CHAPTER 2 THE CHEMICAL BASIS OF LIFE I: ATOMS, MOLECULES, AND WATER

Prepared by

Brenda Leady, University of Toledo

Copyright (c) The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Biology
Based on the principles of chemistry and physics All living organisms are a collection of atoms and molecules

Atoms
Smallest functional units of matter that form all chemical substances and that cannot be further broken down into other substances by ordinary chemical or physical means Each specific type of atom is a chemical element
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Three subatomic particles

Protons- positive, found in nucleus, same number as electrons Neutrons- neutral, found in nucleus, number can vary Electrons- negative, found in orbitals, same number as protons

Entire atom has no net electric charge

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Electrons occupy orbitals

Scientists initially visualized an atom as a mini solar system
This is an oversimplified but convenient image

Electrons travel within regions surrounding the nucleus (orbitals) in which the probability is high of finding that electron Can be depicted as a cloud
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Orbitals
S orbitals are spherical P orbitals are propeller or dumbbell shaped Each orbital can hold only 2 electrons
An atom with more than 2 electrons has more than 1 orbital

Atoms with progressively more electrons have orbitals within electron shells that are at greater and greater distances from the center of the nucleus
1st shell - 1 spherical orbital (1s) - holds 2 electrons 2nd shell - 1 spherical orbital (2s) and 3 dumbbell-shaped orbitals (2p) can hold 4 pairs of electrons

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Nitrogen example
An atom of nitrogen has seven protons and seven electrons 2 electrons fill 1st shell 5 electrons in 2nd shell
2 fill 2s orbital 1 each in the 3 p orbitals

Outer 2nd shell is not full

Electrons in the outer shell that are available to combine with other atoms are called the valence electrons
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Protons
Number of protons in an atom is its atomic number The atomic number is also equal to the number of electrons in the atom so that the net charge is zero

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Periodic table
Organized by atomic number Rows correspond to number of electron shells Columns, from left to right, indicate the numbers of electrons in the outer shell Similarities of elements within a column occur because they have the same number of electrons in their outer shells, and therefore they have similar chemical bonding properties
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Atomic mass
Protons and neutrons are nearly equal in mass, and both are more than 1,800 times the mass of an electron Atomic mass scale indicates an atoms mass relative to the mass of other atoms Most common form of carbon has six protons and six neutrons, is assigned an atomic mass of exactly 12
A hydrogen atom has an atomic mass of 1, indicating that it has 1/12 the mass of a carbon atom A magnesium atom, with an atomic mass of 24, has twice the mass of a carbon atom
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Mass or weight?
Weight is derived from the gravitational pull on a given mass If a man who weighs 154 pounds on earth were standing on the moon, for example, he would only weigh about 25 pounds, but he would weigh 21 trillion pounds if he could stand on a neutron star. However, his mass is the same in all locations.
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Units
Dalton
Unit of measurement for atomic mass One dalton (d) equals 1/12 the mass of a carbon atom Carbon has an atomic mass of 12 Daltons

Mole
1 mole of any element contains the same number of atoms6.022 x 1023 Avogadros number
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Isotopes
Multiple forms of an element that differ in the number of neutrons 12C contains 6 protons and 6 neutrons 14C contains 6 protons and 8 neutrons Atomic masses are averages of the weights of different isotopes of an element

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Hydrogen, oxygen, carbon, and nitrogen

Typically make up about 95% of the atoms in living organisms
Hydrogen and oxygen occur primarily in water Nitrogen is found in proteins Carbon is the building block of all living matter

Mineral elements - less than 1% Trace elements - less than 0.01%

Essential for normal growth and function
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Chemical bonds and molecules

Molecule
2 or more atoms bonded together

Molecular formula
Contains chemical symbols of elements found in a molecule Subscript indicates how many of each atom are present

Compound
Molecule composed of 2 or more elements
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3 types of bonds
1. 2. 3.

Covalent
Polar covalent

Hydrogen Ionic

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Covalent bonds
Atoms share a pair of electrons Occurs between atoms whose outer electron shells are not full Covalent bonds are often the strongest of all chemical bonds, because the shared electrons behave as if they belong to each atom Can share
1 pair of electrons single bond H-F 2 pairs of electrons double bond O=O 3 pairs of electrons triple bond
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Octet rule
Atoms are stable when their outer shell is full For many atoms, the outer shell fills with 8 electrons One exception is hydrogen, which fills its outer shell with 2 electrons

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Polar covalent bonds

When two atoms with different electronegativities form a covalent bond, the shared electrons are more likely to be in the outer shell of the atom of higher electronegativity rather than the atom of lower electronegativity Polar covalent bonds occur because the distribution of electrons around the atoms creates a polarity, or difference in electric charge, across the molecule

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Water
Classic example of polar covalent bonds Electrons tend to be in the more electronegative oxygen atom rather than either of the less electronegative hydrogen atoms Molecule has partial negative charge region and a partial positive charge region
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Hydrogen bonds
Weak polar covalent bonds Represented as dashed or dotted lines Collectively, can form strong bond overall
Holds DNA strands together

Individually, weak bonds can form and break easily

Substrate and enzyme bonding
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Ionic bonds
An ion is an atom or molecule that has gained or lost one or more electrons It now has a net electric charge Cations- net positive charge Anions- net negative charge Ionic bond occurs when a cation binds to an anion
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Chemical Reactions
Occurs when one or more substances are changed into other substances
Reactants products

Share many properties

All require a source of energy Reactions in living organisms often require a catalyst (enzymes) Tend to proceed in a particular direction but will eventually reach equilibrium Occur in liquid environment - water
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Properties of water
A solution is made up of the
Solvent- liquid Solutes- substances dissolved in solvent

Aqueous solution- water is the solvent Ions and molecules that contain polar covalent bonds will dissolve in water

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Hydrophillic- water-loving
Readily dissolve in water Ions and molecules that contain polar covalent bonds

Hydrophobic- water-fearing
Do not readily dissolve in water Nonpolar molecules like hydrocarbon

Amphipathic molecule
Have both polar or ionized regions at one or more sites and nonpolar regions at other sites May form micelles in water
Polar (hydrophilic) regions at the surface of the micelle and nonpolar (hydrophobic) ends are oriented toward the interior of the micelle
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Solutions
Concentration
Amount of a solute dissolved in a unit volume of solution 1 gram of NaCl was dissolved in 1 liter of water = 1 g/L

Molarity
Number of moles of a solute dissolved in 1 L of water 1 mole of a substance is the amount of the substance in grams equal to its atomic or molecular mass
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H2O in 3 states of matter

Solid (ice), liquid (water), and gas (water vapor) Changes in state, such as changes between the solid, liquid, and gas states of H2O, involve an input or release of energy Water is extremely stable as a liquid

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Colligative properties of water

Depend strictly on the concentration of dissolved solute particles and not on the specific type of particle Addition of solutes to water lowers its freezing point below 0C and raises its boiling point above 100C Some animals produce antifreeze molecules that dissolve in their body fluids, thereby lowering the freezing point of the fluids and preventing their blood and cells from freezing in the extreme cold
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Not just a solvent

Water has many important functions in living organisms
Participates in chemical reactions
Hydrolysis or dehydration

Provides force or support Remove toxic waste components Evaporative cooling Cohesion and adhesion
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Acids and Bases

Pure water has the ability to ionize to a very small extent into hydrogen ions (H+) and hydroxide ions (OH-) In pure water [H+][OH-] = [10-7 M][10-7 M] 10-14 M

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Acids are molecules that release hydrogen ions in solution

A strong acid releases more H+ than a weak acid

Bases lower the H+ concentration

Some release OHOthers bind H+

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pH
pH = log10 [H+] Acidic solutions are pH 6 or below pH 7 is neutral Alkaline solutions are pH 8 or above

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The pH of a solution can affect

The shapes and functions of molecules The rates of many chemical reactions The ability of two molecules to bind to each other The ability of ions or molecules to dissolve in water

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Buffers
Organisms usually tolerate only small changes in pH Buffers help to keep a constant pH An acid-base buffer system can shift to generate or release H+ to adjust for changes in pH

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