Chapter 2- Water and Carbon: The Chemical Basis of Life

2.1 Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution

• An atom is the smallest identifiable unit of matter. 
• Just four types of atoms:
  • hydrogen (H)
  • carbon (C)
  • nitrogen (N) 
  • oxygen (O)
• Elements are defined as substances that consist entirely of a single type of atom. 
• Each atom of a given element contains a characteristic number of protons, called its atomic number.
• The sum of the protons and neutrons in an atom is called its mass number
• Although the masses of protons, neutrons, and electrons can be measured in grams, the numbers involved are so small that biologists prefer to use a special unit called the dalton (Da).
•  Forms of an element with different numbers of neutrons are known as isotopes 
• The atomic weight of an element is an average of all the masses of the naturally occurring isotopes based on their abundance in nature.
• Electrons move around atomic nuclei in specific regions called orbitals.
• Orbitals are grouped into levels called electron shells.
• ==Electron shells are numbered 1, 2, 3, and so on, to indicate their relative distance from the nucleus. Smaller numbers are closer to the nucleus.==
• Each electron shell contains a specific number of orbitals.
• The electrons of an atom fill the innermost shells first, before filling outer shells. 
• The outermost shell of each element is the atom’s valence shell.
• The electrons found in this shell are referred to as valence electrons.
• The number of unpaired electrons found in an atom’s valence shell is referred to as its valence.
• One way that valence shells can be filled is through the formation of chemical bonds-attractions that bind atoms together.
• When two atoms share electrons, the chemical bond is called a covalent bond, and the connected atoms are termed a molecule.
• Compounds, in which atoms of different elements are bonded together.
• Electronegativity is a property when atoms of different elements form a bond, they may pull shared electrons toward their nuclei with varying lengths
• A bond that involves equally shared electrons is called a nonpolar covalent bond. 
• In contrast, asymmetric sharing of electrons results in a polar covalent bond. 
• Ionic bonds are similar in principle to covalent bonds, but instead of being shared between two atoms, the electrons in ionic bonds are completely transferred from one atom to the other. 
• An atom or molecule that carries a full charge, rather than the partial charges that arise from polar covalent bonds, is called an ion.
• Positively charged ions are called cations.
• Negatively charged ions are called anions.
• Atoms with more than one unpaired electron in the valence shell can also form double bonds or triple bonds.
• Molecular formulas are compact, but don’t contain a great deal of information-they indicate only the numbers and types of atoms in a molecule 
• Structural formulas indicate which atoms in a molecule are bonded together.
• Ball-and-stick models take up more space than structural formulas, but provide information on the three-dimensional shape of molecules and often indicate the relative sizes of the atoms involved
• Space-filling models are more difficult to read than ball and-stick models but more accurately depict the relative sizes of atoms and their spatial relationships 
• Researchers postulate that most of the critical reactions in chemical evolution occurred in an aqueous, or water-based, environment.

2.2 Properties of Water and the Early Oceans

• Solvent is an agent for dissolving or getting substances into solution.
• Substances are most likely to come into contact with one another and react when they are solutes-meaning, when they are dissolved in a solvent like water.
• ==Water’s small size, highly polar covalent bonds, and bent shape resulting in overall polarity are unique among molecules.== 
• Hydrogen bond is a weak electrical interaction and an attraction between a hydrogen atom with a partial positive charge and another atom, usually oxygen or nitrogen, with a partial negative charge. 
• Substances that interact with water in this way are said to be hydrophilic
• Substances that do not interact with water are said to be hydrophobic 
• The interactions between nonpolar molecules that result from being brought together in an aqueous solution are called hydrophobic interactions.
• Once hydrophobic molecules are close to one another, their association is further stabilized by weak electrical attractions known as van der Waals interactions. 
• Attraction between like molecules is called cohesion
• Attraction between unlike molecules, in contrast, is called adhesion.
• A meniscus forms as a result of 
  • Adhesion: At the perimeter of the surface, partial positive charges on water molecules adhere to the negative charges on glass, resulting in an upward pull. 
  • Cohesion: Along the surface, water molecules hydrogen-bond to those next to them and below them, resulting in a net lateral and downward pull that resists the upward pull of adhesion.
• Surface tension is the cohesive force caused by attraction between the molecules at the surface of a liquid.
• Specific heat is the amount of energy required to raise the temperature of 1 gram of a substance by 1 °C. W
• Water’s heat of vaporization- the energy required to change 1 gram of water from a liquid to gas-is higher than that of most molecules that are liquid at room temperature.
• When a chemical reaction occurs, one substance is combined with others or broken down into another substance. 
• The initial, or reactant, molecules are shown on the left and the resulting, or product, molecules are shown on the right.
• A dynamic but stable state such as this is termed a chemical equilibrium. 
• Substances that give up protons during chemical reactions and raise the hydronium ion concentration of water are called acids.
• Molecules or ions that acquire protons during chemical reactions and lower the hydronium ion concentration of water are called bases.
• A chemical reaction that involves a transfer of protons is called an acid-base reaction. 
• A mole refers to the number 6.022 × 10^23-just as the unit dozen refers to the number 12 or the unit million refers to the number 1 × 10^6
• The mass of one mole of a molecule, called its molecular weight, is the sum of the atomic weights of all the atoms in the molecule.
• Molarity is the number of moles of the solute present per liter of solution. 
•  Compounds that minimize changes in pH are called buffers because they reduce the impact of adding acids or bases on the overall pH of a solution. 
• Buffers are important in maintaining relatively constant conditions, or homeostasis, in organisms.

2.3 Chemical Reactions, Energy, and Chemical Evolution 

•  Three types of systems used to evaluate chemical reactions:
  • Open system: can exchange energy with environment, can exchange matter with environment
  • Closed system: can exchange energy with environment, cannot exchange matter with environment 
  • Isolated system: cannot exchange energy with environment, cannot exchange matter with environment
• Endothermic (“within heating”) because thermal energy is absorbed by the system during the process. 
• The transformation of water vapor to liquid water releases thermal energy to the environment and is exothermic
• Energy can be defined as the capacity to do work or supply heat.
• Stored energy is called potential energy. 
• A molecule’s potential to form stronger bonds is a type of potential energy called chemical energy. 
• Energy of motion is called kinetic energy.
• The kinetic energy of molecular motion is called thermal energy.
  • The temperature of an object is a measure of how much thermal energy its molecules possess. 
  • When two objects with different temperatures come into contact, thermal energy is transferred between them. This transferred energy is called heat.
• First law of thermodynamics, energy is conserved-it cannot be created or destroyed, but only transferred and transformed. 
• ==Reactions tend to be spontaneous if the products hαve lower potential energy thαn the reactants==
• Reactions tend to be spontaneous when the product molecules are less ordered thαn the reactant molecules. 
• The amount of disorder in a system ( or the surrounding environment) is called entropy.
• The second law of thermodynamics states that in all spontaneous reactions, entropy always increases when both the system and its environment are taken into account. 

2.4 Investigating Chemical Evolution 

• Chemical evolution was first taken seriously in 1953 when a graduate student named Stanley Miller performed a breakthrough experiment.

2.5 Life is Carbon Based

• ==Many molecules that contain carbon bonded to other elements, such as hydrogen, are called organic compounds.== 

• The critically important H-, N-, O-, P-, and S-containing groups found in organic compounds are called functional groups. 

• These large molecules, made up of smaller molecular subunits joined together, are called macromolecules. 

• In general, a molecular subunit used to build a macromolecule is called a monomer (“one-part”). 

• When a large number of monomers are bonded together, the resulting structure is called a polymer

• The process of linking monomers together is called polymerization.

• Monomers polymerize through condensation reactions, also known as dehydration reactions.

• The reverse reaction, called hydrolysis, breaks polymers apart by adding a water molecule.

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