The Nature of Molecules Chapter 2

2 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.

3 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.

4 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

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

6 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

7 Electrons Each orbital can contain only 2 electrons. Electrons possess potential energy, with electrons far from the nucleus having the most energy

8 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

9 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.

10 Periodic Table of the Elements Arranges all elements according to their atomic number.

11 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

12 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.

13 Nature of Chemical Bonds Ionic bonds are formed by the attraction of oppositely charged ions.

14 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

15 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

16 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. 6H 2 O + 6CO 2 C 6 H 12 O 6 + 6O 2 reactantsproducts Chemical reactions are often reversible. C 6 H 12 O 6 + 6O 2 6H 2 O + 6CO 2

17 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

18 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

19 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. 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

20 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. H 2 O  OH -1 + H +1 hydroxide ion hydrogen ion

21 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

22 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

23 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 ). 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. This product was funded by a grant awarded under the President’s High Growth Job Training Initiative, as implemented by the U.S. Department of Labor’s Employment & Training Administration. The information contained in this product was created by a grantee organization and does not necessarily reflect the official position of the U.S. Department of Labor. All references to non-governmental companies or organizations, their services, products, or resources are offered for informational purposes and should not be construed as an endorsement by the Department of Labor. This product is copyrighted by the institution that created it and is intended for individual organizational, non-commercial use only.

24 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

25 Elements

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27 Properties of Water

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

29 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 ). 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. “This workforce solution was funded by a grant awarded under the President’s Community-Based Job Training Grants as implemented by the U.S. Department of Labor’s Employment and Training Administration. The solution was created by the grantee and does not necessarily reflect the official position of the U.S. Department of Labor. The Department of Labor makes no guarantees, warranties, or assurances of any kind, express or implied, with respect to such information, including any information on linked sites and including, but not limited to, accuracy of the information or its completeness, timeliness, usefulness, adequacy, continued availability, or ownership. This solution is copyrighted by the institution that created it. Internal use by an organization and/or personal use by an individual for non-commercial purposes is permissible. All other uses require the prior authorization of the copyright owner.”