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Biochemical Basis of Life Atoms Atoms are the basic units of matter. The atom is the smallest particle of a substance that still remains the properties of that substance. Atoms are composed of protons, neutrons, and electrons. Atoms (continued) Protons: positive charge Neutrons: no charge Electrons: negative charge Protons and neutrons have about the same mass and are found in the center of the atom, the nucleus. Electrons are very light and in constant motion surrounding the nucleus. Elements A chemical element is a pure substance that consists entirely of one type of atom. More than 100 are currently known to exists; however, only about 20 to 24 are commonly found in living organisms. Symbols for Elements Chemists use symbols of one or two letters to represent elements. The first letter is always capitalized. If there is a second letter, it is not capitalized. C represents carbon. Al represents aluminum. Au represents gold. (The Latin name for gold is aurum.) Periodic Table There are four pieces of information for each element. Atomic Number Atomic Symbol Atomic Name Atomic Mass Periodic Table Atomic number is the number of protons (or electrons) Atomic mass is the mass of the nucleus, protons and neutrons. Compounds A compound is a substance formed by the chemical combination of two or more elements in definite proportions. The composition of compounds are represented by a kind of shorthand known as a chemical formula. H20: 2 elements of hydrogen and 1 element of oxygen The physical and chemical properties of a compound are usually very different from the individual elements. http://vimeo.com/4433312 Chemical Bonds The atoms in compounds are held together by various types of chemical bonds. Bond formation involves the electrons that surround each atomic nucleus. The tendency of elements to combine and form compounds depends on the number and the arrangement of electrons in their outermost energy level. The main types of bonds are ionic and covalent bonds. Ionic Bonds An ionic bond is formed when one or more electrons are transferred. An atom that loses electrons becomes positively charged. An atoms that gains electrons becomes negatively charged. Atoms with a charge are called ions. Ionic bonds form between sodium and chlorine to form table salt (NaCl). Electrons Electrons have energy levels surrounding the nucleus. 1st energy level has 2 electrons 2nd energy level has 8 electrons 3rd energy level has 18 electrons 4th through 7th energy levels like bond in 8 or groups of 8 or have full electron shells. (An electron’s happy state is 8: octet rule) Ionic Bonds Protons +11 Protons +17 Electrons - 11 Electrons - 17 Charge 0 Charge 0 Protons +11 Protons +17 Electrons - 10 Electrons -18 Charge +1 Charge -1 Covalent Bonds A covalent bond is formed when electrons are shared by atoms. When atoms of the same element join together, they also form a molecule. Covalent bonds form between hydrogen and oxygen to form H2O, water. What type of bond is the cartoon illustrating? Answer The cartoon is illustrating an ionic bond. An ionic bond is an electrical attraction between two oppositely charged atoms. The positively charged atoms are inside the classroom are attracted to the negatively charged atoms on the outside of the window. Properties of Water A water molecule (H20), is made up of three atoms: two hydrogen and one oxygen. Water is one of the few compounds found in a liquid state over most of the surface of Earth. In its solid state, ice has a low density allowing objects to float. Water is polar. The charges are unevenly distributed. The hydrogen end is positive and the oxygen end is negative. Because water is a polar molecule, it is able to perform multiple hydrogen bonds, which account for many of water’s special properties. Properties of Water The attraction between a hydrogen atom on one water molecule and the oxygen atom on another water molecule is called a hydrogen bond. Hydrogen bonds are not as strong as ionic or covalent bonds, and they can form in other compounds as well. Properties of Water High Heat Capacity is the amount of heat energy required to increase its temperature. Adhesion is an attraction between molecules of different substances. Adhesion forms capillary action which give water the ability to climb structures. (Ex. Water in the stem of plant stalks) Cohesion is attraction between molecules of the same substance. Cohesion causes water molecules to be drawn together . This results in surface tension. https://www.youtube.com/watch?v=HVT3Y3_gHGg Properties of Water Surface tension – cohesion of water with a film-like quality on the surface of a liquid Capillary action – tendency of a liquid to draw up into a narrow tube due to the liquid’s properties of cohesion and adhesion Solutions A solution is composed of two parts: solute and solvent. - In a salt water solution, table salt is the solute – the substance that is dissolved. - Water is the solvent – the substance in which the solute dissolves. Water is the universal solvent. A homogenous mixture is a solution where the substance looks the same throughout . Van der Waals Van der Waals forces include attractions and repulsions between atoms, molecules, and surfaces, as well as other intermolecular forces. Geckos can stick to walls and ceilings because of Van der Waals forces. Let’s Practice Identify the property of water that best describes the following statements: 1. Water forms raindrops as is flows through the air. ________________ 2. Fish and other aquatic life are able to survive in subzero temperatures. _______________ 3. Water is able to ascend very tall trees. ______________ 4. Many types of materials are able to be dissolved in water. _________________ Answers 1. Water forms raindrops as is flows through the air. Cohesion 2. Fish and other aquatic life are able to survive in subzero temperatures. low density of ice 3. Water is able to ascend very tall trees. adhesion 4. Many types of materials are able to be dissolved in water. polarity Acids and Bases Some compounds break into ions when they dissolve in water. An acid is any compound that forms hydrogen ions (H+) in a solution. A base is a compound that produces hydroxide ions (OH-) in a solution. pH The pH scale is a measurement system used to indicate the concentration of H+ ions in a solution. pH scale ranges from 0 to 14. 7 is neutral. Solutions with a pH below 7 are called acidic because they have more H+ ions than OH- ions. The lower the pH, the greater the acidity. Solutions with a pH above 7 are called basic because that have more OH- ions than H+ ions. The higher the pH, the more basic the solution. Buffers The pH of the fluids within most cells in the human body must generally be kept between 6.5 and 7.5 in order to maintain homeostasis. If the pH is lower or higher, it will affect chemical reactions that take place within the cells. One of the ways that organisms control pH is through dissolved compounds called buffers, which are weak acids or weak bases that can react with strong acids or bases to prevent sharp, sudden changes in pH. pH Scale Practice #2 Use the diagram below to answer the following: 5. Which is more basic: blood or ammonia? _______ 6. What is the pH of drain cleaner? ____________ 7. Would a lemon have more hydrogen or hydroxide ions? _____________ 8. What is the pH of lemon?_______________ 9. Is water an acid, a base, or neutral? ___________ Answers 5. Which is more basic: blood or ammonia? ammonia 6. What is the pH of drain cleaner?14 7. Would a lemon have more hydrogen or hydroxide ions? hydrogen 8. What is the pH of lemon?2 9. Is water an acid, a base, or neutral? neutral Let’s Practice - 3 10. John consumes large amounts of black coffee and tomato juice daily. Sometimes these fluids cause digestive discomforts, and he takes antacids to reduce the symptoms. Use your knowledge of acids, bases, and pH to explain why antacids reduce the symptoms. Answer Coffee and tomatoes are acidic fluids. Antacids are bases. A base reacts with an acid to form a less acidic product. Antacids help neutralize digestive juices by changing its pH. Carbon Compounds Carbon can bond with many elements, including hydrogen, oxygen, phosphorus, sulfur, and nitrogen to form the molecules of life. Carbon can share its electrons with other atoms to form up to four covalent bonds. Carbon-carbon bonds can be single, double, or triple covalent bonds. Chains of carbon atoms can even close up on themselves to form rings. Macromolecules Many of the molecules in living cells are very large and known as macromolecules. Most macromolecules are formed by a process known as polymerization through which large compounds are built by joining smaller ones together. The smaller units or monomers join together to form polymers. Polymer Train monomer + monomer + monomer + monomer Polymers Polymers are formed by dehydration synthesis because water is given off. Polymers are broken apart by hydrolysis because water is added. Types of Macromolecules Carbohydrates Lipids Proteins Nucleic Acids Macromolecules: Carbohydrates Type Structures Monomers Function Sugar, starches, and cellulose Carbon:Hydrogen: Oxygen Glucose Living things use carbohydrates as their main source of energy. Monosaccharide 1:2:1 ratio C6H12O6 Disaccharides Polysaccharides Types of Carbohydrates Monosaccharide: one simple sugar. Examples are glucose, fructose(fruit sugar), galactose(milk sugar) The formula for glucose is C6H12O6. Plants use this during photosynthesis Disaccharide: two simple sugars joined by a saccharide bond. Examples are sucrose(table sugar), lactose(milk sugar), and maltose (malt beverage sugar) Polysaccharide: three or more monosaccharides combined. Examples are cellulose(cell walls), chitin (exoskeleton), glycogen (stores glucose in liver cells), starch (stores glucose in roots of plants) http://www.youtube.com/watch?v=QckfYvIlVu4 Isomers Isomers have the same elements, but are arranged differently. An example of an isomer is glucose and fructose. Macromolecules: Lipids Type Structure Fats, Oils, Waxes Carbon, Hydrogen, 3 Fatty Acids and and Oxygen Glycerol NOT in the same 1:2:1 ratio as carbohydrates Monomer Function Lipids form part of biological membranes, store energy, help insulate the body, and cushion and protect organs. Lipids Lipids are made of glycerol and three fatty acids. Lipids contain fewer oxygen than carbohydrates Lipids are used for protection, cushion, structure, insulation, and long term energy storage. Two main types of lipids are fatty acids and phospholipids. http://www.youtube.com/watch?v=3xF_LK9pnL0 2 Types of Fatty Acids Saturated: solid at room temperature, example animal fats Unsaturated: liquids at room temperature, example vegetable oil Phospholipids Phospholipids make up cell membranes. They are like fatty acids that contain phosphorus. Macromolecules: Proteins Type Structure Monomer Antibodies, Carbon, Hydrogen, Amino Acids (20) Muscles, Enzymes, Oxygen, and and Hair. Nitrogen Function Proteins control rate of reactions, regulate cell processes, form cellular structures, and fight diseases. Proteins Proteins are composed of carbon, hydrogen, oxygen, and nitrogen with sulfur and two amino acids The building blocks of protein are amino acids held together by a peptide bond. Examples of proteins are antibodies, muscles, enzymes, and hair. http://www.youtube.com/watch?v=w-ctkPUUpUc Macromolecules: Nucleic Acids Type Structure Monomer DNA RNA Carbon, Hydrogen, Nucleotides Oxygen, Nitrogen, Phosphorus Function Nucleic acids store and transmit genetic information. Nucleic Acids Nucleic acids are used for controlling cellular activities and making protein (genes) Nucleic acids are made of: a simple sugar: deoxyribose for DNA and ribose for RNA phosphate group nitrogen base: adenine, cytosine, guanine, and thymine for DNA and adenine, cytosine, guanine, and uracil for RNA http://www.youtube.com/watch?v=jKMwLrbYyJ0 Organic Substances of the Body Organic Compound (Polymer) Carbohydrates Elements Building Blocks (monomer) C, H, and O (H:O ratio of 2:1) Simple sugars Lipids C, H and O Glycerol and Fatty Acids Proteins C, H, O, and N Amino Acids Nucleic Acids (DNA and RNA) C, H, O, N and P Nucleotides (monosaccharaids) Let’s Practice -4 Matching #11 Answer for Practice -4 #11 Chemical Reactions •Chemical reaction is a process that changes one set of chemicals into another set of chemicals. •Reactants are substances that go into a chemical reaction. •Products are substances that result from a chemical reaction. •Reactants and products are separated in a chemical reaction by a yields sign . Enzymes Activation energy is the term used to describe the energy needed to get a reaction started. A catalyst is a substance that accelerates the rate of a chemical reaction. Enzymes are proteins that act as biological catalysts. Enzymes do not cause reactions to happen. They speed up chemical reactions that take place in cells. Enzymes act by lowering activation energies, which has a dramatic effect on how quickly reactions are completed. Without enzymes the reactions of the cells would proceed very slowly. Enzymes are never used up in the reaction. They can be used over and over again. Enzymes get their names from the substances they act on and on the action of the enzyme and end in “ase.” Example: Lipase – breaks down a lipid. How Enzymes Work Enzymes are very specific, generally catalyzing only one chemical reaction. The reactants of the enzyme-catalyzed reactions are known as substrates. The substrates bind to a site on the enzyme called the active site. The active site and the substrate have complementary shapes. The fit is so precise the active site and substrate are often compared to a lock and key. Enzyme Regulation Temperature – Enzymes produced by the human cells generally work best at temperatures close to 37°C, the normal temperature of the human body. pH – Enzymes work best at certain pH values. For example, the stomach enzyme pepsin, which begins protein digestion, works best under acidic conditions. Regulatory Molecules- The activities of most enzymes are regulated by molecules that carry certain chemical signals within cells, switching enzymes “on” or “off” as needed. Let’s Practice – 5 Label as enzyme, active site, products, substrate (reactants) , and enzymesubstrate complex (one is used twice). #12 Answers #12 Review 13. The effect of pH on a certain enzyme is shown in the graph below: At what pH would the enzyme be most effective? A. Above 10 B. between 8 and 10 C. Between 5 and 7 D. below 5 Review 13. The effect of pH on a certain enzyme is shown in the graph below: At what pH would the enzyme be most effective? A. Above 10 B. between 8 and 10 C. Between 5 and 7 D. below 5 Review 14. An enzyme and four different molecules are shown in the diagram below: The enzyme would most likely affect reactions involving: A. molecule A, only B. molecule D, only C. molecules B and D D. molecules A and C Review 14. An enzyme and four different molecules are shown in the diagram below: The enzyme would most likely affect reactions involving: A. molecule A, only B. molecule D, only C. molecules B and D D. molecules A and C Review 15. Ice floats on a lake. This characteristic of water is responsible for A. Suffocation of aquatic organisms B. Mixing a lake’s thermal layers C. Preventing a lake from freezing solid D. Altering migration patterns of fish Review 15. Ice floats on a lake. This characteristic of water is responsible for A. Suffocation of aquatic organisms B. Mixing a lake’s thermal layers C. Preventing a lake from freezing solid (High Heat Capacity is the amount of heat energy required to increase its temperature.) D. Altering migration patterns of fish Review 16. Proteins are formed from monomers (subunits) called: A. Nucleic acids B. Fatty acids C. Nucleotides D. Amino acids Review 16. Proteins are formed from monomers (subunits) called: A. Nucleic acids (it’s a type of macromolecule) B. Fatty acids (monomers of lipids) C. Nucleotides (monomers for nucleic acids) D. Amino acids Review 17. Which of the following macromolecules are a prominent part of animal tissues that function in insulation, helping animals to conserve heat? A. Carbohydrates B. Lipids C. Proteins D. Nucleic Acids Review 17. Which of the following macromolecules are a prominent part of animal tissues that function in insulation, helping animals to conserve heat? A. Carbohydrates B. Lipids C. Proteins D. Nucleic Acids