Covalent bonds – where electrons are shared Typically the strongest bonds in biological systems. Can be polar (where electrons are not equally shared) or non-polar (electrons are equally shared).

Formation of a covalent bond Hydrogen atoms (2 H) Hydrogen molecule (H2) + In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus. 1 When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus. 2 The two electrons become shared in a covalent bond, forming an H2 molecule. 3 Figure 2.10

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)

Covalent bonding in compounds Name (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

The more electronegative an atom 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

A nonpolar covalent bond The atoms have similar electronegativities Share the electron equally Common in hydrocarbons

A polar covalent bond The atoms have differing electronegativities Share the electrons unequally 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

Electron transfer between two atoms creates ions Ions Ionic Bonds Electron transfer between two atoms creates ions Ions Are atoms with more or fewer electrons than usual Are charged atoms An anion Is negatively charged ions A cation Is positively charged

Sodium chloride (NaCl) An ionic bond An attraction between anions and cations These bonds are strong in crystal form, but weak in water 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–

Weak Chemical Bonds – form due to differences in polarity Hydrogen bonds Form when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom  –  + Water (H2O) Ammonia (NH3) O H  +  – N A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. + d+ Figure 2.15  +

Van der Waals Interactions Occur when transiently positive and negative regions of molecules attract each other Weak chemical bonds Reinforce the shapes of large molecules Help molecules adhere to each other

BSC 2010 - Exam I Lectures and Text Pages I. Intro to Biology (2-29) II. Chemistry of Life Chemistry review (30-46) Water (47-57) Carbon (58-67) Macromolecules (68-91) III. Cells and Membranes Cell structure (92-123) Membranes (124-140) IV. Introductory Biochemistry Energy and Metabolism (141-159) Cellular Respiration (160-180) Photosynthesis (181-200)

Water – The Solvent of Life (Ch. 3) Cells are made of 70-95% water, the “SOLVENT OF LIFE”. All living things require water more than any other substance. Solvent - Solute - Aqueous -

Three-quarters of the Earth’s surface is submerged in water The abundance of water is the main reason the Earth is habitable Figure 3.1

The water molecule is a polar molecule The polarity of water molecules Allows them to form hydrogen bonds with each other (negative O ends are attracted to positive H ends) Contributes to the various properties water exhibits Hydrogen bonds + H  – Figure 3.2

Emergent Properties of Water Contribute to Life A. cohesion: (related properties: surface tension and adhesion) B. Water tends to resist rupturing. (related to cohesion) C. Water resists changes in temperature. D. Water expands when it freezes. E. Water is a versatile solvent.

Water molecules exhibit cohesion Cohesion Is the bonding of a high percentage of the molecules to neighboring molecules Water molecules stick together due to hydrogen bonding Causes surface tension and adhesion.

Water conducting cells Cohesion Helps pull water up through the microscopic vessels of plants. Water molecules stick to each other and to the walls of the xylem. Water conducting cells 100 µm Figure 3.3

Is a measure of how hard it is to break the surface of a liquid. Surface tension Is a measure of how hard it is to break the surface of a liquid. Figure 3.4

Moderation of Temperature Water moderates air temperature This is very important for the maintenance of homeostasis by living organisms. Also - ~75% of the earth is covered with water, this helps stabilize climate. Water absorbs heat from air that is warmer and releases the stored heat to air that is cooler

Water’s High Specific Heat The specific heat of a substance Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC

Water’s High Specific Heat Water has a high specific heat, which allows it to minimize temperature fluctuations to within limits that permit life. Heat is absorbed when hydrogen bonds break. Heat is released when hydrogen bonds form.

Evaporative Cooling Heat of vaporization Evaporative cooling Is the quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas Evaporative cooling Is due to water’s high heat of vaporization Allows water to cool a surface

The hydrogen bonds in ice Ice Floats 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

Insulation of Bodies of Water by Floating Ice Solid water, or ice Is less dense than liquid water Floats in liquid water Allows life to exist in frozen lakes and ponds.

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

Forming solutions with ionic solutes. The different regions of the polar water molecule can interact with ionic compounds 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

Forming solutions with polar solutes. Water can also interact with polar molecules such as proteins This oxygen is attracted to a slight positive charge on the lysozyme molecule. This hydrogen 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

Hydrophilic and Hydrophobic Substances Some substances are attracted to water and others are not. A hydrophilic substance Has an affinity for water. Ions and polar molecules. A hydrophobic substance is not attracted to water. Nonpolar molecules.

Life is sensitive to pH (Acids and Bases) Water can dissociate Into hydronium ions and hydroxide ions Changes in the concentration of these ions Can have a great affect on living organisms H Hydronium ion (H3O+) Hydroxide ion (OH–) + – Figure on p. 53 of water dissociating

Acids and Bases An acid A base Is any substance that increases the hydrogen ion concentration of a solution (donates protons) A base Is any substance that reduces the hydrogen ion concentration of a solution (accepts protons)

The pH Scale The pH of a solution Is determined by the relative concentration of hydrogen ions Is low in an acid Is high in a base Most biological solutions range from pH of 6-8, but there are exceptions (stomach acids pH 1-2)

The pH scale and pH values of various aqueous solutions Increasingly Acidic [H+] > [OH–] Increasingly Basic [H+] < [OH–] Neutral [H+] = [OH–] Oven cleaner 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH Scale Battery acid Digestive (stomach) juice, lemon juice Vinegar, beer, wine, cola Tomato juice Black coffee Rainwater Urine Pure water Human blood Seawater Milk of magnesia Household ammonia Household bleach Figure 3.8

The internal pH of most living cells Buffers The internal pH of most living cells Must remain close to pH 7

Buffers Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution Consist of a weak acid-base pair that reversibly combines with hydrogen ions