Learning Objectives. Learning Objectives (cont.) Chapter 2: Basic Chemistry 1. Lectures by Tariq Alalwan, Ph.D.

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1 Biology, 10e Mader Lectures by Tariq Alalwan, Ph.D. Learning Objectives Name the principal chemical elements in living things. Compare the physical properties (mass and charge) and locations of electrons, protons, and neutrons. Distinguish between the atomic number and the mass number of an atom. Define the terms orbital and electron shell; relate electron shells to principal energy levels. Explain how the number of valence electrons of an atom is related to its chemical properties. Learning Objectives (cont.) Distinguish among simplest, molecular, and structural chemical formulas. Distinguish among covalent bonds, ionic bonds and hydrogen bonds. Compare them in terms of the mechanisms by which they form and their relative strengths. Explain how hydrogen bonds between adjacent water molecules govern many of the properties of water. Chapter 2: Basic Chemistry 1

2 Learning Objectives (cont.) Contrast acids and bases, and discuss their properties. Convert the hydrogen ion concentration (moles per liter) of a solution to a ph value. Describe how buffers help minimize changes in ph. Chemical Elements Matter refers to anything that has mass and occupies space Only 92 naturally occurring fundamental types of matter 92 Elements Organisms composed primarily (95%) of only six elements Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulfur CHNOPS Elements Composition of Earth s Crust vs. Organisms Chapter 2: Basic Chemistry 2

3 Atomic Structure Atoms smallest particles of elements Atoms composed of 3 types of subatomic particles Protons: positively charged particles within the nucleus Neutrons: electrically neutral charged particles also found in nucleus Electrons: negatively charged particles orbiting the nucleus Atomic Symbol Each element represented by unique atomic symbol One or two letters Mass First letter capitalized Number 12 C Superscripted number before: 6 Atomic Represents mass number Number Carbon Number of protons & neutrons in nucleus Atomic Subscripted number before: Symbol Represents atomic number Number of protons in nucleus Periodic Table Elements grouped in periodic table based on characteristics Vertical columns = groups; chemically similar Horizontal rows = periods; larger and larger I VIII 1 1 Groups 2 H He II III IV V VI VII Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Ga Ge As Se Br Kr Periods Chapter 2: Basic Chemistry 3

4 Isotopes Isotopes: Atoms of the same element that differ in the number of neutrons. Isotopes of an element have the same chemical properties p but different weights Example: 12 C 6 Carbon C 6 Carbon C 6 Carbon 14 Electron Shells, Orbitals and Energy Levels Atoms normally have as many electrons as protons Opposite charges balance leaving atom neutral Electrons are attracted to the positive nucleus Revolve around nucleus in 3 D space orbitals Can be pushed into higher orbitals with energy Release that energy when they fall back to lower orbital Different energy levels referred to as electron shells The Octet Rule for Distribution of Electrons Bohr models show electron shells as concentric circles around nucleus Each shell has two or more electron orbitals Innermost shell hll has 2 orbitals Others have 8 or multiples thereof Atoms with fewer than 8 electrons in outermost shell are chemically reactive If 3 or less Tendency is to donate electrons If 5 or more Tendency is to receive electrons Chapter 2: Basic Chemistry 4

5 Periodic Table Elements and Compounds Molecule two or more atoms react or bond together If all atoms in molecule are of the same element Material is still an element (e.g. O 2, H 2, N 2, etc.) If at least one atom is from a different element Material formed is a compound CO 2, H 2 O, C 6 H 12 O 6, etc. Characteristics of compounds dramatically different from constituent elements Chapter 2: Basic Chemistry 5

6 Chemical Bonding Bonds between atoms are caused by electrons (valence) in outermost shells The process of bond formation is called a reaction The intensity it of simple reactions can be predicted d by the periodic table If two elements are horizontally close in the table, they usually react mildly If they are horizontally far apart, they usually react vigorously Types of Bonds: Ionic Bonding Octet rule Atoms need 8 electrons in outer shell If have < 4 outers, desire to donate them If have > 4 outers, desire to receive more Consider two elements from opposite ends of periodic table Element from right side: Has 7 electrons in outer shell Desperately needs one more (7+1=8) Element from left side: Has only 1 electron in outer shell Desperately needs to donate it (1 1=0=8) Formation of Sodium Chloride Chapter 2: Basic Chemistry 6

7 Types of Bonds: Covalent Bonds When atoms are horizontally closer together in the periodic table The electrons are not permanently transferred from one atom to the other like in NaCl A pair of (valence) electrons from the outer shell will time share with one atom and then the other This also causes the atoms to remain together Known as covalent bonding Covalently Bonded Molecules A double covalent bond is formed when two pairs of electrons are shared (represented by two parallel solid lines) Example O 2 A triple covalent bond is formed when three pairs of electrons are shared (represented by three parallel solid lines) Example N 2 Nonpolar Covalent Bonds Consider two elements that are equidistant from the edges of the periodic table Atoms will have about equal affinity for electrons One will want to donate electron(s) The other will want to receive electron(s) When bonded covalently: The bond electrons will spend about equal time with both atoms Such covalent bonds are said to be nonpolar Chapter 2: Basic Chemistry 7

8 Polar Covalent Bonds Some atoms attract electrons more strongly than others electronegativity (a measure of an atom s attraction for shared electrons in chemical bonds) Atoms will have unequal affinity for electrons When bonded covalently: The bond electrons will spend more time with one atom than the other The atom that gets the most time with the electrons will be slightly negative The other will be slightly positive Such covalent bonds are said to be polar Types of Bonds: Hydrogen Bonds Water (H 2 O or H O H) is a polar molecule Electrons spend more time with the larger oxygen atom than the smaller hydrogen atom H becomes slightly positive and O slightly negative When polar molecules are dissolved in water The H of water molecules are attracted to the negative parts of the solute molecules Results in a weak bond the hydrogen bond Easily broken, but many together can be quite strong One of the most important interactions in biological molecules (e.g. proteins, DNA, etc.) Water Molecule and Hydrogen Bonding Chapter 2: Basic Chemistry 8

9 The Chemistry of Water: Heat Capacity Water has a high heat capacity Temperature = rate of vibration of molecules When water is heated Hydrogen bonds restrain bouncing Temperature rises more slowly per unit heat Thermal inertia resistance to temperature change Because of hydrogen bonding takes a large heat loss or gain for each 1 C change in temperature Maintains constant environmental temperatures Properties of Water: Heat of Vaporization Water has a high heat of vaporization the energy required to convert 1g of liquid water to a gas To raise water from 99 to 100 C; ~1 calorie To raise water from 100 to 101 C; ~540 calories! Large numbers of hydrogen bonds must be broken to evaporate water This is why sweating (and panting) cools Evaporative cooling is best when humidity is low because evaporation occurs rapidly Great example is when you get out of the shower! Temperature and Water Calorie (cal) Amount of heat energy required to raise 1 g of water 1 degree Celsius (C) Hydrogen bonds must absorb heat to break, and they release heat when they form Chapter 2: Basic Chemistry 9

10 Properties of Water: Water as a Solvent Solution liquid that is a completely homogenous mixture of two or more substances Solvent dissolving agent of a solution Solute substance dissolved in a solution Hydrophilic Water loving, property of having an affinity for H 2 O (polar and ionic molecules) Hydrophobic Water fearing, not water soluble (nonpolar molecules) Ionic Compounds Dissociate in Water Properties of Water: Cohesion & Adhesion Cohesion Hydrogen bonds hold water molecules tightly together Adhesion Hydrogen bonds for between water and other polar materials il Explains how water makes things wet High Surface Tension A measure of how difficult it is to stretch or break the surface of a liquid Allows small nonpolar objects (e.g. water strider) to sit on top of water Chapter 2: Basic Chemistry 10

11 Water as a Transport Medium Cohesion & adhesion are both important because combined together they form an event called capillary action Capillary action defies gravity and helps move water up the plant to its leaves Properties of Water: Uniqueness of Ice Frozen water is less dense than liquid water The density of water: Prevents water from freezing from the bottom up Ice forms on the surface first the freezing of the water releases heat to the water below creating insulation Permits organisms to survive without freezing ph of Water: Acids In pure water, a small number of water molecules dissociate into hydrogen ions (H + ) and hydroxide ions (OH ) HOH H + + OH The concentrations of hydrogen ions and hydroxide ions in pure water are exactly equal Acids Substances that dissociate in water and release hydrogen ions [H + ] Hydrochloric acid (stomach acid) is an inorganic acid with symbol HCl In water, it dissociates into H + and Cl Dissociation of HCl is almost total, therefore it is a strong acid Chapter 2: Basic Chemistry 11

12 ph of Water: Bases Bases: Either take up hydrogen ions [H + ] or release hydroxide ions [OH ] NaOH Na + + OH OH + H + H 2 O Sodium hydroxide is a solid with symbol NaOH In water, it dissociates into Na + and OH Dissociation of NaOH is almost total, therefore it is a strong base Some bases do not dissociate to yield hydroxide ions directly, example? ph Scale ph scale used to indicate acidity and alkalinity of a solution Values range from 0 14 Acidic solution (ph <7) Hydrogen ion concentration is higher than hydroxide ion concentration Basic solution (ph >7) Hydrogen ion concentration is lower than hydroxide ion concentration Neutral solution (ph 7) Equal concentrations of hydrogen ions and hydroxide ions (concentration of each is 10 7 mol/l) The ph Scale Chapter 2: Basic Chemistry 12

13 ph Scale (cont.) Logarithmic Scale Each unit change in ph represents a change of 10 times ph of 4 is 10 times as acidic as ph of 5 ph of 10 is 100 times more basic than ph of 8 Buffers and ph When H + is added to pure water at ph 7, ph goes down and water becomes acidic When OH is added to pure water at ph 7, ph goes up and water becomes alkaline Buffers are substances that resist change in ph When H + is added, buffer may absorb, or counter by adding OH When OH is added, buffer may absorb, or counter by adding H + A buffering system includes a weak acid or a weak base Buffers in Nature Biological buffer system Human blood normally 7.4 (slightly alkaline) Many foods and metabolic processes add or subtract [H + ]or[oh ] Reducing blood ph to 7.0 results in acidosis Increasing blood ph to 7.8 results in alkalosis Both life threatening situations Chapter 2: Basic Chemistry 13

14 Buffers in Nature (cont.) In blood, carbon dioxide reacts with water to form carbonic acid, a weak acid that dissociates to yield H + and bicarbonate: CO 2 + H 2 O H 2 CO 3 H + + HCO 3 Addition of excess hydrogen ions shifts the system to the left, as H + combine with bicarbonate ions to form carbonic acid Addition of hydroxide ions shifts the system to the right Chapter 2: Basic Chemistry 14