The Nature of Molecules

Chapter 2

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Recall from Chapter 1:Levels of Organization

Cellular Organization cells

organellesmolecules

atoms

The cell is the basic unit of life.

Fig. 1.1-1

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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

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Atomic Structure

• Atoms are composed of:1. Protons – positively charged particles

2. Neutrons – neutral particles– Electrons – negatively charged particles

1. Protons and neutrons are located in the nucleus of the atom

2. Electrons are found in orbitals surrounding the nucleus

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Atomic Structure

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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.

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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.

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Atomic Structure:Carbon Isotopes

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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 (-)

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Atomic StructureAtomic 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

Fig. 2.5

• Electrons release energy as they fall from a high energy level to a lower energy level

• Electrons climb from alower energy level to a higher energy level as they absorb energy

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Atomic StructureElectron 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

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• 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

Atomic StructureElectron Orbitals

Fig. 2.4a

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Atomic StructureElectron 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

Fig. 2.4c

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. 2.4

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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

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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

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Atomic Structure

LEO the lion says GER

If it Looses Electrons, it’s Oxidized

If it Gains Electrons, it’s Reduced

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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

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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

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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

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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

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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

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Periodic Table of the Elements

H has 1 e-

Na has 1Valence e-

Ca has 2Valence e-s

C has 4Valence e-s

O has 6Valence e-s

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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

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Elements

• Become Familiar with the Valence Electron

Configuration for the Elements:

Hydrogen (H): 1Carbon (C): 4Oxygen (O): 6Nitrogen (N): 5Chlorine (Cl): 7Sodium (Na): 1

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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

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Elements

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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

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Chemical Bonds

• We will study 3 types of chemical bonds

1. Ionic Bonds2. Covalent Bonds

3. Hydrogen Bonds

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Chemical Bonds1. Ionic bonds

• Ionic Bonds are formed by the attraction of oppositely charged ions

• Cation Na+ and Anion Cl- attract

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Chemical Bonds1. 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

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Chemical Bonds1. 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

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Chemical Bonds1. Ionic bonds

• Cation Na+ and Anion Cl- attract

• Ionic Bonds form crystals

• Ionic Bonds dissociate in water

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Chemical Bonds2. 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

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Chemical Bonds2. 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

• •

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Chemical Bonds2. 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

doublebond

triplebond< <

single bond >

doublebond > triple

bond

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Chemical Bonds 2. Covalent Bonds

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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?

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Periodic Table of Elements

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Chemical Bonds

• Electronegativity is an atom’s affinity for electrons

• The Periodic Table of Elements discloses an Electronegativity Trend

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Electronegativity(EN) Trend in the Periodic Table of Elements

LowestEN

GreatestENIncreasing EN

Table 2.2

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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

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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

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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

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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’

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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

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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

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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

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Water Chemistry

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Water Chemistry3. 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.

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Water Chemistry3. 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

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Water Chemistry

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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

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Water ChemistrySurface Tension

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Water ChemistryCapillary Action

Look for the meniscus

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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.

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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

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Properties of WaterWater dissolves ionic molecules

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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

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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

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Properties of Water6. 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

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Properties of Water6. 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

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Properties of Water6. 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

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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?

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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

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Acids and Bases

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Acids and BasesThe 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)

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Acids and BasesThe 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

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Acids and Bases

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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

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Acids and Bases

Base: a chemical that accepts H+1 ions

• Sodium Hydroxide, NaOH

NaOHNa+1 + OH-1

OH-1 + H+1H2O

• Bicarbonate, HCO3-

HCO3- + H+ H2CO3

carbonic acid

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Acids and BasesAcid-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-

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Acids and BasesBuffer 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

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Acids and Bases

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

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Acids and Bases

Table 2.1

The Nature of Molecules

End Chapter 2