The electron configuration of carbon gives it covalent compatibility with many different elements • The valences (number of H atoms an atom can bind with) of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules Hydrogen (valence = 1) Oxygen (valence = 2) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Nitrogen (valence = 3) Carbon (valence = 4) Ethane Propane Butane 2-methylpropane (commonly called isobutane) Length Molecular Diversity Arises from Carbon Skeleton Variation • • Branching Carbon chains form the skeletons of most organic molecules 1-Butene Double bonds 2-Butene Carbon chains vary in length and shape Cyclohexane Rings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Benzene 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 Mammalian adipose cells A fat molecule Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fat droplets (red) 100 µm Isomers • Isomers are compounds with the same molecular formula but different structures and properties: – Structural isomers have different covalent arrangements of their atoms – Geometric isomers have the same covalent arrangements but differ in spatial arrangements – Enantiomers are isomers that are mirror images of each other Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. L isomer D isomer Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enantiomers and medicine • Enantiomers are very important in the pharmaceutical industry • Two enantiomers of a drug may have different effects • Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules L-Dopa (effective against Parkinson’s disease) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings D-Dopa (biologically Inactive) Functional groups are the parts of molecules involved in chemical reactions • Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it • Certain groups of atoms are often attached to skeletons of organic molecules • The functional groups of compounds are the most Important determinant in the chemistry of life • Functional groups are the components of organic molecules that are most commonly involved in chemical reactions Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemistry Determines Organism Characteristics estradiol testosterone Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Functional Groups of organic molecules • The six 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS Alcohols (their specific names PowerPoint Lectures for usually end in -ol) Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars. Acetone, the simplest ketone STRUCTURE EXAMPLE Acetone, the simplest ketone NAME OF COMPOUNDS Ketones if theLectures carbonyl group PowerPoint for is within a carbon skeleton Biology, Seventh Edition Aldehydes if the carbonyl group is Neil Campbell and Jane Reece at the end of the carbon skeleton Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Propanal, an aldehyde FUNCTIONAL PROPERTIES A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. STRUCTURE EXAMPLE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS Carboxylic acids, or organic acids PowerPoint Lectures for Biology, Seventh Edition FUNCTIONAL PROPERTIES Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Neil Campbell and Jane Reece Acetic acid Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Acetate ion In cells, found in the ionic form, which is called a carboxylate group. STRUCTURE EXAMPLE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. NAME OF COMPOUNDS Amine PowerPoint Lectures for Biology, Seventh Edition FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: Neil Campbell and Jane Reece (nonionized) (ionized) Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ionized, with a charge of 1+, under cellular conditions STRUCTURE EXAMPLE (may be written HS—) Ethanethiol NAME OF COMPOUNDS PowerPoint Lectures for Biology, Seventh Edition Thiols Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure. STRUCTURE EXAMPLE Glycerol phosphate NAME OF COMPOUNDS PowerPoint Lectures for Organic phosphates Biology, Seventh Edition Neil Campbell and Jane Reece FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules. Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Methyl STRUCTURE Methylated compounds EXAMPLE Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. 5-Methyl cytidine 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Arrangement of methyl groups in male and female sex hormones affects their shape and function. NAME OF COMPOUND FUNCTIONAL PROPERTIES