Atoms and Molecules: The Chemical Basis of Life Chapter 2

Learning Objective 1  What principal chemical elements are found in living things?  What are the most important functions of these elements?

Element  A substance that cannot be decomposed into simpler substances by normal chemical reactions

The Periodic Table

Element Functions  Carbon backbone of organic molecules backbone of organic molecules  Hydrogen and oxygen components of water components of water  Nitrogen component of proteins and nucleic acids component of proteins and nucleic acids

Learning Objective 2  Compare the physical properties (mass and charge) and locations of electrons, protons, and neutrons  What is the difference between the atomic number and the mass number of an atom?

Atom  Nucleus protons (positive) protons (positive) neutrons (uncharged) neutrons (uncharged)  Electrons encircle the nucleus encircle the nucleus negative negative

Atomic Number and Mass  Each atom is a particular element identified by number of protons (atomic number) identified by number of protons (atomic number)  Atomic mass sum of protons and neutrons sum of protons and neutrons

AMU  Atomic Mass Unit Mass of a single proton or neutron Mass of a single proton or neutron  Mass of an electron about 1/1800 amu about 1/1800 amu

Isotopes

Fig. 2-2, p. 28 Carbon-12 ( 12 C) (6p, 6n) 6 Carbon-14 ( 14 C) (6p, 8n)

Learning Objective 3  What are orbitals and electron shells?  How are electron shells related to principal energy levels?

Orbitals  Electrons move rapidly in electron orbitals Outside the nucleus Outside the nucleus  Electron shell Electrons in orbitals at the same principal energy level Electrons in orbitals at the same principal energy level Electron in shell far from nucleus has more energy than electron in shell close to nucleus Electron in shell far from nucleus has more energy than electron in shell close to nucleus

Atomic Orbitals

Fig. 2-4a, p. 30 (a) The first principal energy level contains a maximum of 2 electrons, occupying a single spherical orbital (designated 1s). The electrons depicted in the diagram could be present anywhere in the blue area. Nucleus

Fig. 2-4b, p. 30 (b) The second principal energy level includes four orbitals, each with a maximum of 2 electrons: one spherical (2s) and three dumbbell-shaped (2p) orbitals at right angles to one another.

Fig. 2-4c, p. 30 (c) Orbitals of the first and second principal energy levels of a neon atom are shown superimposed. Note that the single 2s orbital plus three 2p orbitals make up neon's full valence shell of 8 electrons. Compare this more realistic view of the atomic orbitals with the Bohr model of a neon atom at right.

Fig. 2-4d, p. 30 (d) Neon atom (Bohr model)

Learning Objective 4  How does the number of valence electrons of an atom relate to its chemical properties?

Valence Electrons  Electron in the outer shell most energetic electrons most energetic electrons  Number and arrangement of an atom’s valence electrons determine its chemical properties determine its chemical properties

Valence Electrons  An atom tends to lose, gain, or share electrons to fill its valence shell  Electrons needed to fill valence shell Most atoms: 8 electrons Most atoms: 8 electrons Hydrogen or helium: 2 electrons Hydrogen or helium: 2 electrons

Learning Objective 5  What is the difference between simplest, molecular, and structural chemical formulas?

Compounds  Atoms are joined by chemical bonds to form compounds  A chemical formula gives the types and relative numbers of atoms in a substance

Chemical Formulae  Simplest formula smallest whole-number ratio of component atoms smallest whole-number ratio of component atoms  Molecular formula actual numbers of each type of atom actual numbers of each type of atom  Structural formula the arrangement of atoms in a molecule the arrangement of atoms in a molecule

Learning Objective 6  Why is the mole concept so useful to chemists?

Avogadro’s Number  Avogadro’s number 6.02 x  One mole (atomic or molecular mass in grams) of any substance contains 6.02 x atoms, molecules, or ions  Enables scientists to “count” particles by weighing a sample

Learning Objective 7  What is the difference between covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions?  How does each differ in the mechanisms by which they form and in relative strength?

Covalent Bonds  Strong, stable bonds  Formed when atoms share valence electrons  Form molecules  May rearrange the orbitals of valence electrons (orbital hybridization)

Covalent Bonds

Fig. 2-5, p. 32 Molecular hydrogen (H2) HH HH or Hydrogen (H) (a) Single covalent bond formation. Two hydrogen atoms achieve stability by sharing a pair of electrons, thereby forming a molecule of hydrogen. In the structural formula on the right, the straight line between the hydrogen atoms represents a single covalent bond. Molecular oxygen (O2) (double bond is formed) O O O O Oxygen (O) or (b) Double covalent bond formation. In molecular oxygen, two oxygen atoms share two pairs of electrons, forming a double covalent bond. The parallel straight lines in the structural formula represent a double covalent bond.

Nonpolar and Polar Covalent Bonds  Covalent bonds are nonpolar if electrons are shared equally between the two atoms nonpolar if electrons are shared equally between the two atoms polar if one atom is more electronegative (greater electron affinity) than the other polar if one atom is more electronegative (greater electron affinity) than the other

Ionic Bonds  Form between a positively charged cation and a negatively charged anion  Are strong in the absence of water but relatively weak in aqueous solution

Ionic Bonds

Fig. 2-9a, p protons 11 electrons Sodium (Na) 17 electrons Chlorine (Cl) 17 protons and 18 electrons Chloride ion (Cl – ) 10 electrons Sodium ion (Na + ) Sodium chloride (NaCl) –

CLICK TO PLAY Animation: How Atoms Bond

CLICK TO PLAY Animation: Spheres of Hydration

Hydrogen Bonds  Relatively weak bonds  Form when A hydrogen atom with a partial positive charge A hydrogen atom with a partial positive charge Is attracted to an atom (usually O or N) with a partial negative charge Is attracted to an atom (usually O or N) with a partial negative charge Already bonded to another molecule or part of the same molecule Already bonded to another molecule or part of the same molecule

Hydrogen Bonds

Fig. 2-11, p. 35 Electronegative atoms Hydrogen bond H H H H H –+ O N

van der Waals interactions  Weak forces  Based on fluctuating electric charges

Learning Objective 8  What are oxidation and reduction reactions?  How do oxidation and reduction reactions relate to the transfer of energy?

Redox Reactions  Oxidation and reduction reactions  Electrons (energy) are transferred from a reducing agent to an oxidizing agent

Oxidation and Reduction  Oxidation Atom, ion, or molecule loses electrons (energy) Atom, ion, or molecule loses electrons (energy)  Reduction Atom, ion, or molecule gains electrons (energy) Atom, ion, or molecule gains electrons (energy)

Learning Objective 9  How do hydrogen bonds between adjacent water molecules govern the properties of water?

Polar Molecules  Water is a polar molecule  One end has a partial positive charge and the other has a partial negative charge  Because it is polar, water is an excellent solvent for ionic or polar solutes

Polar Molecules

Fig. 2-7, p. 34 Hydrogen parts Hydrogen (H)Oxygen (O) Hydrogen (H) Partial negative charge at oxygen end of molecule Oxygen part Water molecule (H 2 O) Partial positive charge at hydrogen end of molecule

Fig. 2-7, p. 34 Hydrogen (H)Oxygen (O) Hydrogen (H) Partial negative charge at oxygen end of molecule Water molecule (H 2 O) Partial positive charge at hydrogen end of molecule Oxygen part Hydrogen parts Stepped Art

Cohesion and Adhesion  Water molecules exhibit cohesion because they form hydrogen bonds with one another  Water molecules exhibit adhesion by hydrogen bonding to substances with ionic or polar regions

Hydrogen Bonds in Water

Specific Heat  Water has high specific heat  Hydrogen bonds must break to raise water temperature  Specific heat of water helps organisms maintain relatively constant internal temperature organisms maintain relatively constant internal temperature keep large bodies of water (ocean) at a constant temperature keep large bodies of water (ocean) at a constant temperature

Heat of Vaporization  Water has a high heat of vaporization  Hydrogen bonds must break for molecules to enter vapor phase  Molecules carry heat, causing evaporative cooling

Ice  Hydrogen bonds between water molecules make ice less dense than liquid water  Because ice floats, the aquatic environment is less extreme

Three Phases of Water

Learning Objective 10  What is the difference between an acid and a base?  What are the properties of acids and bases?

Acids and Bases  Acids proton (hydrogen ion, H + ) donors proton (hydrogen ion, H + ) donors dissociate in solution to yield H + and an anion dissociate in solution to yield H + and an anion  Bases proton acceptors proton acceptors dissociate in solution to yield hydroxide ions (OH - ) dissociate in solution to yield hydroxide ions (OH - )

Learning Objective 11  How does the hydrogen ion concentration (moles per liter) of a solution relate to its pH value?  How do buffers help minimize changes in pH?

pH  The negative log of the hydrogen ion (H +) concentration of a solution (measured in moles per liter)

pH of Solutions  Neutral solution equal concentrations of H + and OH - equal concentrations of H + and OH - (10 -7 mol/L), pH 7 (10 -7 mol/L), pH 7  Acidic solution pH less than 7 pH less than 7  Basic solution pH greater than 7 pH greater than 7

Buffers  Buffering system based on a weak acid or a weak base based on a weak acid or a weak base  Buffer resists changes in pH of a solution when acids or bases are added resists changes in pH of a solution when acids or bases are added

Learning Objective 12  What is the composition of a salt?  Why are salts are important in organisms?

Salts  Salt a compound in which the hydrogen atom of an acid is replaced by some other cation a compound in which the hydrogen atom of an acid is replaced by some other cation  Salts provide many mineral ions essential for life functions

CLICK TO PLAY Animation: Shell Models of Common Elements

CLICK TO PLAY Animation: Electron Arrangements in Atoms