1. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chapter 2

2. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.1 Atoms Matter is any substance in the universe that has mass and occupies space All matter is composed of extremely small particles called atoms Every atom has the same basic structure Core nucleus of protons and neutrons Orbiting cloud of electrons

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4. 2.1 Atoms Atomic number Number of protons Atomic mass Number of protons and neutrons Element A substance that cannot be broken down by ordinary chemical means

5. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Energy is the ability to do work Electrons have energy due to their relative orbital position (potential energy) Electrons

6. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Each electron shell has a specific # of orbitals Each orbital holds up to two electrons Electrons Atoms with incomplete electron orbitals are more reactive

7. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.2 Ions and Isotopes Ions are atoms in which the number of electrons does not equal that of protons

8. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.2 Ions and Isotopes Isotopes are atoms with the same number of protons but different numbers of neutrons Different atomic mass Same atomic number 99% of all carbon

9. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.3 Molecules A molecule is a group of atoms held together by energy The holding force is called a chemical bond There are three kinds of chemical bonds 1. Ionic bonds 2. Covalent bonds 3. Hydrogen bonds

10. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Formed by the attraction of oppositely charged ions Two key properties 1. Strong But not as strong as covalent bonds 2. Not directional They are not formed between particular ions in the compound Ionic Bonds

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12. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Formed when two atoms share electrons Two key properties 1. Strong The strength increases with the number of shared electrons 2. Very directional They are formed between two specific atoms Covalent Bonds

13. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Covalent Bonds Fig. 2.9 Water molecules contain two covalent bonds

14. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Formed by the attraction of opposite partial electric charges between two polar molecules Two key properties 1. Weak They are not effective over long distances 2. Highly directional Polar molecules must be very close for the weak attraction to be effective Hydrogen Bonds

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16. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.4 Hydrogen Bonds Give Water Unique Properties Water molecules are polar molecules They can thus form hydrogen bonds with each other and with other polar molecules Each hydrogen bond is very weak However, the cumulative effect of enormous numbers can make them quite strong Hydrogen bonding is responsible for many of the physical properties of water

17. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.4 Hydrogen Bonds Give Water Unique Properties Heat Storage A large input of thermal energy is required to disrupt the organization of liquid water This minimizes temperature changes Ice Formation At low temperatures, hydrogen bonds don’t break Water forms a regular crystal structure that floats High Heat of Vaporization At high temperatures, hydrogen bonds do break Water is changed into vapor

18. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.4 Hydrogen Bonds Give Water Unique Properties Cohesion Attraction of water molecules to other water molecules Adhesion Attraction of water molecules to other polar molecules Example: Capillary action Example: Surface tension Water strider

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20. 2.4 Hydrogen Bonds Give Water Unique Properties High Polarity Polar molecules are termed hydrophilic Water-loving All polar molecules that dissolve in water are termed soluble Nonpolar molecules are termed hydrophobic Water-fearing These do not form hydrogen bonds and are therefore not water soluble

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22. 2.5 Water Ionizes Covalent bonds within a water molecule sometimes break spontaneously H2OH2O + OH – hydroxide ion H+H+ hydrogen ion This process of spontaneous ion formation is called ionization It is not common because of the strength of covalent bonds

23. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display A convenient way to express the hydrogen ion concentration of a solution pH = log [H + ] _ The pH scale is logarithmic A difference of one unit represents a ten-fold change in H + concentration Acid Dissociates in water to increase H + concentration Base Combines with H + when dissolved in water

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25. Hydrogen ion reservoirs that take up or release H + as needed The key buffer in blood is an acid-base pair Buffers Favored reaction when [H + ] is high H2OH2O Water CO 2 Carbon dioxide + H 2 CO 3 Carbonic acid + + – HCO 3 – Bicarbonate ion H + Hydrogen ion Favored reaction when [H + ] is low

26. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.6 Forming Macromolecules An organic molecule consists of a carbon- based core with special groups attached These groups have special properties and are referred to as functional groups

27. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.6 Forming Macromolecules Organisms are primarily made of four kinds of molecules Proteins Nucleic acids Carbohydrates Lipids These are termed macromolecules They constitute the building materials and machinery of the cell

28. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Macromolecules are made by a process termed dehydration synthesis Macromolecules are broken down by a process termed hydrolysis Both types of processes require enzymes HO H H H2OH2O Energy HO H H H2OH2O Energy HO HH

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30. 2.7 Proteins Made up of subunits called amino acids There are 20 common amino acids, and they fall into one of four general groups Six amino acids Five amino acids Three amino acids

31. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.7 Proteins Amino acids are linked together by peptide bonds Long chains of amino acids are called polypeptides

32. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Determined by the sequence of its amino acids There are four general levels Primary Secondary Tertiary Quaternary Protein Structure

33. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Primary structure The specific amino acid sequence of a protein Secondary structure The initial folding of the amino acid chain by hydrogen bonding Tertiary structure The final three-dimensional shape of the protein Quaternary structure The spatial arrangement of polypeptides in a multi-component protein Protein Structure

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35. Changes in a protein’s environment can cause a protein to denature It loses its three- dimensional structure And becomes inactive Protein Structure

36. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Proteins can be divided into two classes Protein Structure 1. Structural Long cables Provide shape/strength 2. Globular Grooves and depressions Enzymes Fibrin Silk Keratin

37. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.8 Nucleic Acids Serve as information storage molecules Long polymers of repeating subunits termed nucleotides A nucleotide is composed of three parts Five-carbon sugar Nitrogen-containing base Phosphate

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39. 2.8 Nucleic Acids Two varieties Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) RNA DNA Sugar = RiboseSugar = Deoxyribose Bases = A, G, C, U Single-strandedDouble-stranded Bases = A, G, C, T

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41. The DNA double helix Nucleotide sequence specifies the amino acid sequence of proteins Space-filling model

42. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2.9 Carbohydrates Also referred to as sugars Provide building materials and energy storage Are molecules that contain carbon, hydrogen and oxygen in a 1:2:1 ratio Are of two main types Simple carbohydrates Complex carbohydrates

43. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Simple Carbohydrates 1. Monosaccharides Consist of one subunit 2. Disaccharides Consist of two subunits Formed by a dehydration reaction Glucose Sucrose Chemical formula: C 6 H 12 O 6

44. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Complex Carbohydrates Consist of long polymers of sugar subunits Also termed polysaccharides Examples: Starch provides energy storage in plants Glycogen provides energy storage in animals Cellulose is found in the cell walls of plants Chitin is found in the cell walls of fungi

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47. 2.10 Lipids Large nonpolar molecules that are insoluble in water Three major types Fats Phospholipids Steroids

48. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Used for long-term energy storage Also termed triglycerides or triacylglycerol Composed of three fatty acid chains linked to glycerol Fats

49. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Fatty acids can be saturated or unsaturated Fats Most animal fats Most plant fats

50. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display A modified fat One of the three fatty acids is replaced by a phosphate and a small polar functional group Phospholipids In water, phospholipids aggregate to form a lipid bilayer Fig. 2.34a

51. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Examples: Cholesterol Found in most animal cell membranes Composed of four carbon rings Steroids Male and female sex hormones