The Nature of Molecules

Chapter 2

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Why should we study atoms?

• Substances with mass and space – Matter

• All matter is composed of atoms.

• Understanding the structure of atoms is critical to understanding the nature of biological molecules.

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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. Electrons are found in orbitals surrounding the nucleus.

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Atomic Number and Mass• Each atom has a

characteristic number of protons (atomic number) in the nucleus.

• Atoms with the same atomic number have the same chemical properties and belong to the same element.

• The sum of protons and neutrons is the atomic mass of atom

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Isotopes

• Isotopes – atoms of the same element that have different atomic mass numbers due to different numbers of neutrons.

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Ions

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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Electrons

• Each orbital can contain only 2 electrons.

• Electrons possess potential energy, with electrons far from the nucleus having the most energy

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Redox reactions• 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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Elements

• Valence electrons are the electrons in the outermost energy level of an atom.

• An element’s chemical properties depend on interactions between valence electrons of different atoms.

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Periodic Table of the Elements

Arranges all elements according to their atomic number.

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Elements

• There are 90 naturally occurring elements.

• Only 12 elements (C, H, O, N, P, S, Na, K, Ca, Mg, Fe and Cl) are found in living organisms in substantial amounts.

• Four elements make up 96.3% of human body weight:- carbon, hydrogen, oxygen, nitrogen

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Chemical Bonds

• Molecules are groups of atoms held together in a stable association.

• Compounds are molecules containing more than one type of element.

• Atoms are held together in molecules or compounds by chemical bonds.

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Nature of Chemical Bonds• Ionic bonds are formed by the attraction of

oppositely charged ions.

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Nature of chemical bonds

• Covalent bonds form when atoms share 2 or more valence electrons.

• Covalent bond strength depends on the number of electron pairs shared by the atoms.

• Single bond<Double bond<Triple bond

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Polar and Nonpolar covlent bonds

• Electronegativity is an atom’s affinity for electrons.

• Differences in electronegativity dictate how electrons are distributed in covalent bonds.

- nonpolar covalent bonds = equal sharing of electrons

- polar covalent bonds = unequal sharing of electrons

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How chemical reactions alter bonds?• Chemical reactions involve the formation or

breaking of 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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What factors influence alteration of chemical bonds?

• Chemical reactions are influenced by three factors

• Temperature – High temperatures must be avoided

• Concentration of reactants and products

• Availability of a catalyst – increases rate of reaction

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What is the unique property of water?• Hydrogen bonds are weak

attractions between the partially negative oxygen of one water molecule and the partially positive hydrogen of a different water molecule (Polarity)

• Hydrogen bonds can form between water molecules (cohesion) or between water and another polar molecule (adhesion)

• Cohesion provides surface tension

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Properties of Water1. 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.

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 and ions. For example: NaCl

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Properties of Water

5. Water organizes nonpolar molecules.-hydrophilic: “water-loving”-hydrophobic: “water-fearing”- Water causes hydrophobic molecules to aggregate or assume specific shapes.

6. Water can form ions.

H2O OH-1 + H+1

hydroxide ion hydrogen ion

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Acids and Bases

• Hydrogen ion (H+1) is the basis of the pH scale.

• Greater H+1 concentration --- lower pH (acidic)

- Acid: a chemical that releases H+1 ions

• Lower H+1 concentration --- higher pH (basic)

- Base: a chemical that accepts H+1 ions

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How do buffers act?

Buffer: a chemical that accepts/releases H+1 as necessary to keep pH constant

• Allows curve to rise or fall (buffering range)

• Minimizes changes in pH

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What is the unique property of water?

• Within a water molecule, the bonds between oxygen and hydrogen are highly polar.

• Partial electrical charges develop:

- oxygen is partially negative

- hydrogen is partially positive

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Elements

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Properties of Water

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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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This project is funded by a grant awarded under the President’s Community Based Job Training Grant as implemented by the U.S. Department of Labor’s Employment and Training Administration (CB-15-162-06-60). NCC is an equal opportunity employer and does not discriminate on the following basis: against any individual in the United States, on the basis of race, color, religion, sex, national origin, age disability, political affiliation or belief; and against any beneficiary of programs financially assisted under Title I of the Workforce Investment Act of 1998 (WIA), on the basis of the beneficiary’s citizenship/status as a lawfully admitted immigrant authorized to work in the United States, or his or her participation in any WIA Title I-financially assisted program or activity.

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