The Nature of Molecules Chapter 2

Recall from Chapter 1: Levels of Organization Cellular Organization cells organelles molecules atoms The cell is the basic unit of life.

Fig. 1.1-1 3

Atomic Structure All matter is composed of atoms Understanding the structure of atoms is critical to understanding the nature of biological molecules: Bonding Reactivity Oxidation/ Reduction pH Energy

Atomic Structure Atoms are composed of: Protons – positively charged particles Neutrons – neutral particles Electrons – negatively charged particles Protons and neutrons are located in the nucleus of the atom Electrons are found in orbitals surrounding the nucleus

Atomic Structure

Atomic Structure Every different atom has a characteristic number of protons in the nucleus. Atomic Number = number of protons Atoms with the same atomic number have the same chemical properties and belong to the same element.

Atomic Structure Each proton and neutron has a mass of approximately 1 dalton. The sum of protons and neutrons is the atom’s atomic mass. Isotopes – atoms of the same element that have different atomic mass numbers due to different numbers of neutrons.

Atomic Structure: Carbon Isotopes

Atomic Structure Neutral atoms have the same number of protons and electrons Ions are charged atoms Cations – have more protons than electrons and are positively charged (+) Anions – have more electrons than protons and are negatively charged (-)

Atomic Structure Atomic Energy Levels Electrons have discrete energy levels around the nucleus - Energy of Position Energy Levels are labelled K-M The distance an electron is from the nucleus is relative to the amount of potential energy of the electron

Electrons release energy as they fall from a high Fig. 2.5 Electrons release energy as they fall from a high energy level to a lower energy level Electrons climb from a lower energy level to a higher energy level as they absorb energy

Atomic Structure Electron Orbitals At each Energy Level, electrons are located in orbitals described as s or p orbitals Orbitals are areas where the electron is most likely to be found Each orbital can contain only 2 electrons

Atomic Structure Electron Orbitals At the K Energy Level, there is one s orbital (referred to as the 1s orbital) There can be two electrons in the K Energy Level Fig. 2.4a

Atomic Structure Electron Orbitals At the L Energy Level, there is one s orbital (referred to as the 2s orbital) and 3p orbitals (each referred to as 2p orbitals) The L Energy Level holds 8 electrons Fig. 2.4b

Atomic StructureElectron Configuration for Neon Neon has 10 electrons The K and L Energy Levels are completely filled The 1s orbital of K and the 2s and three 2p orbitals of L are completely filled Fig. 2.4c

Fig. 2.4

Atomic Structure Valence electrons are the electrons in the outermost energy level of an atom Any level (K-M) can be the outermost level, it depends on how many electrons the atom has An element’s chemical properties depend on interactions between valence electrons of different atoms These chemical properties include: Reactivity - atom’s ability to make or break bonds Electronegativity - atom’s affinity for electrons

Fig. 2.2

Atomic Structure Electrons can be transferred from one atom to another, while still retaining the energy of their position in the atom Oxidation = loss of an electron Reduction = gain of an electron

Atomic Structure LEO the lion says GER If it Looses Electrons, it’s Oxidized If it Gains Electrons, it’s Reduced

Atomic Structure Oxidation and Reduction reactions always occur in pairs If a an atom or molecule is reduced, another atom or molecule must have been oxidized If a an atom or molecule is oxidizied, another atom or molecule must have been reduced For this reason Oxidation and Reduction Reactions are known as Redox Reactions

Atomic Structure Redox Reactions Some Terminology: The entity that lost (donates) the electrons in a redox rxn. is oxidized Therefore, it is known as the Reducing Agent in the Redox Rxn. It caused the other entity to be reduced by providing the electron

Atomic Structure Redox Reactions Conversely: The entity that gained (accepted) the electrons in a redox rxn. is reduced Therefore, it is known as the Oxidizing Agent in the Redox Rxn. It caused the other entity to be Oxidized by accepting the electron

Atomic Structure Redox Reactions Differentiate Oxidation/ Reduction and Oxidizing Agent/ Reducing Agent Remember, LEO says GER describes Oxidation/ Reduction The Oxidizing Agent is Reduced, The Reducing Agent is Oxidized Redox Reactions are very important in biological processes (and easy test questions) Cellular Respiration, Photosynthesis

Elements The Periodic Table arranges all elements according to their atomic number and their number of Valence Electrons Therefore, the Periodic Table identifies and groups elements with similar chemical properties The number of Valence Electrons of an element can be determined by counting across the columns of the Periodic Table

Periodic Table of the Elements O has 6 Valence e-s H has 1 e- C has 4 Valence e-s Na has 1 Valence e- Ca has 2 Valence e-s

Elements There are 90 naturally occurring elements Only 12 elements are found in living organisms in substantial amounts Twelve or so others are found in trace amounts: I, for example Four elements make up 96.3% of human body weight: carbon, hydrogen, oxygen, nitrogen

Elements Become Familiar with the Valence Electron Configuration for the Elements: Hydrogen (H): 1 Carbon (C): 4 Oxygen (O): 6 Nitrogen (N): 5 Chlorine (Cl): 7 Sodium (Na): 1

(H and He are exceptions) Elements Octet rule: States that Atoms typically attempt to achieve 8 valence electrons (H and He are exceptions) Eight valence electrons will fill the outer energy level (H needs 1e-, He needs 2 e-s) Atoms will steal, give up, or share valence electrons in order to fulfill the Octet Rule Atoms with full energy levels are more stable and less reactive than atoms with unfilled energy levels

Elements

Chemical Bonds Atoms can fulfill the octet rule by loosing, gaining or sharing electrons with other atoms, creating chemical bonds Atoms are held together in molecules or compounds by chemical bonds Molecules are groups of atoms held together in a stable association Compounds are molecules containing more than one type of element

Chemical Bonds We will study 3 types of chemical bonds Ionic Bonds Covalent Bonds Hydrogen Bonds

Chemical Bonds 1. Ionic bonds Ionic Bonds are formed by the attraction of oppositely charged ions Cation Na+ and Anion Cl- attract

Chemical Bonds 1. Ionic bonds Na easily gives up its single valence electron to fulfill the octet rule Because Na lost an electron it now has a positive (+) charge

Chemical Bonds 1. Ionic bonds Cl, with 7 valence electrons, easily picks up the extra electron to fulfill the octet rule Because Cl gained an electron it now has a positive (-) charge

Chemical Bonds 1. Ionic bonds Cation Na+ and Anion Cl- attract Ionic Bonds form crystals Ionic Bonds dissociate in water

Chemical Bonds 2. Covalent Bonds Covalent bonds form when atoms share 2 or more valence electrons Covalent bond strength and length depends on the number of electron pairs shared by the atoms Single Covalent Bond - one pair of e-’s is shared Double Covalent Bond - two pairs of e-’s are shared Triple Covalent Bond - three pairs of e-’s are shared Covalent Bonds are the strongest bonds and do not dissociate in water

Chemical Bonds 2. Covalent Bonds Covalent bond strength depends on the number of electron pairs shared by the atoms Single Covalent Bond - one pair of e-’s is shared C C Double Covalent Bond - two pairs of e-’s are shared C C Triple Covalent Bond - three pairs of e-’s are shared C C

Chemical Bonds 2. Covalent Bonds Covalent bond strength depends on the number of electron pairs shared by the atoms Single Covalent Bond - one pair of e-’s is shared Double Covalent Bond - two pairs of e-’s are shared Triple Covalent Bond - three pairs of e-’s are shared Bond Strength: Bond Length: single bond double bond triple bond < < single bond double bond triple bond > >

Chemical Bonds 2. Covalent Bonds

Chemical Bonds Electronegativity is an atom’s affinity for electrons Atoms of each of the elements differ in electronegativity Atomic size, mass, nuclear charge, electron configuration all attribute to the differences in electronegativity Based on what you know about the Na atom, do you think Na has a high or low electronegativity? What about Cl?

Periodic Table of Elements

Chemical Bonds Electronegativity is an atom’s affinity for electrons The Periodic Table of Elements discloses an Electronegativity Trend

Electronegativity(EN) Trend in the Periodic Table of Elements Greatest EN Increasing EN Lowest EN

Table 2.2

Chemical Bonds A covalent bond is formed by a sharing of electrons, but electrons are not always shared equally Differences in electronegativity dictate how electrons are distributed in covalent bonds In a covalent bond between a highly electronegative atom and a weakly electronegative atom, electrons will be drawn more towards the highly electronegative side of the bond

Chemical Bonds The water molecule is an important example of a covalent bond between a highly electronegative atom and a weakly electronegative atom As a result of this unequal sharing of electrons, one side of the molecule (the highly electronegative side) has a partial negative charge and the other side has a partial positive charge

Fig. 2.11a

Chemical Bonds A covalent bond with an unequal sharing of electrons is known as a polar covalent bond Polar because it has two ‘poles’, a partial positive pole and a partial negative pole A covalent bond with an equal sharing of electrons is known as a nonpolar covalent bond A Carbon to Carbon covalent bond is an example of a nonpolar covalent bond C C

Chemical Bonds A molecule with an unequal sharing of electrons is known as a polar molecule Water is an important polar molecule A molecule with an equal sharing of electrons is known as a nonpolar molecule A Carbon to Carbon molecule (like an oil molecule) is an example of a nonpolar molecule Polar molecules mix only with other polar molecules, nonpolar molecules mix only with other nonpolar molecules ‘Like dissolves like’

Chemical Bonds Chemical reactions involve the formation or breaking of chemical bonds The making and breaking of bonds Whether a chemical reaction occurs is influenced by many factors: temperature concentration of reactants and products availability of a catalyst

Chemical Bonds Chemical reactions are written with the reactants first, followed by the products 6H2O + 6CO2 C6H12O6 + 6O2 reactants products Chemical reactions are often reversible C6H12O6 + 6O2 6H2O + 6CO2

Water Chemistry All living organisms are dependent on water The structure of water is the basis for its unique properties The most important property of water is the ability to form hydrogen bonds

Water Chemistry

Water Chemistry 3. Hydrogen Bonds Hydrogen bonds are weak attractions between the partially negative oxygen of one water molecule and the partially positive hydrogen of a different water molecule. Hydrogen bonds can form between water molecules or between water and another charged molecule.

Water Chemistry 3. Hydrogen Bonds Within a water molecule, the bonds between oxygen and hydrogen are highly polar. Partial electrical charges develop: oxygen side is partially negative hydrogen side is partially positive The partially negative oxygen side of one water molecule is weakly attracted to the partially negative hydrogen side of another water molecule to form a hydrogen bond

Water Chemistry

Water Chemistry The polarity of water causes it to be cohesive and adhesive. Cohesion: water molecules stick to other water molecules by hydrogen bonding Adhesion: water molecules stick to other polar molecules by hydrogen bonding

Water Chemistry Surface Tension

Water Chemistry Capillary Action Look for the meniscus

Properties of Water 1. Water has a high specific heat A large amount of energy is required to change the temperature of water. 2. Water has a high heat of vaporization The evaporation of water from a surface causes cooling of that surface.

Properties of Water 3. Solid water is less dense than liquid water Bodies of water freeze from the top down 4. Water is a good solvent Water dissolves polar molecules - “like dissolves like” Water dissolves ionic molecules Water Soluble

Properties of Water Water dissolves ionic molecules

Properties of Water 5. Hyrophobic Interactions Water organizes nonpolar molecules Polar molecules are hydrophilic: “water-loving” Nonpolar molecules are hydrophobic: “water- fearing” Water causes hydrophobic molecules to aggregate or assume specific shapes “Like dissolves like”, oil and water don’t mix A Micelle

Properties of Water 6. Water can form 3 ions: H2O  OH-1 + H+1 water hydroxide ion hydrogen ion H2O + H+1  H3O+1 water hydronium ion

Properties of Water 6. Water can form 3 ions: 1. Hydrogen Ion H2O  OH-1 + H+1 water hydroxide ion hydrogen ion The hydrogen ion is a lone proton with a +1 charge

Fig. 2.2

Properties of Water 6. Water can form 3 ions: 2. Hydroxide Ion H2O  OH-1 + H+1 water hydroxide ion hydrogen ion The hydoxide ion retains the electron yielding a -1 charge

Fig. 2.2

Properties of Water 6. Water can form 3 ions: 3. Hydronium Ion H2O + H+1  H3O+1 water hydronium ion A water molecule can pick up a hydrogen ion (a proton, H+1) to become a hydronium ion with +1 charge

Table 2.3

Is water an Acid or a Base? Acids and Bases Acid: a chemical that releases H+1 ions Base: a chemical that accepts H+1 ions The acidity/basicity of a solution is measured in terms of the pH Scale Is water an Acid or a Base?

Is water an acid or a base? Acids and Bases Is water an acid or a base? H2O  OH-1 + H+1 H2O + H+1  H3O+1 Water acts as an acid and a base Pure water exists as a balance of H2O, OH-1, and H3O+1 Water has a neutral pH

Acids and Bases

Acids and Bases The pH Scale Hydrogen ion concentration [H+1] is the basis of the pH scale pH = -log [H+1] or pH = 1 log [H+1] Greater H+1 concentration = lower pH (acidic) Lower H+1 concentration = higher pH (basic)

Acids and Bases The pH Scale Hydrogen ion concentration [H+1] of pure water is 10-7 moles [H+1] / L pH = 1 pHwater = 1 log [H+] log [10-7] pHwater = 7 The pH scale is based on the pH of pure water

Acids and Bases

Acid: a chemical that releases H+1 ions Acids and Bases Acid: a chemical that releases H+1 ions Hydrochloric acid, HCl HCl  H+1 + Cl- Sulfuric acid, H2SO4 H2SO4  2H+1 + SO4-2 Carbonic acid, H2CO3 (Example from text) H2CO3  H+1 + HCO3- Bicarbonate ion

Base: a chemical that accepts H+1 ions Acids and Bases Base: a chemical that accepts H+1 ions Sodium Hydroxide, NaOH NaOH  Na+1 + OH-1 OH-1 + H+1  H2O Bicarbonate, HCO3- HCO3- + H+  H2CO3 carbonic acid

Acids and Bases Acid-Base Pairs Acids and Bases come in pairs H2CO3  H+1 + HCO3- Carbonic acid Bicarbonate HCO3- + H+  H2CO3 Bicarbonate Carbonic acid H2CO3 H+1 + HCO3-

Acids and Bases Buffer Systems Buffer: a chemical that resists a change in pH Buffers accept/release H+1 as necessary to keep pH constant Buffers accept hydrogen ions in acidic solutions and release hydrogen ions in basic solutions, minimize a change in hydrogen ion concentration The key buffer in human blood is the carbonic acid/ bicarbonate acid-base pair

Acids and Bases Most biological buffers consist of a pair of molecules, one an acid and one a base.

Acids and Bases

Table 2.1

The Nature of Molecules End Chapter 2