Chapter 2 - Chemical Evolution PDF

Chapter 2 Water and Carbon: The Chemical Basis of Life Link between chemistry and biology Chemical evolution: – Leading explanation for origin of life on Earth – Formation of increasingly complex carbon-containing substances – Led to molecule that could replicate itself – Switch...

Chapter 2 Water and Carbon: The Chemical Basis of Life Link between chemistry and biology Chemical evolution: – Leading explanation for origin of life on Earth – Formation of increasingly complex carbon-containing substances – Led to molecule that could replicate itself – Switch from chemical to biological evolution Evolution by natural selection took over: – Original molecule multiplied – Descendant of original molecule became metabolically active and acquired membrane – Five characteristics of life fulfilled Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution Four types of atoms make up 96% of matter in organisms: – Hydrogen, carbon, nitrogen, and oxygen How did simple substances evolve into complex structures in living cells? 1. What are the physical structures of hydrogen, carbon, nitrogen, and oxygen atoms? 2. What are the structures of simple molecules—water, carbon dioxide, etc.—that served as building blocks of chemical evolution?  Basic Atomic Structure – Nucleus made up of protons and neutrons: ▪ Protons—positive charge (+1) ▪ Neutrons—neutral charge – Surrounded by orbiting electrons: ▪ Negative charge (-1) – Atom with equal number of protons and electrons: ▪ Charges balance ▪ Electrically neutral  Understanding Elements Elements: – Consist entirely of a single type of atom Atomic number: – Characteristic number of protons in nucleus of any atom – Written as subscript left of its symbol Mass number: – Sum of protons and neutrons in atom Atoms are tiny, so how do we weigh them? Dalton (Da): – Each proton and each neutron has a mass of one dalton (Da) Mass of electron so small that it can be ignored Therefore, mass of atom is equal to its mass number Number of protons in element does not vary: – Neutrons in element may vary – Forms element with different numbers of neutrons (isotope): ▪ Isotopes of element have different masses Example: All carbon atoms have 6 protons: – Carbon-12 has 6 neutrons; atomic mass 12 Da – Carbon-13 has 7 neutrons; atomic mass 13 Da – Carbon 14 has 8 neutrons; atomic mass 14 Da Atomic weight of element: – Average of all masses of naturally occurring isotopes based on their abundance ▪ Atomic number of carbon is 12.01, what is the most abundant isotope of carbon? Radioactive isotopes: Unstable isotopes that decay over time Weight of molecules in grams Mole refers to 6.022 × 1023: – Mass of one mole of an atom is the same as its atomic weight expressed in grams – Molecular weight: ▪ Mass of one mole of molecule ▪ Sum of atomic weights of all atoms in molecule The Atomic Structure of the First 18 Elements C, H, N, O, P and S make up over 99% of atoms in body  Atomic Structure and Electron Shells Arrangement of electrons around nucleus is key to understanding how elements behave: – Electrons move around atomic nuclei in specific regions called orbitals – Each orbital can hold up to two electrons – Orbitals grouped into levels called electron shells Electron shells numbered 1, 2, 3, and so on: – Numbers indicate their relative distance from nucleus – Smaller numbers are closer to nucleus – Each electron shell contains specific number of orbitals – Electron shell comprising single orbital can hold up to two electrons – Shell with four orbitals can contain up to eight electrons – Electrons of an atom fill innermost shells first, then fill outer shells Outermost shells of elements: – Atom’s valence shell is outermost shell – Electrons in this shell called valence electrons Different atoms have different numbers of unpaired electrons Covalent Bonding Hold Molecules Together By Sharing Electrons Atoms become more stable by making covalent bonds Hydrogen does not have full valence shell: ▪ Two hydrogen atoms share electrons ▪ Outer shell filled—more stable Electrons in Covalent Bonds are Not Always Shared Equally Water is an example of a compound – which are molecules in which atoms of different elements are bonded together Nonpolar vs Polar Covalent Bonds Nonpolar covalent bond: – Electrons are evenly shared between two atoms – Bond is symmetrical – Example: C – H bond Polar covalent bond: – Electrons are shared unevenly (asymmetrical) – Electrons in polar covalent bonds spend most of their time close to nucleus of more electronegative atom Electronegativity: Strength with which atoms pull electrons toward themselves Atom’s electronegativity determined by: – Number of protons – Distance of valence shell from nucleus Moving up and to the right on periodic table → higher electronegativity – O > N > S,C,H,P  Polar Bonds Produce Partial Charges on Atoms Examples of Consequences of differences in electronegativity Polar covalent bonds in water molecule: – Consists of oxygen atom bonded to two hydrogen atoms – Electrons in covalent bond not shared equally – Held more tightly by oxygen nucleus than hydrogen nuclei: ▪ Gives oxygen partial negative charge – Partial charges symbolized as delta    and    Ionic Bonding Ionic bonds - Unlike covalent bond, electron is not shared; it is completely transferred from one atom to another: – Transfer gives each atom a full valence shell Ions—atom or molecule that carries charge: – Cation—Atom loses electron and becomes positively charged – Anion—Atom gains an electron and becomes negatively charged The Electron-Sharing Continuum Unpaired Electrons in the Valence Shell Can Participate in Double and Triple Covalent Bonds Number of unpaired electrons determines number of bonds an atom can make Molecule’s shape often dictates its behavior Shape of simple molecule governed by geometry of its bonds The Geometry of Methane and Water: – Methane (C H4)—tetrahedron forms due to repulsive forces between electrons – Water (H2O) is planar and bent because of two unshared electron pairs – Will come back to shapes of other molecules Molecules Can Be Represented Several Ways Properties of Water and the Early Oceans Life is based on water: – 75% of cell is water Water is an excellent solvent: – Solute dissolved into solvent makes a solution – Substances more likely to react when they are dissolved in solvent like water What properties are correlated with water’s structure? A Water Can Interact with other Water Molecules Water is polar: – Oxygen atoms have partial negative charge – Hydrogen atoms have partial positive charge Water is Polar and Participates in Hydrogen Bonds: – Water molecules have bent geometry – Partial charge on hydrogen attracts partial negative charge on oxygen: ▪ These weak electrical interactions are called hydrogen bonds Water Is an Efficient Solvent Hydrogen bonds can also form between water molecules and polar solutes Hydrophilic (“water-loving”) molecules: ▪ Ions and polar molecules stay in solution due to their interactions with water’s partial charges Hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in water Not everything dissolves in water Hydrophobic (“water-fearing”) molecules: – Uncharged and nonpolar compounds – Do not dissolve in water Hydrophobic molecules interact with each other through hydrophobic interaction van der Waals interactions increase stability of clustered hydrophobic molecules Cohesion and Adhesion Cohesion and adhesion: – Attraction between like molecules is called cohesion – Attraction between unlike molecules is called adhesion Water is cohesive: ▪ Stays together because of hydrogen bonds ▪ Adheres to surfaces with polar or charged components How does water move from roots of plants to their leaves against gravity? Surface Tension Cohesion instrumental in phenomenon known as surface tension: – Surface tension: ▪ Cohesive force caused by attraction between molecules at surface of liquid Water resists any force that increases its surface area: – Resistance makes water surface act like elastic membrane Water Is Denser as a Liquid than as a Solid Most substances shrink as they solidify Water expands as it freezes: – Denser as a liquid than a solid – Forms relatively open crystal structure – This is why ice floats! – Ice forms an insulating “blanket” on water surfaces Water Has a High Capacity for Absorbing Energy Water has high capacity for absorbing energy: – Specific heat—amount of energy needed to raise temperature of 1 gram of substance by 1°C: ▪ Water has very high specific heat ▪ Many hydrogen bonds must be broken for water molecules to move faster – As molecules increase in polarity, it takes more energy to change their temperature With extensive hydrogen bonding Specific Heat Water (H2O) 4.18 With some hydrogen bonding Blank Ethanol (C2H6O) 2.44 Glycerol (C3H8O3) 2.38 With little or no hydrogen bonding Blank Benzene (C6H6) 1.74 Xylene (C8H10) 1.72  The Role of Water in Acid–Base Chemical Reactions Chemical reactions occur when substance is: – Combined with another – Broken down into another substance In most chemical reactions, chemical bonds are broken and new bonds form Chemical reactions are written as equations: Reactant(s) Product(s) – For example: Water molecules dissociate into a hydrogen ion (H+) and a hydroxide ion (O H−): Chemical equilibrium: – Reaction is reversible, happens in both directions at approximately the same time Since protons (H+) don’t exist by themselves, reaction produces hydronium ions (H3O+): Measuring the Concentration of Protons Mole refers to 6.022 × 1023: – Mass of one mole of an atom is the same as its atomic weight expressed in grams – Molecular weight: ▪ Mass of one mole of molecule ▪ Sum of atomic weights of all atoms in molecule Molarity (M): – Concentration of substance in solution – Number of moles of solute present per liter of solution The Role of Water in Acid–Base Chemical Reactions Acids—substances that give up protons during chemical reactions and raise hydronium ion concentration (H3O+): – Adding acid to solution increases proton concentration of solution Bases—substances that acquire protons during chemical reactions and lower (H3O+): ‒ Adding base to solution decreases proton concentration  The pH of a Solution Reveals Whether It Is Acidic or Basic Concentration of protons in water is very low (1 × 10-7M) pH (power of hydrogen): – Logarithmic notation used to express concentration of protons in solution The pH Scale: – One unit of pH represents change in concertation of hydrogen ions equal to factor of 10 Acids have a p H of less than 7 Bases have a p H of greater than 7 Neutral indicates neither acidic or basic: – Solution inside living cells is about p H 7 Buffers minimize changes in p H: – Buffers help maintain homeostasis, relatively constant conditions, in organisms Chemical Reactions Most common reaction in mix of gases from volcanoes produces carbonic acid: Expression is balanced: – Same number of atoms on each side System—set of interacting components: If this system absorbs enough thermal energy from environment: – Liquid water H2O(l) will convert to gas H2O(g) Endothermic reactions must absorb thermal energy to proceed Exothermic reactions release thermal energy What Is Energy? Energy—capacity to do work or supply heat This capacity exists in one of the two ways: 1. Stored potential—potential energy Object gains or loses ability to store energy due to its position Position of shared electrons in covalent bonds: 1. Shared electrons are far from atoms’ nuclei—bonds are long and weak 2. Electrons are shifted closer to one or both nuclei—bond becomes shorter and stronger Molecule’s potential to form stronger bonds is type of potential energy called chemical energy 2. Active Molecular Motion—kinetic energy – Thermal energy – Molecules are constantly in motion – Temperature—measure of thermal energy in molecule: ▪ Cold object has low temperature; molecules are moving slowly – Heat—measure of thermal energy being transferred between two objects: ▪ Objects have different temperatures Thermodynamics and the Early Earth The first law of thermodynamics: – Energy is conserved – It cannot be created or destroyed – It can be transferred or transformed Energy transformation heart of chemical evolution: – Molecules of early Earth were exposed to massive inputs of energy Kinetic energy in form of heat present in gradually cooling molten mass that formed planet The second law of thermodynamics: – Entropy (disorder) always increases Physical and chemical processes proceed in direction that results in: – Lower potential energy – Increased entropy – Or both What Makes a Chemical Reaction Spontaneous? Chemical reactions are spontaneous if: – They proceed on their own—without any continuous external influence – No added energy is needed Two factors determine if reaction will proceed spontaneously: 1. Products have lower potential energy than the reactants 2. Products are less ordered than reactants Entropy is the amount of disorder in the system Stanley Miller’s Spark-Discharge Experiment in 1953 – Miller had simple question: ▪ Can complex organic compounds be synthesized from simple molecules present in Earth’s early atmosphere? ▪ Experimental setup designed to produce microcosm of early Earth Miller’s apparatus showed that complex molecules could be formed from simple molecules: – Used heat and electrical charges – Formed precursors to life molecules: ▪ Samples contained newly synthesized amino acids—building blocks of proteins Concluded that chemical evolution occurs readily if simple molecules with high free energy are exposed to kinetic energy Life is Carbon Based Carbon: – Except for water, almost all molecules found in organisms have this atom – Forms four covalent bonds due to its four valence electrons Organic compounds—molecules that contain carbon bonded to other elements: – Limitless array of molecular shapes – With different combinations of single and double bonds Carbon provides a molecular skeleton – Molecules with more than one carbon atom have a more complex shape Functional Groups define the Chemical Behavior of Organic Molecules Small Organic Molecules Can Assemble into Large Molecules For chemical evolution to continue, smaller molecules had to form larger, more complex ones Macromolecules: – Large molecules made of smaller molecular subunits (monomers) joined together – Polymer—large number of monomers bonded together via polymerization (process of linking monomers together): Polymers can be Extended or Broken Apart Condensation reactions (dehydration reactions): ▪ Monomers polymerize via condensation reactions ▪ Newly formed bond results in production of a water molecule – Reverse reaction is called hydrolysis: ▪ Water molecules reacts with bond linking monomers, separating them from polymer chain Small Organic Molecules Can Assemble into Large Molecules Hydrolysis dominates: – Increases entropy – Is favorable energetically – Polymerization would occur only in high concentration of monomers to push reaction Equilibrium favors free monomers over polymers Macromolecules of life (proteins, nucleic acids, carbohydrates etc.): – May have polymerized early in chemical evolution End of Chapter Questions to Practice Chapter 2 Review Questions 1, 2, 3, 5, 8, 12, 16 (for question 16 you will have to read the case study that this question is part of)