The Chemical Context of Life PDF

Chapter 2 The Chemical Context of Life PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Be...

Chapter 2 The Chemical Context of Life PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Overview: 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 Fig. 2-2 EXPERIMENT Cedrela Insect sapling barrier Duroia Outside, tree Inside, protected unprotected Inside, protected Devil’s Outside, garden unprotected RESULTS Dead leaf tissue (cm2) 16 after one day 12 8 4 0 Inside, Inside, Outside, Outside, unprotected protected unprotected protected Cedrela saplings, inside and outside devil’s gardens Fig. 2-2a EXPERIMENT Cedrela Insect sapling barrier Duroia Outside, tree Inside, protected unprotected Inside, protected Devil’s Outside, garden unprotected Fig. 2-2b RESULTS Dead leaf tissue (cm2) 16 after one day 12 8 4 0 Inside, Inside, Outside, Outside, unprotected protected unprotected protected Cedrela saplings, inside and outside devil’s gardens 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 Fig. 2-3a Sodium Fig. 2-3b Chlorine Fig. 2-3c Sodium chloride Essential Elements of Life About 25 of the 92 elements are essential to life Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are those required by an organism in minute quantities Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Table 2-1 Fig. 2-4 (a) Nitrogen deficiency (b) Iodine deficiency Fig. 2-4a (a) Nitrogen deficiency Fig. 2-4b (b) Iodine deficiency Concept 2.2: An element’s properties depend on the structure of its atoms Each element consists of unique atoms An atom is the smallest unit of matter that still retains the properties of an element 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 Neutron mass and proton mass are almost identical and are measured in daltons Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-5 Cloud of negative charge (2 electrons) Electrons Nucleus (a) (b) Atomic Number and Atomic Mass 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 Atomic mass, the atom’s total mass, can be approximated by the mass number Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Isotopes All atoms of an element have the same number of protons but may differ in number of neutrons Isotopes are two atoms of an element that differ in number of neutrons Radioactive isotopes decay spontaneously, giving off particles and energy Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  Some applications of radioactive isotopes in biological research are: – Dating fossils – Tracing atoms through metabolic processes – Diagnosing medical disorders Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-6 TECHNIQUE Compounds including Incubators radioactive tracer 1 2 3 (bright blue) 10°C 15°C 20°C Human cells 4 5 6 25°C 30°C 35°C 1 Human cells are 7 8 9 incubated 40°C 45°C 50°C with compounds used to make DNA. One compound is labeled with 3H. 2 The cells are DNA (old and new) placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. 3 The test tubes are placed in a scintillation counter. RESULTS Counts per minute Optimum 30 temperature for DNA ( 1,000) 20 synthesis 10 0 10 20 30 40 50 Temperature (ºC) Fig. 2-6a TECHNIQUE Compounds including Incubators radioactive tracer 1 2 3 (bright blue) 10ºC 15ºC 20ºC Human 4 5 6 cells 25ºC 30ºC 35ºC 1 Human cells are 7 8 9 incubated 40ºC 45ºC 50ºC with compounds used to make DNA. One compound is labeled with 3H. 2 The cells are DNA (old and new) placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. Fig. 2-6b TECHNIQUE 3 The test tubes are placed in a scintillation counter. Fig. 2-6c RESULTS Counts per minute Optimum 30 temperature ( 1,000) for DNA 20 synthesis 10 0 10 20 30 40 50 Temperature (ºC) Fig. 2-7 Cancerous throat tissue The Energy Levels of Electrons Energy is the capacity to cause change Potential energy is the energy that matter has because of its location or structure The electrons of an atom differ in their amounts of potential energy An electron’s state of potential energy is called its energy level, or electron shell Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-8 (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons Third shell (highest energy level) Second shell (higher Energy energy level) absorbed First shell (lowest energy level) Energy lost Atomic nucleus (b) 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 Hydrogen 2 Atomic number Helium 1H He 2He Atomic mass 4.00 Element symbol First shell Electron- distribution diagram Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 3Li 4Be 5B 6C 7N 8O 9F 10Ne Second shell Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon 11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar Third shell  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 Electron Orbitals An orbital is the three-dimensional space where an electron is found 90% of the time Each electron shell consists of a specific number of orbitals Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-10-1 Neon, with two filled shells (10 electrons) (a) Electron-distribution diagram First shell Second shell Fig. 2-10-2 Neon, with two filled shells (10 electrons) (a) Electron-distribution diagram First shell Second shell (b) Separate electron orbitals 1s orbital Fig. 2-10-3 Neon, with two filled shells (10 electrons) (a) Electron-distribution diagram First shell Second shell (b) Separate electron orbitals x y z 1s orbital 2s orbital Three 2p orbitals Fig. 2-10-4 Neon, with two filled shells (10 electrons) (a) Electron-distribution diagram First shell Second shell (b) Separate electron orbitals x y z 1s orbital 2s orbital Three 2p orbitals (c) Superimposed electron orbitals 1s, 2s, and 2p orbitals 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 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 molecule consists of two or more atoms held together by covalent bonds 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 Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  The notation used to represent atoms and bonding is called a structural formula – For example, H–H This can be abbreviated further with a molecular formula – For example, H2 Animation: Covalent Bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-12 Name and Electron- Lewis Dot Space- Molecular distribution Structure and filling Formula Diagram Structural Model Formula (a) Hydrogen (H2) (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4) Fig. 2-12a Name and Electron- Lewis Dot Space- Molecular distribution Structure and filling Formula Diagram Structural Model Formula (a) Hydrogen (H2) Fig. 2-12b Name and Electron- Lewis Dot Space- Molecular distribution Structure and filling Formula Diagram Structural Model Formula (b) Oxygen (O2) Fig. 2-12c Name and Electron- Lewis Dot Space- Molecular distribution Structure and filling Formula Diagram Structural Model Formula (c) Water (H2O) Fig. 2-12d Name and Electron- Lewis Dot Space- Molecular distribution Structure and filling Formula Diagram Structural Model Formula (d) Methane (CH4)  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 Bonding capacity is called the atom’s valence Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  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 Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  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. 2-13 Polar covalent bonds in a water molecule – O H H + + H2O Ionic Bonds Atoms sometimes strip electrons from their bonding partners 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 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 Chlorine atom Sodium ion Chloride ion (a cation) (an anion) 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 Animation: Ionic Bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (table salt), are often found in nature as crystals Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-15 Na+ Cl– Weak Chemical Bonds Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Weak chemical bonds, such as ionic bonds and 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 − + Water (H2O) + Hydrogen bond − Ammonia (NH3) + + + Van der Waals Interactions If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge Van der Waals interactions are attractions between molecules that are close together as a result of these charges Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-UN1 gecko’s toe hairs and a wall surface Molecular Shape and Function A molecule’s shape is usually very important to its function A molecule’s shape is determined by the positions of its atoms’ valence orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-17 z Four hybrid orbitals s orbital Three p orbitals x y Tetrahedron (a) Hybridization of orbitals Space-filling Ball-and-stick Hybrid-orbital Model Model Model (with ball-and-stick model superimposed) Unbonded electron pair 104.5º Water (H2O) Methane (CH4) (b) Molecular-shape models Fig. 2-17a z Four hybrid orbitals s orbital Three p orbitals x y Tetrahedron (a) Hybridization of orbitals Fig. 2-17b Space-filling Ball-and-stick Hybrid-orbital Model Model Model (with ball-and-stick model superimposed) Unbonded electron pair 104.5º Water (H2O) Methane (CH4) (b) Molecular-shape models  Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-18 Key Carbon Nitrogen Hydrogen Sulfur Natural endorphin Oxygen Morphine (a) Structures of endorphin and morphine Natural endorphin Morphine Endorphin Brain cell receptors (b) Binding to endorphin receptors Fig. 2-18a Key Carbon Nitrogen Hydrogen Sulfur Natural endorphin Oxygen Morphine (a) Structures of endorphin and morphine Fig. 2-18b Natural endorphin Morphine Endorphin Brain cell receptors (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 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 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 Fig. 2-19  Some chemical reactions go to completion: 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 Fig. 2-UN3 Nucleus Protons (+ charge) determine element Electrons (– charge) form negative cloud Neutrons (no charge) and determine determine isotope chemical behavior Atom Fig. 2-UN4 Fig. 2-UN5 Single Double covalent bond covalent bond Fig. 2-UN6 Ionic bond Electron transfer forms ions Na Cl Na+ Cl– Sodium atom Chlorine atom Sodium ion Chloride ion (a cation) (an anion) Fig. 2-UN7 Fig. 2-UN8 Fig. 2-UN9 Fig. 2-UN10 Fig. 2-UN11 You should now be able to: 1. Identify the four major elements 2. Distinguish between the following pairs of terms: neutron and proton, atomic number and mass number, atomic weight and mass number 3. Distinguish between and discuss the biological importance of the following: nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings  Chapter 1 Introduction: Themes in the Study of Life PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Overview: Inquiring About the World of Life Evolution is the process of change that has transformed life on Earth Biology is the scientific study of life Biologists ask questions such as: – How a single cell develops into an organism – How the human mind works – How living things interact in communities Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-1 Fig. 1-2  Life defies a simple, one-sentence definition Life is recognized by what living things do Video: Seahorse Camouflage Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-3 Some properties of life Order Response to the environment Evolutionary adaptation Regulation Reproduction Energy processing Growth and development Fig. 1-3a Order Fig. 1-3b Evolutionary adaptation Fig. 1-3c Response to the environment Fig. 1-3d Reproduction Fig. 1-3e Growth and development Fig. 1-3f Energy processing Fig. 1-3g Regulation Concept 1.1: Themes connect the concepts of biology Biology consists of more than memorizing factual details Themes help to organize biological information Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Evolution, the Overarching Theme of Biology Evolution makes sense of everything we know about living organisms Organisms living on Earth are modified descendents of common ancestors Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Theme: New properties emerge at each level in the biological hierarchy Life can be studied at different levels from molecules to the entire living planet The study of life can be divided into different levels of biological organization Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-4 Levels of biological organization The biosphere Cells Organs and 10 µm organ systems Cell Ecosystems Organelles Communities 1 µm Atoms Tissues 50 µm Populations Molecules Organisms Fig. 1-4a The biosphere Ecosystems Communities Populations Organisms Fig. 1-4b Cells Organs and 10 µm organ systems Cell Organelles 1 µm Atoms Tissues 50 µm Molecules Fig. 1-4c The biosphere Fig. 1-4d Ecosystems Fig. 1-4e Communities Fig. 1-4f Populations Fig. 1-4g Organisms Fig. 1-4h Organs and organ systems Fig. 1-4i Tissues 50 µm Fig. 1-4j 10 µm Cell Cells Fig. 1-4k 1 µm Organelles Fig. 1-4l Atoms Molecules  Emergent Properties Emergent properties result from the arrangement and interaction of parts within a system Emergent properties characterize nonbiological entities as well – For example, a functioning bicycle emerges only when all of the necessary parts connect in the correct way Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The Power and Limitations of Reductionism Reductionism is the reduction of complex systems to simpler components that are more manageable to study – For example, the molecular structure of DNA An understanding of biology balances reductionism with the study of emergent properties – For example, new understanding comes from studying the interactions of DNA with other molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Systems Biology A system is a combination of components that function together Systems biology constructs models for the dynamic behavior of whole biological systems The systems approach poses questions such as: – How does a drug for blood pressure affect other organs? – How does increasing CO2 alter the biosphere? Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Theme: Organisms interact with their environments, exchanging matter and energy Every organism interacts with its environment, including nonliving factors and other organisms Both organisms and their environments are affected by the interactions between them – For example, a tree takes up water and minerals from the soil and carbon dioxide from the air; the tree releases oxygen to the air and roots help form soil Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Ecosystem Dynamics The dynamics of an ecosystem include two major processes: – Cycling of nutrients, in which materials acquired by plants eventually return to the soil – The flow of energy from sunlight to producers to consumers Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-5 Sunlight Nutrient cycling and energy flow Ecosystem in an ecosystem Producers (plants and other photosynthetic Cycling organisms) Heat of chemical nutrients Chemical energy Consumers (such as animals) Heat  Energy Conversion Work requires a source of energy Energy can be stored in different forms, for example, light, chemical, kinetic, or thermal The energy exchange between an organism and its environment often involves energy transformations Energy flows through an ecosystem, usually entering as light and exiting as heat Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Theme: Structure and function are correlated at all levels of biological organization Structure and function of living organisms are closely related – For example, a leaf is thin and flat, maximizing the capture of light by chloroplasts Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-6 (a) Wings (b) Bones Infoldings of membrane Mitochondrion 100 µm 0.5 µm (c) Neurons (d) Mitochondria Fig. 1-6a (a) Wings Fig. 1-6b (b) Bones Fig. 1-6c 100 µm (c) Neurons Fig. 1-6d Infoldings of membrane Mitochondrion 0.5 µm (d) Mitochondria  Theme: Cells are an organism’s basic units of structure and function The cell is the lowest level of organization that can perform all activities required for life All cells: – Are enclosed by a membrane – Use DNA as their genetic information The ability of cells to divide is the basis of all reproduction, growth, and repair of multicellular organisms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-7 25 µm  A eukaryotic cell has membrane-enclosed organelles, the largest of which is usually the nucleus By comparison, a prokaryotic cell is simpler and usually smaller, and does not contain a nucleus or other membrane-enclosed organelles Bacteria and Archaea are prokaryotic; plants, animals, fungi, and all other forms of life are eukaryotic Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-8 Prokaryotic cell Eukaryotic cell DNA (no nucleus) Membrane Membrane Cytoplasm Organelles Nucleus (contains DNA) 1 µm  Theme: The continuity of life is based on heritable information in the form of DNA Chromosomes contain most of a cell’s genetic material in the form of DNA (deoxyribonucleic acid) DNA is the substance of genes Genes are the units of inheritance that transmit information from parents to offspring Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  DNA Structure and Function Each chromosome has one long DNA molecule with hundreds or thousands of genes DNA is inherited by offspring from their parents DNA controls the development and maintenance of organisms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-9 Sperm cell Nuclei containing DNA Fertilized egg Embryo’s cells with with DNA from copies of inherited DNA Egg cell both parents Offspring with traits inherited from both parents  Each DNA molecule is made up of two long chains arranged in a double helix Each link of a chain is one of four kinds of chemical building blocks called nucleotides Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-10 Nucleus DNA Nucleotide Cell (a) DNA double helix (b) Single strand of DNA  Genes control protein production indirectly DNA is transcribed into RNA then translated into a protein An organism’s genome is its entire set of genetic instructions Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Systems Biology at the Levels of Cells and Molecules The human genome and those of many other organisms have been sequenced using DNA- sequencing machines Knowledge of a cell’s genes and proteins can be integrated using a systems approach Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-11 Fig. 1-12 Outer membrane and cell surface Cytoplasm Nucleus  Advances in systems biology at the cellular and molecular level depend on – “High-throughput” technology, which yields enormous amounts of data – Bioinformatics, which is the use of computational tools to process a large volume of data – Interdisciplinary research teams Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Theme: Feedback mechanisms regulate biological systems Feedback mechanisms allow biological processes to self-regulate Negative feedback means that as more of a product accumulates, the process that creates it slows and less of the product is produced Positive feedback means that as more of a product accumulates, the process that creates it speeds up and more of the product is produced Animation: Negative Feedback Animation: Positive Feedback Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-13 A Negative feedback − Enzyme 1 B D Enzyme 2 Excess D blocks a step D D C Enzyme 3 D (a) Negative feedback W Enzyme 4 X Positive feedback + Enzyme 5 Excess Z Z Y stimulates a Z step Z Enzyme 6 Z (b) Positive feedback Fig. 1-13a A Negative feedback – Enzyme 1 B D Enzyme 2 Excess D blocks a step D D C Enzyme 3 D (a) Negative feedback Fig. 1-13b W Enzyme 4 X Positive feedback + Enzyme 5 Excess Z Z Y stimulates a Z step Z Enzyme 6 Z (b) Positive feedback  Concept 1.2: The Core Theme: Evolution accounts for the unity and diversity of life “Nothing in biology makes sense except in the light of evolution”—Theodosius Dobzhansky Evolution unifies biology at different scales of size throughout the history of life on Earth Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Organizing the Diversity of Life Approximately 1.8 million species have been identified and named to date, and thousands more are identified each year Estimates of the total number of species that actually exist range from 10 million to over 100 million Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Grouping Species: The Basic Idea Taxonomy is the branch of biology that names and classifies species into groups of increasing breadth Domains, followed by kingdoms, are the broadest units of classification Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-14 Species Genus Family Order Class Phylum Kingdom Domain Ursus americanus (American black bear) Ursus Ursidae Carnivora Mammalia Chordata Animalia Eukarya  The Three Domains of Life The three-domain system is currently used, and replaces the old five-kingdom system Domain Bacteria and domain Archaea comprise the prokaryotes Domain Eukarya includes all eukaryotic organisms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-15 (a) DOMAIN BACTERIA (b) DOMAIN ARCHAEA (c) DOMAIN EUKARYA Protists Kingdom Plantae Kingdom Fungi Kingdom Animalia Fig. 1-15a (a) DOMAIN BACTERIA Fig. 1-15b (b) DOMAIN ARCHAEA  The domain Eukarya includes three multicellular kingdoms: – Plantae – Fungi – Animalia Other eukaryotic organisms were formerly grouped into a kingdom called Protista, though these are now often grouped into many separate kingdoms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-15c Protists Kingdom Plantae Kingdom Fungi (c) DOMAIN EUKARYA Kingdom Animalia Fig. 1-15d Protists Fig. 1-15e Kingdom Fungi Fig. 1-15f Kingdom Plantae Fig. 1-15g Kingdom Animalia Unity in the Diversity of Life A striking unity underlies the diversity of life; for example: – DNA is the universal genetic language common to all organisms – Unity is evident in many features of cell structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-16 15 µm 5 µm Cilia of Paramecium Cilia of windpipe cells 0.1 µm Cross section of a cilium, as viewed with an electron microscope  Charles Darwin and the Theory of Natural Selection Fossils and other evidence document the evolution of life on Earth over billions of years Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-17  Charles Darwin published On the Origin of Species by Means of Natural Selection in 1859 Darwin made two main points: – Species showed evidence of “descent with modification” from common ancestors – Natural selection is the mechanism behind “descent with modification” Darwin’s theory explained the duality of unity and diversity Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-18 Fig. 1-19  Darwin observed that: – Individuals in a population have traits that vary – Many of these traits are heritable (passed from parents to offspring) – More offspring are produced than survive – Competition is inevitable – Species generally suit their environment Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Darwin inferred that: – Individuals that are best suited to their environment are more likely to survive and reproduce – Over time, more individuals in a population will have the advantageous traits In other words, the natural environment “selects” for beneficial traits Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-20 1 Population 2 Elimination 3 Reproduction 4 Increasing with varied of individuals of survivors. frequency inherited traits. with certain of traits that traits. enhance survival and reproductive success.  Natural selection is often evident in adaptations of organisms to their way of life and environment Bat wings are an example of adaptation Video: Soaring Hawk Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-21  The Tree of Life “Unity in diversity” arises from “descent with modification” – For example, the forelimb of the bat, human, horse and the whale flipper all share a common skeletal architecture Fossils provide additional evidence of anatomical unity from descent with modification Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Darwin proposed that natural selection could cause an ancestral species to give rise to two or more descendent species – For example, the finch species of the Galápagos Islands Evolutionary relationships are often illustrated with tree-like diagrams that show ancestors and their descendents Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-22 Warbler finches Insect-eaters Green warbler finch Certhidea olivacea COMMON Gray warbler finch ANCESTOR Certhidea fusca Seed-eater Sharp-beaked ground finch Bud-eater Geospiza difficilis Vegetarian finch Platyspiza crassirostris Mangrove finch Cactospiza heliobates Insect-eaters Tree finches Woodpecker finch Cactospiza pallida Medium tree finch Camarhynchus pauper Large tree finch Camarhynchus psittacula Small tree finch Camarhynchus parvulus Cactus-flower- Large cactus eaters ground finch Geospiza conirostris Cactus ground finch Ground finches Seed-eaters Geospiza scandens Small ground finch Geospiza fuliginosa Medium ground finch Geospiza fortis Large ground finch Geospiza magnirostris Fig. 1-22a Warbler finches Insect-eaters Green warbler finch Certhidea olivacea Gray warbler finch Certhidea fusca Seed-eater Sharp-beaked ground finch Bud-eater Geospiza difficilis Vegetarian finch Platyspiza crassirostris Fig. 1-22b Mangrove finch Cactospiza heliobates Insect-eaters Tree finches Woodpecker finch Cactospiza pallida Medium tree finch Camarhynchus pauper Large tree finch Camarhynchus psittacula Small tree finch Camarhynchus parvulus Fig. 1-22c Cactus-flower- Large cactus eaters ground finch Geospiza conirostris Cactus ground finch Ground finches Seed-eaters Geospiza scandens Small ground finch Geospiza fuliginosa Medium ground finch Geospiza fortis Large ground finch Geospiza magnirostris  Video: Albatross Courtship Ritual Video: Blue-footed Boobies Courtship Ritual Video: Galápagos Islands Overview Video: Galápagos Marine Iguana Video: Galápagos Sea Lion Video: Galápagos Tortoise Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Concept 1.3: Scientists use two main forms of inquiry in their study of nature The word Science is derived from Latin and means “to know” Inquiry is the search for information and explanation There are two main types of scientific inquiry: discovery science and hypothesis-based science Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Discovery Science Discovery science describes natural structures and processes This approach is based on observation and the analysis of data Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Types of Data Data are recorded observations or items of information Data fall into two categories – Qualitative, or descriptions rather than measurements – Quantitative, or recorded measurements, which are sometimes organized into tables and graphs Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-23  Induction in Discovery Science Inductive reasoning draws conclusions through the logical process of induction Repeat specific observations can lead to important generalizations – For example, “the sun always rises in the east” Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Hypothesis-Based Science Observations can lead us to ask questions and propose hypothetical explanations called hypotheses Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The Role of Hypotheses in Inquiry A hypothesis is a tentative answer to a well- framed question A scientific hypothesis leads to predictions that can be tested by observation or experimentation Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  For example, – Observation: Your flashlight doesn’t work – Question: Why doesn’t your flashlight work? – Hypothesis 1: The batteries are dead – Hypothesis 2: The bulb is burnt out Both these hypotheses are testable Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-24 Observations Question Hypothesis #1: Hypothesis #2: Dead batteries Burnt-out bulb Prediction: Prediction: Replacing batteries Replacing bulb will fix problem will fix problem Test prediction Test prediction Test falsifies hypothesis Test does not falsify hypothesis Fig. 1-24a Observations Question Hypothesis #1: Hypothesis #2: Dead batteries Burnt-out bulb Fig. 1-24b Hypothesis #1: Hypothesis #2: Dead batteries Burnt-out bulb Prediction: Prediction: Replacing batteries Replacing bulb will fix problem will fix problem Test prediction Test prediction Test falsifies hypothesis Test does not falsify hypothesis  Deduction: The “If…Then” Logic of Hypothesis Based Science Deductive reasoning uses general premises to make specific predictions For example, if organisms are made of cells (premise 1), and humans are organisms (premise 2), then humans are composed of cells (deductive prediction) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  A Closer Look at Hypotheses in Scientific Inquiry A hypothesis must be testable and falsifiable Hypothesis-based science often makes use of two or more alternative hypotheses Failure to falsify a hypothesis does not prove that hypothesis – For example, you replace your flashlight bulb, and it now works; this supports the hypothesis that your bulb was burnt out, but does not prove it (perhaps the first bulb was inserted incorrectly) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The Myth of the Scientific Method The scientific method is an idealized process of inquiry Hypothesis-based science is based on the “textbook” scientific method but rarely follows all the ordered steps Discovery science has made important contributions with very little dependence on the so-called scientific method Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  A Case Study in Scientific Inquiry: Investigating Mimicry in Snake Populations Many poisonous species are brightly colored, which warns potential predators Mimics are harmless species that closely resemble poisonous species Henry Bates hypothesized that this mimicry evolved in harmless species as an evolutionary adaptation that reduces their chances of being eaten Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  This hypothesis was tested with the poisonous eastern coral snake and its mimic the nonpoisonous scarlet kingsnake Both species live in the Carolinas, but the kingsnake is also found in regions without poisonous coral snakes If predators inherit an avoidance of the coral snake’s coloration, then the colorful kingsnake will be attacked less often in the regions where coral snakes are present Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-25 Scarlet kingsnake (nonpoisonous) Key Range of scarlet kingsnake only Overlapping ranges of scarlet kingsnake and eastern coral snake North Carolina Eastern coral snake (poisonous) South Carolina Scarlet kingsnake (nonpoisonous)  Field Experiments with Artificial Snakes To test this mimicry hypothesis, researchers made hundreds of artificial snakes: – An experimental group resembling kingsnakes – A control group resembling plain brown snakes Equal numbers of both types were placed at field sites, including areas without poisonous coral snakes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-26 (a) Artificial kingsnake (b) Brown artificial snake that has been attacked Fig. 1-26a (a) Artificial kingsnake Fig. 1-26b (b) Brown artificial snake that has been attacked  After four weeks, the scientists retrieved the artificial snakes and counted bite or claw marks The data fit the predictions of the mimicry hypothesis: the ringed snakes were attacked less frequently in the geographic region where coral snakes were found Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-27 RESULTS 100 Artificial kingsnakes 83% 84% Percent of total attacks Brown 80 on artificial snakes artificial snakes 60 40 20 17% 16% 0 Coral snakes Coral snakes absent present  Designing Controlled Experiments A controlled experiment compares an experimental group (the artificial kingsnakes) with a control group (the artificial brown snakes) Ideally, only the variable of interest (the color pattern of the artificial snakes) differs between the control and experimental groups A controlled experiment means that control groups are used to cancel the effects of unwanted variables A controlled experiment does not mean that all unwanted variables are kept constant Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Limitations of Science In science, observations and experimental results must be repeatable Science cannot support or falsify supernatural explanations, which are outside the bounds of science Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Theories in Science In the context of science, a theory is: – Broader in scope than a hypothesis – General, and can lead to new testable hypotheses – Supported by a large body of evidence in comparison to a hypothesis Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Model Building in Science Models are representations of natural phenomena and can take the form of: – Diagrams – Three-dimensional objects – Computer programs – Mathematical equations Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-28 From From body lungs Right Left atrium atrium Right Left ventricle ventricle To lungs To body  The Culture of Science Most scientists work in teams, which often include graduate and undergraduate students Good communication is important in order to share results through seminars, publications, and websites Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-29  Science, Technology, and Society The goal of science is to understand natural phenomena The goal of technology is to apply scientific knowledge for some specific purpose Science and technology are interdependent Biology is marked by “discoveries,” while technology is marked by “inventions” Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The combination of science and technology has dramatic effects on society – For example, the discovery of DNA by James Watson and Francis Crick allowed for advances in DNA technology such as testing for hereditary diseases Ethical issues can arise from new technology, but have as much to do with politics, economics, and cultural values as with science and technology Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 1-30 Fig. 1-UN1 Fig. 1-UN2 Fig. 1-UN3 Producers Consumers Fig. 1-UN4 Fig. 1-UN5 Fig. 1-UN6 Fig. 1-UN7 Fig. 1-UN8 Population of organisms Hereditary Overproduction variations and competition Environmental factors Differences in reproductive success of individuals Evolution of adaptations in the population Fig. 1-UN9  You should now be able to: 1. Briefly describe the unifying themes that characterize the biological sciences 2. Distinguish among the three domains of life, and the eukaryotic kingdoms 3. Distinguish between the following pairs of terms: discovery science and hypothesis- based science, quantitative and qualitative data, inductive and deductive reasoning, science and technology Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Chapter 3 Water and the Fitness of the Environment PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Overview: The Molecule That Supports All of Life 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 Fig. 3-1 Why does the abundance of water allow life to exist on the planet Earth? Concept 3.1: 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 Animation: Water Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-2 – Hydrogen + bond H O – + H – + – + Fig. 3-UN1 Concept 3.2: 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 and Adhesive behavior – Ability to moderate temperature – Expansion upon freezing – Versatility ( ‫ )براعه‬as a solvent Copyright © 2008 Pearson Education, Inc., publishing as Pearson 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 is an attraction between different substances, for example, between water and plant cell walls Animation: Water Transport Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-3 Adhesion Water-conducting cells Direction Cohesion of water 150 µm movement  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 Fig. 3-4 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Heat and Temperature Kinetic energy is the energy of motion Heat is a measure of the total amount of kinetic energy due to molecular motion Temperature measures the intensity of heat due to the average kinetic energy of molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The Celsius scale is a measure of temperature using Celsius degrees (°C) A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1°C The “calories” on food packages are actually kilocalories (kcal), where 1 kcal = 1,000 cal The joule (J) is another unit of energy where 1 J = 0.239 cal, or 1 cal = 4.184 J Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 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  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 The high specific heat of water minimizes temperature fluctuations to within limits that permit life Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-5 The effect of a large body of water on climate Burbank San Bernardino Santa Barbara 73° 90° 100° Los Angeles Riverside 96° (Airport) 75° Santa Ana Palm Springs 70s (°F) 84° 106° 80s Pacific Ocean 90s 100s San Diego 72° 40 miles Evaporative Cooling Evaporation is transformation of a substance from liquid to gas Heat of vaporization is the heat a liquid must absorb for 1 g 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 and bodies of water Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Insulation )‫(عازلة‬of 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 Fig. 3-6 Ice: crystalline structure and floating barrier Hydrogen bond Ice Liquid water Hydrogen bonds are stable Hydrogen bonds break and re-form Fig. 3-6a Hydrogen bond Ice Liquid water Hydrogen bonds are stable Hydrogen bonds break and re-form 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-8 A water-soluble protein (a) Lysozyme molecule in a (b) Lysozyme molecule (purple) in an aqueous (c) Ionic and polar regions nonaqueous environment environment on the protein’s surface attract water molecules. Fig. 3-8ab A water-soluble protein (a) Lysozyme molecule in a (b) Lysozyme molecule (purple) in an aqueous nonaqueous environment environment Fig. 3-8bc A water-soluble protein (b) Lysozyme molecule (purple) in an aqueous (c) Ionic and polar regions environment on the protein’s surface attract water molecules. Hydrophilic and Hydrophobic Substances A hydrophilic substance is one that has an affinity for water A hydrophobic substance is one that does not have an affinity for water Oil molecules are hydrophobic because they have relatively nonpolar bonds A colloid is a stable suspension of fine particles in a liquid Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Solute Concentration in Aqueous Solutions Most biochemical reactions occur in water Chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Molecular mass is the sum of all masses of all atoms in a molecule Numbers of molecules are usually measured in moles, where 1 mole (mol) = 6.02 x 1023 molecules Avogadro’s number and the unit dalton were defined such that 6.02 x 1023 daltons = 1 g Molarity (M) is the number of moles of solute per liter of solution Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 3.3: Acidic and basic conditions 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+), though it is often represented as H+ – The molecule that lost the proton is now a hydroxide ion (OH–) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 3-UN2 water molecules dissociation H H O H O O H O H H H H 2H2O Hydronium Hydroxide ion (H3O+) 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Effects of Changes in pH Concentrations of H+ and OH– are equal in pure water Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH– 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 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The pH Scale In any aqueous solution at 25°C the product of H+ and OH– is constant and can be written as [H+][OH–] = 10–14 The pH of a solution is defined by the negative logarithm of H+ concentration, written as pH = –log [H+] For a neutral aqueous solution [H+] is 10–7 = –(–7) = 7 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  The pH scale and pH pH Scale 0 values of some aqueous 1 Battery acid solutions Gastric juice, 2 lemon juice H+ H+ + – H H+ OH 3 Vinegar, beer, OH– H H+ + wine, cola H+ H+ Acidic 4 Tomato juice solution Black coffee 5 Rainwater 6 Urine OH– Saliva OH– Neutral OH– 7 Pure water H+ H+ [H+] = [OH–] OH– OH– + Human blood, tears H+ H+ H 8 Seawater Neutral solution 9 10 Milk of magnesia OH– OH– OH– H+ OH– 11 OH– OH – Household ammonia H+ OH– 12 Basic solution Household 13 bleach Oven cleaner 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 © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 0 More 1 acidic 2 3 Acid 4 rain 5 Normal 6 rain 7 8 9 10 11 12 13 More 14 basic  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 ‫الشعب المرجانية‬to form calcified reefs ‫الشعاب المرجانية‬ Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Fig. 3-11 What is the effect of carbonate ion concentration on coral reef calcification? RESULTS 40 0 20 EXPERIMENT 200 150 250 [CO32–] (µmol/kg) 300 Fig. 3-11a EXPERIMENT What is the effect of carbonate ion concentration on coral reef calcification? Fig. 3-11b RESULTS 40 20 0 150 200 250 300 [CO32–] (µmol/kg) Fig. 3-UN3 – Hydrogen + bond H + – O H – + + – Fig. 3-UN4 Ice: stable hydro- Liquid water: gen bonds transient hydrogen bonds Fig. 3-UN5 0 Acidic [H+] > [OH–] Acids donate H+ in aqueous solutions Neutral [H+] = [OH–] 7 Bases donate OH– or accept H+ in Basic aqueous solutions [H+] < [OH–] 14 Fig. 3-UN6 Surface of Mars Surface of Earth Fig. 3-UN7 You should now be able to: 1. List and explain the four properties of water that emerge as a result of its ability to form hydrogen bonds 2. Distinguish between the following sets of terms: hydrophobic and hydrophilic substances; a solute, a solvent, and a solution 3. Define acid, base, and pH 4. Explain how buffers work Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Chapter 4 Carbon and the Molecular Diversity of Life PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Overview: Carbon: The Backbone of Life Although cells are 70–95% water, the rest consists mostly of carbon-based 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 © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-1 What properties of carbon underlie its role as the molecular basis of life? Concept 4.1: Organic chemistry is the study of carbon compounds Organic chemistry is the study of compounds that contain carbon Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds Mechanism is the view that all natural phenomena are governed by physical and chemical laws Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  EXPERIMENT conditions believed to simulate those on the “Atmosphere” CH4 Water vapor Can organic molecules form under Electrode Condenser early Earth? Cooled water containing Cold organic water molecules H2O “sea” Sample for chemical analysis 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Formation of Bonds with Carbon 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 © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-3 The shapes of three simple organic molecules Molecular Structural Ball-and-Stick Space-Filling Name Formula Formula Model Model (a) Methane (b) Ethane (c) Ethene (ethylene)  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” that governs the architecture of living molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-4 Valences of the major elements of organic molecules Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C  Carbon atoms can partner with atoms other than hydrogen; for example: – Carbon dioxide: CO2 O=C=O – Urea: CO(NH2)2 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-UN1 Urea Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Animation: Carbon Skeletons Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-5 Variation in carbon skeletons Ethane Propane 1-Butene 2-Butene (a) Length (c) Double bonds Butane 2-Methylpropane (commonly called isobutane) Cyclohexane Benzene (b) Branching (d) Rings Fig. 4-5a Variation in carbon skeletons Ethane Propane (a) Length Fig. 4-5b Variation in carbon skeletons Butane 2-Methylpropane (commonly called isobutane) (b) Branching Fig. 4-5c Variation in carbon skeletons 1-Butene 2-Butene (c) Double bonds Fig. 4-5d Variation in carbon skeletons Cyclohexane Benzene (d) Rings 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-6 The role of hydrocarbons in fats Fat droplets (stained red) 100 µm (a) Mammalian adipose cells (b) A fat molecule 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 ‫مكاني‬ arrangements – Enantiomers are isomers that are mirror images of each other Animation: Isomers Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-7 Three types of isomers Pentane 2-methyl butane (a) Structural isomers cis isomer: The two Xs are trans isomer: The two Xs are on the same side. on opposite sides. (b) Geometric isomers L isomer D isomer (c) Enantiomers Fig. 4-7a Three types of isomers Pentane 2-methyl butane (a) Structural isomers Fig. 4-7b Three types of isomers cis isomer: The two Xs are trans isomer: The two Xs are on the same side. on opposite sides. (b) Geometric isomers Fig. 4-7c Three types of isomers L isomer D isomer (c) Enantiomers  Enantiomers are 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 Animation: L-Dopa Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-8 The pharmacological importance of enantiomers Effective Ineffective Drug Condition Enantiomer Enantiomer Ibuprofen Pain; inflammation S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it A number of characteristic groups are often attached to skeletons of organic molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Chemical Groups Most Important in the Processes of Life 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-9 A comparison of chemical groups of female (estradiol) and male (testosterone) sex hormones Estradiol Testosterone  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 Copyright © 2008 Pearson Education,