The Chemical Context of Life Atoms, Bonding, Molecules Lecture 2 8/31/05 The Chemical Context of Life Atoms, Bonding, Molecules

Website to get LECTURE NOTES Before we start… Website to get LECTURE NOTES http://www.uvm.edu/~dstratto/bcor011_handouts/ Questions from last time?

Types of atoms bonded together Matter Elements Compounds Pure substances Made up of only One type of atom Bonded Elements Made up of two or more Types of atoms bonded together In a fixed ratio NEW SUBSTANCE Different Properties Sodium Chloride Sodium Chloride + Figure 2.2

ATOMS are the smallest unit of matter that maintain the properties of an element Why ATOMS bond together chemically is because of their subatomic structure

Basis for Chemical Bonding Atomic Structure Electrons (-) Atomic number = protons nucleus Protons (+) Electron number Chemical properties Neutrons (o) Atomic mass = protons + neutrons Atoms are electrically neutral !

Atoms differ by the number of protons and electrons Atomic“character”

Electrons are arranged in SHELLS 1 outer shell electron 4 outer shell electrons 1 outer shell electron 7 outer shell electrons

Character determined by Outer Shell Electrons

The periodic table of the elements Shows the electron distribution for all the elements Second shell Helium 2He First Third Hydrogen 1H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3Li Beryllium 4Be Boron 3B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Figure 2.8

Bonding: achieve electronic stability “full outer shells of electrons” Ionic Bonding Covalent Bonding “Theft” “Sharing”

Ionic or Covalent Bonding? What determines Ionic or Covalent Bonding? Electronegativity Electronegativity Is the attraction of a particular kind of atom for the electrons in a covalent bond The more electronegative an atom The more strongly it pulls shared electrons toward itself

Atoms have very different electronegativities Ionic bonding Atoms have very different electronegativities Second shell Helium 2He First Third Hydrogen 1H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3Li Beryllium 4Be Boron 3B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Figure 2.8 Electronically Stable Full Outer Shells NON- REACTIVE Strong Electro- Negative Nearly Full Outer shells Weak Electro- Negativity Nearly Empty Outer Shells

Attraction between ions Ionic Bonding:“Theft & Abandonment” (Na) (Cl) (Na+) (Cl-) Unfilled outer shells Electronically neutral Filled outer shells CHARGED SPECIES No longer atoms: IONS Attraction between ions is very strong

An anion Is negatively charged ions A cation Is positively charged

Sodium chloride (NaCl) An ionic bond Is an attraction between anions and cations Cl– Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Sodium atom (an uncharged atom) Chlorine atom Na+ Sodium on (a cation) Sodium chloride (NaCl) Figure 2.13

Ionic compounds Are often called salts, which may form crystals Na+ Figure 2.14 Na+ Cl–

Covalent Bonding: sharing between atoms of similar electronegativity Second shell Helium 2He First Third Hydrogen 1H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3Li Beryllium 4Be Boron 3B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Figure 2.8 Intermediate Electro- Negativity

Covalent Bonding: “Sharing” H-H Same electronegativity physical overlap between atoms full outer shells physically tied at the hip geometrical/spatial orientation fixed MOLECULES

Specific Geometry O H C Figure 2.11 C, D Name Electron- Structural (molecular formula) Electron- shell diagram Structural formula Space- filling model (c) Methane (CH4). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. Water (H2O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. (d) H O C Figure 2.11 C, D Specific Geometry

Each electron shell Consists of a specific number of orbitals Orbitals are defined areas of space that electrons occupy within electron shells Electron orbitals. Each orbital holds up to two electrons. 1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals (a) First shell (maximum 2 electrons) (b) Second shell 8 electrons) (c) Neon, with two filled shells (10 electrons) Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. x Z Y Figure 2.9

In a covalent bond The s and p orbitals may hybridize, creating specific molecular shapes s orbital Z Three p orbitals X Y Four hybrid orbitals (a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink). Tetrahedron Figure 2.16 (a)

Space-filling Ball-and-stick Hybrid-orbital model model (with ball-and-stick model superimposed) Unbonded Electron pair 104.5° O H Water (H2O) Methane (CH4) C Ball-and-stick (b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules Figure 2.16 (b)

COVALENT BONDING: Sharing Products of Covalent bonding are called MOLECULES

A molecule A single bond A double bond Consists of two or more atoms held together by covalent bonds A single bond Is the sharing of one pair of valence electrons A double bond Is the sharing of two pairs of valence electrons

Single and double covalent bonds Name (molecular formula) Electron- shell diagram Structural formula Space- filling model Hydrogen (H2). Two hydrogen atoms can form a single bond. Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond. H O Figure 2.11 A, B (a) (b)

Missing: 2 3 4 always makes 2 3 4 bonds outer shell electrons water 2 3 4 outer shell electrons Valence Electrons always makes 2 3 4 bonds water cytosine

Molecular Shape and Function The precise shape of a molecule Is usually very important to its function in the living cell Is determined by the positions of its atoms’ valence orbitals Molecular shape Determines how biological molecules recognize and respond to one another with specificity

Figure 2.17 Carbon Nitrogen Hydrogen Sulfur Oxygen Natural endorphin Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Endorphin receptors Brain cell Figure 2.17

Two Types of Covalent Bonds nonpolar covalent bond The atoms have similar electronegativities Share the electron equally polar covalent bond The atoms have fairly different electronegativities - Share the electrons, but unequally

Water polar covalent bond The atoms have differing electronegativities Share the electrons unequally Water This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2O d– O H d+ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. Figure 2.12

POLAR COVALENT BOND the sharing of electrons in a bond is unequal negative pole the molecule is LOPSIDED NO NET CHARGE JUST ASYMMETRY positive pole

Asymmetry of Electrons within Water has some interesting Consequences Individual Water Molecules have Considerable attraction for one another Cohesion / Cohesive Properties Water molecules act as little magnets

- + Dipole Hydrogen Bonds Electron withdrawing weak, dynamic, electrostatic interactions * additive

S N S N S N + + + + + + + +

The polarity of water molecules Allows them to form hydrogen bonds with each other Contributes to the various properties water exhibits Hydrogen bonds + H  – Figure 3.2

Properties of water due to Polarity Cohesion/surface tension Temperature moderation High specific heat Evaporative cooling Ice floats Solvent Ability Hydrophilicity and hydrophobicity Ionization ability (pH)

Summary Points of Lecture 2 Atomic Structure Atoms bond to achieve full outer electron shells Ionic bonding “theft and abandonment” - consequence: IONS, charged species - Consequence: strong attraction of ions Covalent Bonding “sharing” - consequence: molecules - consequence: atoms physically tied at the hip - consequence: precise 3-D spatial geometries POLAR Covalent Molecules - Asymmetric charge distribution within molecule - “little magnets” - water is most common example

Water conducting cells Emergent properties of water contribute to Earth’s fitness for life 1. Cohesion - water molecules stick to one another Figure 3.4 Surface Tension Water conducting cells 100 µm Figure 3.3

Gas = Steam + + + + + + + + + + + + + + + + + + + + + + Liquid + +

Emergent properties of water contribute to Earth’s fitness for life 2. Temperature Moderation - water has a high specific heat (energy to raise 1g of substance 1oC) heat is absorbed when Hydrogen bonds break heat is released when Hydrogen bonds form keeps temperature of earth from fluctuating wildly heat capacities in change of state (solid-liquid-gas) (heat of vaporization, heat of fusion)

Gas = Steam + + + + + + + + + + + + + + + + + + + + + + Liquid + +

Some consequences Water hydrogen bonding Evaporative cooling Is due to water’s high heat of vaporization Allows water to cool a surface Solid Water – ICE Is less dense than Water – SO FLOATS - Insulates bodies of water

The hydrogen bonds in ice Are more “ordered” than in liquid water, making ice less dense Liquid water Hydrogen bonds constantly break and re-form Ice Hydrogen bonds are stable Hydrogen bond Figure 3.5

The Solvent of Life Water is a versatile solvent due to its polarity It can form aqueous solutions

The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them Negative oxygen regions of polar water molecules are attracted to sodium cations (Na+). + Cl – – Na+ Positive hydrogen regions of water molecules cling to chloride anions (Cl–). Cl– Figure 3.6

Water can also interact with polar molecules such as proteins This oxygen is attracted to a slight positive charge on the lysozyme molecule. This oxygen is attracted to a slight negative charge on the lysozyme molecule. (a) Lysozyme molecule in a nonaqueous environment (b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva (c) Ionic and polar regions on the protein’s Surface attract water molecules. + – Figure 3.7