1. Chapter 2 The Chemical Basis of Life Outline 2.1 Atoms and Atomic Bonds Matter is anything that takes up space and has mass. Atomic Structure 2.2 Water's Importance to Life The Structure of Water Properties of Water 2.3 Acids and Bases pH and the pH Scale

2. 2.1 The Nature of Matter Matter ( 物質 ) refers to anything that takes up space and has mass. can exist as a solid, liquid, or gas composed of elements, –elements --substances that cannot be broken down into another substance –There are 92 natural elements. –Four elements make up about 96% of the body weight of most living organisms—carbon, hydrogen, oxygen, and nitrogen. Figure 2.1 Elements in living organisms.

3. Atomic Structure The atomic theory states that elements consist of atoms atoms. Atomic symbol—name of the atom or element –Hydrogen = H –Sodium = Na –Chloride = Cl Subatomic elements Neutrons ( 中子 ) —no electrical charge, found in nucleus Protons ( 質子 ) —positive charge, found in nucleus Electrons ( 電子 ) —negative charge, found outside of nucleus Mass number ( 質量數 ) is equal to sum of protons and neutrons—electrons have about zero mass Atomic weight changes with gravity 6 12 C Mass number Atomic number Chemical symbol + – – – = proton= neutron = electron outside nucleusinside nucleus nucleus b. a. + + – + + Figure 2.2 Two models of helium (He).

4. Arrangements of Electrons in an Atom  Electrons are constantly moving.  Useful to construct models of atoms with energy levels or electron shells  Each shell contains a certain number of electrons.  For atoms up through number 20 2 electrons fill first shell 8 electrons fill each additional shell  Octet rule ( 八階法則 ) for valence ( 原子價 ) shell Valence shell—outermost shell If an atom has more than 2 shells, the outer shell is most stable with 8 electrons Atoms can give up, accept, or share electrons to have 8  Chemical properties of atoms are largely determined by the arrangement of their electrons

5. Atomic number  All atoms of an element have this same number of protons  Also gives number of electrons if an atom is electrically neutral Periodic table  Elements’ chemical and physical characteristics recur in a predictable manner  Atoms are arranged in periods (rows) and groups (columns) Figure 2.3 A portion of the periodic table.

6. Isotopes Atoms of the same element that differ in the number of neutrons Isotopes have the same number of protons but a different number of neutrons (different mass numbers) Unstable and may decay, emitting radiation Radioactive isotope behavior is essentially the same as a stable isotope of same element Can be used as tracer—PET scan Can cause damage to cells leading to cancer Can be used to sterilize medical equipment C 12 6 C 14 6 P 31 15 P 32 15

7. Figure 2.4 PET scan. Figure 2.5 High levels of radiation.

8. Types of Chemical Bonds  Molecule ( 分子 ) —group of atoms bonded together O 2, H 2 O, C 6 H 12 O 6, N 2  Compound ( 化合物 ) —molecule containing atoms of more than one element H 2 O, C 6 H 12 O 6  2 types of bonds Ionic ( 離子鍵 ) —attraction between opposite charges Covalent ( 共價鍵 ) —sharing electrons to complete outer shell

9. Types of Chemical Bonds (cont.) Covalent bonding  2 atoms share electrons  2 hydrogen atoms can share electrons to fill their outer shell—orbitals overlap.  Structural formula ( 結構式 ) —uses straight lines H-H  1 line indicates 1 pair of shared electrons.  Molecular formula ( 分子式 ) —simply shows number of atoms involved H2

10. Double covalent bond—sharing 2 pairs of electrons  Oxygen gas O 2 or O=O Triple covalent bond—sharing 3 pairs of electrons  Nitrogen gas N 2 or N≡N Single atom may form bonds with more than one atom  May be represented by ball-and-stick models or space-filling models

11. Chemical formulas and reactions  Reactants—molecules that participate in reactions Shown to the left of the arrow  Products—molecules formed by reactions Shown to the right of the arrow  Equation is balanced if the same number of each type of atom occurs on both sides of the arrow. An overall equation for photosynthesis Molecular formula for glucose 6 CO 2 carbon dioxide 6 H 2 O water C 6 H 12 O 6 glucose + 6 O 2 oxygen + C 6 H 12 O 6 one molecule indicates 6 atoms of carbon indicates 6 atoms of oxygen indicates 12 atoms of hydrogen

13. 2.2 Water’s Importance to Life Life began in water Single most important molecule on Earth All organisms are 70–90% water Water has unique properties that make it a life-supporting substance Properties stem from the structure of the molecule

14. The Structure of Water  Polar covalent bond Atoms do not share electrons equally. Oxygen is more electronegative than hydrogen. Electrons spend more time around the oxygen nucleus than the hydrogen nuclei. Oxygen end becomes slightly negative/hydrogens become slightly positive—NOT an ionic bond or ions  Hydrogen bond—slightly positive hydrogen of one water molecule attracted to the slightly negative oxygen in another water molecule O HH Oxygen is slightly negative (–) a. Hydrogens are slightly positive (+) b. hydrogen bond

15.  Solvency  Cohesion and adhesion  High surface tension  High heat capacity  High heat of vaporization  Varying density Properties of Water

16. Water is a solvent  Due to polarity and H-bonding, water dissolves many substances  Hydrophilic—molecules attracted to water  Hydrophobic—molecules not attracted to water  Water causes NaCl to dissociate

17. Cohesion ( 內聚 )  Ability of water molecules to cling to each other due to hydrogen bonding Adhesion ( 黏附 )  Ability of water molecules to cling to other polar surfaces Allows water to be excellent transport system both in and outside of living organisms Contributes to water transport in plants

18. Properties of Water (cont.) Water also has a high surface tension ( 表面張力 ). Water molecules at the surface cling more tightly to each other than to the air above. Mainly due to hydrogen bonding Water strider Water has a high heat capacity ( 容量 ). The many hydrogen bonds linking water molecules allow water to absorb heat without greatly changing its temperature. Temperature of water rises and falls slowly Water has a high heat of vaporization ( 蒸發 ). Takes a great deal of energy to break H bonds for evaporation Heat is dispelled as water evaporates. Ice is less dense than water. Unlike other substances, water expands as it freezes. Ice floats rather than sinks. It makes life possible in water. Ice acts as an insulator.

19. Figure 2.12 Properties of ice.

21. 2.3 Acids and Bases Water dissociates into an equal number of hydrogen ions (H + ) and hydroxide ions (OH – ) Acidic Solutions (High H + Concentration) Lemon juice, vinegar, and coffee Acids release hydrogen ions Basic Solutions (Low H + Concentration) Milk of magnesia and ammonia Either take up hydrogen ions or release hydroxide ions

22. pH and the pH scale Mathematical way to indicate the number of hydrogen ions in solution pH scale ranges from 0 to 14 pH below 7 is acidic—more [H + ] than [OH – ] pH above 7 is basic—more [OH – ] than [H + ] pH of 7 is neutral—[H + ] equal to [OH – ]

23. Buffers ( 緩衝溶液 ) and pH Figure 2.14 Acidosis.  Chemical or combination of chemicals that keeps pH within normal limits  Resists pH change by taking up excess H + or OH –  pH of blood is about 7.4—maintained by buffer

24. Chapter 3 The Organic Molecules of Life Outline 3.1 Organic Molecules The Carbon Atom The Carbon Skeleton and Functional Groups 3.2 The Biological Molecules of the Cells Carbohydrates Lipids Proteins Nucleic Acids

25. 3.1 Organic Molecules Organic chemistry Biological molecules Organic molecules contain carbon and hydrogen. Inorganic molecules do not (H 2 O and NaCl) Figure 3.1 Organic molecules as structural materials.

26. The Carbon Atom  Total of six electrons—4 in outer shell  Almost always shares electrons with elements such as hydrogen, nitrogen, and oxygen  Can bond with as many as 4 other elements  Most often shares electrons with other carbon atoms Carbon chains can vary in length, and/or have double bonds, and/or be branched. Carbon chains can form rings of different sizes and have double bonds. Figure 3.2 Hydrocarbons are highly versatile.  Hydrocarbons—chains of carbon atoms bonded only to hydrogen atoms  Isomers—same number and kinds of atoms in a variety of arrangements May have different properties

27. The Carbon Skeleton and Functional Groups 1.Size and shape of carbon skeleton or backbone 2.Functional group—specific combination of bonded atoms that always has the same chemical properties and always reacts the same way  Reactivity of organic molecule largely dependent on attached functional groups  Often use R to stand for the rest of the molecule

28. 3.2 The Organic Molecules of Cells 4 categories—carbohydrates, lipids, proteins, and nucleic acids As your body digests food, these compounds are released and used to assemble the large macromolecules that make up your cells. Corn Pasta Rice Bread Potato Cheese Lard Ice cream Oil Butter Tofu Meat Milk Nuts Beans Eggs Protein foods Lipid foods Carbohydrates.

29. 3.2 The Organic Molecules of Cells (cont.) Monomers—subunits Polymer—monomers joined together Dehydration synthesis reaction  Joins monomers to form polymers  Equivalent of removing a water molecule Hydrolysis  Breaks polymers apart  Water is used to break the bond

30. Carbohydrates Almost universally used as immediate energy source in living things Play structural roles Polymers of monomers called saccharides or sugars Monosaccharide, disaccharide, polysaccharide Monosaccharides: Ready Energy  Single sugar molecule  Simple sugars  3–7 carbon backbone  Glucose C 6 H 12 O 6 2 isomers—fructose ( 果糖 ) and galactose ( 半乳糖 ). Cells use glucose as the energy source of choice. Ribose ( 核醣 ) and deoxyribose are found in RNA and DNA. Figure 3.8 Glucose.

31. Disaccharides: Varied Uses  2 monosaccharides bonded together  Maltose ( 麥芽糖 ) —yeast breaks down maltose in beer for energy and produces ethyl alcohol Fermentation  Sucrose ( 蔗糖 ) —table sugar

32. Polysaccharides as Energy Storage Molecules  Polymers of monosaccharides  Some function as energy storage molecules Plants store glucose as starch ( 澱粉 ). Animals store glucose as glycogen ( 肝糖 ).  Some function as structural components Cellulose—plant cell walls  Most abundant of all organic molecules  Digested only by some microbes Chitin—crab, lobster, insect exoskeletons

33. Polysaccharides as Structural Molecules Cellulose ( 纖維素 ) is the most abundant polysaccharide on earth because it comprises the cell walls of plants. Chitin ( 幾丁質 ) is a polysaccharide that forms the exoskeleton of crabs, lobsters, and insects.

34. Lipids  All are insoluble in water  Long nonpolar hydrocarbon chains  Relative lack of hydrophylic functional groups  Very diverse structures and functions  Fats and oils used for long-term energy storage  Oil may help waterproof skin, hair, and feathers.

35. Fats and Oils: Long-term Energy Storage Triglycerides are composed of 1 glycerol ( 甘油 ) and 3 fatty acids ( 脂肪酸 ). A fat or oil is formed when a dehydration reaction adds fatty acids to the – OH groups of glycerol and broken down by hydrolysis reactions. Since three fatty acids are attached to a glycerol, fats and oils are often called triglycerides ( 三酸甘油酯 ).

36. Fatty Acids Fatty acids are either...  Saturated—no double bonds between carbon atoms Butter is solid at room temperature.  Unsaturated—one or more double bonds between carbon atoms Oil is liquid at room temperature. Trans fatty acids have been artificially hydrogenated to make them more solid.

37. Fatty Acids (cont.) The saturation of fats affects human health. –Saturated fats such as trans fats contribute to heart disease. –Unsaturated oils, such as monounsaturated and polyunsaturated oils, can have a protective effect against atherosclerosis. Elaidic acid, a trans fatty acid (one double bond) found in many snack foods. C 18 H 34 O 2 carboxyl group donut characteristic of a trans fat

38. Fatty Acids (cont.) 菜籽油 紅花 椰子

39. Phospholipids ( 磷脂 ) : Membrane Components  Form the bulk of the plasma membrane  One end of the molecule is water- soluble. Polar phosphate head  Other end of the molecule is not water- soluble Nonpolar fatty acid tails

40. Steroids: Four Fused Rings Figure 3.14 Steroid diversity.  Lipids made of 4 fused rings  No fatty acids but are insoluble in water  Derived from cholesterol ( 膽固醇 )  Differ only in functional groups ( 睪丸素 ) ( 雌激素 )

41. Proteins Many functions: support, metabolism, transport, defense, regulation, and motion –Proteins such as keratin ( 角質 ) and collagen ( 膠原 ) have structural roles. –Proteins are also enzymes that speed up the chemical reactions of metabolism. –Proteins such as hemoglobin ( 血紅素 ) are responsible for the transport of substances within the body. –Proteins form the antibodies ( 抗體 ) of the immune system that defend the body from disease. –Proteins such as insulin ( 胰島素 ) are hormones that regulate cellular function. –Contractile proteins such as actin ( 肌動蛋白 ) and myosin ( 肌凝蛋白 ) allow parts of cells to move and muscles to contract.

42. Amino Acids: Subunits of Proteins Proteins are composed of amino acid monomers Amino acids have three elements to their structure. –An amino (–NH 2 ) group –A carboxyl (–COOH) group –The R (Residual) group 20 different amino acids Differ according to R group

43. Peptides Peptide—two or more amino acids covalently linked Peptide bond ( 胜鍵 )—formed by dehydration reaction between two amino acid monomers Polypeptide—chain of many amino acids joined by peptide bonds Amino acid sequence determines the final three-dimensional shape of protein.

44. Shape of Proteins  Function determined by three-dimensional shape Loss of structure and function—denature  Usually due to pH or temperature  Primary structure—amino acid sequence

45. Shape of Proteins (cont.) Secondary structure—portions of chain form helices ( 螺旋 ) or pleated ( 起褶的 ) sheets ( 薄板,).

46. Shape of Proteins (cont.) Tertiary structure—overall three- dimensional shape of interacting secondary structures Quaternary structure—more than one polypeptide chain interacting. Quaternary structure: more than one polypeptide

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48. Nucleic Acids Deoxyribonucleic acid (DNA) Stores genetic information Ribonucleic acid (RNA) Helps to make proteins Nucleic acids ( 核酸 ) are polymers of nucleotides ( 核甘酸 ). Nucleotides have three parts. –A phosphate group (–PO 4 - ) –A 5-carbon sugar –A nitrogen-containing base The 5-carbon sugar differs between DNA and RNA. – Ribose is the sugar found in RNA. – Deoxyribose is the sugar found in DNA. There are four possible nitrogen-containing bases in DNA or RNA. –The bases in DNA are thymine ( 胸腺嘧啶 ), adenine ( 腺嘌呤 ), cytosine ( 胞嘧啶 ) and guanine ( 鳥糞嘌呤 ). –The bases in RNA are uracil ( 尿嘧啶 ), adenine, cytosine, and guanine.

49. Nucleic Acids (cont.) The phosphate groups and sugars of nucleotides are linked to form the backbone of a DNA or RNA molecule. The nitrogen-containing bases show specific complementary ( 互補 的 ) base pairing. –In DNA or RNA, guanine is always paired with cytosine. –In DNA, thymine is always paired with adenine. –In RNA, uracil is always paired with adenine. DNA is a double helix formed from two spiral strands.

50. Relationship Between Proteins and Nucleic Acids  Sequence of bases in DNA determines sequence of amino acids in a protein  Sequence of amino acids determines a protein's structure and function  Small changes in the DNA may cause large changes in a protein.  Sickle cell disease Individual’s red blood cells are sickle-shaped One amino acid difference Inherited disease