Chapter 2! Chapter 2 Chemistry. The Chemical Level of Organization! SECTION 2-1! Atoms are the basic particles of matter! Subatomic Particles!

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1 Chapter 2 The Chemical Level of Organization SECTION 2-1 Atoms are the basic particles of matter Note: Although we will not cover the first parts of these notes during lecture, you are responsible for understanding everything in the notes. We are skipping the basic chemistry that you learned in the prerequisite you took to get into this class (to slide 21). If you need help reviewing this material, let me know soon. 2 Subatomic Particles Protons - Found in nucleus Positive charge Weight of approximately 1 Dalton Neutrons - Found in nucleus No charge Weight similar to protons Electrons - Found in electron shells Negative charge Weight of approximately 1/1836 Dalton An atom has same number of protons and electrons 3 1

2 Atomic Number and Atomic Mass Atomic number = number of protons Atomic mass number = protons + neutrons All atoms with the same atomic number are called elements e.g. Oxygen (O) Atomic number = 8 Atomic mass number = 16 How many protons, electrons and neutrons? e.g. Sodium (Na) Atomic number = 11 Atomic mass number 23 How many protons, electrons and neutrons? 4 Atoms and Subatomic Particles Figure Some Important Elemental Symbols Oxygen (O) Carbon (C) Hydrogen (H) Nitrogen (N) Calcium (Ca) Chlorine (Cl) Phosphorus (P) Sulfur (S) Sodium (Na) Potassium (K) Iron (Fe) 6 2

3 Chapter 2 Chemistry Electron Energy Levels (Electron Shells) The outermost electron shell (valence shell) determines the reactivity of the element. Octet rule or Rule of Eight First shell can hold up to 2 electrons All other shells THAT YOU NEED TO KNOW ABOUT can hold up to 8 electrons 7 Atoms and Electron Shells Figure Atoms Combine Through Chemical Reactions Molecule = a chemical structure consisting of atoms held together by covalent bonds Compound = a chemical substance composed of atoms of two or more different elements Types of bonds: 1. Ionic 2. Covalent 3. Hydrogen 9 3

4 Chapter 2 Chemistry 1. Ionic Bonding Figure 2-4 Giving something away is a positive thing to do Covalent Bonds - Atoms Sharing Electrons Single and double covalent bonds Single = one pair of electrons shared Double = two pairs of electrons shared Non-polar covalent bonds Electrons shared equally between atoms Polar covalent bonds Electrons shared unequally 11 Nonpolar Covalent Bonds Figure

5 Polar Covalent Bonds - e.g. Water Figure Hydrogen Bonds H-bonds are the weakest bonds (that we ll cover) Involve polar covalent bonds that occur when hydrogen covalently bonds with another element Partial positive (δ + ) and negative (δ - ) charges attract each other Help determine molecular shapes (e.g. DNA), properties of water H-bonds hold the two strands of DNA to one another. 14 Hydrogen Bonding in Water Figure

6 Chapter 2 Chemistry Matter and Chemical Notation Matter can exist as a solid, liquid or gas. Depends on the interaction of the component atoms or molecules Molecular weight is the sum of the atomic weights of the component atoms Mole: a quantity of a substance having a weight in grams equal to the atomic or molecular weight of that substance. e.g. MW for H = 1; MW for O = 16 1 mole of O 2 = 32 g 1 mole of H 2 O = 18 g 16 Chemical Notation An example: General formula for Carbohydrates = (CH 2 O) n Glucose = a six-carbon sugar (n = 6) (CH 2 O) 6 = C 6 H 12 O 6 See Spotlight Figure 2-3, page 32 for additional examples of chemical notation 17 SECTION 2-3 Decomposition, synthesis, and exchange reactions are important chemical reactions in physiology Reactants What go into the reaction Products What come out of the reaction 18 6

7 Chapter 2 Chemistry Basic Energy Concepts Work = movement of an object or change in its physical structure Energy = the capacity to perform work Kinetic energy = the energy of motion Potential energy = energy of position or structure Energy conversions are not 100% efficient. This results in the release of heat. 19 Types of Reactions Decomposition (or hydrolysis = breaking bonds) A-B + H 2 O A-H + B-OH + energy Synthesis (or dehydration = forming new bonds) A-H + B-OH + energy A-B + H 2 O Exchange A-B + C-D A-C + B-D Metabolism is the sum of all reactions Catabolism releases energy (exergonic) Anabolism requires energy input (endergonic) 20 Reversible Reactions All reactions are theoretically reversible. e.g. AB A + + B - e.g. H 2 CO 3 H + + HCO 3 - At equilibrium, the rates of two opposing reactions are equal (in balance). i.e. At equilibrium, the rates of anabolism and catabolism are equal. (In the examples above, which direction (right or left) depicts anabolism?) 21 7

8 SECTION 2-4 Enzymes catalyze specific biochemical reactions by lowering the reaction s activation energy 22 Activation Energy and Enzymes Activation energy is the amount of energy needed to begin a reaction Enzymes are catalysts. Properties of catalysts: 1. Increase rates of chemical reactions 2. Reduce activation energy 3. Not permanently changed by reaction 4. Highly selective 5. Sensitive to environmental conditions (e.g. ph) 6. Can be saturated 7. Can be regulated 23 Enzymes and Activation Energy Figure 2-8 High Low 24 8

9 Enzymes Sensitivity to Environment 25 Enzymes Saturation 26 SECTION 2-5 Inorganic and organic compounds Inorganic compounds Carbon and hydrogen are generally not primary structural ingredients Organic compounds Carbon and hydrogen are always primary structural ingredients 27 9

10 Aqueous Solutions A solution is a fluid containing dissolved materials. A solute is the substance dissolved in a solvent. A solvent is the medium in which molecules of solute are dispersed. Water is the solvent in biological aqueous solutions. 28 SECTION 2-6 Physiological systems depend on water Water is the solvent in aqueous systems. About 2/3 of human body weight is water. 29 Water Molecules and Solutions Figure 2-9 Note error in this figure in some printings of your text

11 Chapter 2 Chemistry Biologically Important Properties of Water H 2 O is a polar molecule, forms H-bonds with itself 1. Is a good solvent (solubility) 2. Very reactive (reactivity: synthesis, dehydration rxns) 3. Has a high heat capacity 4. Is a good lubricant - little friction between water molecules 5. Has high surface tension 6. Ice floats Notice the importance of hydrogen bonds. 31 Electrolytes Undergo Ionization Electrolytes dissociate to form ions that carry electrical current. Ionization: NaCl Na + + Cl - Compounds that interact readily with water are called hydrophilic. Compounds that do not interact with water are called hydrophobic. 32 Important Electrolytes in Body Fluids 33 11

12 SECTION 2-7, 2-8 Body fluid ph; acids and bases, salts, buffers ph = -log [H + ] This definition is VERY important. If you have trouble with ph and buffers, it is likely that you forgot this definition. (Hint) 34 ph is a Measure of Hydrogen Ion Concentration ph = - log[h + ] (concentration in moles per liter) Examples of log usage: log(100) = log(10 2 ) = 2 log(0.01) = log(10-2 ) = -2 Pure water at 25 C has [H + ] of 10-7 moles/liter ph = -log[10-7 ] = -(-7) = 7 ph 7 (at 25 C) is said to be neutral. 35 Acids and Bases Acids release hydrogen ions into solution. Bases remove hydrogen ions from solution. Strong acids and bases ionize completely. e.g. HCl H + + Cl - (HCl is not present in the solution.) Weak acids and bases do not completely ionize. e.g. H 2 CO 3 H + + HCO 3 - (H 2 CO 3 is present in the solution.) 36 12

13 Chapter 2 Chemistry The ph Scale Figure 2-10 Blood: ; Vaginal fluid: ; Semen: ; Urine: ph = -log[h + ] ph 7 = -log[10-7 ] = -(-7) = 7 37 Salts and Buffers Salt = an electrolyte whose cation is not hydrogen (H + ) and whose anion is not hydroxide (OH - ) Buffers resist a change in ph. Consist of a weak acid and a weak base Remove or replace hydrogen ions in solution Buffer systems maintain the ph of body fluids 38 Carbonic Acid-Bicarbonate Buffer System CO 2 + H 2 O H 2 CO 3 H + + HCO 3 - carbonic acid bicarbonate ion Carbonic acid functions as a weak acid. Gives up H + Does not completely dissociate Bicarbonate functions as a weak base. Takes up H + Does not completely dissociate 39 13

14 SECTION 2-9 Carbohydrates contain carbon, hydrogen and oxygen in a 1:2:1 ratio 40 Review Important Functional Groups Table Carbohydrates from Figure 2-11 General formula = (CH 2 O) n (i.e. a 1:2:1 ratio) General functions: Energy source for metabolism (e.g. glucose) Energy reserve (e.g. glycogen) Structural molecules (e.g. DNA backbone) 42 14

15 Carbohydrate Classes Table 2-4 Monosaccharides e.g. glucose, fructose Disaccharides e.g. sucrose, maltose Polysaccharides e.g. glycogen (and starch and cellulose in plants) 43 Formation and Breakdown of Complex Sugars (Figure 2-12) Hydrolysis 44 The Structure of a Polysaccharide Figure 2-13 Glycogen 45 15

16 SECTION 2-10 Lipids contain a carbon-to-hydrogen ratio of 1:2 46 Lipids Include Fats, Oils, and Waxes Five classes: 1. Fatty acids 2. Eicosanoids 3. Glycerides 4. Steroids 5. Phospholipids and glycolipids Summarized in Table 2-5, page Fatty Acids Figure 2-14 Example: Lauric acid Functions: Energy source (2 x CH 2 O energy/gram) Saturated: Solid at room temperature Unsaturated: Liquid at room temperature 48 16

17 2. Eicosanoids Figure 2-15 Derived from arachadonic acid (a fatty acid) Examples: Prostaglandins Leukotrienes Functions: Chemical messengers (local hormones) E.g. released from damaged tissues E.g. released by uterus contractions E.g. released by T lymphocytes Glycerides Examples: Mono-, di- and triglycerides 1, 2 or 3 fatty acid(s) + glycerol Functions: Energy source Energy storage Thermal insulation Physical cushioning (protection) 50 Triglyceride Formation Figure 2-16 Triglycerides: glycerol + 3 fatty acids Saturated fatty acids Unsaturated fatty acid 51 17

18 Chapter 2 Chemistry 4. Steroids Examples: Cholesterol and derivatives Functions: Hormones E.g. sex hormones Cell membrane structure Digestion E.g. Bile, Vitamin D (for Ca 2+ absorption) 52 Steroid Structure Figure Phospholipids and Glycolipids Derived from diglyceride + nonlipid components E.g. phosphate and choline, or a CH 2 O Phospholipid example = lecithin Very important components of cell membranes Polar molecules Hydrophilic heads Hydrophobic tails Also form micelles with bile salts 54 18

19 Phospholipid Structure Figure 2-18 Note charges SECTION 2-11 Proteins are formed from amino acids and contain carbon, hydrogen, oxygen and nitrogen 56 Protein Functional Classes (1 of 2) Support - structural proteins E.g. collagen, keratin Movement - contractile proteins E.g. actin and myosin Transport proteins E.g. hemoglobin, albumin, transferrin Metabolic regulation - enzymes Kinases, proteases, lipases, carbohydrases 57 19

20 Protein Functional Classes (2 of 2) Buffering proteins E.g. hemoglobin, plasma proteins Coordination and control - Hormones E.g. insulin, growth hormone Defense proteins E.g. antibodies, clotting proteins, complement proteins 58 Proteins are Chains of Amino Acids Amino acids contain an amino group, a carboxylic acid group and a radical (R) group Polypeptides are linear sequences of amino acids held together by peptide bonds A polypeptide is not necessarily a functional protein E.g., Hemoglobin, a functional protein, is formed from four individual polypeptides. 59 Amino Acid Structure Figure

21 Peptide Bonds Figure 2-20 Energy?? 61 Four Levels of Protein Structure 1. Primary structure Linear sequence of amino acids in polypeptide 2. Secondary structure Local folding of parts of the polypeptide e.g. alpha helix, beta-pleated sheet 3. Tertiary structure Complex folding - 3-D shape of entire molecule 4. Quaternary structure Two or more polypeptides involved 62 Protein Structure Figure 2-21 Structure determines function 63 21

22 Enzymatic Reactions: Protein Structure/Function Reactants (substrates) interact to yield a product by binding to the active site of the enzyme. Cofactors must bond to the enzyme before substrate binding can occur. Coenzymes are organic cofactors commonly derived from vitamins. Enzymes may also have allosteric site(s) 64 Enzyme Structure and Function Figure 2-22 Allosteric site Product can bind to allosteric site and turn enzyme off. 65 Enzyme Properties (see also slide #23) 1. Specificity (Isozymes: have a slightly different structure, but catalyze the same reaction) 2. Regulation (e.g. allosteric sites, cofactors, coenzymes) Cofactors (e.g. Ca 2+, Mg 2+ ) must be present for enzyme to function Coenzymes are organic molecules (e.g. vitamins) that function as cofactors 3. Saturation 66 22

23 Chapter 2 Chemistry Enzyme Saturation: Draw your own curve. 67 A Protein s Shape Determines Its Function Proteins pushed outside their optimal temperature and ph range become temporarily or permanently denatured and will cease to function E.g. heat, ph, osmotic concentration 68 Environmental Effects on Enzyme Function 69 23

24 Chapter 2 Chemistry SECTION 2-12 DNA and RNA are nucleic acids 70 Nucleic Acids DNA and RNA Store and process information at the molecular level Contain purines and pyrimidines (nitrogenous bases) General formula: Sugar-Phosphate-Sugar-Phosphate-Sugar-Phosphate Base Base Base 71 Nucleic Acids are Chains of Nucleotides Nucleotides are composed of a sugar, a phosphate and a nitrogenous base Sugar = deoxyribose (DNA) or ribose (RNA) DNA nitrogenous bases adenine, thymine, cytosine, guanine RNA nitrogenous bases adenine, uracil, cytosine, guanine 72 24

25 Purines and Pyrimidines Figure Nucleic Acids: RNA and DNA Figure 2-24 RNA Found in both nucleus and in cytoplasm Single stranded Participates in protein synthesis Types: mrna rrna trna DNA Found in nucleus, except during cell division Double stranded Contains the information for protein synthesis 74 Comparison of DNA and RNA Table

26 Chapter 2 Chemistry SECTION 2-13 ATP is a high-energy compound used by cells 76 High Energy Compounds Store cellular energy in high energy bonds e.g. Adenosine triphosphate (ATP) Made by adding a phosphate group to adenosine diphosphate (ADP) Process referred to as phosphorylation ADP + P i + energy ATP + H 2 O ATP contains nucleosides (adenosines) and is therefore more closely related to nucleic acids than to the other macromolecules. 77 The Structure of ATP Figure 2-25 (top) 78 26

27 The Structure of ATP Figure 2-25 (bottom) 79 Metabolic Turnover Table 2-8 Organic molecules are continually being built up and broken down (i.e. turned over)