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Chapter 2: The Chemical Level of Organization 1 Introduction to Chemistry • Matter is made up of atoms • Atoms join together to form chemicals with different characteristics • Chemical characteristics determine physiology at the molecular and cellular level 2 Atomic Particles • Proton: – positive, 1 mass unit • Neutron: – neutral, 1 mass unit • Electron: – negative, low mass 3 Particles and Mass • Atomic number: – number of protons • Mass number: – number of protons plus neutrons • Atomic weight: – exact mass of all particles (daltons) 4 Isotopes • 2 or more elements with equal numbers of protons but different numbers of neutrons Electron shell n e p+ (a) Hydrogen-1 (electron-shell model) p+ e (b) n Hydrogen-2 deuterium e p+ (c) n Hydrogen-3, tritium 5 Elements in the Human Body 6 Table 2–1 How do atoms form molecules and compounds? 7 Molecules and Compounds • Molecules: – atoms joined by strong bonds • Compounds: – atoms joined by strong or weak bonds 8 Chemical Bonds • Ionic bonds: – attraction between cations (+) and anions (-) • Covalent bonds: – strong electron bonds – Non polar covalent bonds: equal sharing of electrons – Polar covalent bonds: unequal sharing of electrons • Hydrogen bonds: – weak polar bonds 9 Ionic Bonds Are atoms with positive or negative charge 10 Figure 2–3a Covalent Bond • Formed between atoms that share electrons Molecule Electron-Shell Model and Structural Formula Hydrogen (H2) H–H Oxygen (O2) O=O Carbon Dioxide (CO2) O=C=O Nitric Oxide (NO) N=O Free Radicals: Ion or molecule that contain unpaired electrons in the outermost shell. - Extremely Reactive -Typically enter into destructive reactions -Damage/destroy vital compounds 11 Hydrogen Bonds • Attractive force between polar covalent molecules • Weak force that holds molecules together • Hydrogen bonds between H2O molecules cause surface tension 12 Figure 2–6 How is it possible for two samples of hydrogen to contain the same number of atoms, yet have different weights? A. One sample has more bonds. B. One sample contains fewer electrons, decreasing weight. C. One sample contains more of hydrogen’s heavier isotope(s). D. One sample includes more protons, increasing weight. 13 Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why? A. Neon has 8 electrons in its valence shell, oxygen has only 6. B. Neon cannot undergo bonding due to its polarity. C. Neon is exergonic. D. Neon’s molecular weight is too low to allow bonding. 14 Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why? A. Neon has 8 electrons in its valence shell, oxygen has only 6. B. Neon cannot undergo bonding due to its polarity. C. Neon is exergonic. D. Neon’s molecular weight is too low to allow bonding. 15 Which kind of bond holds atoms in a water molecule together? What attracts water molecules to one another? A. polar covalent bonds; hydrogen bonds B. ionic bonds; charge interactions C. hydrogen bonds; charge interactions D. covalent bonds; hydrogen bonds 16 Why are chemical reactions important to physiology? 17 Energy • Energy: – the capacity to do work • Work: – a change in mass or distance 18 Forms of Energy • Kinetic energy: – energy of motion • Potential energy: – stored energy • Chemical energy: – potential energy stored in chemical bonds When energy is exchanged, heat is produced - cells cannot capture it or use it for work 19 Break Down, Build Up • Decomposition reaction (catabolism): AB A + B • Synthesis reaction (anabolism): A + B AB • Exchange reaction (reversible): AB + CD AD + CB If Water is Involved: • Hydrolysis: A—B—C—D—E + H2O A—B—C—H + HO—D—E • Dehydration synthesis (condensation): A—B—C—H + HO—D—E A—B—C—D—E + H2O 20 KEY CONCEPT • Reversible reactions seek equilibrium, balancing opposing reaction rates • Add or remove reactants: – reaction rates adjust to reach a new equilibrium 21 How do enzymes control metabolism? 22 Activation Energy • Chemical reactions in cells cannot start without help • Activation energy gets a reaction started 23 Figure 2–7 Materials in Reactions • Reactants: – materials going into a reaction • Products: – materials coming out of a reaction • Enzymes: – proteins that lower the activation energy of a reaction 24 Energy In, Energy Out • Exergonic reactions: – produce more energy than they use – Heat will be the by-product • Endergonic reactions: – use more energy than they produce • Most chemical reactions that sustain life cannot occur unless the right enzymes are present 25 In cells, glucose, a six-carbon molecule, is converted into two threecarbon molecules by a reaction that releases energy. How would you classify this reaction? A. endergonic B. exergonic C. decomposition D. B and C 26 In cells, glucose, a six-carbon molecule, is converted into two threecarbon molecules by a reaction that releases energy. How would you classify this reaction? A. endergonic B. exergonic C. decomposition D. B and C 27 Why are enzymes needed in our cells? A. to promote chemical reactions B. for chemical reactions to proceed under conditions compatible with life C. to lower activation energy requirements D. all of the above 28 What is the difference between organic and inorganic compounds? 29 Organic and Inorganic Molecules • Organic: – molecules based on carbon and hydrogen • Inorganic: – molecules not based on carbon and hydrogen 30 Essential Molecules • Nutrients: – essential molecules obtained from food • Metabolites: – molecules made or broken down in the body 31 Why is water so important to life? 32 Properties of Water • Solubility: – water’s ability to dissolve a solute in a solvent to make a solution • Reactivity: – most body chemistry uses or occurs in water • High heat capacity: – water’s ability to absorb and retain heat • Lubrication: – to moisten and reduce friction Water is the key structural and functional component of cells and their control mechanisms, the nucleic acids 33 Aqueous Solutions Polar water molecules form hydration spheres around ions and small polar molecules to keep them in solution 34 Figure 2–8 Electrolytes • Inorganic ions: conduct electricity in solution • Electrolyte imbalance seriously disturbs vital body functions 35 Molecules and Water • Hydrophilic: – hydro = water, philos = loving – reacts with water • Hydrophobic: – phobos = fear – does not react with water 36 Solutions • Suspension: – a solution in which particles settle (sediment) • Concentration: – the amount of solute in a solvent (mol/L, mg/mL) 37 What is pH and why do we need buffers? 38 pH: Neutral, Acid, or Base? • pH: – the concentration of hydrogen ions (H+) in a solution • Neutral pH: – a balance of H+ and OH— – pure water = 7.0 • Acid (acidic): pH lower than 7.0 – high H+ concentration, low OH— concentration • Base (basic): pH higher than 7.0 – low H+ concentration, high OH— concentration 39 pH Scale • Has an inverse relationship with H concentration: + – more H+ ions mean lower pH, less H+ ions mean higher pH 40 Figure 2–9 KEY CONCEPT • pH of body fluids measures free H+ ions in solution • Excess H+ ions (low pH): Acidosis – damages cells and tissues – alters proteins – interferes with normal physiological functions • Excess OH— ions (high pH): Alkalosis – Uncontrollable and sustained skeletal muscle contractions 41 Controlling pH • Salts: – positive or negative ions in solution – contain no H+ or OH— (NaCl) • Buffers: – weak acid/salt compounds – neutralizes either strong acid or strong base 42 Why does a solution of table salt conduct electricity, but a sugar solution does not? A. Electrical conductivity requires ions. B. Sugar forms a colloid, salt forms a suspension. C. Electricity is absorbed by glucose molecules. D. Table salt is hydrophobic, sugar is hydrophilic. 43 How does an antacid help decrease stomach discomfort? A. by reducing buffering capacity of the stomach B. by decreasing pH of stomach contents C. by reacting a weak acid with a stronger one D. by neutralizing acid using a weak base 44 Organic Compounds What kinds of organic compounds are there, and how do they work? 45 Functional Groups of Organic Compounds • Molecular groups which allow molecules to interact with other molecules 46 Table 2–4 Carbohydrates • Consist of C:H:O in 1:2:1 ratio 1. Monosaccharides: – simple sugars with 3 to 7 carbon atoms (glucose) • Glucose: important metabolic fuel 2. Disaccharides: – 2 simple sugars condensed by dehydration synthesis (sucrose) 47 Simple Sugars Structural Formula: • Straight-chain form • Ring from • 3-D Isomers: Glucose vs. Fructose: - Same chemical formula but different shape 48 Figure 2–10 Polysaccharides • Chains of many simple sugars (glycogen) • Formation: – Dehydration synthesis • Breakdown: – Hydrolysis synthesis Glycogen: made and stored in muscle cells 49 Figure 2–12 Carbohydrate Functions Polysaccharides Glycogen: made and stored in muscle cells Cellulose: structural component of plants -Ruminant Animals: Cattle, sheep, and deer 50 Table 2–5 The Ruminant Stomach Ruminant stomach is polygastric: four compartments -Rumen -Reticulum -Abomasum -Omasum 51 Rumen Occupies 80% of the stomach Muscular Pillar Contract to mix feed Digest starch and fibers Microbes produce VFA’s Lined with Papillae pH of 5.8-7.0 Provide a suitable environment for bacteria and protozoa 52 KEY CONCEPT • Carbohydrates are quick energy sources and components of membranes • Lipids have many functions, including membrane structure and energy storage – Provides 2x more energy then carbohydrates 53 Lipids • Mainly hydrophobic molecules such as fats, oils, and waxes • Made mostly of carbon and hydrogen atoms (1:2), and some oxygen – Less oxygen then carbon 54 Classes of Lipids • • • • • Fatty acids Eicosanoids Glycerides Steroids Phospholipids and glycolipids 55 Fatty Acids • Carboxyl group -COOH – Hydrophilic • Hydrocarbon tail: – Hydrophobic – Longer tail = lower solubility • Saturated vs. Unsaturated – Saturated: solid at room temp. • Cause solid plaques in arteries – Unsaturated: liquid at room temp. • Healthier 56 Figure 2–13 Eicosanoids • Used for cellular communication • Never burned for energy 1. Leukotrienes: – active in immune system – Used by cells to signal injury 2. Prostaglandins: local hormones – Used for cell-to-cell signaling to coordinate events 57 Steroids • 4 carbon ring with attached carbon chains • Not burned for energy 58 Figure 2–16 Types of Steroids • Cholesterol: – cell membrane formation and maintenance, cell division, and osmotic stability • Estrogens and testosterone: – Regulation of sexual function • Corticosteroids and calcitrol: – Tissue metabolism and mineral balance • Bile salts: – Processing of dietary fats 59 Glycerides • Glycerides: are the fatty acids attached to a glycerol molecule • Triglyceride: are Fat Deposits are Important the 3 fatty-acid 1. Energy Storage tails, fat storage 2. Insulation molecule 3. Mechanical Protection -Knees and Eye Sockets 60 Figure 2–15 Phospholipids Vs. Glycolipids Combination Lipids Cell Membranes are Composed of these lipids Hydrophilic Diglyceride Hydrophobic 61 Figure 2–17a, b Phospholipids Vs. Glycolipids Combination Lipids Spontaneous formation of Micelle 62 Figure 2–17c 5 Lipid Types 63 Table 2–6 A food contains organic molecules with the elements C, H, and O in a ratio of 1:2:1. What class of compounds do these molecules belong to, and what are their major functions in the body? A. lipids; energy source B. proteins; support and movement C. nucleic acids; determining inherited characteristics D. carbohydrates; energy source 64 When two monosaccharides undergo a dehydration synthesis reaction, which type of molecule is formed? A. B. C. D. polypeptide disaccharide eichosanoid polysaccharide 65 Which kind of lipid would be found in a sample of fatty tissue taken from beneath the skin? A. B. C. D. eichosanoid steroid triglyceride phospholipid 66 Which lipids would you find in human cell membranes? A. B. C. D. cholesterol glycolipids phospholipids all of the above 67 Protein Structure • Proteins are the most abundant and important organic molecules • Basic elements: – carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) • Basic building blocks: – 20 amino acids 68 Protein Functions • 7 major protein functions: – – – – – – – support: structural proteins movement: contractile proteins transport: transport proteins buffering: regulation of pH metabolic regulation: enzymes coordination and control: hormones defense: antibodies 69 Proteins • Proteins: – control anatomical structure and physiological function – determine cell shape and tissue properties – perform almost all cell functions 70 Amino Acid Structure 1. 2. 3. 4. central carbon hydrogen amino group (—NH2) carboxylic acid group (—COOH) 5. variable side chain or R group 71 Figure 2-18 Peptide Bond • A dehydration synthesis between: – amino group of 1 amino acid – and the carboxylic acid group of another amino acid – producing a peptide 72 Primary Structure • Polypeptide: – Linear sequence of amino acids • How many amino acids were bound together • What order they are bound 73 Figure 2–20a Secondary Structure • Hydrogen bonds form spirals or pleats 74 Figure 2–20b Tertiary Structure • Secondary structure folds into a unique shape • Global coiling or folding due to R group interaction 75 Figure 2–20c Quaternary Structure • Final protein shape: – several tertiary structures together Fibrous proteins: - structural sheets Globular proteins: - soluble spheres with active functions 76 Figure 2–20d Shape and Function • Protein function is based on shape • Shape is based on sequence of amino acids • Denaturation: – loss of shape and function due to heat or pH 77 Enzymes • Enzymes are catalysts: – proteins that lower the activation energy of a chemical reaction – are not changed or used up in the reaction 78 How Enzymes Work Substrates: reactants in enzymatic reactions Active site: location on an enzyme that fits a particular substrate 79 Figure 2–21 Enzyme Helpers • Cofactor: – an ion or molecule that binds to an enzyme before substrates can bind • Coenzyme: – nonprotein organic cofactors (vitamins) • Isozymes: – 2 enzymes that can catalyze the same reaction 80 Enzyme Characteristics • Specificity: – one enzyme catalyzes one reaction • Saturation limits: – an enzyme’s maximum work rate • Regulation: – the ability to turn off and on 81 Conjugated Protein • Glycoproteins: – large protein + small carbohydrate • includes enzymes, antibodies, hormones, and mucus production • Proteoglycans: – large polysaccharides + polypeptides • promote viscosity 82 Proteins are chains of which small organic molecules? A. B. C. D. saccharides fatty acids amino acids nucleic acids 83 Which level of protein structure would be affected by an agent that breaks hydrogen bonds? A. the primary level of protein structure B. the secondary level of protein structure C. the tertiary level of protein structure D. the protein structure would NOT be affected by this agent 84 Why does boiling a protein affect its structural and functional properties? A. Heat denatures the protein, causing unfolding. B. Heat causes the formation of additional quaternary structure. C. Heating rearranges the primary structure of the protein. D. Heat alters the radical groups on the amino acids. 85 Why does boiling a protein affect its structural and functional properties? A. Heat denatures the protein, causing unfolding. B. Heat causes the formation of additional quaternary structure. C. Heating rearranges the primary structure of the protein. D. Heat alters the radical groups on the amino acids. 86 How might a change in an enzyme’s active site affect its functions? A. increased activity due to a better fit with the substrate B. decreased activity due to a poor substrate fit C. inhibited activity due to no substrate fit D. all of the above 87 Nucleic Acids • C, H, O, N, and P • Large organic molecules, found in the nucleus, which store and process information at the molecular level • DNA – deoxyribonucleic acid • RNA – ribonucleic acid 88 DNA and RNA DNA • Determines inherited characteristics • Directs protein synthesis • Controls enzyme production • Controls metabolism RNA • Codes intermediate steps in protein synthesis 89 KEY CONCEPT • DNA in the cell nucleus contains the information needed to construct all of the proteins in the body 90 Nucleotides • Are the building blocks of DNA • Have 3 molecular parts: – sugar (deoxyribose) – phosphate group – nitrogenous base (A, G, T, C) 91 The Bases 92 Figure 2–22b, c Complementary Bases • Purines pair with pyrimidines: • DNA: – adenine (A) and thymine (T) – cytosine (C) and guanine (G) • RNA: – uracil (U) replaces thymine (T) 93 RNA and DNA • RNA: – a single strand • DNA: – a double helix joined at bases by hydrogen bonds 94 Protein Synthesis: Three forms of RNA • messenger RNA (mRNA) – Protein blueprint or instructions • transfer RNA (tRNA) – Carry amino acids to the place where proteins are being synthesized • ribosomal RNA (rRNA) – Forms the site of protein synthesis in the cell • Factory = ribosomes 95 High-Energy Compounds: ADP and ATP - Assembled using RNA Nucleotides - Bonds are broken easily by cells to release energy as needed - During digestion and cellular respiration: - energy from food is transferred to high energy compounds for quick and easy access. 96 ADP to ATP: Phosphorylation ADP vs. ATP: • adenosine diphosphate (ADP): – 2 phosphate groups (di = 2) • adenosine triphosphate (ATP): – 3 phosphate groups (tri = 3) Adding a phosphate group to ADP with a highenergy bound to form the high-energy compound ATP • ATPase: – the enzyme that catalyzes phophorylation 97 The Energy Molecule • Chemical energy stored in phosphate bonds 98 Figure 2–24 A large organic molecule composed of the sugar ribose, nitrogenous bases, and phosphate groups is which kind of nucleic acid? A. B. C. D. DNA ATP tRNA RNA 99 What molecule is produced by the phosphorylation of ADP? A. B. C. D. ATPase ATP Adenosine Diphosphate Uridine Triphosphate 100 Compounds Important to Physiology 101 Table 2–8 SUMMARY • Atoms, molecules, and chemical bonds control cellular physiology • Metabolism and energy work within the cell • Importance of organic and inorganic nutrients and metabolites 102 SUMMARY • Role of water and solubility in metabolism and cell structure • Chemistry of acids and bases, pH and buffers • Structure and function of carbohydrates, lipids, proteins, and nucleic acids 103