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Chemistry UEQ: What is the relationship between water, the four essential macromolecules and an organism’s regulation by chemical processes? LEQ: How do valence electrons affect living organisms? LEQ: How can I identify an ionic, covalent or hydrogen bonds? 2.1 Everything is made of atoms. An element is a substance that cannot be broken down chemically into any other substances. An atom is a bit of matter that cannot be subdivided any further without losing its essential properties. Atomic Structure: The nucleus, protons, and neutrons Atomic Structure: Electrons Atomic Numbers Insert new figure 2.3 Isotopes insert new fig 2.4 Radioactive Atoms A few atomic nuclei are not stable and break down spontaneously. These They atoms are radioactive. release, at a constant rate, a tiny, highspeed particle carrying a lot of energy. 25 Elements Found in Your Body and the Big 4 Take-home message 2.1 Everything around us, living or not, is made from atoms, the smallest unit into which material can be divided. Atoms They all have the same general structure. are made up of protons and neutrons in the nucleus and electrons, which circle far around the nucleus. 2.2 An atom’s electrons determine how (and whether) the atom will bond with other atoms. Electron shells Electron Shells Insert new fig 2-6 The Versatility of Carbon Insert fig 2-7 Ions Insert new fig 2-8 Take-home message 2.2 The chemical characteristics of an atom depend upon number of electrons in their outermost shells. Atoms are most stable and least likely to bond with other atoms when their outermost electron shell is full. 2.3 Atoms can bond together to form molecules or compounds. Molecules Products of bonding! Covalent Bonds Insert fig 2-9 to right side of slide Ions and Ionic Bonds Insert fig 2-10 Hydrogen Bonds Insert fig 2-11 Insert fig 2-12 Take-home message 2.3 • Atoms can be bound together in three different ways: covalent bonds, ionic bonds, hydrogen bonds. Covalent bonds, in which atoms share electrons, are the strongest. • In ionic bonds, one atom transfers its electrons to another and the two oppositely charged ions are attracted to each other, forming a compound • Hydrogen bonds, which are weaker than covalent and ionic bonds, involve the attraction between a hydrogen atom and a polar molecule. • 2.4–2.6 •LEQ: How does the arrangement of covalent bonds within a water molecule add to its polarity? •LEQ: How do the special properties of water contribute to Earth’s suitability as an environment for life? 2.4 Hydrogen bonds make water cohesive. Insert fig 2-13 Take-home message 2.4 Water molecules easily form hydrogen bonds, giving water great cohesiveness. 2.5 Water has unusual properties that make it critical to life. Cohesion Large Low heat capacity density as a solid Good solvent Cohesion Heat Capacity Why do coastal areas have milder, less variable climates than inland areas? Low Density as a Solid Why don’t oceans freeze as easily as fresh water lakes? Take home message 2.5 The hydrogen bonds between water molecules give water several of its most important characteristics: • • • • cohesiveness reduced density as a solid the ability to resist temperature changes broad effectiveness as a solvent for ionic and polar substances 2.6 Living systems are highly sensitive to acidic and basic conditions. Hydrogen Ions and Hydroxide Ions OH - O H Ionized Hydroxide Molecule H2O O H H Non-Ionized Water Molecule pH Scale The amount of H+ in a solution is a measure of its acidity and is called pH. Acids Bases H+ Ions and Acids H+ very reactive Acids can donate H+ to other chemicals Stomach acids Bases Low H+ High OH Antacids Baking soda, seltzer, milk of magnesia Blood pH Buffers • can quickly absorb excess H+ ions to keep a solution from becoming too acidic • can quickly release H+ ions to counteract any increases in OH concentration Take-home message 2.6 The pH of a fluid is a measure of how acidic or basic a solution is and depends on the concentration of dissolved H+ ions present. The lower the pH, the more acidic the solution Acids, such as vinegar, can donate protons to other chemicals while bases, including baking soda, bind with free protons. 2·7–2·10 Carbohydrates are fuel for living machines. 2.7 Carbohydrates include macromolecules that function as fuel. Health topics of the year Low-carb diet? Hi-carb diet? “Carbo-loading”? Fiber intake? What are carbohydrates? Four Types of Macromolecules Carbohydrates Lipids Proteins Nucleic acids Carbohydrates C, H, and O Primary fuel for organisms Cell structure Energy is in the chemical bonds! Take-home message 2-7 Carbohydrates are the primary fuel for running all cellular machinery and also form much of the structure of cells in all life forms. Take-home message 2.7 Carbohydrates contain carbon, hydrogen, and oxygen, and generally have the same number of carbon atoms as they do H2O units. Take home message 2.7 The C-H bonds of carbohydrates store a great deal of energy and are easily broken by organisms. The simplest carbohydrates, including glucose, are monosaccharides or simple sugars. They contain from three to six carbon atoms. Take home message 2.7 As the chemical bonds of carbohydrates are broken down and other more stable bonds are formed, a great deal of energy is released that can be used by organisms. 2.8 Glucose provides energy for the body’s cells. Fuel for cellular activity Stored temporarily as glycogen Converted to fat Glucose Most carbohydrates — ultimately converted into glucose Blood sugar What is “carbo-loading”? Take home message 2.8 Glucose is the most important carbohydrate to living organisms. Glucose in the bloodstream can be used as an energy source, can be stored as glycogen in the muscles and liver for later use, or can be converted to fat. 2.9 Many complex carbohydrates are time-released packets of energy. More than 1 sugar (monosaccharide) unit Disaccharides • • sucrose lactose Polysaccharides • • starch cellulose Chemical Fuel Preliminary Processing Starch > 100’s of glucose molecules joined together Barley, wheat, rye, corn, and rice Glycogen—“animal starch” Complex Carbohydrates “Time-release” fuel pellets Take-home message 2.9 Multiple simple carbohydrates sometimes link together into more complex carbohydrates. Types of complex carbohydrates include starch, the primary form of energy storage in plants, and glycogen, a primary form of energy storage in animals. 2.10 Not all carbohydrates are digestible. Chitin Cellulose Insert new fig 2-26 Fiber “Roughage” Colon cancer prevention/reduction Termites ecological role Take-home message 2.10 Some complex carbohydrates, including chitin and cellulose, cannot be digested by most animals. Such indigestible carbohydrates in the diet, called fiber, aid in digestion and have numerous health benefits. 2.11–2.13 Lipids store energy for a rainy day. 2.11 Lipids are macromolecules with several functions, including energy storage. Why does a salad dressing made with vinegar and oil separate into two layers shortly after you shake it? Hydrophobic Hydrophilic In making a homemade salad dressing you mix olive oil, vinegar, and water together. You notice when you add the vinegar to the water it mixes immediately. When you add the olive oil it floats on top of the solution. The vinegar is ____________ and the oil is ____________. 1. 2. 3. 4. hydrophobic; hydrophilic acidic; basic hydrophilic; hydrophobic basic; acidic Take-home message 2.11 Lipids are non-soluble in water and greasy to the touch. They are valuable to organisms in longterm energy storage and insulation, membrane formation, and as hormones. 2.12 Fats are tasty molecules too plentiful in our diets. Glycerol: “head” region Fatty acid “tails” Triglycerides Fat molecules contain much more stored energy than carbohydrate molecules. Saturated and Unsaturated Fats # of bonds in the hydrocarbon chain in a fatty acid Health considerations Which answer below is solid at room temperature? 1. 2. 3. 4. Saturated fat (like animal fat) Unsaturated fat (like canola oil) Trans fat (like margarine) Both 1 and 3 are correct. Chocolate lipids. chip cookie recipes call for some How will the “chewy-ness” of the cookies differ depending on whether you use butter or vegetable oil as the lipid? Which cookies will be healthier? Many snack foods contain “partially hydrogenated” vegetable oils. Why might it be desirable to add hydrogen atoms to a vegetable oil? What are trans fats? Olestra is a recently developed “fake fat” chemical that gives foods the taste of fat, without adding the calories of fats. What chemical structure might make this possible? If you analyze the nutrition label of some commercially available chocolate chip cookies you will find that they say they have zero trans fats. Many times this is false because when you look in the list of ingredients you find… 1. 2. 3. 4. 5. Butter Canola oil Partially hydrogenated canola oil Lard Palm oil Take-home message 2.12 Fats, including the triglycerides common in the food we eat, are one type of lipid. Take-home message 2.13 Characterized by long hydrocarbon tails, fats effectively store energy in the many carbonhydrogen and carbon-carbon bonds. Their caloric density is responsible for humans’ preferring fats to other macromolecules in the diet, and is also responsible for their association with obesity and illness in the modern world. 2.13 Cholesterol and phospholipids are used to build sex hormones and membranes. Not all lipids are fats The sterols Cholesterol Important component of most cell membranes. Can attach to blood vessel walls and cause them to thicken. Cells in our liver produce almost 90% of the circulating cholesterol. Steroid Hormones Estrogen Testosterone • synthetic variants of testosterone Phospholipids and Waxes Phospholipids are the major component of the cell membrane. Waxes are strongly hydrophobic. Take-home message 2.13 Cholesterol and phospholipids are lipids that are not fats. Both are important components in cell membranes. Cholesterol also serves as a precursor to steroid hormones, important regulators of growth and development. 2.14–2.18 Proteins are versatile macromolecules that serve as building blocks. 2.14 Proteins are bodybuilding macromolecules. Amino Acids Twenty Strung different amino acids together to make proteins Take-home message 2.14 Unique combinations of 20 amino acids give rise to proteins, the chief building blocks of physical structures that make up all organisms. Proteins perform myriad functions, from assisting chemical reactions to causing blood clotting to building bones to fighting microorganisms. 2.15 Proteins are an essential dietary component. Growth Repair Replacement Food labels indicate an item’s protein content. Why is this insufficient for you to determine whether you are protein deficient, even if your protein intake exceeds your recommended daily amount? Complete Proteins Have all essential amino acids Incomplete proteins Complementary proteins Insert new fig 2-38 Which answer below will provide all of the essential amino acids in a meal? 1. 2. 3. 4. Hamburger Corn and a legume (complementary) Apple Both 1 and 2 are correct. Take-home message 2.15 Twenty amino acids make up all the proteins necessary for growth, repair, and replacement of tissue in living organisms. Take-home message 2.15 Of these amino acids, about half are essential for humans: they cannot be synthesized by the body so must be consumed in the diet. Complete proteins contain all essential amino acids, while incomplete proteins do not. 2.16 A protein’s function is influenced by its three-dimensional shape. Peptide bonds Primary Structure The sequence of amino acids Secondary Structure Hydrogen bonding between amino acids The two most common patterns: • twist in a corkscrew-like shape • zig-zag folding Tertiary Structure Folding and bending of the secondary structure Due to bonds such as hydrogen bonds or covalent sulfursulfur bonds. Quaternary Structure When two or more polypeptide chains are held together by bonds between the amino acids on the different chains. Hemoglobin Egg whites contain much protein. Why does beating them change their texture, making them stiff? Egg Why whites contain much protein. does beating them change their texture, making them stiff? Why is wet hair easier to style than dry hair? Why do some people have curly hair and others have straight hair? Getting hair straightened at a hair salon involves… 2. nd 1a p. .. he ng t ng i Ch a in fo rm Re Ch a ng i ng t he gh yd r.. t.. . . 1. Changing the tertiary 25% 25% 25% 25% structure of the hair proteins. 2. Reforming hydrogen bonds that have been broken. 3. Changing the primary structure of the hair proteins. 4. 1 and 2. Take-home message 2.16 The particular amino acid sequence of a protein determines how it folds into a particular shape. This shape determines many of the protein's features, such as which molecules it will interact with. When a protein's shape is deformed, the protein usually loses its ability to function. 2.17 Enzymes are proteins that initiate and speed up chemical reactions. Activation Energy Chemical reactions occurring in organisms can either release energy or consume energy. In either case, the reaction needs a little “push” in order to initiate the reaction―called activation energy. Enzymes act as catalyst by lowering the activation energy. An enzyme can reduce the activation energy in a variety of ways. 1. By stressing, bending, or stretching critical chemical bonds 2. By directly participating in the reaction 3. By creating a microhabitat that is conducive to the reaction 4. By simply orienting or holding substrate molecules in place so that they can be modified. Classroom Catalyst Why can’t we digest cellulose? The polysaccharides amylose and cellulose are both made of glucose. Why can’t the enzyme salivary amylase breakdown both? 1. The orientation of the covalent bonds are different. 2. The active site of the enzyme cannot bind to glucose. 3. The enzyme cannot digest cellulose at normal body temperatures (32oC). 4. The covalent bonds in cellulose are stronger than in amylose. Take-home message 2.17 Enzymes are proteins that help initiate and speed up chemical reactions. They aren’t permanently altered in the process but rather can be used again and again. 2-18 Enzymes regulate reactions in several ways (but malformed enzymes can cause problems). The rate at which an enzyme catalyzes a reaction is influenced by several chemical and physical factors. Insert new figure 2-43, preferably broken into 4 stepped segments Insert fig 2-43, pt 2 Insert fig 2-43, pt 3 Insert fig 2-43, pt 4 “Misspelled” Proteins Incorrect Active amino acid sequence site disruptions Phenylketonuria Insert fig 2-44 to right Why do some adults get sick when they drink milk? Lactase cannot function properly in this example because the…. 1. shape is incorrect. 2. amino acid sequence is incorrect. 3. color is incorrect. 4. 1 and 2 When lactase is functioning correctly it… ac t.. . an ac ts as an as ac ts ea se in cr 25% in h. .. ... 25% 25% st he ac t.. . 4. th e 3. 25% er s 2. lowers the activation energy required to digest lactose. increases the activation energy required to digest lactose. acts as an inhibitor to decrease the activity of enzymes that breakdown lactose. acts as an activator to increase the activity of enzymes that breakdown lactose. lo w 1. Take-home message 2.18 Enzyme activity is influenced by physical factors such as temperature and pH, as well as chemical factors, including enzyme and substrate concentrations. Take-home message 2.18 Inhibitors and activators are chemicals that bind to enzymes, and by blocking the active site or altering the shape or structure of the enzyme can change the rate at which the enzyme catalyzes reactions. 2.19–2.21 Nucleic acids store information on how to build and run a body. 2.19 Nucleic acids are macromolecules that store information. Insert fig 2-45 Two Types of Nucleic Acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) Both play central roles in directing the production of proteins. Insert fig 2-45 to right Information Storage The information in a molecule of DNA is determined by its sequence of bases. Adenine, guanine, cytosine, and thymine • CGATTACCCGAT Take-home message 2.19 The nucleic acids DNA and RNA are macromolecules that store information in their unique sequences of bases contained in nucleotides, their building-block molecules. Both nucleic acids play central roles in directing protein production in organisms. 2.20 DNA holds the genetic information to build an organism. Insert new fig 2-46 Base-Pairing A &T G &C What is the complimentary strand to this strand: CCCCTTAGGAACC? What is the complimentary strand to this strand: CCCCTTAGGAACC? 1. 2. 3. 4. CCCCTTAGGAACC GGGGTTAGGAACC GGGGAATCCTTGG GGTTCCTAAGGCC Take-home message 2.20 DNA is shaped like a ladder in which the long vertical sides of the ladder are made from a sequence of sugar-phosphatesugar-phosphate molecules and the rungs are pairs of nucleotide bases. The sequence of nucleotide bases contains the information about how to produce a particular protein. 2.21 RNA is a universal translator, reading DNA and directing protein production. Insert fig 2-47 RNA differs from DNA in three important ways. The sugar molecule of the sugarphosphate backbone Single-stranded Uracil (U) replaces thymine (T) Which sequence below is the RNA synthesized from the DNA sequence below: CCCCTTAGGAACC 1. 2. 3. 4. GGGGAATCCTTGG CCCCTTAGGAACC GGUUCCUAAGGGG GGGGAAUACCUUGG Take-home message 2.21 RNA acts as a middleman molecule— taking the instructions for protein production from DNA to another part of the cell where, in accordance with the RNA instructions, amino acids are pieced together into proteins. Learning Objectives Describe what atoms are, their structure, and how they bond. Understand water’s features that help it support all life. Describe carbohydrates—their structure and function. Describe lipids—their structure and function. Describe proteins—their structure and function. Describe nucleic acids—their structure and function.