Campbell Biology In Focus Ch 2 2024 PDF

CAMPBELL BIOLOGY IN FOCUS URRY CAIN WASSERMAN MINORSKY REECE 2 The  Chemical Context of Life Lecture Presentations by Kathleen Fitzpatrick and Nico...

CAMPBELL BIOLOGY IN FOCUS URRY CAIN WASSERMAN MINORSKY REECE 2 The  Chemical Context of Life Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge, Simon Fraser University SECOND EDITION © 2016 Pearson Education, Inc. A Chemical Connection to Biology Biology is a multidisciplinary science  Living organisms are subject to basic laws of physics and chemistry One example is the use of formic acid by ants to maintain “devil’s gardens,” stands of Duroia trees Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-1  Devil’s Garden Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds Organisms are composed of matter  Matter is anything that takes up space and has mass Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Elements and Compounds Matter is made up of elements An element is a substance that cannot be  broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio A compound has characteristics different from those of its elements Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-3  Sodium Chlorine Sodium chloride Essential Elements of Life  About 25 of the 92 elements are essential to live a healthy life and reproduce. Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter [COHN] Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are those required by an organism in minute quantities (Fe, I) Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Table 2.1 © 2016 Pearson Education, Inc. Fig. 2-4 (b) Iodine deficiency (a) Nitrogen deficiency Concept 2.2: An element’s properties depend on the structure of its atoms There are 92 naturally occurring elements Each element consists of unique atoms, different from the atoms of any other element.  An atom is the smallest unit of matter that still retains the properties of an element. That’s 10 million atoms worth! Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Subatomic Particles Atoms are composed of subatomic particles Relevant subatomic particles include: – Neutrons (no electrical charge) – Protons (positive charge) – Electrons (negative charge) Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Neutrons and protons form the atomic nucleus  Electrons form a cloud around the nucleus Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings DEFINITIONS:  Atomic Number and Mass Number Atoms of the various elements differ in number of subatomic particles An element’s atomic number is the number of protons in its nucleus An element’s mass number is the sum of protons plus neutrons in the nucleus Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings 23 Na 11 Mass number = number Atomic number = of protons + neutrons = number of protons = 11 23 for sodium for sodium  there? How many neutrons are © 2016 Pearson Education, Inc. Review Questions What is the mass number of an atom with 16 neutrons, 15 protons, and 15 electrons? Which of these are compounds? H2 H2O O2 CH4 What 4 elements make up 96% of living matter? Electron Distribution and Chemical Properties  The chemical behavior of an atom is determined by the distribution of electrons in electron shells The periodic table of the elements shows the electron distribution for each element Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-9 Electron Distribution Diagram 2 He 1H Hydrogen  Helium 2He Atomic number 4.00 First Electron Atomic mass distribution diagram shell Element symbol 12Mg Oxygen Boron 8O 5B Second shell Sodium Silicon 11Na 14Si Beryllium Sulfur 4Be Aluminum 16S 13Al Fluorine Third Carbon 6C 9F shell Lithium 3Li Magnesium Nitrogen Phosphoru s 7N 15P  17Cl 18Ar Neon 10Ne Chlorine Argon Start with H which has one electron. We build other atoms by adding 1 proton and 1 electron Valence electrons are those in the outermost shell, or valence shell  The chemical behavior of an atom is mostly determined by the valence electrons Elements with a full valence shell are chemically inert Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  QUICK QUESTION: Predict the formula for hydrogen sulfide. H has atomic number of 1, S has an atomic number of 16. Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-11 Hydrogen atoms (2 H)  Hydrogen molecule (H2)  A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons acetylene Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  Covalent bonds can form between atoms of the same element or atoms of different elements A compound is a combination of two or more different elements (H2O or CH4) Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Atoms in a molecule attract electrons to varying degrees  Electronegativity is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom, the more strongly it pulls ‘shared’ electrons toward itself More electrons Smaller atomic radiu s Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings There are two types of covalent bonds…..  In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-14-1 Cl  Ionic Bonds Atoms sometimes strip electrons from their  bonding partners. This occurs when one atom is much more electronegative than the other. An example is the transfer of an electron from sodium to chlorine After the transfer of an electron, both atoms have charges. A charged atom (or molecule) is called an ion Both atoms also have complete valence shells Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-14-1  Na Cl Na Cl Sodium atom Chlorine atom Fig. 2-14-2  Na Cl Na Cl Na Cl Na+ Cl–  Sodium atom Sodium ion (a cation) anion) Chlorine atom Chloride ion (an Sodium chloride (NaCl) A cation is a positively charged ion An anion is a negatively charged ion An ionic bond is an attraction between an anion and a cation  Na + – Cl Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Weak Chemical Bonds Most of the strongest bonds in organisms  are covalent bonds that form a cell’s molecules Weak chemical bonds, such as hydrogen bonds, are also important Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Hydrogen Bonds  A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-16 δ− δ+ Water (H2O) Ammonia (NH3) δ+ δ− δ+ Hydrogen bond δ+ δ+  + - - + - - - ++ + - + + - +- + + --  Molecular Shape and Function All molecules have a characteristic size and shape Angular, bent, or V-shaped A molecule’s shape is usually very important to its function Molecular shape determines how biological molecules recognize and respond to one another Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with  similar shapes can have similar biological effects (“morphine” pain-killing drug and natural endorphins) Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-18 Carbon Hydrogen Nitrogen Sulfur Natural Oxygen endorphin Morphine Key (a) Structures of endorphin and morphine receptors Same 3D Brain cell Natural shape! endorphin Morphine Endorphin  (b) Binding to endorphin receptors Concept 2.4: Chemical reactions make and break chemical bonds Chemical reactions are the making and breaking of chemical bonds 2H2 + O2 → 2H20 The starting molecules of a chemical reaction are called reactants  The final molecules of a chemical reaction are called products Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-UN2 Matter is conserved!  2 H2 O2 2 H2O Reactants Reaction Products Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen  6 CO2 + 6 H20 → C6H12O6 + 6 O2 Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Some chemical reactions go to completion where all reactants are converted to products All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction  Chemical equilibrium is reached when the forward and reverse reaction rates are equal Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Quiz time….. The atomic number of magnesium is 12. The atomic number of chlorine is 17. What is the formula for magnesium chloride?  What indicates the number of protons? How do you calculate atomic mass? If an atom has an atomic number of 15, how many electrons does this atom have? How many electrons does an atom of sulfur have in its valence shell? (atomic number is 16) Which of the following has a strong polar covalent bond? H20, CO2, or CH4 What is the maximum number of covalent bonds an element with atomic number 8 can make with hydrogen?  When two atoms are equally electronegative, what types of bonds will they form? Polar or nonpolar? What type of bond holds the H to the O in a water molecule? What type of bond forms between 2 water molecules? Concept 2.5: Hydrogen bonding gives water properties that help make life possible on Earth  Water is the biological medium on Earth. All living organisms require water more than any other substance 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 2.5: The polarity of water molecules results in hydrogen bonding The water molecule is a polar molecule: The opposite ends have opposite charges. The oxygen region has a partial negative charge (δ−) and the hydrogen region has a slight positive charge (δ+) Polarity allows water molecules to form hydrogen bonds with each other  Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 2.16 δ− Hydrogen δ+ bond H Polar covalent δ− δ+ H δ+ bonds δ− δ+ δ− O © 2016 Pearson Education, Inc. Four emergent properties of water contribute to Earth’s fitness for life Four of water’s properties that facilitate an environment for life are: – Cohesive behavior – Ability to moderate temperature – Expansion upon freezing – Versatility as a solvent  Water is a polar molecule 4 min TedEd video Amoeba Sisters 7 min Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Cohesion and Adhesion Water molecules are linked by multiple hydrogen bonds Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion Cohesion helps the transport of water against gravity in plants Adhesion is an attraction between different substances, for example, between water and plant cell walls Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 2.17 H2O Adhesion  Two types of water conducting cells Cohesion Direction of water movement 300 ∝m H2O H2O © 2016 Pearson Education, Inc.  Surface tension is a measure of how hard it is to break the surface of a liquid Surface tension is related to cohesion  Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Moderation of Temperature Water absorbs heat from warmer air and releases stored heat to cooler air Water can absorb or release a large amount of heat with only a slight change in its own temperature Chattahoochee  River Fig. 3-5 San Bernardino Santa Barbara 73° Burbank 90° 100° Los Angeles Riverside 96° Santa 70s (°F) 80s Ana 90s 84° (Airport) 75° Palm Springs 106° Pacific Ocean  100s 40 miles San Diego 72° The high specific heat of water minimizes temperature fluctuations to within limits that permit life Water’s High Specific Heat 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 1ºC Or in simpler terms… how much heat energy it takes to warm a  substance The specific heat of water is 1 cal/g/ºC Water resists changing its temperature because of its high specific heat Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Here is a chart with the specific heat of various  substances: Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Water’s high specific heat can be traced to hydrogen bonding  – Heat is absorbed when hydrogen bonds break – Heat is released when hydrogen bonds form Copyright © 2008 Pearson Education, Inc., publishing as Pearson 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 Water reaches its greatest density at 4°C If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Water -- 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 An aqueous solution is one in which water is the solvent Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Water is a versatile solvent due to its polarity, which allows it to form hydrogen  bonds easily When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-7  – – 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 C6H12O6 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-8 Lysozyme is an enzyme found in tears, saliva, sweat and other body fluids. It protects us from bacterial invaders!  nonaqueous environment (b) Lysozyme molecule (purple) in an aqueous environment (c) Ionic and polar regions on the protein’s surface attract water molecules. (a) Lysozyme molecule in a Definitions: Hydrophilic and Hydrophobic Substances A hydrophilic substance is one that has an affinity for water (they are polar too so water is attracted to them!)  A hydrophobic substance is one that does not have an affinity for water Oil molecules are hydrophobic because they have Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin relatively nonpolar bondsCummings Lots of equal sharing of electrons here! No partial + or -! Switching gears…. Acids and BasesConcentrations of H+ and OH– are equal in pure water Solutes called acids and bases can be added to water to  disrupt the balance between H+ and OH− in pure water Biologists use something called the pH scale to describe whether a solution is acidic or basic (the opposite of acidic) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Acidic solutions have pH values less than 7 Basic solutions have pH values greater than 7 Most biological fluids have pH values in the range of 6 to 8  Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 2.23 H+ + _ H+ [H ]> [OH ] Increasingly Acidic 1 Battery acid 2 Gastric juice, lemon juice There is a 10-fold difference between  H+ H+ Vinegar, wine, OH− 3 numbers H+ OH− H+ H H+ + Tomato juice Beer Black coffee Rainwater 4 Urine Acidic 5 Saliva solution 6 OH− on the scale. Neutral OH− cola H+ OH− 7 + [H ]= Pure [OH_] water H+ OH− OH− blood, tears intestine Milk Basic + Neutral H+ H H+ Seawater solution + _ Inside of [H ]< [OH ] of magnesia 8 OH−OH− OH−H+ OH− small 9 10 11 Increasingly Human OH− OH−OH− H+ Household  ammonia 12 Basic Household 13 bleach solution Oven 14 cleaner © 2016 Pearson Education, Inc. Acids and Bases + 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 because it accepts the H ion. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 (Buffers help maintain a constant pH when either acids or bases are added to them)  Most buffers consist of an acid-base pair that + reversibly combines with H Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Blood always contains a combination of H2CO3 and HCO3-  Threats to Water Quality on Earth 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 and can fall at some distance from the source of pollutants Acid precipitation can damage life in lakes and streams Effects of acid precipitation on soil chemistry are contributing to the decline of some forests Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-10 More 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 acidic Acid rain Normal rain More basic  Ca+ and Mg+ Human activities such as burning fossil fuels threaten water quality CO2 is released by fossil fuel combustion and contributes to: – A warming of earth called the “greenhouse” effect – Acidification of the oceans; this leads to a decrease in  the ability of corals to form calcified reefs Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Acidification: A Threat to Our Oceans Video 3 min Human activities such as burning fossil fuels also threaten water quality CO2 is a product of fossil fuel combustion  About 25% of human-generated CO2 is absorbed by the oceans CO2 dissolved in seawater forms carbonic acid; this causes ocean acidification © 2016 Pearson Education, Inc. As seawater acidifies, hydrogen ions combine with carbonate ions to form bicarbonate ions – (HCO3 ) It is predicted that carbonate ion concentrations will decline by 40% by the year  2100 This is a concern because organisms that build coral reefs or shells require carbonate ions © 2016 Pearson Education, Inc. Figure 2.24 More on this part later! → H ions CO2 + H2O H2CO3 released → making H2CO3 H+ + HCO3− ocean more acidic! → H+ + CO32− HCO3− → CO32− + Ca2+ CaCO3 © 2016 Pearson Education, Inc.